Dicentrarchus labrax), a highly prized marine fish species. Full‐sib families  were produced and reared in a common environment. Parentage assignment of 7,200 individuals was performed with seven microsatellite markers. Generalized linear models showed significant additive effects for both traits and pleiotropy between traits. A significant nonadditive genetic effect was detected. Different expression of traits and distinct relative performances were found for reciprocal crosses involving populations located on each side of the main hybrid zone located at the Almeria‐Oran front, illustrating asymmetric reproductive isolation. The poor fitness performance observed for the Western Mediterranean population of sea bass is discussed as it represents the main source of seed hatchery production, but also because it potentially illustrates nonadaptive introgression and maladaptation.Describing and explaining the geographic within‐species variation in phenotypes (“phenogeography”) in the sea over a species distribution range is central to our understanding of a variety of eco‐evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five origins) and 26 dams  in a factorial diallel cross in order to investigate geographic variation for early survival and sex ratio in the metapopulation of the European sea bass ( The integration of phenogeography and phylogeography should contribute to better understanding of functional phenotypic evolution, and then fitness performance within and among lineages  has been the subject of numerous studies for approximately 30 years  and performed a factorial diallel cross to test for the relationship between genetic distance and observed variation in juvenile survival and sex ratio in F22.1Wild sea bass used to produce the broodstock for this study was collected from five distinct origins in the Northeastern Atlantic or the Mediterranean Sea recognized as the main subpopulations of wild sea bass  to induce reproduction. The egg collection of each dam was carried out 3 days after the injection, and spawns of nine NAT and 17 WEM dams were obtained. Eggs were mixed in equal proportions  in two batches (NAT and WEM). Each batch of eggs was then divided in 75 aliquots, which were individually fertilized (no intersire competition) with the sperm of 15 sires from each geographic origin to produce a theoretical number of 1,950 families of sea bass (26 dams × 75 sires). Sperm cell quality was checked as described in Ky, Vergnet, Molinari, Fauvel, and Bonhomme (n = 5) × dam (n = 2) origins and incubated in 10 different incubators. After 48 hr of incubation, the live eggs . The temperature gradually increased from 16 to 20°C at 40 dpf, then fish were transferred to a 15 m3 nursery tank. The fish were fed with Artemia starting at 13 dpf, then with commercial pellets afterward. Temperature was kept constant around 20°C (19–21°C) until 111 dpf, when 3,000 randomly selected fish were transported to another pregrowing location , while the majority remained in the initial site (Viveiro Vila Nova). Therefore, full‐sib families of sea bass grew in a common environment until 111 dpf in order to minimize early‐life genotype‐by‐environment (G×E) interactions. The range of rearing temperatures used until 111 dpf is known to produce an excess of male sea bass . Potential G×E interactions introduced after transfer to each pregrowing locations were tested prior to model use and were not found significant (not reported). Furthermore, maternal effects are weak in sea bass because of lecithotrophic embryos. These effects are restricted to the first weeks of life  1,800 of them were randomly chosen, and PIT‐tagged in the muscle, on the left dorsal anterior part of the body. A fin‐clip was taken from each tagged fish for further DNA extraction and kept in 90% ethanol. On 26 September 2007 (216 dpf), the Portugal fish had reached an estimated mean body mass of ~20 g, and 5,400 of them were tagged, measured, and sampled as described before. All fish were reared until sexing was possible at 2.4n = 101; 26 dams and 75 sires) with seven microsatellite markers: Dla016, Dla020, Dla105, Dla116, Dla119, Lab13, and Lab3 , and 10 ml proteinase K (20 mg ml−1). DNA extraction was performed with the Wizard SV Genomic DNA Purification System kit (Promega), according to manufacturer recommendations. Extracts were stored at −20°C. Amplification was performed in a 20‐μl polymerase chain reaction (PCR) mixture containing 25 ng of genomic DNA, 2.0 μl PCR buffer, 1.2 μl MgCl2, 0.4 units Amplitaq Gold (Applied Biosystems), 1.25 mmol/L dNTPs mix (Applied Biosystems), and 10 pmol for each primer. The reverse primers were 5′ end‐labelled with FAM, NED, or VIC fluorochromes. The samples were amplified on a Geneamp® PCR System 9600 (Invitrogen) according to the following protocol: 10‐min initial denaturation at 95°C (hot start) followed by 30 cycles of 1 min at 94°C, 30 s at 55°C, 1 min at 72°C and extension at 72°C for 60 min. The polymorphism was screened on an ABI PRISM® 3100 DNA Analyzer (Life Technologies).The 7,200 PIT‐tagged sea bass juveniles were assigned to their parents  of no significant departure from panmixia was tested by randomly permuting alleles  from the original matrix of genotypes. Pairwise levels of population differentiation among broodstocks were investigated using θ^  and corrected for multiple tests. We attempted to assign individuals of each broodstock  to their population of origin using arlequin v3.5  of each full‐sib family in the 7,200 genotyped offspring. Sex ratio was determined by visual examination of the gonads of 2,877 genotyped and tagged fish that were sacrificed.Yijk is the number of survivors in the offspring of paternal line j and maternal line k reared in pregrowing location i, μ is the population mean, li is the fixed effect of pregrowing location i , pj is the fixed effect of paternal (sire) line j (j = 1–5), mk is the fixed effect of maternal (dam) line k , pmjk is the fixed interaction term between paternal line j and maternal line k (nonadditive sire × dam effects), and εijk is the random residual. This model was fitted with the SAS‐GENMOD procedure, with a logarithm link function and a Poisson residual distribution, which is appropriate for count data. Individual sire and dam effects on full‐sib family counts were also tested within each paternal and maternal line crosses. Sex‐ratio differences were tested with the same model where Yijk was the proportion of females in the offspring of sire line j and dam line k reared in pregrowing location i. In the case of the sex ratio, logit was used as the link function, with a binomial residual, which is appropriate for binary variables . The family within line information was available, but it could not be used in the analysis owing to the very high number of potential families  compared to sample size  which precluded model convergence. This GLM was also used with j = 2 for sire lines. In this case, sires from the Mediterranean  and from the Atlantic  were grouped before analyses.The number of fish per population cross at tagging was used as a surrogate for survival, under the hypothesis of equal initial numbers per population cross, and was tested with a generalized linear model (GLM) to assess the existence of differences linked to population and population cross:pm.., above) were regressed on the pairwise values of θ^ between the NAT and each of the five paternal lines. NAT was retained as a reference because it was one of the extreme populations in terms of genetic distance . The mean genetic differentiation among broodstocks was estimated to θ^ = 0.038 (p < .001), with all pairs of broodstocks found significantly differentiated with θ^ ranging from θ^ = 0.006 (NS) for the Atlantic NAT‐SAT comparison  for comparisons of SEM with each Atlantic population. Results confirmed the genetic homogeneity within the Atlantic, and that the Atlantic samples were genetically distinct of Mediterranean samples. Relative genetic differentiation observed among Atlantic and Mediterranean populations of sea bass is illustrated in Fig. arlequin, except for SAT (93%) and NAT (92%) because of above‐mentioned nonsignificant genetic differentiation .No deviation from Hardy–Weinberg equilibrium was observed within each broodstock of noninbred fish that initiated the experiment  were assigned to a unique parental pair when using the six or seven microsatellite markers. Among the unassigned fish, 41 (0.6%) did not provide reliable DNA amplification, 35 (0.5%) were assigned to two or more parent pairs, and only 4 (0.05%) were not assigned to any parent pair. Unassigned fish were discarded from the analysis.3.3The representation of parental lines was found to be highly unbalanced at 20 g (step for tagging and DNA collection). This was observed among the sire and the dam lines for both the initial five paternal lines × two maternal lines data set, and for the two paternal lines × two maternal lines data set . The difference is significant for the number of families produced .Impacts of the fertilization and/or the standardization procedure were also evaluated. The number of fish per cross at tagging was plotted against the percentage of floating  eggs at 48 hr Fig. . No signp < .001, details not reported). The number of progeny per full‐sib family is reported in Figure The representation of the different sires and dams was quite unbalanced within each line cross, where both sire and dam effects were highly significant in all 10 line crosses . Low proportions of female are the rule in aquaculture conditions . Female proportions were found to vary according to paternal line (p < .01), maternal line (p < .05), and paternal line × maternal line interaction (p < .05) when both pregrowing locations were combined  are reported in Fig. p < .01; Figure sensu stricto (see “Discussion” section for further comments).When we grouped the sire and dam populations by origin (Atlantic [ATL] vs Mediterranean [MED]), significantly higher proportions of females were detected for crosses that carried different genomes, i.e., the paternal origin × maternal origin interaction was found significant .We further analyzed the relationship between the proportion of females within sire and the mean body mass of progeny of each sire at tagging in order to test whether body mass at tagging could significantly predict family sex ratio. This relationship was not significant for both the 10 crosses and when grouping sires and dams by their oceanic origin . Namely, when one sire line showed higher survival of progenies with one dam line compared to the other, then this sire line also produced more females with this dam line, indicating pleiotropic effects between traits.Finally, a significant relationship was found between the log‐transformed number of fish that survived at 6 months and the proportion of females observed at ~1 year . The sire population appeared important to survival in sea bass, supporting recent evidence for a paternal role in increased survival of young fish . These results are consistent with reports that pure fitness traits such as survival showing fitness traits more prone to exhibit nonadditive components than traits indirectly related to fitness . If this was the case, this could also lead to underestimation of the nonadditive effects, which were significant on sex ratio and survival, but with apparent lower influence than sire “additive” effects. Despite this limitation, results showed that survival and sex ratio were prone to exhibit nonadditive components of genetic variance, which were not found in previously investigated traits such as, e.g., carcass or fillet yields  ). When populations were grouped by oceanic origin , larger proportions of females and higher survival were observed in crosses involving both Atlantic and Mediterranean individuals compared to crosses of individuals with the same oceanic origin. Note, however, that this pattern is not found when Mediterranean populations remained ungrouped. For instance, the reciprocal NAT × WEM crosses did not report systematic increase in performance compared to their respective parental crosses. This particular case is further discussed below, but results proved that adding the Eastern Mediterranean populations in the analysis to more clearly oppose the two ancestral genomic backgrounds increased the significance of the nonadditive genetic effect. If we cannot rigorously interpret these patterns as heterosis Edmands, . We hereThe observation of positive nonadditive genetic effects among Western and Eastern Mediterranean populations of sea bass may also have practical implications. Indeed, population genetics studies have showed that cultured WEM fish escaped from farms in Greece impacted local Eastern Mediterranean populations in a relatively enclosed natural environment   demonstrated no recovery of fitness in hybrid populations . This is probably unlikely because lower performance for distinct sets of traits was also observed when WEM fish were reared locally  and G×E interactions were not significant in this study. WEM individuals may also have poor fitness because they inherited and still not purged the deleterious alleles initially present in each parental population. This seems theoretically unlikely as recombination and segregation should bring together favorable alleles within the same individuals  and hence improve the efficiency of natural selection by reducing the load  > parental(♂NAT × ♀NAT) > hybrid(♂WEM × ♀NAT) > parental(♂WEM × ♀WEM). Ky et al. ((♂NAT × ♀WEM) outperformed parental(♂NAT × ♀NAT) for hatching rate. Asymmetric performances of F1 crosses are commonly reported in a wide range of organisms even though—contrary to sea bass—F1s rarely outcompete their parents as observed in, e.g., numerous freshwater fish species (Bolnick, Turelli, Lopez‐Fernández, Wainwright, & Near, The performance of the two reciprocal crosses between ♂y et al.  also rep2 or backcrosses have not been determined in sea bass yet and certainly needs further investigation to gain insight on the basis and strength of reproductive isolation.The observation of such asymmetric barriers to reproductive isolation has been coined as the “Darwin's corollary to Haldane's rule” (Turelli & Moyle, 4.6NAT × ♀WEM hybrid cross for early survival and production of females compared to the reciprocal ♂WEM × ♀NAT cross is interesting as it correlates with the relative success of these genotypes in the wild. Indeed, Atlantic mtDNA haplotypes of sea bass have not been observed to naturally introgress the Western Mediterranean Sea population so far, while the reverse was regularly observed (Coscia et al., WEM × ♀NAT cross as males as suggested by Lemaire et al. (T. californicus (Alexander et al., Cottus sp.; Cheng, Czypionka, & Nolte, In the present study, the superior performance of the ♂e et al. . Situati5Using individuals derived from wild populations and covering major genetic subdivisions currently recognized for the European sea bass, we performed a phenogeographic study of several phenotypic traits that complements previous phylogeographic studies performed in this species. We showed that both significant additive variance and nonadditive genetic variance were present for early survival and sex ratio. Performance for early survival and sex ratio as measured by the proportion of females may reflect a pleiotropic effect. While potentially suffering from incomplete interpopulation crosses, the expression of nonadditive effects was found related to levels of population divergence and could be indicative of heterosis at the metapopulation level. The relative survival performance of available reciprocal crosses showed correlations with genetic structure observed in the wild, but also highlighted low performance of WEM, the main source of seed hatchery production in sea bass. Genomic resources that accumulated in sea bass should now contribute to a more detailed crosstalk between the genotypic and phenotypic levels of variation to better understand the underpinnings of molecular variation governing expression of traits and DM incompatibilities in the wild or in aquaculture programs. Because the sea bass is only a representative of many marine species studied in this area (Patarnello et al., None declared.10.5061/dryad.8r0q8.Data of this study are deposited in Dryad under accession: doi: Click here for additional data file.


Skeletonema marinoi) and dinoflagellates , spanning ca. a century. Phenotypic and genotypic analyses of these time series have revealed effects of past environmental changes on population genetic structure. Future perspectives include direct comparisons of phenotypes and genotypic data of populations, for example, by genomewide assays that can correlate phenotypic trends with genotypes and allele frequencies in temporally separated strains. Besides their usefulness as historical records, “seed” banks of phytoplankton resting stages also have the potential to provide an inoculum that influences present populations through “dispersal from the past” (the storage effect) and are important for adaptation to future environments through their standing genetic diversity.Undisturbed records of resting stages produced in the past and stored in coastal sediments are very valuable to science, because they may provide unique insights into past evolutionary and ecological trajectories. Within marine phytoplankton, multidecadal time series of monoclonal strains germinated from resting stages have been established for diatoms ( A main functional group in the plankton is the phytoplankton, that is, the photosynthesizing fraction, which broadly speaking comprises the planktic microalgae. Many planktic organisms form a resting stage as part of their life cycle and these resting stages sink through the water column and may accumulate in the sediments  they were found to have long temporal extent of viability in sediment cores and were found alive furthest down‐core in highest numbers in studies targeting all potentially viable dinoflagellate cysts , which also affects the abundance of P. dalei cysts in the sediments , corresponding to the maximal and minimal salinities expected in negative and positive modes of the NAO, respectively. The study showed that there was large variability between strains but that there were no significant differences in response to salinity or in maximal pH tolerance between the three tested layers . Lundholm et al. , which, under ideal circumstances, can be applied to sediments up to ca. 120–150 years old  or enriched sediment slurries . In the case of sexual stages such as dinoflagellate cysts, this isolation must be done twice to achieve monoclonal strains (first by isolating the diploid resting cyst and thereafter isolating a single haploid vegetative cell). Both the work involved and the availability of viable cells back in time limit the number of strains that can be resurrected Figure .3. HowevP. dalei from a Greenlandic fjord  and S. marinoi  from the Swedish inlet Havstens fjord and Mariager fjord attempt to increase the analysis depth by employing genomewide methodologies. Thus, in the study on S. marinoi the entire genomes of hundreds of individuals have been resequenced and single nucleotide polymorphisms (SNPs) have been identified in candidate genes. In the study on P. dalei, amplified fragment length polymorphisms have been developed for studying temporal population genetic structure (Figure The studies published so far have used microsatellite markers to study population genetic structure. Microsatellites are very suitable for such studies, but due to difficulties and cost of development, so far <10 different loci have been used, making the coverage of the genome limited and restricting the data to noncoding sites. Ongoing studies of The availability of temporal data series on environmental conditions in a potential sampling site is another central factor Figure .2. To te33.12 adaptations are of interest, different temperatures or pCO2 can be tested (Lohbeck, Riebesell, & Reusch, pCO2 (as done with salinity in Ribeiro et al., FST analyses will indicate outlier loci and may reveal genes that are affected by the environmental trend (Narum & Hess, Given the short mitotic generation time of phytoplankton and the large population sizes and genetic standing stock, phytoplankton resurrected from sediment cores provide a splendid material for studying adaptation to past and ongoing changes. Phytoplankton populations germinated from discrete layers of a sediment record can be kept side by side in the laboratory. This allows direct comparisons of phenotypes and genotypes of original and adapted populations. Establishing populations from several discrete layers permits trend analyses of phenotypic changes and changes in allele frequencies. For ecophysiological studies, it is crucial to select experimental treatments that mimic past or ongoing environmental change, and the phenotypic trait that best illustrates adaptive changes Figure .4. When,Chlamydomonas reinhardtii P.A. Dangeard 1888 and a rotifer predator, which showed that changes in prey traits in response to predation influenced predator abundance over time scales of months and that there was a genetic component to these trait changes (Becks et al., A key potential of studies using temporal series of strains is to explore if and how populations can undergo evolutionarily significant changes in ecologically important traits on the same time scales as the changes that drive them (e.g., Becks, Ellner, Jones, & Hairston Jr., 3.2As seen above, undisturbed records of resting stages produced in the past and stored in coastal sediments may provide unique insights into past evolutionary and ecological trajectories. Alongside with their potential as historical records, however, “seed banks” also have the potential to provide an inoculum that will influence present populations through “dispersal from the past.” In order for old resting stages buried in the sediment to germinate, the sediments have to be disturbed and resuspended, so that germination can be triggered. Hairston and Kearns  argued tThe maintenance of a phytoplankton “seed bank” that incorporates germinated cells from viable resting stages formed over several years implies that there is generation overlap. Overlapping generations in a fluctuating environment allow for the maintenance of diverse populations and the coexistence of competitors (the storage effect, Warner & Chesson, Climate change is an important driver of long‐term species evolution and extinction rates, and “seed banks” of microbial organisms have been suggested to play an important role in adaptation to future environments (Lennon & Jones,


Salix purpurea were determined with the use of AFLP (amplified length polymorphism), RAPD (randomly amplified polymorphic DNA) and ISSR (inter-simple sequence repeats). The genetic relationships between 91 examined S. purpurea genotypes were evaluated by analyses of molecular variance (AMOVA), principal coordinates analyses (PCoA) and UPGMA (unweighted pair group method with arithmetic mean) dendrograms for both single marker types and a combination of all marker systems. The locations were assigned to distinct regions and the analysis of AMOVA  revealed a high genetic diversity within locations. The genetic diversity between both regions and locations was relatively low, but typical for many woody plant species. The results noted for the analyzed marker types were generally comparable with few differences in the genetic relationships among S. purpurea locations. A combination of several marker systems could thus be ideally suited to understand genetic diversity patterns of the species. This study makes the first attempt to broaden our knowledge of the genetic parameters of the purple willow (S. purpurea) from natural location for research and several applications, inter alia breeding purposes.In this study, the genetic diversity and structure of 13 natural locations of  Recent years have witnessed the growing popularity of natural remedies, which increased the demand for high-quality herbal material ,2. WilloSalix .,53.S. puterature ,29,54. Ta et al. ,55. The EcoRI and MseI restriction enzymes , and double stranded EcoRI+/− and MseI+/− adapters were ligated to restriction fragments. Restriction and ligation were carried out overnight at room temperature, and the obtained mixture was diluted (1:5). Preamplification was carried out using 1× Reaction buffer B 2SO4, 0.2% w/v Tween-20; Solis BioDyne, Tartu, Estonia), 2.5 mM MgCl2, 0.2 μM dNTP, 0.2 μM of the preselective primers MseI + C or G and EcoRI + A, 0.3 U FIREPol® DNA Polymerase  in 20 cycles , with a preliminary step (72 °C for 2 min) and a final step (60 °C for 30 min). In our study, 12 combinations of selective AFLP primers , followed by 24 cycles with annealing temperature of 56 °C, and a final polymerization at 60 °C for 30 min.AFLP amplification products  were gen primers  were tesThe obtained AFLP products were separated by capillary electrophoresis with the use of the ABI Prism 3100 genetic analyzer  and internal size standard GS 500 ROX™ . AFLP fragments were scored using the software Genotyper 3.7 .S. purpurea generating clear and repeatable bands , 0.2 mM of each dNTP , 0.4 μM of the primer and 0.625 U of DreamTaq™ Green DNA Polymerase . The PCR reaction was performed in 37 cycles  with an initial denaturation (94 °C for 10 min) and a final elongation (72 °C for 8 min). A total of 64 RAPD primers with 10 nucleotides each  were tested, and 62 primers were used in genetic diversity analyses of le bands . All samThe PCR-ISSR reaction mix 25 μL) contained 10 ng of DNA, 1× DreamTaq™ Green Buffer , 0.2 mM of each dNTP , 0.4 μM of the primer and 0.625 U of DNA polymerase . The reaction was carried out in 37 cycles  with an initial denaturation (94 °C for 1 min) and a final elongation (72 °C for 8 min). ISSR primers were selected based on literature data  μL conta,57. The The amplification products of RAPD and ISSR reactions  were sepS. purpurea: the number and percentage of polymorphic amplification products , the number and percentage of private products for each location , the scored products ratio (SPR) describing the number of scored products per primer/combination of primers, the number of detected products (Na) [uHe) [I) [STΦ) among the analyzed locations was calculated and presented in principal coordinate analyses (PCoA) [SD) matrix [S. purpurea genotypes. These analyses were also performed for single marker systems and for a combination of all methods.The results for all amplification products were transferred to a binary matrix where “1” denoted the presence and “0” denoted the absence of a product. Genetic diversity analyses were performed in GenAlEx 6.5  , AFLPsurcts (Na) , unbiasea) [uHe)  and the uHe) [I) . These puHe) [I) . Genetics (PCoA) . A genet) matrix  was used) matrix  to illusS. purpurea from natural localities. The observed genetic diversity is representative for willow species whose genetic structure was largely determined by the geographical regions of the studied localities. Purple willow stands are sometimes small and fragmented, which partially influences their diversity and differentiation. As expected, gene flow and migration could play an important role in wind-pollinated tree species whose small seeds are also widely dispersed by wind. This study relied on three well-established marker systems which are often used in genetic analyses of Salix populations. The results of single marker systems were mostly comparable, but a combined analysis of all systems is a reproducible and highly suitable method for analyzing genetic diversity and variation of S. purpurea. A combination of neutral genetic marker systems with different levels of genetic diversity revealed a significant discriminative power allowing for characterization and identification of genotypes and locations that constitute valuable breeding material for the pharmaceutical industry. However, the applied marker systems could be replaced in the next important breeding steps by new methods and technologies. Effective sequencing techniques reveal thousands of SNPs and contribute to the search for adaptive variation. Nevertheless, our study shows that genetic diversity and structure of natural plant locations can be effectively described with neutral, anonymous, but well-established molecular marker methods.This is the first study presenting the genetic diversity of S. purpurea locations expand our knowledge about the biology and biogeography of the species. They indicate that analyses combining various types of DNA marker systems produce more reliable results with regard to in understand genetic diversity patterns in the species. The resulting knowledge could be valuable and useful support for breeding programs of S. purpurea, conducting variety surveys and construction of mapping purple willow populations.The presented data relating to the genetic diversity and genetic relationships between


Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14%  of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97–99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1–89.2% attributable to differences within groups.The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179  Although the International Rice Research Institute (IRRI) genebank in the Philippines conserves the largest collection of rice germplasm, the Africa Rice Center (AfricaRice) genebank also conserves approximately 22,000 registered rice samples that represent five African indigenous wild species , as well as both modern and traditional O. glaberrima and O. sativa varieties. O. glaberrima accounts for approximately 14% of the collection at the AfricaRice genebank. Efforts have been made to characterize the O. glaberrima germplasm conserved at the AfricaRice genebank using phenotypic traits  investigate the genetic variation, relatedness and population structure of O. glaberrima collection available at the AfricaRice genebank and (ii) create core and mini-core sets of accessions that capture most of the genetic variation of the whole O. glaberrima collection conserved at the AfricaRice genebank. This will aid breeders to efficiently tap the available sequence diversity of the collection to create improved cultivars.Rice is the second largest crop in total global production after maize , genebank was initially used in this study (Supplementary Table Oryza species from the Office de la Recherche Scientifique et Technique d'Outre-Mer (ORSTOM) in France, Institute de Recherche d'Afrique Tropicale (IRAT) in France, the International Institute for Tropical Agriculture (IITA) in Nigeria, the Central Agricultural Research Institute (CARI) in Liberia, and the Kogoshima University in Liberia. Additional collections were made by AfricaRice scientists and collaborators to fill collection gaps of the different Oryza species growing across floating, mangrove, swamp, hydromorphic, irrigated lowland, rainfed lowland, and upland growing ecologies in Africa. Nearly 92% of the 2,223 accessions used in the present study originate from eight countries, which includes Nigeria (25.9%), Liberia (23.5%), Mali (12.2%), Togo (10.3%), Guinea Conakry (6.8), Côte d'Ivoire (Ivory Coast) (4.9%), Senegal (4.8%) and Burkina Faso (3.3%) . Seeds were directly sown in the field with a spacing of 0.20 m between rows and 1 m between accessions in August 2016 using randomized incomplete block design with a single replication; standard agronomic practices and inputs were used. For each accession, seven phenotypic traits were recorded on 5 randomly selected plants from the inner row of each plot using the Standard Evaluation System for Rice . Days to heading was recorded as the number of days from seeding until 50% of the panicles had headed. Total number of tillers per plant was counted at maximum tillering, while number of fertile tillers per plant were counted at maturity when about 50% of the panicles in a plot lost their greenness. Plant height was measured from the base of the plants to the tip of heads, excluding awns, at maturity. Panicle length was measured from the panicle neck to the panicle tip, excluding awns, at maturity.To update the phenotypic descriptors of the whole TM technology  and SNPs were called using the DArTsoft analytical pipeline (http://www.diversityarrays.com/dart-technology-package-dartSoft). A total of 31,739 SNPs were successfully called, of which approximately 18% of the SNPs had missing data points ranging from 0 to 79.7%, with an overall average missing data points of 11% (data not shown). The missing alleles of SNPs with <50% missing data points  method  using the scatter plot option with the following categorical variables: countries of origin and ecologies of accessions, and group memberships obtained from cluster analysis and the model-based STRUCTURE.For each SNP, polymorphism information content (PIC) values were computed using PowerMarker v.3.25  method implemented in DARwin v.6.0.14. Sphericity index  was used in deciding the most informative number of genotypes to be retained or removed. In the presence of redundant genotypes, the sphericity index curve would be linear (in a plateau) with the initial value obtained before any genotype is removed, which is indicative of the number of redundant genotypes to be removed. The curve increases as each redundancy is removed until it reaches another plateau, at which point the minimum number of genotypes that can be retained while conserving maximum diversity has been reached  and minimum (mini-core) number of Oryza species, nearly 60%  were polymorphic across the 2,223 O. glaberrima accessions. Minor allele frequency in the O. glaberrima data set ranged from 0.010 to 0.498  of the pairs of accessions had a genetic distance of < 0.05, which is extremely small as compared with just 2.7% of the pairs of accessions that had genetic distance > 0.300  were polymorphic among the remaining 2,179 accessions ) increased between K = 1 and K = 5, and mostly reached a plateau between K = 5 and K = 10, while the ad hoc statistic ΔK declined between K = 2 and K = 5  and PC2 (5.8%) revealed 5 groups  and highest (97.8%) polymorphism was observed within accessions originating from Chad and Nigeria, respectively, which may be due mainly to the size of samples from each country. Nucleotide diversity varied from 0.055 for accessions originated from Togo to 0.161 for those from Mali. When polymorphism and nucleotide diversity among ecology groups were compared, polymorphism was the lowest in mangrove (52.8%) and highest in irrigated lowland (100%), while nucleotide diversity was the lowest in upland (0.118) and the highest (0.160) in lowland irrigated/rainfed ecologies. Accessions that belong to the first group predicted based on cluster analysis and the model-based STRUCTURE analysis showed the least polymorphism (71.2–73.9%), while those accessions in the third group had the highest gene and nucleotide diversity  between pairs of countries (Supplementary Table O. glaberrima accessions from Liberia showed very great genetic differentiation from those from Cameroon (0.302), Chad (0.310), and Gambia (0.282), and great differentiation from those from Burkina Faso (0.221), Ghana (0.246) and Guinea Bissau (0.218). Accessions from Mali showed great genetic differentiation from those from Liberia (0.241), Cameroon (0.175) Chad (0.165) and Gambia (0.154), and moderate differentiation from all other countries. Similarly, accessions from Nigeria showed great differentiation from those accessions from Liberia (0.217) and moderate differentiation as compared with all other countries  the Liberia, Senegal, Guinea Conakry, Guinea Bissau, Burkina Faso and Mali group ; (ii) the Nigeria, Gambia, Cameroon and Chad group, and (iii) the Ghana and Togo group, which showed the greatest within-group differentiation  among eight ecologies varied from 0.026 to 0.250  than either countries of origin or ecologies. Pairwise FST values among accessions that belong to group 1 predicted based on cluster analysis and the model-based STRUCTURE was the highest (0.268–0.469) as compared to the other four groups. A random permutation test indicated that the proportion of variance attributable for all hierarchical levels were highly significant (p < 0.001).Results from partitioning of the overall molecular variance into different hierarchical levels revealed that differences in ecology and country of origin accounted for 10.8 and 18.1% of the genetic variation, respectively Table . Higher O. glaberrima germplasm  and 125 (3.3%), respectively. Both allele and genotype frequencies in the core and mini-core sets were the same as the whole set  frequency, and genetic distance. For the 3,834 SNPs that were polymorphic in the whole t Figure . As expet Figure . The proon Table . Using ton Table  and 6 econ Table .O. glaberrima collection; however, 46% of the polymorphisms were due to just 44 accessions  and O. longistaminata (30.3%) . In another study, we used the same set of 27,560 SNPs for genotyping 331 widely used rice genotypes in Africa, which includes 85 “New Rice for Africa (NERICA)” improved varieties, 11 “Advanced Rice for Africa (ARICA)” varieties, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes. Sixty six percent of the SNPs  were polymorphic across all 331 genotypes, of which 15,020 SNP (82.6%) were physically mapped in to one of the rice chromosomes. Of the 15,020 physically mapped SNPs, nearly 37, 43, 48, and 49%, respectively, were polymorphic within ARICA, japonica, indica, and NERICA genotypes ; therefore, the level of polymorphism observed in O. sativa and interspecific NERICA genotypes was from 2.5 to 3.5 times higher than that of O. glaberrima. Several previous molecular studies conducted on O. glaberrima have also reported a narrow genetic base compared to other Oryza species  were polymorphic within the remaining 2,179 g et al.  suggesteO. glaberrima is a selfing species with outcrossing rates ranging from 2 to 5% . This was seen with ~95% of the accessions, but the remaining ~4%  had observed heterozygosity exceeding 5%  than among countries and ecologies. Therefore, there was more genetic divergence among the predicted groups that was not fully explained by geographical proximity or ecology. The development of core and mini-core collections and selection of parental lines for breeding programs need to consider such genetic divergence.Knowledge of population structure is important for different purposes, including understanding the relative effect of evolutionary processes of migration/gene flow, mating system, selection, adaptation, and genetic drift on populations (including breeding populations) . In the maximization strategy, the main objective is to preserve the highest number of alleles, which is ideal for germplasm conservation, while the distance-based methods primarily aim to maintain most combinations of alleles in specific genotypes , which is appropriate in breeding , which allowed them in identifying 286 unique samples to represent a core collection (Egea et al., In rice, previously suggested core collections contain from 1% (Chung et al., O. glaberrima collection conserved at the AfricaRice genebank, and in creating a core and mini-core collections. Overall, O. glaberrima showed very low genetic variation, but clear population structure, primarily by countries of origin, and less so by ecology. The mini-core collection accounts ~16% of the whole O. glaberrima germplasm and represents all countries and ecologies of origin, and all groups predicted based on both cluster and population STRUCTURE analyses, proportionally to the size of each cluster. This mini-core collection will be highly valuable for various purposes, including allele mining and donor parent selection for developing new improved rice germplasm for target traits of interest.The present study demonstrated the usefulness of DArTseq in effectively characterizing the genetic variation and population structure of All relevant results are included within this article and its additional files. The original DArTseq data are available from the corresponding author on request.MNN conceived, designed, and supervised the experiments, secured funding, and partly drafted the paper; ACG, SBK, DDT, and AGo were responsible for sample preparation, phenotyping, DNA extraction and/or compilation of passport information; KS analyzed the data and wrote most part of the paper; XP contributed to data analysis to create core and mini-core collection; MSo, MSi, and AGh provided valuable suggestions on the paper; MLW contributed to and edited the paper. All authors read and approved the paper.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Erianthus arundinaceus is not only a candidate plant for sugarcane breeding programs, but also a potential bioenergy grass. Genetic variation that is affected by geographic environments and ploidy level is very important for the utilization of Erianthus arundinaceus. In this study, effects of geographic environments and ploidy level on genetic variation were studied through analyzing the genetic diversity, genetic similarity and cluster analysis of 46 E. arundinaceus materials from natural habitats in China by using 7 ISSRs and 15 SSRs. Results showed that: 1) Seven ISSRs generated total 66 bands, of which 77% were polymorphic bands, the Nei's genetic similarity coefficient of tested materials ranged from 0.642 to 0.904 with an average value of 0.765. Fifteen SSRs generated 138 bands, of which 81% were polymorphic bands, the Nei's genetic similarity coefficient of tested materials ranged from 0.634 to 0.963 with an average value of 0.802. The results indicated great genetic diversity existed in the tested materials. 2)The tested materials were clustered into 3 groups and 7 subgroups, which demonstrated a strong geographic effect on variation of the local E. arundinaceus, and weak relationship was found between genetic distance and geographic distance. Five tetraploid materials were not clustered together, and were clustered together with materials from similar geographical location. 3) The genetic variation and cluster results were affected by geographic landforms and environments, the gene flow was blocked by Ocean and mountains, and promoted by river. The effect of ploidy level on genetic variation was little. E. arundinaceus is a warm-season, and caespitose perennial tall grass in Erianthus (Poaceae) native to China which are widely distributed in south China . After electrophoresis, the gel was stained in AgNO3 solution. The gel image was then photographed by Gel Doc(TM) XR System .Fifteen SSR primer pairs were synthesized by Shanghai Biochemical Engineering Technology  . PCR reaClearly amplified PCR bands were visually scored for presence as “1” or absence as “0” and input into an Excel matrix for the following analysis. Total bands, polymorphic bands and percent polymorphic bands were figured out respectively. A UPGMA tree based on Nei’s  genetic Seven ISSR markers which produced clear and previous bands were screened out from 100 random markers. A total of 66 bands were obtained through these 7 markers after amplification, of which 51 bands were polymorphic . For eacA total of 138 bands were obtained by 15 SSR markers from amplification, of which 112 bands were polymorphic . Five toFor ISSRs, values of genetic similarity (GS) ranged from 0.634 to 0.963 with an average of 0.802 among the 46 materials, 0.634 to 0.963 with an average of 0.802 in the materials of Sichuan, 0.835 to 0.902 with an average of 0.878 for Yunnan materials, 0.795 to 0.907 with an average of 0.849 for Guizhou materials, 0.833 to 0.963 with an average of 0.887 for Guangxi materials, 0.841 to 0.962 with an average of 0.865 for Guangdong materials, and 0.892 to 0.986 with an average of 0.865 for Hainan materials, respectively .For SSRs, values of GS ranged from 0.642 to 0.904 with an average of 0.765 in the 46 materials, 0.744 to 0.907 with an average of 0.821 for the materials from Sichuan, 0.776 to 0.912 with an average of 0.828 for Yunnan materials, 0.807 to 0.877 with an average of 0.851 for Guizhou materials, 0.807 to 0.896 with an average of 0.849 for Guangxi materials, 0.805 to 0.904 with an average of 0.859 for Guangdong materials, and 0.807 to 0.915 with an average of 0.872 for Hainan materials, respectively .For ISSRs, the UPGMA tree was constructed based on the values of genetic distance. Total 46 materials were divided into 3 groups . Group 1For SSRs, the UPGMA tree was composed of 3 major groups from 46 materials which was consistent with the results of ISSRs . Group 1The Mantel tests indicated that medium relationship existed between genetic distance and geographic distance among these materials . The relationship between SSR gene diversity (HE) values and ISSR HE values was in a medium high level .E. arundinaceus. The first impact was that the low level of genetic diversity of island E. arundinaceus due to ocean isolation. Materials with similar geographical distances were gathered into different groups because of the isolation effects of Qiongzhou Strait. For example, E40  was located at a distance of 128.98 km from E38  and 267.34 km from E45  although it was separated from E38 and gathered together with E45. The second impact showed that the low level of genetic diversity of E. arundinaceus was generated by mountains isolation, which caused materials with similar geographical distances in different groups due to the isolation effects of the mountains. For example, E23  was located at a distance of 470.90 km from E18  and 651.20 km from E38  although it was separated from E18 and gathered together with E38. The third impact was caused by the river systems which was the reason for the materials from the same basin or from different basins gathering together at the river confluence reaches. The fourth impact that the effects of ploidy level on cluster was identified little in this study because 5 tetraploid materials from different geographical locations were not clustered together.There were 4 impacts of geographic environments and ploidy level on cluster structure of E. arundinaceus in this study were 77% (ISSR) and 81% (SSR), lower than 99.3% (AFLP) in the study of Cai [E. arundinaceus in China. The level of genetic diversity varied among the materials in different regions of China. The materials from Hainan province showed the lowest level of genetic diversity and the value of GS was 0.865 and 0.872 for ISSR and SSR, respectively. The genetic diversity level of E. arundinaceus in this study was similar with that detected in Cai's study in which was 0.846.The percentage of polymorphic bands (PPB) of y of Cai , higher y of Cai ,15, 69.2y of Cai , respectE. arundinaceus in this study was similar with that detected in Cai's study [E. arundinaceus was generated by ocean isolation, which may have effectively blocked gene flow from germplasm outside the islands, consequently reducing genetic diversity [The genetic diversity level of 's study . These riversity .E. arundinaceus, and influence the diversity of E. arundinaceus as well as the genetic relationship among different groups of E. arundinaceus [The “isolation effect” of ocean not only affected the level of genetic diversity, but also the cluster results of materials in different regions. From the cluster analysis of ISSRs and SSRs, the materials from Hainan, Guangxi except Nandan, and Guangdong province were divided into the same subgroup, and the materials from Hainan were separated clearly from others, which showed a large influence of the Qiongzhou Strait on the cluster structure. Similarly, mountains, especially the high mountains, could impact on the cluster results. From the cluster analysis of SSR, the materials were divided into 3 groups. The materials from Sichuan and a material from Hanzhong of Shanxi around Sichuan Basin formed the group 1. Four materials seperated by the Yunnan-Guizhou Plateau from southern tip of Yunnan were clustered in the group 2. The materials from Guizhou, Guangxi, Guangdong and Hainan province formed the group 3. The group 3 was located in the south of Sichuan and in north of the Yunnan, which were just separated by mountains of the Yunnan-Guizhou Plateau. The cluster analysis of ISSRs was consistent with SSRs. Therefore, the ocean and the big mountains could hinder the gene exchange of dinaceus .E. arundinaceus may be promoted through confluence of river systems. Meanwhile, the materials from near location tended to be grouped together through gene flow, due to E. arundinaceus's characteristic of outcrossing with higher level of gene flow [E. arundinaceus could be blocked by geographical environment (like ocean and mountains). However, the blocked effects of geographical environments on gene flow could also be removed by rivers to provide channels for gene flow, and promote the gene exchange among the materials in the same river basin. Thus, the river systems should be an important factor for the consistent genetic background among the materials from the same river basin.The group 1 from cluster analysis of ISSRs was composed of 2 subgroups. The subgroup contained the materials from the middle reaches of Minjiang River basin. The second subgroup included the materials from the Qinyi River basin, one material from the middle reaches of Minjiang River basin, and one material from the lower reaches of Minjiang River basin. For the two subgroups in group 1 SSRs, the materials from the middle reaches of Minjiang River basin were divided into one subgroup, and the materials from the Qinyi River basin and the lower reaches of Minjiang River basin were divided into another subgroup. From the cluster analysis of ISSRs and SSRs, some interesting results were found that the materials from the same river basin were firstly grouped together, while some materials from different river basin were also grouped together, such as the materials from the Qinyi River basin and the lower reaches of Minjiang River basin, which indicated the gene exchange of ene flow . Gene flE. arundinaceus, which could hinder or promote the gene exchange between different regions. Previously, genetic variation was affected by geographical environments through limited gene exchange [The mantel tests showed a weak associated relationship existed between genetic distance and geographic distances among these materials. Because the geographical environment has a great influence on the genetic diversity of exchange , 25, whiE. arundinaceus materials had a high level of genetic diversity although the correlation coefficient between SSR gene diversity (HE) values and ISSR HE values was small . For the geographic factors, the results indicated that the ocean and the big mountains could hinder the gene exchange of E. arundinaceus and the gene exchange of E. arundinaceus could be promoted through confluence of river systems.In this study, both ISSRs and SSRs revealed that the native Chinese Dactylis glomerata was studied by Zeng, which showed the ploidy level was the primary factor of the effect on Orchardgrass cluster structure and the genetic variation. And the genetic diversity of among the materials with same ploidy level were smaller than the materials with difference ploidy level [E. arundinaceus germplasm since gene flow between plants of altered ploidy is likely limited [E. arundinaceus. The effects of polyploidization on the plant genome may be little in some polyploid species, which led to chromosome recombination and sequence elimination. Moreover, polyploidization were not tested in these species [Polyploidization is a common phenomenon in plant evolution which is also useful for the formation of new species . Shock ody level . In prev limited . However species .S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file.


Streptopelia decaocto) is one of the most successful biological invaders among terrestrial vertebrates. However, little information is available on the genetic diversity of the species. A total of 134 Eurasian Collared Doves from Europe, Asia and the Caribbean (n = 20) were studied by sequencing a 658-bp length of mitochondrial DNA (mtDNA) cytochrome oxidase I (COI). Fifty-two different haplotypes and relatively high haplotype and nucleotide diversities (Hd±SD = 0.843±0.037 and π±SD = 0.026±0.013) were detected. Haplotype Ht1 was particularly dominant: it included 44.03% of the studied individuals, and contained sequences from 75% of the studied countries. Various analyses  distinguished 2 groups on the genetic level, designated ‘A’ and ‘B’. Two groups were also separated in the median-joining network and the maximum likelihood tree. The results of the neutrality tests were negative  and significantly different from zero (P≤0.001) for group A, whereas both values for group B were positive  and not significant (P>0.05). Statistically significant positive autocorrelation was revealed among individuals located up to 2000 km apart . The present results provide the first information on the genetic diversity and structure of the Eurasian Collared Dove, and can thereby serve as a factual and comparative basis for similar studies in the future.The Eurasian Collared Dove ( Streptopelia decaocto) is one of the most successful biological invaders among terrestrial vertebrates [2 [The Eurasian Collared Dove , cytochrome oxidase I (COI), NADH dehydrogenase subunit 2 (ND2) and the nuclear gene β-fibrinogen intron 7 (FIB7). Despite the lower homoplasmy presented in the FIB7 sequences, mitochondrial genes provided better resolution for the phylogeny of Streptopelia. Other barcoding and phylogenetic studies were later also carried out mostly in the COI region [Although the species attracts wide scientific interest, very little is known about its genetic diversity and structure. In spite of the fact that genetic studies may reveal such elements of the expansion that would be hidden if only classical ornithological methods are used . Expansion can be caused by genetic change in the peripheral area of the species' geographical range ,17. AlreI region –23.Here we present the results of the first large-scale study on the variability of the mitochondrial COI region in Eurasian Collared Doves from Europe, Asia and the Caribbean. We determined the level of genetic variability, the demographic events and the possible structuring of the populations, and looked for association between genetic similarity and geographical distance.calamus size–the Eurasian Collared Dove’s feathers do not contain enough blood for the extraction method used in the study. Muscle tissues and eggshells were stored in Eppendorf tubes filled with 96% ethanol at -20°C.Samples (n = 134) were collected from altogether 14 countries between 2013 and 2015 . In the DNA was extracted from feathers (n = 86) using a special method developed by Vili , and fro5'-TTCTCCAACCACAAAGACATTGGCAC-3'; reverse: 5'-ACGTGGGAGATAATTCCAAATCCTG-3'. The 10 μl reaction volume contained 1 μl dNTP (2 mM), , 2 μl buffer (5 u/μl) , 2 μl MgCl2 (2 mM) , 0.4 μl primer (10 pmol/μl) , 0.2 μl GoTaq polymerase (1.25 U) , 2.4 μl dH2O and 2 μl DNS template.Amplification of the 749 bp fragment of the mitochondrial DNA COI was performed using the following primer pairs  forward:PCR reaction conditions were the following: 94°C for 5 minutes, then for 35 cycles: 94°C for 1 minute, 60°C for 1 minute, 72°C for 1 minute, followed by 72°C for 5 minutes. PCR products were checked under UV illumination and, if considered useable, prepared for sequencing. Prepared samples were stored at -20°C until sequencing. Sequencing was performed by Macrogen Europe Laboratory in the Netherlands.https://net.jogtar.hu/jr/gen/hjegy_doc.cgi?docid=a0400079.fvm).Moulted primary feathers (n = 86) were collected, but muscle tissue (n = 45) and hatched eggshells (n = 3) were also collected. Sampling of moulted feathers and eggshells is considered as a non-invasive method, which meets the standards of science ethics and does not require special permits. Feather samples from the different countries were obtained from collaborating ornithologists, and were used with their permission. Fresh muscle tissues were sampled only in Hungary from legally hunted unprotected Eurasian Collared Doves or from individuals hit by cars on roadsides. Animals were not shot only for the purpose of this study. No ethics statement was required. Hunters collected samples in accordance with Hungarian national regulations on Eurasian Collared Dove management (decree: 79/2004. (V. 4.) FVM rendelet a vad védelméről, a vadgazdálkodásról, valamint a vadászatról szóló 1996. évi LV. törvény végrehajtásának szabályairól d) and nucleotide diversity (π)) were determined by ARLEQUIN 3.5.2. software [Streptopelia decaocto (GenBank: KX372273) was used as a reference sequence for the determination of variable positions. All the available Eurasian Collared Dove sequences  was used as outgroup.An analysis of molecular variance (AMOVA) –30 was psoftware . The boosoftware  softwaresoftware  and implsoftware . PhasianFs [D [SSD [Population structure and the most likely genetic classification were determined using the admixture model of the STRUCTURE 2.3.4 software , which cFs , Tajima'Fs [D  and the  [D [SSD  and Harp [D [SSD  with sigSpatial autocorrelation analysis was performed using GenAlEx 6.501 software , 41. ThiBased on the 658 bp mitochondrial DNA COI sequence of 134 animals, 171 polymorphisms and 52 haplotypes were identified . All hapA haplotype network was created from data of the present study and 18 Genbank mtDNA COI sequences . Ht1, whIn addition to the haplotype network tree, a phylogenetic tree  providedST = 0.912, p = 0.000), and indicated strong genetic differentiations between groups ‘A’ and ‘B’. Variation within (98.70%) and among populations (1.3%) was also analysed for all samples as one group , which can support the weak geographical genetic structure in our samples. However, the analysis based on the two newly described groups gave the opposite result , whereas Fu FS and Tajima D for group ‘B’ were positive and not significant, indicating a non-expanding population.In accordance with the network patterns , Fig 2, S. decaocto located up to 2000 km apart , suggesting that individuals of S. decaocto located within 2000 km of each other were more similar genetically than expected at random, whereas those individuals separated by greater distances were less similar than expected. The correlation value was considerably higher in the 1000 km class , then steeply declined, indicating that genetic structuring can be detected up to this distance.As shown by Europe has been colonised by the Eurasian Collared Dove in less than a century. This remarkable achievement has attracted keen interest from researchers, although information on the genetic diversity and structure of the species has been scarce. In the present work we used only a female-specific marker, and analysed mtDNA COI region sequences from 152 samples (134 of our own samples and 18 from GenBank) covering a wide distribution range. High genetic diversity and two genetic structures without geographical localisation were detected. To our knowledge, similarly detailed studies on genetic diversity and structure have been very rare even in the case of other Columbidae species.Columbidae species studied all over the world using different parts of mitochondrial DNA as markers [Streptopelia turtur) from Europe  yielded 40 haplotypes [Sylvia atricapilla) [Perisoreus canadensis) [Terastes bonasia) [Accipter striatus) and the Great Blue Heron (Ardea herodias) [The number of polymorphisms (171) and haplotypes 52) were high in the studied species, the European Collared Dove, which suggests population expansion , similar markers –48. For plotypes . The higcapilla) , the Greadensis) , the Hazbonasia) , but con were higerodias) . Certainerodias) . Lee [55erodias) .S. decaocto in the Netherlands [Grus canadensis) [Chiroxiphia caudata) [Tetrao urogallus) [Passer domesticus) [S. decaocto was in agreement with the results of our analysis of population differentiation.Our 134 sequenced animals together with all 18 mtDNA COI sequences obtained from GenBank were aligned in order to extend the geographical area studied. An NJ tree was constructed. The most frequent haplotype was Ht1, previously described in herlands . The topherlands . This stadensis) , the Blucaudata) , the Wooogallus)  and the esticus) . In the Spermophilus citellus) [Anthus berthelotii) [Passer domesticus) [Alectoris rufa) [Streptopelia turtur) [Passer domesticus) [Zenaida galapagoensis) [Columba janthina nitens) [Zenaida galapagoensis) among the five Galapagos Islands [The AMOVA test clearly indicated that 91.25% of the genetic variation occurred between groups ‘A’ and ‘B’ , which citellus)  and Berthelotii) . Howeveresticus) , the Redis rufa)  and the  turtur) . A low lesticus) , the Galgoensis)  and the  nitens) . Geograp Islands , where n Islands  did not FS and Tajima’s D test, analysis for mismatch distribution to study the historical demographic expansions of S. decaocto, which could have an important role in the patterns of genetic variability. All tests and analysis supported our hypothesis about the demography history of the newly described groups ‘A’ and ‘B’, indicating the rapid and sudden expansion of group ‘A’. Similar results were found for the Chinese Egret (Egretta eulophotes) [Columba janthina) [The presence of two groups was further verified by the results of the analysis using STRUCTURE . In thisophotes)  and the anthina) .S. decaocto located within 2000 km of each other were genetically more similar than expected at random, whereas those individuals separated by greater distances were less similar than expected. Other studies concluded that short-distance (<50 km) bird movements serving natal dispersal are typical of the Eurasian Collared Dove, however a 650-km dispersal distance is also observed in the species based on banding records [Columbidae are usually recognized as good flyers, potential dispersal associated with such capabilities cannot be observed in every case [Statistically significant positive autocorrelation suggested that individuals of  records , 54. Now records , 67–70. ery case  in spiteResults from this study, based on mtDNA COI sequences, showed high genetic diversity, signs of global demographic expansion and two genetically–but not geographically–separated groups in Eurasian Collared Dove. Given that mtDNA variation in this work is highly structured genetically, a strong female natal philopatry is suggested. However these results are still not decisive, it is necessary to use nuclear data (microsatellite DNA) and more samples in further analysis.S1 Table(PDF)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S1 FigRate of change in the log probability (prob.) of data between successive runs of K (ΔK).(TIF)Click here for additional data file.S2 FigThe plot depicts results obtained from all geographic regions. The analysis considered geographic distances with even distance classes of 1000 km. Lines “U” and “L” represent the 95% confidence values of the null hypothesis (there is no structure), with “r” representing the correlation coefficient.(TIF)Click here for additional data file.


I.‘Genetic testing can reveal crucial information to guide your training and nutrition strategies based on predispositions built into your DNA. Genetic testing identifies the ideal nutrition, training and recovery strategies for you and helps explain why athletes given the same training and nutrition plans respond differently. In short gene testing provides the ultimate in personalized nutrition and training guidance…’Direct-to-consumer (DTC) genetic testing has been in the news in recent years, especially since November 2013, when the US Food and Drug Administration (FDA) shut down 23andMe, one of several firms that offered people general health information based on their genetic test results.It seems inevitable that, unless the regulatory environment changes, this trend will continue, with genetic testing being offered to the public for an ever-increasing range of reasons not directly related to disease. In this paper, we map the policy issues associated with the marketing and use of genetic testing products outside of the context of disease risk. We focus on companies and providers that offer testing for a wide range of genetic traits, and consider the potential implications of offering these products for use in children and adolescents. While the size of the market for these services remains unknown, it is probably still relatively small.For example, the present analysis affords an opportunity to consider the possible harms, if any, and available policy options for regulating genetic testing services not focused on disease risk and that reside on the margins of credibility. As we will see, some tests are being marketed for purposes that are clearly scientifically absurd (eg for targeting homeopathic therapies and naturopathic detoxification regimens)Looking at these, and other,II.Numerous policy guidelines have addressed the genetic testing of minors in the clinical context. Most of these guidelines were crafted in response to the availability of disease and predisposition testing.If a minor is suspected of having a condition where obtaining genetic information is considered clinically useful—be it for diagnostic or treatment purposes—testing is, in general, viewed as an appropriate course of action.Given these concerns, it is not a surprise that most clinical guidelines and position papers are also critical of DTC genetic testing companies that test minors. The most recent guideline on the testing of minors was published by the American Academy of Pediatrics and the American College of Medical Genetics and Genomics. In their statement, both societies ‘strongly discourage the use of direct-to-consumer and home kit genetic testing of children because of the lack of oversight on test content, accuracy, and interpretation’.Existing policy documents, however, also note that not all concerns apply equally to all types of tests. The UK Human Genetics Commission, for example, acknowledged the importance of considering both the type of test provided and the impact of that test. In situations where tests could have a ‘significant or potentially detrimental impact on consumers’ appropriate support and professional advice is more important than in situations where testing might not create that type of impact.This distinction between ‘medically significant’ genetic tests on one hand and lifestyle-oriented, recreational, or informational types of genetic tests on the other hand creates room for a policy debate. Do these latter types of services that are aimed at issues not tied directly to health—such as athletic ability—or do not relate to something of immediate clinical relevance—such as diet—but that are often based on less-than-robust science, give rise to similar potential harms as ‘medically significant’ tests? Are the potential harms significant enough to trigger regulatory oversight?Most policy debates have focused on tests pertaining to predisposition to disease offered by DTC companies such as 23andMe and there has been little attention, at least from a policy perspective, on these more lifestyle-oriented genetic testing services. Indeed, many of the policy responses, such as those by professional societies, seem to assume, without much, if any, discussion, that there is potential for real clinical or health relevance, which requires oversight. Below we review in greater detail some of these ‘lifestyle’ types of tests and the potential policy issues they raise, especially when made available for use in children and adolescents.III.(i)Companies throughout the world offer genetic testing for the purpose of assessing athletic ability. Atlas Sports Genetics, for example, provides a testing service that promises to ‘show athletes, trainers and interested individuals where their genetic advantage lies’.We know of no evidence about how many minors (or their parents) are using these services.In addition, abundant evidence shows that adolescents will often go to great lengths to gain a competitive edge in their chosen sport. Given that a significant portion of teenagers are willing to take illegal performance enhancing drugs,The actual performance value of these tests, if any, is far from clear. Can these DTC genetic testing services really provide useful, actionable information? The existing evidence on point can, at best, be described as equivocal. There is absolutely no doubt that genes play an important part in athletic performance.(ii)One of the core concepts behind personalized medicine is that genetic testing can be used to tailor our lifestyles in order to maximize health promotion.In addition to being marketed directly to consumers, genetic testing services are also being offered by a range of health care practitioners, such as naturopaths,Once again, it is unclear how big the genetic testing market is for these ‘healthy living’ type of services or how many children and adolescents are being tested. But it is worth noting that there are some musings in both the academic and popular media about testing children for a genetic predisposition to obesity.Can these tests really provide useful information that will change behavior? Is a personalized approach really more effective?First, the associations being tested are usually very weak. Even the most scientifically valid genetic tests are far from being highly predictive of, for example, a future risk of obesity.Second, there is no evidence that people use this information to make behavioral changes.IV.Given the questionable scientific validity or predictive power of many of these testing services and the lack of any evidence of clear health benefit, what are the harms of testing children and adolescents in this context and are they significant enough to warrant a policy response?(i)Concerns exist about direct psychological or physical harms to children that could result from genetic testing. In the context of ‘healthy living’ tests, it is possible that parents purchasing these tests to use on their children could have misunderstandings about the validity and relevance of these tests which could lead to harmful interventions. For example, testing children for obesity or their ability to tolerate second-hand smoke might lead to physical harm if parents unnecessarily restrict their children's dietsThere is also the possibility that children or adolescents might face subtle forms of stereotyping from parents, coaches, schools, peers, and others based on the mistaken belief that the information is more powerful than it is.While studies examining how people actually react to genetic information regarding predisposition for disease show that receiving this information generally does not have a significant effect on people's psychological outcomes (eg it does not result in significant anxiety or depression),(ii)As noted above, parental genetic testing of children raises concerns about respect for children's autonomy, including the decision to pursue testing when they reach the age of capacity. In clinical genetic testing, the norm is to let children exercise their autonomy by making choices when adults about conditions that do not affect children. Whether the reasons for this position exist to the same extent in relation to athletic and ‘healthy living’ types of genetic testing is less clear.On one hand, the fact that the information provided by many of these tests is poorly predictive and of no real benefit may weigh in favor of preserving a child's ability to decide whether or not to undergo genetic testing when the child has sufficient capacity. On the other hand, given the poor quality of information that is often provided it is questionable in some cases how much genetic information is actually being disclosed. For example, test results indicating a strong ‘propensity for teenage romance’ or poor ‘general wellness’ are not likely a reflection of a child's actual genetic make-up. The harm here appears to be more a problem of misleading claims in the marketing and advertising of these tests. To the extent that the information from these tests limits a child's or adolescent's ability to make decisions that are consistent with their goals, however, there may nevertheless be an autonomy concern. This concern may be more pronounced in some tests, such as many of the athletically focused tests, which actually look for specific variants of a particular gene and have the potential to limit a child's ability to explore different sports and activities. However, the question then becomes whether disclosing a child's genetic predisposition for endurance sports, for example, warrants the same kind of protection as disclosing a child's genetic predisposition for developing disease.If an individual's genetic information in and of itself, regardless of its lack of clinical relevance, is something that only autonomous individuals should have access to and control of, then perhaps all forms of athletic and ‘healthy living’ genetic testing of children by parents should be prohibited. However, unless something about genetic information is inherently different, perhaps inherently more convincing, it is difficult to rationalize why a genetic indicator of a child's sprinting ability, for example, should be prohibited while empirical indicators  should not.In the clinical genetic testing context, what's at stake is the child's ability to decide whether or not to discover his or her genetic likelihood of developing future health problems. In the context of an athletic or ‘healthy living’ genetic test that does not provide any clinically relevant or meaningful health information, the impact of the information will rarely if ever reach that level.It is also important to consider the autonomy interests of the child or adolescent who wants to undergo genetic testing and the potential for restrictive policies to interfere with a child's right to know his or her personal genomic information. Should the choice to undergo athletic and ‘healthy living’ genetic testing be treated like a medical decision where a child or adolescent has to reach a certain level of capacity to be able to consent? Or should these tests be treated like any other consumer product, and if so should there be age restrictions for access as is the case with alcohol, tobacco, and pornography? Age restrictions on the ability to purchase these products exist because there are demonstrated health risks and social harms associated with their use. In the case of DTC genetic tests where proof of harm remains lacking, it is less clear whether children and adolescents should be prohibited from purchasing these testing services if they so wish.(iii)The lack of any demonstrated benefit for these types of athletic and ‘healthy living’ tests certainly suggests that charging money for them—either to parents or children and adolescents themselves—under the auspices of providing useful information is financially exploitative. Many of these companies seem to be simply leveraging the excitement surrounding genetics to market productsV.While few would dispute the idea that these kinds of athletic and ‘healthy living’ genetic tests raise social issues, are the potential harms significant enough to trigger a regulatory response? For example, in the absence of evident harmsSome European countries have taken a restrictive stance on genetic testing more generally with legislation that limits or prohibits DTC genetic testing.There may also be a role for health authorities and regulatory agencies to address these genetic tests. The FDA in the United States, for example, asserted its jurisdiction over 23andMe's test for disease predisposition on the basis that this test was a ‘diagnostic device’.service does not.However, it is less likely that athletic DTC genetic tests or some of the ‘healthy living’ tests with less clinical relevance would similarly come within the FDA's jurisdiction. Additionally, it is unlikely that the analogous regulatory bodies in Canada or the United Kingdom would have jurisdiction over any of these tests as these bodies have taken the position that although DTC genetic testing kits themselves may fall within their respective jurisdictions the actual testing As many of the potential harms associated with these types of genetic tests pertain to a lack of accurate information and understanding about the validity and relevance of the genetic information provided, there may be a role for regulatory bodies responsible for enforcing truth in advertising standards. These bodies address complaints about potential misrepresentations in advertisements and have the authority to limit the types of representations that companies can make. For example, the US Federal Trade Commission (FTC) recently took action against GeneLink, Inc., which offered genetic testing in conjunction with the sale of nutritional supplements that were purportedly tailored to its customers’ DNA profiles. The FTC issued an order prohibiting GeneLink from making any representations ‘about the health benefits, performance, or efficacy’ of its product ‘unless … possesses and relies upon competent and reliable scientific evidence that is sufficient in quality and quantity based on standards generally accepted in the relevant scientific fields’.In addition, it may be useful to provide educational interventions aimed at physicians or the general public about the lack of scientific validity and relevance of many of these tests. There is evidence that consumers of disease-risk DTC genetic testing sometimes consult health care providers about test results.Finally, future research should focus on evaluation of the more subtle and nuanced benefits and harms of athletic and ‘healthy living’ genetic testing of children and adolescents. Socially relevant outcomes would include impact on self-esteem, feelings of vulnerability, and experiences of social stigma and discrimination, among others. The lack of sufficient evidence of the benefits and harms of these services highlights the need for further empirical research to guide policy development.


Congenital malformations (due to genetic causes) represent a hidden danger for animal production, above all when genetic selection is undertaken for production improvements. These malformations are responsible for economic losses either because they reduce the productivity of the farm, or because their spread in the population would decrease the total productivity of that species/breed. River buffalo is a species of increasing interest all over the world for its production abilities, as proved by the buffalo genome project and the genetic selection plans that are currently performed in different countries. The aim of this review is to provide a general view of different models of congenital malformations in buffalo and their world distribution. This would be useful either for those who performed buffalo genetic selection or for researchers in genetic diseases, which would be an advantage to their studies with respect to the knowledge of gene mutations and interactions in this species.Bubalus bubalis) world population, the present status of the congenital malformations, due to genetic causes, to identify their frequency and distribution in order to develop genetic breeding plans able to improve the productive and reproductive performance, and avoid the spreading of detrimental gene variants. Congenital malformations most frequently reported in literature or signaled by breeders to the Department of Veterinary Medicine and Animal Production of the University Federico II  in river buffalo are: musculoskeletal defects  and disorders of sexual development. In conclusion this review put in evidence that river buffalo have a great variety of malformations due to genetic causes, and TH and omphalocele are the most frequent and that several cases are still not reported, leading to an underestimation of the real weight of genetic diseases in this species.The world buffalo population is about 168 million, and it is still growing, in India, China, Brazil, and Italy. In these countries, buffalo genetic breeding programs have been performed for many decades. The occurrence of congenital malformations has caused a slowing of the genetic progress and economic loss for the breeders, due to the death of animals, or damage to their reproductive ability or failing of milk production. Moreover, they cause animal welfare reduction because they can imply foetal dystocia and because the affected animals have a reduced fitness with little chances of survival. This review depicts, in the river buffalo ( The world’s water buffalo population is about 168 million: 95% are in Asia , 2% in Africa (Egypt), 2% in South America and the Caribbean, 1% in Europe and Oceania [Breeding programs are carried out in many countries, such as China, India, and Brazil; however, Italy represents the international point of reference for buffalo breeding as a result of the innovations brought in management, dairy technologies, cheese manufacturing, feeding, and reproduction. Despite the aim of breeding plans being to obtain healthy animals with good morphology and high production, it is not uncommon for animals to be born showing congenital defects due to gene mutations inherited from the parents or caused by new mutations or changes to the DNA. The occurrence of congenital malformations, above all when due to gene variants passed down by parents, in livestock production, causes the slowing of genetic progress, economic loss for the breeders due to the death of animals, or damage to their reproductive and productive ability, such as milk production. Moreover, congenital malformations imply a reduction of animal welfare directly in the affected animals because they have a reduced fitness and a lower adaptability to farming conditions and indirectly because can provoke foetal dystocia. To study the genetic bases of these diseases, and to find strategies to eradicate them in livestock populations is, for breeders, an issue to avoid economic losses .With respect to the worldwide presence of congenital malformations in River buffalo, there are few papers, and a systematic report is still lacking. Purohit et al.  reportedBubalus bubalis) in the literature or that have been signaled (and still unpublished) to the Department of Veterinary Medicine and Animal Production of University of Naples Federico II by ANASB and veterinarians, most likely due to genetic causes, according to available information, because of their increasing impact in the world livestock production chain. Moreover, the completion of buffalo genome sequencing and annotation will allow the identification of gene mutations underlying these malformations. This paper aims to provides an overview of the congenital malformations reported in river buffalo  is a congenital malformation characterized by total or partial lack of distal limb structures. It is also known as congenital amputation, since the malformed limb is similar to a stump normally developed proximally and distally, but cut off at different points. In river buffalo, and particularly in MIRB, this is the most frequent congenital malformation diagnosed previously and, similar to other species, all of the cutaneous annexes are present so that in the terminal part of the stump, the sketch of hooves are visible. It was reported for the first time in some farms located in the province of Salerno , and theSMARCA4 and WNT7A genes are the main drivers for this type of TH malformation. Moreover, the accumulation of homozygous mutations in modifier genes appears to impact the severity of the TH phenotype, resulting in animals that vary from the lack of a single transverse bone in one limb to the complete lack of both hindlimbs with malformation of one forelimb [At birth buffalo calves with TH are alive and lively, the only symptom is difficulty in moving due to the malformed limb or limbs. At necropsy they show no macroscopic lesions incompatible with life and their karyotype is normal. In forelimb , and proforelimb , that obforelimb . In bothISG15, HES4, and AGRN genes in the American Angus breed [CHRNB1 [SMN gene on BTA20q13.1 [Arthrogryposis is a congenital disease characterized by non-progressive joint contractures that can affect upper or lower limbs and/or the vertebral column, leading to various degrees of flexion or extension limitations, evident at birth. It is not a specific diagnosis, but rather a clinical finding of congenital contractures causing severe mobility difficulties in affected individuals. Arthrogryposis has been reported in livestock and pets and is often associated with muscle atrophy or other malformations. It has more than one etiological factor, including physical limitation of in utero movement causing fetal akinesia/hypokinesia syndrome, maternal illness, intrauterine viral infection , toxin exposure, and genetic disorders affecting the fetus . In Horsus breed ; and in  [CHRNB1 ; furtherA20q13.1 . In SoutA20q13.1  reportedA20q13.1  observedA variety of other musculoskeletal malformations have been reported in river buffalo. Mehmood et al.  describecampylorrhacchis contorta in a calf born from a primiparous Indian buffalo; the fetus was under-weighed and showed brachignathism/parrot mouth, malformation of the pelvis, lumbar, and sacral regions, and ankylosis of all of the limbs with atrophy of musculature. According to the author, this malformation being a congenital defect is most likely caused by a defective gene or a genetic insult.Kumar et al.  observedCLCN1; the gene coding for the main skeletal muscle chloride channel ClC-1 [CLCN1 associated to a synonymous SNP in exon-3 (c.396C>T). All animals showed generalized muscular hypertrophy and action myotonia, especially after being startled with difficulties in rising from recumbency and stiffness at the beginning of the movements [Another congenital musculoskeletal defect reported in river buffalo is myotonia congenita; a specific inherited disorder of muscle membrane hyperexcitability. It is caused by reduced sarcolemmal chloride conductance due to mutations in el ClC-1 . It has el ClC-1 , inheritovements .COLQ gene in cats [Congenital megaesophagus (ME) consists of esophageal dilation and dysmotility that progressively leads to the inability to drive the food/bolus into the stomach. It has been reported in cats , dog 3030, horse in cats , and genNine cases of ME have been reported in Murrah buffaloes  in whichSHH, GLI3, WNT7A, Fgfs, BMPs, ALX4, PRMT5, and SMARCA4; thus, they can all be considered candidate genes for these malformations. Recently, a duplication of exon 2 of the ALX4 has been observed in Galloway Cattle affected by tibial hemimelia syndrome and assumed to be the candidate causative mutation for this malformation [In addition to the previously described congenital malformations involving limbs, at the Department of Veterinary Medicine and Animal Production of the University Federico II of Naples, in MIRB, we have examined a case of forelimb amelia and a calf with a complex of skeletal malformation involving only limbs characterized by hypoplasia of the radius and ulna, the absence of medial femoral condyle, and tibial agenesis (unpublished data). Embrionic limb development is a complex process under the control of several genes, like ormation .SWR1928 on SSC7 and SW830 on SSC10 [CDC73 gene is assumed to be responsible for the malformation [Congenital umbilical hernia  is the protrusion, in a newborn, of the peritoneal sac and, eventually, of other abdominal organs that are covered by skin and subcutaneous tissue through the abdominal wall at the umbilical level . It is don SSC10 . In thisormation . In cattormation  and it sormation . Additioormation  found a ormation .Schistosoma Reflexum or schistosomus reflexus (SR) syndrome is a rare and fatal congenital malformation characterized by exposed abdominal, and sometimes thoracic, viscera , failureGLI2 as a candidate gene [Atresia ani is a congenital malformation of the anorectum due to the failure of the urorectal fold to divide the cloaca completely or of the failure of the perforation of the fetal anal membrane that divides the rectus and anus during fetal development. As a consequence, the anal opening is closed and feces are accumulated in the large intestine. This is the most common defect of the lower gastrointestinal tract reported in mammals  and, in ate gene . In cattate gene ,53,54,55ate gene  reportedate gene .Hydrocephalus is a multifactorial, congenital, or acquired disorder characterized by an abnormal accumulation of cerebrospinal fluid (CSF) within the cranial cavity. It is defined as internal when the CFS is accumulated in the ventricles, and external when CFS is accumulated in the subarachnoid space . The incPolycephaly is a congenital malformation in which an individual with two  or more heads, probably due to partial or total union of two developing embryos or to a partial duplication of a body, or to the anteroposterior compression of the embryonic disk . It is vIn buffaloes several cases of duplication of the head with different characteristics have been reported: monster with varying degrees of duplication of the face or diprosopus  and diceIn MIRB, we have seen a case of a dicephalic derodymus calf  characteOther congenital craniofacial malformations are very rare in domestic animals and the most frequent reported are brachygnatia, prognathia, micrognathia, clefts of palate, of the face, or of specific facial boneshave. In some cases an inherited condition has been demonstrated ,72 and sIn India, three cases of “Bull Dog” buffalo calves have been observed; the first one was from a Murrah buffalo fetus of 8.5 months characterized by complete alopecia, broad head, bulging forehead, malocclusions of the jaw, prognathism of the mandible, and pot belly ; the secDisorders of sexual development (DSDs) are congenital conditions in which chromosomal, gonadal, or anatomical sex development is atypical . Sexual The abnormalities of chromosomal sex are linked to abnormalities in sex chromosome number or structure. In the river buffalo, cases of X-monosomy (Turner’s syndrome) ,79, X-trSRY, SOX9, RSPO1, and WNT. These abnormalities are defined as sex reversal disorders and classified according to the chromosomal complement detected in the individual  and the presence/absence of SRY gene [The abnormalities of gonadal sex are related to mutation, deletion, or translocation of small parts of chromosome containing one or more genes which regulate the testis and ovarian developing pathways, like SRY gene . TherefoSRY gene . SRY condition) showed Müllerian duct atrophy. In domestic animals sex reversal disorders are rare and described in horses ,85,86, cMISRII gene, causes the failure of the regression of Müllerian ducts in males during embryo development [The abnormalities of phenotypic sex are related to developmental alterations of internal and external genitalia, which is strictly dependent on secretions from testis in males. In carriers, defined pseudohermaphrodites, the chromosomal and gonadal sex are in agreement, but the internal or external genitalia are ambiguous. The causes of this condition are often unknown because multiple genes are involved in the differentiation of genital apparatus and their roles are still not clear. In dogs, the iatrogenic administration of androgen or progesterone to the dam during gestation could induce masculinization of female fetuses  . In Perselopment .Another disorder of sexual development is cryptorchidism, a condition in which one or both testicles fail to descend into the scrotum and it is an abnormality in the development of phenotypic sex without sexual ambiguity. In addition to environmental factors, like endocrine disruptors, cryptorchidism is at least in part determined by genetic causes and, until now, many candidate genes have been identified . It is vThis condition is very rare and characterized by a reddish skin that is easy to lacerate, with detachment of the epidermic tissue. At birth the animal is normal, but at 2–3 days of age tufts of hair fall out and the skin starts to lacerate; moreover, injuries to the corneal layer of the hoof may occur. With respect to river buffalo, it has been reported in four Murrah calves transmitted with an autosomal recessive gene and due to the reduced functionality of cadherins .Congenital malformations due to genetic factors represent a significant limit for selection plans and for animal welfare when the underlying gene mutations are unknown and carrier identification is not possible until the mutation is so widespread as to be phenotypically evident. This is typically due to an increase of the inbreeding rate and the spreading of negative alleles responsible for genetic diseases. To avoid this problem, it is necessary not only to set up breeding plans that avoid the increase in inbreeding, but also to know genetic conditions underlying the diseases and exclude carriers from mating. The completion of buffalo genome sequencing would represent another useful tool to discover those conditions, but in order that these mutations are discovered, a good recording system is necessary and breeders and institutions must be sensitized to the importance of reporting and examining all new cases of malformations, sampling all cases in which genetic causes are assumed. According to the literature and our personal experience, river buffalo have a great variety of malformations due to genetic causes, and TH and omphalocele are the most frequent. However, several cases are still not reported, leading to an underestimation of the real weight of genetic diseases in this species. This theory is confirmed by the fact that, despite 95% of the world buffalo population being bred in Asia, the number of malformations reported in the literature is extremely small, in contrast to what is observed in countries, such as Brazil and Italy, where only 2% of the buffalo world population is bred. Moreover, except for DSDs for which genetic causes have been identified and diagnostic tests are available, for all other malformations, the genetic causes are unknown. In conclusion this report represents a reference point to focus future studies on the most important malformations that affect river buffalo and that compromise the results of genetic improvement plans and the welfare of the animals.