Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to  The world’s food system is threatened by over-dependence on a limited number of crops with low nutritional value and the negative impact of climate change on agriculture . AccordiSphenostylis stenocarpa) and winged bean (Psophocarpus tetragonolobus) which produces edible pods, seeds and tubers, and others like yard long bean , lablab bean (Lablab purpureus) and horse gram (Macrotyloma uniflorum) which produce seeds and pods can help to diversify the food system  seeds contain vicilin which is remarkable against pathogenic microorganisms (Lathyrus sativus) seeds have been found to prevent cardiovascular disease and cancer tumour development (Vigna angularis) is known as the “weight loss bean” in Asia because it contains low caloric and fat content and can be recommended to people looking to lose weight  populations are widespread at the roadsides in southern Manitoba  in the Mediterranean.Research remains scant on the genomic impacts on feralization and local adaptation as well as gene flow between domesticated, feral and wild populations in plants at large and legumes in particular. A selective advantage under stress allows feral plants to successfully germinate their seed, survive, reproduce and establish a self-perpetuating population. Hence, studying this domestication legacy seen in many feral types will give insights on adaptation to varying sites in minor food legumes, e.g. grass pea or vetch  there are 4.2 million plant accessions conserved. Encouragingly a relatively large number of accessions are not improved cultivars and instead are landraces (20.1%) or wild accessions (10.8%), suggesting that genetic diversity is, at least for some crops and their wild relatives, likely being preserved.Based on the publicly available Genesys database of germplasm conserved in genebanks worldwide (Triticum aestivum), rice (Oryza sativa) and barley (Hordeum vulgare), which together comprise nearly 25% of the 4.2 million accessions. In contrast, for the focal minor grain legumes, only tens [Kersting’s groundnut (Macrotyloma geocarpum)] to a few thousand [Lima bean (Phaseolus lunatus) and grass pea] accessions are conserved . Based on a minimum of 10 accessions in a genebank, these 13 crops are found in between one (Kersting’s groundnut) and 29 genebanks (grass pea) (median = 10). The top five genebanks for conserving these minor legumes are the World Vegetable Center , Centro Internacional de Agricultura Tropical , Western Regional Plant Introduction Station, USDA-ARS , International Institute of Tropical Agriculture , and International Centre for Agricultural Research in Dry Areas , although for the latter all accessions are grass pea. Overall, these data highlight the risk to some of these crops of both low numbers of accessions being conserved as well as a lack of broad representation in genebanks , or simply reduced, for example if seed from a wild population are grown up and only a tiny number grow to form the next batch of seed. Another arguably more significant risk is that ex situ preservation is unlikely to preserve any indigenous knowledge associated with that crop. Therefore, even if the seed are viable, researchers and farmers lack knowledge pertaining to the timing of planting, companion crops, and crop husbandry  was of similar quality  as those of cereals and pulses  may lead to identifying genetically diverse, stable, and agronomically beneficial germplasm. Genebanks worldwide contain accessions preserved Use of only limited germplasm in crop improvement programs has resulted in a narrow genetic base in many crops. Representative subsets in the form of core or mini core collections  have bee-1, pod length, seed thickness, and seed weight  following morpho-agronomic descriptors to identify diverse accessions with agronomically beneficial traits in nine underutilized grain legume species . Analysid weight . A detaid weight . Charact factors .Vigna contains many underutilized pulses  in addition to some major grain legumes (cowpea and mungbean). Adzuki bean in widely grown across China in a wide range of agroecological environments. A comparison of 475 adzuki bean germplasms including cultigens, landraces and wild relatives revealed significant variation among accessions of different germplasm types, and grouped the accessions into five clusters , and link average diameter (mm) were 04.33–2549.20, 0.06–0.29, and 0.27–0.61, respectively , pubescence (glabrous to pubescent), fragrance (absent to high), constriction, colour, attachment, and pod colour at physiological maturity. Diverse seed colours and shapes were noted. Cluster analysis based on 14 quantitative traits grouped the accessions into four groups, with weak association between group membership and the place of origin. Variation between clusters meant that, for example, one cluster had more locules podnd yield . Gene pond yield .Orobanche spp.) was investigated in grass peas because this weed is a root holoparasitic plant that cause substantial loss to pulses production in the Mediterranean and sub-Saharan Africa. Assessment of wild grass pea accessions against two common broomrape species  detected complete resistance to O. crenata and O. foetida in Lathyrus articulatus and moderate resistance in L. aphaca and L. ochrus , while energy dissipation by non-photochemical quenching (NPQ) in the form of heat and the coefficient of non-photochemical dissipation (qN) were higher in cultivated regressive and wild accessions, which probably contributed to differences in adaptation to combined stress of high temperature and acidic soil conditions. Six and 19 accessions of cultivated and wild groups, respectively, had grain yields above 1.8 t ha-1, which may be deployed in breeding program to improve productivity of tepary beans in such environments  grown under high temperature and acid soil conditions with aluminum toxicity produced more pods plantronments .The daylength-neutral accession MY0-01 from Bago (Myanmar) is adapted to southern Australia and is an excellent genetic resource to breed photoperiod sensitive winged bean cultivars. The small pod and hard-seededness, respectively, may lower its potential for vegetable production and adversely affect germination and plant establishment .Single nucleotide polymorphism (SNP)-based diversity assessment involving 169 AYB grouped the accessions into three subpopulations with high genetic differentiation. Subpopulation 1 accessions were high yielding, while those in those in subpopulation 2 were highly polymorphic and heterozygous . AnotherVigna minima. Accessions could be distinguished from each other based on their origins, which suggests that geographic regions of adaptation of wild adzuki bean shaped their genetic variation. Further unfolding of relationship between Chinese adzuki bean cultivars and wild adzuki bean accessions highlights their closeness to Japanese wild adzuki beans than to domestic accessions, suggesting greater involvement of Japanese adzuki bean accessions in Chinese adzuki bean breeding (A study involving 261 adzuki bean accessions from China and 163 simple sequence repeats (SSRs) grouped the accessions into 10 clusters. Accessions from northern China were genetically distinct than those from southern China . Wild adbreeding .Profiling of 93 South African Bambara groundnut accessions using 2,286 SNPs and morpho-agronomic traits, revealed moderate genetic differentiation and two distinct clusters . Highly Validation and diversity analysis involving 33 polymorphic SSRs and 58 horse gram germplasm detected wide variation and grouped the accessions into 3  or 4 (UPGMA and PCA) distinct clusters. The early flowering types are clearly separated from late flowering group . AnotherProfiling of 25,039 DNA markers  data on 65 lablab bean germplasm showed low discriminating ability and three subpopulations unrelated to site of origin. High within population variance suggests a greater degree of gene exchange or low genetic differentiation among the populations . AnotherThe presence of β-N-oxalyl-L-a,b-diaminopropionic acid (β-ODAP) causes neurological disorders in humans. Analysis of 56 SSRs on 400 accessions of grass pea germplasm showed highly diverse structure, with two main and one admixed population . AnalysiLima bean germplasm was extensively analyzed for assessing population structure and diversity. A combined analysis of genotyping (12 SSRs) and phenotyping  data of 183 Brazilian lima bean landraces detected high diversity and three distinct subpopulations, one predominantly from the Andean gene pool with large seeds (mean 100-seed weight 80 g) and the other two predominantly from the Mesoamerican gene pool (mean 100-seed weight 34 g), with considerable introgression between the Andean and the Mesoamerican gene pools . AnalysiMolecular profiling of 472 rice bean accessions (388 cultivated and 84 wild) detected high gene diversity in cultivated populations, which was ∼83% of that for wild populations. East Asian populations formed a distinct gene pool. The cultivars from Indonesia had a genetic structure like the wild accessions. Accessions from western Nepal were quite distinct from others and formed a specific group, thereby being a unique gene source for rice bean breeding . NortheaMolecular profiling of 158 cultivated and wild tepary bean populations with high quality SNPs (768) separated domesticated and cultivated tepary beans, with two distinct groups within the domesticated types . FurtherMolecular profiling of 457 accessions winged bean accessions with 14 SSRs revealed moderate gene diversity and high genetic admixture. Seed exchange and relatively high outcrossing probably contributed to high genetic admixture in this germplasm set. Structure analysis grouped the accessions into three subpopulations, unrelated to geographic origins, with most accessions having long pods (30 cm or greater in length), purple seed coats or young purple pods grouped together .Overall, assessment of population structure and diversity among gene pools provides greater insights into the genetic makeup of populations, which will help in conservation strategy, management, and utilization of diversity in crops breeding and genetics. Unlike major pulses where there has been extensive use of genetic resources in crop breeding, the diversity in underutilized pulses remains largely untapped as a source of alleles for introgression. Hence the primary gene pool can harbor unexploited genes for crop improvement.-1 and 19%–24%. The accessions also showed significant variation in their physicochemical, cooking hydration and textural properties. Soaked grain hardness ranged between 69 and 120 N and had significant positive association with gumminess and chewiness , flavonoids (0.01–2.51 mg QUE g-1) and anthocyanins (0.03–1.31 mg CYE g-1), with caffeic and catechin discriminating the landraces , with antioxidant activity discovered in Bambara groundnut suggests that seed could be used as natural sources of antioxidants to reduce inflammation in humans  but contain high level of polyunsaturated fatty acids. L sativus accessions had relatively low level of β-ODAP content, average 733 mg with a range of 0.583–1.340 mg kg-1 DM, while those from L. cicero accessions had slightly higher β-ODAP, average 1,168 mg with a range of 0.911–1.349 mg kg-1 DM. L. cicera seeds on average contain greater (6.4 g kg-1 DM) tannins than L. sativus seeds, 3.3 g kg-1 DM. The tannin content in L. sativus seeds were significantly correlated with flowers and seeds colour, darker colour associated with higher levels of tannins  and β-ODAP (0.32%–0.47% and 0.38%–0.53%), and reported accessions low in seed protein and β-ODAP contents (-1 DM) contents, with a few identified as low in seed β-ODAP and high protein contents , than those obtained from lower . Chemotype-based PCA formed three distinct clusters, with cluster 3 accessions containing the nutritionally best metabolites , phytic acid (0.26–1.22 mg g-1 DM), radical scavenging activity (5.63–38.26), and tannins (1.4–3.2 mg g-1 DM), were reported among moth bean germplasm  and omega-3 linolenic acid , in addition to containing high amounts (24%) of proteins and minerals but low (1%) in phytate content . Low phyermplasm .-1 DM) content and antioxidant activity (9.36–18.56%) among rice bean germplasm, with some accessions showing highest in vitro protein (63.84%) and starch (44.6%) digestibility. Accessions with high antioxidant activity, protein content, increased in vitro protein and starch digestibility and reduced oligosaccharides could be used as a donor parent or promote them for human consumption.-1 DW  are the ideal set of genetic resources for detailed characterization to dissect population structure and diversity, discovering trait-specific accessions, gene discovery and allele mining. The underutilized pulses, unlike major grain legume crops, received low priority in management and utilization of genetic resources in genetic enhancement programs. To date, core collections have been reported in adzuki bean , BambaraGenetic variation can increase through the formation of new genetic combinations resulting from gene flow or introgression between domesticated species and their wild relatives. These combinations of hybrids that survive through time expand the genetic diversity of domesticated crops, serve as the basis for the evolution of domesticated species, and carry traits that can be exploited by breeders . There mGene flow between wild relatives and domesticated species occurs in regions where both species are found; this could be centers of diversity especially where traditional cultivation is still practiced . The sugP. lunatus) using SSRs in both local and regional scales at the Yucatan Peninsula region of Mexico concluded that there was evidence of a bidirectional gene flow at the local scale, as well as an asymmetry in crop-to-wild introgression in some accessions. However, these processes do not seem to be affecting the genetic structure and diversity of the species in the longer term, which could be because of low gene flow. Furthermore, results from SSR marker and SNPs have been used to estimate the degree and direction of gene flow in major and minor crops . ResearcStrong gene flow and introgression from wild relatives into domesticated species bring about increased genetic diversity which can cause heterogeneity in the population structure of domesticated species. This could also increase the similarity of populations that are geographically distant thereby reducing genetic differentiation between populations and increase the genetic diversity of a larger, more interconnected population . AdditioAn advantage of gene flow and introgression can be seen in the work of Finally, this reveals that gene flow and introgression which formulate new genetic combinations may contribute to increase in the ecological fitness of wild species and adaptation of domesticated species to harsh weather conditions. In addition, gene flow and introgression can be useful in the improvement of underutilized legumes and their wild relative as shown in the introgression between tepary bean and common bean. Evidently, strong gene flow and introgression from wild-crop type can be advantageous in breeding for underutilized legumes cultivars that are high-yielding under abiotic stress. With the advent of molecular breeding, the process of gene flow and introgression could be faster, easier and cheaper, thereby ensuring the fat release of underutilized legume varieties well adapted to biotic and abiotic stress. .The availability of genetic markers discussed above allows evolutionary and genomic insight into crop origins and the genetic basis of adaptive traits. These markers have revolutionised the identification of QTL; i.e., regions of the genome controlling one or more traits of interest . Small nEven dense linkage maps may give poor resolution of causative genes if recombination is low, or the number of plants required is prohibitively large . However, identifying a genomic region and knowing the sequence of the entire region can remedy this, allowing the researchers to find candidate genes based on likely gene function. The sequencing, assembly and annotation of crop genomes is therefore a significant step in any analysis of agronomic traits. Once available, this can fast-track the identification of causative genes and alleles, as well as identify markers for marker-aided breeding .Whilst modern high throughput sequencing technologies can sequence a genome many times over for a fraction of the cost required for the first genome assemblies, the most accurate and complete assembly requires significant investment, aided by very long read sequencing, and large mapping populations to help unify scaffolds into chromosomes. This means that while many minor legume crops have been investigated with genome sequencing, the availability of high-quality contiguous genome sequences of minor legumes is low, with the two best examples probably being pigeonpea and chickpea, which, due to their widespread use and research investment, probably cannot be considered ‘minor’ legumes. Therefore, focussing on those in Brachypodium  genome and comparison to common bean was used to enumerate a chromosome numbering system in legumes. In this comparison six of the 11 chromosomes are largely syntenic, and five of the cowpea chromosomes are formed from parts of two common bean chromosomes . Associating sequence variation and GWAS data for growth sites at three widely divergent latitudes of rice bean landraces unlocked loci  associated to the adaptation of rice bean from low to higher latitudes. Landraces pyramiding early flowering alleles for these loci were earliest to flower. Copy number variation for VumCYP78A6 regulate seed-yield traits, while an InDel in TFL1 among landraces from mountainous region in South-Central China affect stem determinacy  that confer drought tolerance in horse Gram were isolated and functionally characterized  and determinate (GNIB 21) lablab bean germplasm. A splice site SNP in TFL locus confers determinate growth habit in GNIB 21. The transition from G to A at the end of the third exon differentiated GNIB21 from GPKH 120, which may modulate growth habit in other legumes through genome editing  in adzuki beans. VaSDC1 expression activates the flavonoid metabolic pathways structural genes to substantially accumulate anthocyanins, while low VaSDC1 expression results in a lower anthocyanin accumulation  of soybean GmBADH2 with a high degree of similarity (97%) contains one and three non-synonymous and synonymous SNPs, respectively. Substitution of the amino acid tyrosine (fragrant accessions) with phenylalanine (non-fragrant accessions) in the LpBADH2 protein suggests involvement in fragrance, which could be deployed in breeding programs to develop lablab bean cultivars with high fragrance  and tepary bean. The inability to hybridize could be caused by many factors, which can include large genetic distance between the wild relative and domesticated crop species. In cases where crosses were possible, the fertility of hybrids were mainly dependent on compatible chromosomal arrangement of the wild parent . They may be utilized for the development of toxin free Lathyrus cultivars. Crossbreeding has resulted in the release of several high yielding grass pea cultivars with low β-ODAP content in many countries in Africa, Asia, Australia, and America. Impressive progress has been achieved towards applying biotechnological resources, including transgene technology, in the genetic enhancement of grass peas (β-ODAP content varied widely (0.02%–2.59%) among ass peas .-1 dry seeds, differentiated contrasting accessions, and showed moderate correlation (0.65) between α- and β-ODAP contents, reinforces independent quantification of both ODAP isomers -based method for β-L-ODAP quantification facilitates accurate identification and characterization of grass pea lines with a very low ODAP content . An impr isomers .in vivo, which may pave the way to engineer β-ODAP–free grass pea cultivars  and Medicago truncatula (MtAAE3) homologs. Substituting LsOCS with oxalate oxidase or decarboxylase could reduce the level of β-ODAP in grass peas. Inactivating LsOCS in grass pea using genetic engineering has potential to reduce the biosynthesis of β-ODAP, however, it may increase grass pea susceptibility to pathogens such as Sclerotinia sclerotiorum. Thus, replacing LsOCS with an exogenous oxalate-oxidase or decarboxylase could enable plants to regulate cellular oxalate levels while reducing the levels of β-ODAP in grass pea (β-ODAP synthase (BOS), a recently discovered enzyme of the benzylalcohol O-acetyltransferase, anthocyanin O-hydroxycinnamoyltransferase, anthranilate N-hydroxycinnamoyl/benzoyltransferase, deacetylvindoline 4-O-acetyltransferase superfamily of acyltransferases, provides catalytic activity linked with β-ODAP formation. It is structurally similar to hydroxycinnamoyl transferase. BOS expression in the presence of its substrates causes β-ODAP production ultivars . Oxalic rass pea . Germplarass pea .Arcelin (Arl), an insecticidal gene from lablab bean, is homologous to Arl-3 and Arl-4 alleles from Phaseolus spp, with about 70% amino acid similarity. The artificial diet containing Arl  retarded growth of cowpea weevil, which may be deployed to incorporate bruchid resistance through transgenesis in pulses  suggests it may be used to develop weevil resistance in other cultivated pulses , drastically reduces adult emergence and seed damage, thereby demonstrating the effectiveness against the bruchid beetle  cause substantial damage to pulse grains during storage. Early research shows that n pulses . Exceptid pulses . An insed beetle .Rcc confers beetle resistance in moth bean. One major (qVacBrc2.1) and one modifying (qVacBrc5.1) QTL residing in Rcc control resistance. qVacBrc2.1, mapped on LG2 between SSRs CEDG261 and DMB-SSR160, accounted for 50%–64% variation for resistant traits. qVacBrc2.1 is the same as QTL Brc2.1, which confers beetle resistance in wild adzuki bean (VacPGIP1 coding sequences between TN67 (resistant) and ICMP0056 (susceptible) accessions revealed eight SNPs, three of which altered the amino-acid sequence of the predicted domains of polygalacturonase inhibitors in ICPMO056 (The single dominant gene uki bean . Fine maICPMO056 .Mungbean yellow mosaic India virus (MYMIV) causes significant yield losses in pulses including black gram (Vigna mungo) and green gram (Vigna radiata). High level of resistance to MYMIV was reported in a black gram variety Mash114. A large effect QTL, qMYMIV6.1.1 spanning 3.4 Mb on chromosome 6, identified as an inter-specific introgression from rice bean, accounted for 70% of total phenotypic variation. KASP markers closely associated with MYMIV delineated 500 kb genomic region linked with MYMIV, which can be deployed for marker-assisted transfer of introgressed region into improved genetic backgrounds of Vigna species  led to identifying lines tolerant to sub-zero temperature at seedling stage. Their subsequent evaluation revealed that few outyielded their common bean parent under cold stress and drought, thereby suggesting that introgression of a proportion of tepary bean genome into common bean is a promising strategy to enhance abiotic stress adaptation in the latter , all cloned from horse Gram, improved drought tolerance in peanuts ( peanuts . TransgeThe pulses we have focused on have lagged in the development and use of genetic and genomic resources in applied breeding compared to more mainstream legume crops. The priority areas of research over the past three decades have been to develop and use these types of resources for uplifting the productivity of major food legume crops . The decUnderutilized pulses included in this review have different levels of resources available (both genetic and genomic) . These cMuWRKY3, MuHSP70, MuNAC4) or simultaneous expression of MuMYB96, MuWRKY3, and MuNAC4 provided multiple abiotic stress adaptation in Arabidopsis or groundnut and overexpression of a lablab R2R3-MYB gene in Arabidopsis increased drought and salt tolerance (The levels of research also vary among underutilized pulses. While some crops such as African Yam bean, adzuki bean, Bambara groundnut, grass pea, horse Gram, lablab bean, and lima bean have had their germplasm to some extent characterized for genetic diversity , such reolerance . Clearlyolerance .Underutilized pulses are often adapted to harsh environments and their seeds are nutritionally packed with protein, fiber, minerals, vitamins, and phytochemicals. Although inherently low yielding, they produce where crops such as maize, rice, and wheat fail. These minor legumes are still underutilized because they possess some phenotypically undesired traits, which can be removed or suppressed while improving desirable traits through breeding methods.One of the first steps to breeding for improved cultivars of underutilized legumes should be to track viable materials, use consistent labelling system and use a universal descriptor to phenotype germplasm. Hence, precision-led characterization and optimum conservation of accessions are required to provide adequate information for selection, which is the basis for crop improvement. Furthermore, reference genome, pangenomics, and population-level sequencing are important in investigating the crop genome of underutilized legumes to know where alleles responsible for adaptive traits lie. This knowledge may help accelerate the breeding of underutilized pulses to improve their productivity under harsh environmental conditions.de novo domestication of crops.The degree of research investment varied, with some crops researched more than other underutilized grain legumes. Presently, a few functionally characterized genes impacting stem determinacy, photoperiod induced flowering, stress tolerance, and nutritional quality as well numerous QTL and putative candidate genes associated with domestication related traits, pod and seed characteristics, stress tolerance, and seed quality were uncovered, they may be deployed, after validation, in genomic-aided breeding. Such genomic resources will also be helpful in detecting introgression of these genes from wild relatives to cultivated type and vice versa, as well as for Future research on underutilized pulses should focus on on-farm diversity and preservation of indigenous knowledge associated with cultivation and use of underutilized legumes, standard crop ontology and regeneration protocol to catalogue and preserve diversity, machine learning and algorithms to obtain robust phenomics data on minor legume germplasm characterization, whole genome resequencing involving diverse germplasm, and genetic stocks with specific attributes.


A total of 324 treatments were evaluated, which consisted of 200 half-sib families (100 from Pop1 and 100 from Pop2), 100 full-sib families from the two populations and 24 controls. The field experiment was arranged in a lattice design with three replications in two environments, in the north and northwest regions of the State of Rio de Janeiro, Brazil. The genotype × environment interaction was partitioned and the genetic parameters, heterosis and predicted gains were estimated by the Mulamba and Mock index, based on selection results in both environments. The genetic parameters detected variability that can be explored in successive interpopulation recurrent selection cycles. Exploring heterosis for GY, PE and yield components is a promising option to increase grain yield and quality. The Mulamba and Mock index was efficient in predicting the genetic gains in GY and PE. Interpopulation recurrent selection proved effective to provide genetic gains for traits with predominantly additive and dominance inheritance.In view of the need to develop new popcorn cultivars and considering the uncertainties in choosing the most appropriate breeding methods to ensure consistent genetic progress, simultaneously for both popping expansion and grain yield, this study addressed the efficiency of interpopulation recurrent selection regarding genetic gains, the study of the response in genetic parameters as well as heterotic effects on the control of the main agronomic traits of popcorn. Two populations were established, Pop Zea mays var. Everta L.) is native to the American continent and is used exclusively for human consumption [The species popcorn  , the con99 , the To date, only one study on interpopulation recurrent selection in popcorn has been published . Thus, tFor all the above reasons, it was deemed appropriate to carry out this research with interpopulation recurrent selection in popcorn to assess possible genetic gains and investigate the behavior of genetic parameters as well as heterotic effects on the genetic control of the main agronomic traits.Pop1, HSFPop2 and controls) for all traits. Although the genotype × environment (G × E) interaction caused significant phenotypic differences for all evaluated characteristics, the partitioning of the effects of this interaction showed no significance in the source of variation groups × environment for EL, as well as in the source of variation control × environment for GY, and in HSFPop1 × environment for PE. On the other hand, when analyzing the type of G × E interaction, a simple type interaction was predominant for PE (54.76%); on the other hand, for GY and yield components  there was a predominance of the complex type interaction .The results of the F test in the combined analysis of variance  indicateRegarding the experimental variation coefficient (CVe), only that of GY exceeded 20%, while the values of the other evaluated characteristics were lower than 10% .p ≤ 0.01) for G × E in the combined analysis, individual analysis of variance was performed for each environment. A significant treatment effect was found for all traits in both environments  than in Itaocara . On the other hand, in the environment of Itaocara, the means for 100 GW (14.91 g), EL (16.18 cm) and ED (31.60 mm) were higher than in Campos .In a comparison of the environments, overall mean estimates for GY and PE were higher in Campos (2.34 t haConsidering the full-sib families (FSFs) and estimated heterosis values (H), the estimates varied between positive and negative. The estimated values were highest for GY (30.25% in Itaocara and 16.66% in Campos). In Itaocara and Campos, the percentage values for PE (3.02 and 2.31%) and 100 GW (2.23 and 3.23%) were low and positive. The estimates for the yield components EL and ED were negative in both environments . The mean grain yields of HSFs of both studied populations were equivalent in the environment of Itaocara (2.06 t ha−1). On the other hand, HSFPop1 in Campos produced higher yields (2.32 t ha−1) than HSFPop2 (2.13 t ha−1)  .−1 in Itaocara and 28.93 mL g−1 in Campos). For HSFPop1, the PE estimate was 24.34 and 25.85 mL g−1, in Itaocara and Campos, respectively. In general, PE was highest for HSFs derived from population UENF-14, followed by HSFPop2, with estimates of 31.04 mL g−1 in Itaocara and 28.93 mL g−1 in Campos.For popping expansion, the mean PE of FSFs was close to that of HSFs  as well as GY, the means tended to be higher for FSFs compared to HSFs. The FSF means for the environments of Itaocara and Campos were 15.13 and 13.29 g, respectively. For HSFectively .Pop1 for UENF-synthetic, the mean estimates were 16.25 and 16.19 cm in Itaocara and Campos, respectively. The means of HSFPop2 progenies from population UENF-14 were 16.15 and 16.22 cm in Itaocara and Campos, respectively (For mean ear length (EL), the FSF means were 16.17 cm for Itaocara and 16.19 cm for Campos. Considering HSFectively .Pop1; and 30.39 and 29.73 mm for HSFPop2, respectively (For mean ear diameter (ED) in Itaocara and Campos, the means of the tested FSFs were 31.57 and 29.73 mm; 32.88 and 31.59 mm for HSFectively .Pop1, were estimated as: Pop2) in Itaocara and Campos: For GY, the estimates of the variance components in the FSFs tested in Itaocara and Campos were as follows: genetic variance  for FSFs in the environments of Itaocara and Campos, the variance components were estimated as: ectively .Pop1 the estimates of variance components were Pop2, the estimates were The estimates of the variance components for mean ear diameter (ED) of the FSF tested in the Itaocara and Campos environments were ectively . Likewisectively .Based on the economic weights obtained by the estimated values of r Campos .When ectively .From the estimated ectively .From the economic weights assigned based on the redicted .By means of the economic weights assigned by the breeder, it was possible to obtain simultaneous and approximately equal predicted gains in both environments for the traits GY (8.72 and 8.55%), PE (8.71 and 9.68%) and EL (3.27 and 4.26%), in Itaocara and Campos, respectively. In addition, decreases in 100 GW (0.96 and 0.39%) and ED (0.39 and 1.13%), respectively, were observed .In Itaocara, considering the selection of the 30 best FSFs based on the economic weights assigned by the breeder for mean grain yield, 29 FSFs performed better in relation to the mean of population UENF-14, while 28 FSFs stood out over the mean of UENF-synthetic. For PE, a similar situation occurred with 13 FSFs of population UENF-14 and for the synthetic population all FSFs performed better. In a simultaneous analysis of GY and PE, 12 FSFs were superior to UENF-14 and 28 in comparison with the synthetic population .In Campos, a higher mean GY was estimated for 29 FSFs in relation to that of population UENF-14, and a higher mean GY for the same number of progenies (29 FSF) in relation to the mean of the synthetic population. For mean PE, 20 FSFs performed better than population UENF-14, whereas for the synthetic population, all FSFs performed better. For both GY and PE, 12 FSFs were superior to UENF-14, while 28 stood out over the synthetic population .−1 and 2.417 mL g−1 in Itaocara, and 0.362 t ha−1 and 2.621 mL g−1 in Campos, respectively , CVe values ≤10% indicate excellent experimental precision, 10 to 20% good experimental precision, and ≥20% low experimental precision. In both environments, the CVe of PE, 100 GW, CL and CD was lower than 10%, while the experimental variations for GY exceeded 20%. According to Scapim et al. (1995)  and FritPop1 and HSFPop2 reflect the allelic distribution of the FSF base populations. In this context, the positive heterosis values for GY and 100 GW in the FSFs suggest higher yields than in the HSF progenies, highlighting the predominance of dominance effects of genes in the expression of these traits, due to the superiority of the mean deviation of F1 from the parents [In this study, HSF parents ,32,43. 1 generation. In this situation, the equivalence of the mean performance of the FSFs and HSFs for PE, EL and ED shows the predominance of additive effects on the expression of these characteristics.According to Falconer (1996) , predomiThe predominance of additive gene action on PE and dominant for GY was observed by Larish and Brewbaker (1999)  in a diaBased on the results for PE, minor heterotic effects associated with the tendency of the mean FSF to be equivalent to the mean HSF indicates the high likeliness that additive genes control this characteristic. Thus, additive genetic variance was confirmed to be more relevant than dominance effects in the genetic control of PE ,44. HoweAmong the grain yield components, 100 GW was the only trait with positive heterosis and evidence of dominance deviations. In a study on the inheritance of the main popcorn traits by means of a diallel in irrigated and water-stressed environments, Lima et al. (2019)  suggesteThe heterotic effects for the traits EL and ED were negative and tended to be zero. This does not necessarily imply absence of dominance, since the sum of dominance deviations can be zero when the signs are positive and negative . HoweverThe application of breeding methods that include the exploitation of hybrids seems to be an auspicious option to raise grain yield and 100 GW . HoweverThe covariance in FSFs corresponds to 0.5 of the additive variance 5 of σa2 . ApparenThe heritability coefficient expresses the reliability of the phenotypic value as a guide to the genotypic value ,43. LoweEstimates of the coefficients of genetic variation (CVg) allow breeders to foresee the relative magnitude of changes that can be obtained by selection throughout a breeding program, since this parameter is directly proportional to genetic variance . In geneThe ratio between CVg and CVe, known as the variation index, can be used to predict the success in the selection of superior genotypes, which will depend on its magnitude . For 100 GW, CL and CD, the For PE, the Pop2 and FSF progenies indicate possibilities of future gains through selection. However, for HSFPop1, although the frequency of favorable alleles for GY was high in the parents of the synthetic population, values lower than 0.50% were observed for the characteristic in both environments. The reason may be that the population had not been subjected to any selection cycle so far.Values greater than 0.50% for GY regarding HSFThe key factors that can impair selection gains are selection intensity, the genetic properties of populations and environmental conditions . In addiAnother important factor for the breeding program is the application of economic weights. The economic weights established by Cruz et al. (2012)  can be cThe use of the estimator The estimates of The use of The arbitrary economic weights assigned by the breeder provided the highest gains for GY (8.72 and 8.55%) and PE (8.71 and 9.68%). By favoring higher simultaneous gains for GY and PE, the weights assigned by the breeder overcome the existence of a negative correlation between the two main economic characteristics in popcorn . The intIn this respect, estimates of genetic gains show that interpopulation hybrids established at the end of each selection cycle may not only become genetic sources for the development of lines, but also have a yield, quality and competitive potential that can be marketed, serving as proof of the technical feasibility and economic viability of this methodology. It is noteworthy that the production costs of interpopulation hybrid seeds are lower than those of developing a single-cross hybrid; therefore, the first option is less costly for the breeder and, consequently, for the producer.In popcorn, recurrent intrapopulation selection is being used to increase the frequencies of favorable alleles, predominantly for traits with high additive genetic effects ,20,38. H1), resulting from random crosses of nine lines of the germplasm bank of the UENF popcorn breeding program. These lines had previously been evaluated and selected, based on the estimates of general combining ability for the two main characteristics of interest of the crop—grain yield and popping expansion—and on differences in their genealogical origins [2) consisted of the intrapopulation recurrent selection C10 cycle from UNB-2U, which became designated UENF-14 from the sixth selection cycle. Cultivar UENF-14 started with the UNB-2U population, being an open-pollinated variety. Before arriving at UENF, this variety was made up of an indigenous population donated to the Universidade de Brasília by the Universidade de São Paulo/EALQ, which was named UNB-1. Subsequently, UNB-1 was brought to UENF by Professor Joachim Friedrich Wilhelm Von Bülow in 1993 and crossed with the popcorn variety SAM (South American Mushroom). This first filial generation was then crossed with a popcorn variety resistant to Exserohilum turcicum. After two mass selection cycles, three backcrosses were made with the SAM variety, thus originating the UNB-2 population. This population, after two rounds of mass selection, gave rise to the UNB-2U population. Nine cycles of recurrent selection were then carried out in order to obtain gains for the main characteristics of economic importance of the crop—expansion capacity and grain yield [The composite populations for this study consisted of: (i) Population 1  ; therefoThe full-sib families and S1 progenies were obtained by planting the two populations at Colégio Estadual Agrícola Antônio Sarlo, in Campos dos Goytacazes. The populations were sown in alternate rows measuring 6.00 m in length, with 1.00 m spacing between rows and 0.40 m spacing between plants. The rows and the plants of each row were numbered to facilitate identification when crossing. For each pair of plants, two reciprocal crosses (interpopulation hybrid) and two self-fertilizations (one in each population) were performed, thus constituting 100 full-sib families and 200 S1 progenies. The S1 seeds were stored in a cold room and the full-sib families were used in competition trials.Pollinations were carried out manually, adopting the following procedure: the ear were covered before releasing the style–stigma with plastic bags suitable for this purpose. Simultaneously, the tassels were covered so that unwanted pollen contamination did not occur. This procedure is extremely necessary, as the pollen loses its viability eight hours after the beginning of its release; therefore, any viable pollen found in the paper bag the day after grooming could only have come from the covered tassel. Crosses occurred in prolific plants, selected within each pair of rows, so that the first (uppermost) ear resulted in the hybrid from which full-sibs were derived and the second ear resulted from selfing, to form the remaining seeds. The plants in each row were numbered for better control in identifying crosses.The evaluation tests were carried out in the growing season of 2020/2021 in two environments: (i) Colégio Estadual Agrícola Antônio Sarlo in the district of Campos dos Goytacazes, northern region of the State of Rio de Janeiro , with a mean annual precipitation of 1023 mm and potential evapotranspiration of 1601 mm per year, at a mean annual temperature of 23 °C; and (ii) Experimental Station PESAGRO-RIO in Itaocara, Rio de Janeiro, in the northwest of the State of Rio de Janeiro , with a mean annual precipitation of 1041 mm and a mean annual temperature of 22.5 °C. The total distance between the locations is 110 km.1 and 100 of Pop2), 100 full-sib families and 24 controls including the 10 cycles of recurrent intrapopulation selection of UENF-14, six populations from the popcorn germplasm bank of the State University of Northern Rio de Janeiro Darcy Ribeiro (UENF) and eight single-cross hybrids registered by the Ministry of Agriculture, Livestock and Food Supply. Crop treatments, fertilization and phytosanitary control were applied as recommended for the crop [The experimental units consisted of 3.00 m long rows, spaced 0.90 m apart, with 15 plants per row. The experiment was arranged in an 18 × 18 lattice design, with three replicates. Thus, a total of 324 treatments were evaluated, i.e., 200 half-sib families , determined by popping 30 g of kernels in the microwave oven for 2 min, measuring the popcorn volume in a 2000 mL beaker and dividing the popped volume by 30 g; mean 100-grain weight , obtained by assessing the weight of 100 randomly collected grains and weighing on an analytical balance; mean ear length , by measuring five randomly picked ears without husk per plot; and mean ear diameter , measured with a digital caliper in the middle of five random ears per plot.The following agronomic characteristics were evaluated: mean grain yield (GY), estimated as the weight of grains harvested from the entire plot area and converted to t hai-th genotype in the j-th block within the k-th repetition in the l-th environment; µ is the overall experimental constant; i-th genotype, which is normally independently distributed (NID) ; l-th environment; j-th block within the k-th repetition and within the l-th environment, which is NID ; k-th repetition within the l-th environment; l-th environment, which is NID ; and σ2).Initially, combined variance analysis was performed to detect the occurrence of significant interactions between the environments. For this purpose, we considered the main genotype effects as random and environment effects as fixed, in order to capitalize on possible interactions between them. The following statistical model was adopted: When a significant genotype × environment (GE) interaction effect was detected, the type of interaction (simple or complex) was specified, according to the method proposed by Cruz and Castoldi (1991) .i-th treatment in the k-th block, within the j-th repetition; µ is the overall experimental constant; σ2G); j-th repetition; k-th incomplete block, ranked within the j-th repetition, which is NID ; and ijkY, observation, according to the NID distribution, with mean 0 and variance σ2.Based on the significance of the GE interaction, individual variance for each environment was analyzed based on the statistical model: To estimate the genetic and environmental parameters, the following estimators were used: (a) Genotypic variance: Selection gains were estimated and superior full-sib families were selected by assigning different economic weights, at a selection pressure of 30% (30 families). To this end, covariances were estimated for all characteristics in both environments simultaneously, using the methodology of the sum-of-ranks index .j-th characteristic; and n is the number of characteristics considered in the index.This sum-of-ranks index  consistsj-th characteristic and j-th characteristic.Using this method, different weights can be assigned to order the ranks of characteristics, as specified by the breeder. In this way, the economic weights were given by: gSD), genetic variation coefficient (gCV), variation index (Iv), heritability (h2) and economic weights assigned by the breeder (AW). In this context, after several arbitrary attempts, greater weights were applied to the most relevant characteristics for the crop under study: 10 for GY and PE and 1 for 100 GW, CL and CD. For all statistical genetic analyses, the resources of the program GENES [1)  .In popcorn breeding, exploiting heterosis is a promising strategy, mainly with a view to increasing grain yield (GY) and its components.−1 and PE was higher than 30 mL g−1, indicating genetic potential for breeding new varieties.The first cycle of recurrent selection among popcorn populations in the framework of the UENF breeding program produced seven hybrids in the environment of Itaocara and ten in Campos. The hybrid GY exceeded 3 t haThe Mulamba and Mock index was efficient in predicting crosses for satisfactory genetic gains for grain yield and popping expansion, favoring the continuity of the popcorn breeding program. The economic weights assigned arbitrarily by the breeder provided the highest genetic gains for GY and PE in the first cycle of interpopulation recurrent selection.Two cycles of intrapopulation recurrent selection in the UENF-synthetic population for the subsequent use in recombination with population UENF-14 would favor more marked gains in popping expansion in FSFs, which are also associated with relevant gains in GY.


Common bean is one of the widely consumed food security crop in Africa, Asia, and South America. Understanding genetic diversity and population structure is crucial for designing breeding strategies.Two hundred and eighty-nine germplasm were recently collected from different regions of Ethiopia and introduced from CIAT to estimate genetic diversity and population structure using 11,480 DArTSeq SNP markers.The overall mean genetic diversity and polymorphic information content (PIC) were 0.38 and 0.30, respectively, suggested the presence of adequate genetic diversity among the genotypes. Among the geographical regions, landraces collected from Oromia showed the highest diversity (0.39) and PIC (0.30). The highest genetic distance was observed between genotypes collected from SNNPR and CIAT (0.49). In addition, genotypes from CIAT were genetically more related to improved varieties than the landraces which could be due to sharing of parents in the improvement process. The analysis of molecular variance revealed that the largest proportion of variation was due to within the population both in geographical region (63.67%) and breeding status (61.3%) based classification. Model-based structure analysis delineated the 289 common bean genotypes into six hypothetical ancestoral populations.The genotypes were not clustered based on geographical regions and they were not the main drivers for the differentiation. This indicated that selection of the parental lines should be based on systematic assessment of the diversity rather than geographical distance. This article provides new insights into the genetic diversity and population structure of common bean for association studies, designing effective collection and conservation for efficient utilization for the improvement of the crop.The online version contains supplementary material available at 10.1007/s11033-023-08498-y. Phaseolus vulgaris L.) is a diploid (2n = 2x = 20) annual leguminous self-pollinated crop with estimated genome size ranged from 588 to 637 Mbp 48] who rBased on the breeding status, the highest genetic diversity and PIC were observed in the improved varieties compared with the landraces. From the landraces, those collected from Oromia and Amhara region showed higher genetic diversity and PIC. The higher genetic diversity of landraces collected from Oromia region indicated that landraces could have useful traits which pave the way for the collection of additional landraces in areas where there is an expected rich genetic diversity.Pre-grouping of the genotypes showed that the highest genetic distance was observed between genotypes collected from CIAT and SNNPR (0.49). The CIAT genotypes were closer to improved varieties than all other regions of collection. This supports the fact that many of the improved varieties in Ethiopia and Africa are introduced from the CIAT collections and breeding lines and many of them have close pedigree , 55. CluK = 6 subgroups and the result indicated that the greatest variability was observed within populations in both geographical region and breeding status-based classification followed by among populations.The AMOVA was conducted to display the variation among and within the K value occurred at K = 6 and grouped the 289 common bean genotypes into six subpopulations with a membership coefficient (qi) ≥ 0.70. At K = 2, the genotypes were classified into Andean and Mesoamerican genepool. The classification was mostly based on seed size in which Mesoamerican genotypes contained genotypes with small to medium seed size, while the Andean genotypes contained genotypes with medium to large seed size. At K = 6, the Mesoamerican genepool further separated into five subclusters, while the Andean genepool remains the same as the K value was increasing, except four genotypes. A second peak was observed at K = 9 which might be associated with the presence of different races within the Andean and Mesoamerican genepool. In agreement with this study, two peaks were reported in common bean at K = 3 and K = 7 [In the present study, the highest delta nd K = 7 , 43 haveK varied with the number of populations, source of germplasm, and number and type of markers used. Accordingly, various studies reported different delta K values. In other studies, an optimal population structure at K = 6 was reported [In Ethiopia, the majority of the landraces and commercial cultivars were Mesoamerican type and are widely cultivated both for consumption and export, while the Andean genepool (large seeded) have relatively shorter period of cultivation history and the majority of them were introduced from CIAT as breeding lines and some are released after multi-location trial. In addition, the longtime cultivation and planting of mixed landraces in the same plot may result in the variation among the Mesoamerican genepool. The population structure detected by delta reported .K = 6, the Mesoamerican genepool was separated into five subpopulations, while the Andean genepool remained unseparated. In agreement with this result, [K = 5, while the Andeans remained unseparated. The results of population structure revealed that the Mesoamerican genepool was more diverse than the Andean genepool. This could be due to large sample size of Mesoamerican genepool and long years of cultivation in Ethiopia under different cropping system.The eastern African region is considered as the secondary center of origin of common bean which could be the reason for such wide population structure . In the  result,  reportedThe present study revealed the presence of wide genetic diversity and structured population in common bean. The average overall genetic diversity, PIC, MAF, and inbreeding coefficient were 0.38, 0.30, 0.28, and 0.85, respectively. Genetic diversity based on geographical locations showed that landraces collected from Oromia region showed the highest genetic diversity, PIC, and inbreeding coefficient.K = 6). The results showed that common bean collections revealed a wide range of diversity. At K = 2, the genotypes were clustered into Andean and Mesoamerican genepool. Further separation of the genotypes was due to the diversity, large sample size, and long years of cultivation of the Mesoamerican genepool, while the Andeans remained unseparated. The genotypes were not clustered based on geographical regions and they were not the main drivers for the differentiation and. This indicated that selection of the parental lines should be based on systematic assessment of the diversity rather than geographical distance.Pre-grouping of the genotypes based on geographical origin showed that genotypes form SNNPR and CIAT were the most distant (0.492). Genotypes collected from CIAT were distant than genotypes collected from regions in Ethiopia. However, it is relatively close to the improved varieties due to sharing of parents in the improvement process. Clustering also showed that the genotypes were not clustered based on their origin, which could be due to transboundary movement of the germplasm across the regions. This showed that geographical regions were not the main drivers for differentiation and selection of the parents should be based on systematic assessment of the diversity. The population structure revealed that the optimal number of subpopulation was six Supplementary file2 (TXT 10418 KB)Supplementary file3 (DOCX 105 KB)Supplementary file4 (DOCX 334 KB)Below is the link to the electronic supplementary material.


The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds.ST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (Neb) to effective population size (Ne).The k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (Feb to Ne was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB.Distinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of NThe online version contains supplementary material available at 10.1186/s12711-023-00827-w. To achieve this, controlling the rate of inbreeding and preserving effective population size  is an Irish native pony breed that is popular worldwide, but particularly in Ireland and the UK. CP were originally used for agriculture, including transportation of heavy weights across rough landscape, which led to a hardy native pony type. Breeds such as the Arabian, Shire, Thoroughbred, Welsh Cob, Hackney, Andalusian and Irish Draught all contributed to the formation of the early CP breed . The ConSince the 1970s, the aims of the CP Breeders’ Society (CPBS) shifted from breeding a traditional working pony, with the associated hardiness and bone width, to breeding a sports pony  “of neceThe CP has a relatively small population size compared to many popular horse breeds: 108 stallions and 1204 mares were registered in Volume 24 of the CPBS Studbook in 2012 , and theHowever, in spite of its popularity, there is at least one known autosomal recessive disease specific to the CP breed that is regularly tested for as part of the registration process, i.e. hoof wall separation disease (HWSD) . The carCP have previously been compared to other UK native pony breeds –18 usingAnother horse breed that is popular in equestrian sports similar to those of the CP is the Warmblood horse (WB). The WB is a middleweight horse type that has been selectively bred in various European countries for light farm work and cavalry use since the eighteenth century , 22. SinUnlike the CP, the WB is not a closed population breed and is traditionally defined by the country or region from which the horse originates, forming regional subpopulations . While tPetersen et al.  comparede), which is an idealised population size that undergoes genetic drift at the rate of the real-life population and was first described by Wright in 1931 [e can be calculated in a variety of ways, including based on linkage disequilibrium (LD) as r2 using genome-wide genotype data [eb), which describes the number of breeding adults in the previous generation. Neb is nearly equal to Ne in populations in which the generations do not overlap and the population consists of reproductive adults [eb is the molecular coancestry method, based on alleles that are identical-by-state between individuals [Several parameters based on genetic data measure the genetic diversity of a population. Effective population size  and Warmblood horses (n = 97) used in this project were collected for another study using a combination of random sampling, voluntary response sampling and snowball sampling. Briefly, we had access to muscle biopsy samples from 62 horses (16 CP and 46 WB), and blood samples from six horses (2 CP and 4 WB). Sixty-three other horses (16 CP and 47 WB) were recruited via the Royal Veterinary College website, social media and stakeholder groups, from across the UK and a range of different sporting disciplines, with a hair root sample provided for each one. Thirty four CP represents just over 1/3 of the number of foals registered with the BCPS in 2019 . The meap value for the Hardy–Weinberg equilibrium test > 10e−6. After quality control, 152 samples (36 CP and 116 WB) and 446,878 SNPs remained for further analysis, referred to hereafter as genotype data.DNA was extracted using the following three methods: for muscle tissue, the Qiagen DNEasy Blood and Tissue kit was used according to manufacturer’s instructions; for whole blood, the Illustra Nucleon BACC kit was used according to manufacturer’s instructions; for hair root, the Qiagen Gentra Puregene kit was used according to manufacturer’s instructions  were computed both within and across breeds, and decomposed through principal component analysis (PCA) that was performed using the GEMMA algorithm . PrincipK-means clustering based on the PCA was used to identify any within-breed genetic groups. Elbow plots  and silhouette plots were produced using the R package factoextra  to deter2 using the PLINK 1.9 software, with the maximum window size being equal to the largest equine chromosome 1, i.e. 188.26 Mb in EquCab3.0). LD decay was plotted using the R packages dplyr [The genotype data were split according to the within-breed genetic groups identified with k-means clustering, and SNPs were thinned to 20 SNPs per Mb using the mapthin (v1.11) program , resulties dplyr , stringres dplyr  and ggples dplyr , and maxe) was calculated based on the full genotyping data from the autosomes, which were split according to within-breed genetic groups, from 13 to 999 prior generations using the LD-based method of the SNeP program [e at e at the current generation  using NeEstimator [eb were calculated for each within-breed genetic group.The thinned PLINK files were recoded to GENEPOP format for the autosomes only using PGDSpider , in ordestimator  with thestimator :\documenO), within-population gene diversity (HS), and Wright’s F-statistics, including fixation index (FST) and individual inbreeding coefficient by expected heterozygosity (FIS), were calculated. Overall FST was calculated hierarchically for within-breed genetic groups and within-breed breed types in the total population.Metrics for genetic diversity and hierarchical F-statistics were calculated using the hierfstat package in R  on the nST was calculated per marker between all CP and all WB samples using PLINK 1.9 [ST values per marker were calculated using PLINK 2 [ST was also calculated from the pairwise comparisons using the Scipy package [ST pairwise estimates: between all pairwise CP within-breed genetic group comparisons; between all pairwise WB within-breed genetic group comparisons; and between the three within-breed comparisons for each of the eight genetic groups individually. Results were plotted using the R package qqman [ST values or from all SNPs with an FST > 0.1  from each of the 11 comparisons were identified.Furthermore, FLINK 1.9 . Then, p PLINK 2  for each package  in Pythoge qqman . The SNPEquus caballus background, an EASE threshold of 0.1, and a Benjamini-Hochberg-corrected p-value of 0.05.Genes within 1 Mb of the top 0.5% of markers from the breed comparison and the two harmonic mean comparisons were extracted using the BiomaRt package in R , 68. TheEquus caballus background, an EASE threshold of 0.1, and a Benjamini-Hochberg-corrected p-value of 0.05.Runs of homozygosity (ROH) were detected for each individual sample on the autosomes using the detectRUNS package in R  on the nGenomic inbreeding was then calculated based on the extent of ROH for each individual as follows :\documenbreeding .CP and WB separated along PC1, with only some WB individuals that include Irish Sports Horses in their pedigree overlapping with CP Fig. : Fig. S1Genetic groups identified in the k-means analyses were compared with the breed subtypes using Chi-square tests (to assess overrepresentation of particular subtypes in certain within-breed genetic groups) . LD decayed exponentially in both CP and WB, with the maximum r2 also varied considerably, ranging from 0.077 to 0.130 in the CP within-breed genetic groups and from 0.016 to 0.370 in the WB within-breed genetic groups.When comparing different genetic groups, the maximum LD varied greatly, ranging from 0.122 to 0.258 in the CP genetic groups and from 0.127 to 0.519 in the WB genetic groups. Mean rIn general, LD in CP within-breed genetic groups showed greater values and a slower decay than in WB within-breed genetic groups Fig. , with a As LD was close to the baseline in all groups by a 8-Mb window size Fig. , this die across all groups proved difficult. Table e intercept (NeH) and molecular co-ancestry estimates (MCoA Neb) for the four within-breed genetic groups with similar sample sizes .With the variation in sample size between within-breed genetic groups and origin groups, comparison of Neb and NeH in C1, the genetic groups C1 and W3 had very similar ratios of Neb to NeH. In contrast, C2 had the largest Neb, but the smallest NeH, while for C3 it was the opposite, with the largest NeH and smallest Neb.In spite of a much larger NO), within-population expected heterozygosity (HS), and individual inbreeding coefficient by expected heterozygosity (FIS) were calculated per genetic group  and the group with the highest level of expected admixture (significantly associated with non-registered CP) respectively. Notably, all genetic groups had higher HS than HO, resulting in negative mean FIS values—but both C4 and W1, which were the smallest sample size genetic groups with the lowest mean FIS, did not have an FIS that significantly differed from 0. These results indicate a greater degree of genetic diversity within groups than expected, possibly due to the non-random mating in these horse breeds [Mean alternate allelic frequency, observed heterozygosity  ranged from 0.01 to 0.251 when comparing CP within-breed genetic groups, from 0.218 to 0.472 when comparing WB within-breed genetic groups, and from 0.334 to 0.626 when comparing the two breeds , while the W1 genetic group (associated with Holsteiners) had the largest median sum of ROH lengths and the C1 genetic group (associated with non-registered CP) had the smallest Fig. .Fig. 7ViCP genetic groups showed a smaller mean length of ROH and fewer ROH on average than the WB genetic groups Fig. . This waOverlapping ROH within breed, genetic group and origin group were identified  and W1 the highest (0.118), with a wider range of mean FROH values observed among WB within-breed genetic groups than among CP within-breed genetic groups (0.095–0.118 compared with 0.047–0.084). FROH differed significantly between genetic groups in CP  but not in WB (p = 0.40). Significant differences were identified between genetic groups C1 and C2 as well as between C1 and C3, using post hoc Tukey's testing.FROH was broken down to the per chromosome level, distinct distribution patterns began to emerge  and C4 . C4 had no ROH at all on ECA21, 22 and 27. W2 and W4 had a very even distribution of inbreeding along all the chromosomes, while the highest FROH observed for ECA12 in W3 and for ECA14 and 30 in W1, with no ROH on ECA29.When FWhen ROH were split by size class, it was noted that C2, C3 and C4 genetic groups had a greater proportion of runs longer than 4 Mb than the other genetic groups Fig. . C2, C3 e and Neb; ROH and FROH. We found that the genetic substructure in the WB population was not associated with traditional subtypes (registered studbook), and that WB genetic groups tended to be, although not significantly, more inbred than registered CP genetic groups. We also identified a possible population structure in the CP population. While the number of US CP was too small to draw strong conclusions regarding geographical location, the basis of the separation of the remaining two UK-based, registered, non-admixed clusters could potentially be associated with various factors not analysed here including differences between breeding lines, breeder preferences, or diverging breeding goals. Both registered and unregistered CP genetic groups appeared to have a degree of popular sire choice comparable to that for WB based on the ratio of Neb to Ne, as well as indicators of a greater degree of recent inbreeding.The aim of this study was to characterise the genetic profiles of the little-studied Connemara pony breed and the well-documented Warmblood horse. These two breeds are very distinct with different origins, although both are now selected for performance in equestrian sport. Multiple genetic metrics were calculated and compared, including clustering analysis based on genotypic data; LD decay and LD block size distribution; NCP separated well from WB in the PCA, as might be expected for distinct breeds. Previous studies that compared WB and Scottish Highland ponies, which are among the closest related breeds to CP, also found that the breeds were very distinct , as wellFor WB, in spite of the existence of many different WB subtypes associated with different studbooks, there was, in fact, little genomic differentiation between these subtypes, which implies that it is unlikely that the population sub-structure observed in the WB breed is due the historically location-based studbook of registration. Artificial insemination (AI) has been popular in the WB since the 1990’s, with varying levels of uptake in different countries depending on the managing studbook and availability of AI centres . The GerThe lack of correlation between genetic group and breed subtype found in WB raises the question about whether genetic studies in WB should move away from the traditional use of breed subtype and registered studbook to describe population structure. Usage of genetic clustering as an alternative could reflect more closely the practice of cross-subtype use of particular sires. The presence of these genetic groups is evident in the results of previous phylogenetic, neighbour joining-tree and PCA studies of WB, where WB subtypes often appear in mixed clusters or clades, with some WB more closely related to Thoroughbreds or Standardbreds and others to Arabians or draught breeds , 90–92.A previous study of estimated breeding values for show jumping performance in Swedish Warmbloods demonstrated a clear genetic divergence between animals bred for show jumping versus dressage within subtype . It is pIt is unclear why the Holsteiners would separate more than the Trakehners from other WB subtypes. Trakehners have a defined, closed studbook and are therefore expected to be the only genetically distinct WB subtype. Previous studies have revealed less overlap between Holsteiners and other German WB subtypes  than theSeparation of Anglo European WB and British WB from the continental European studbooks in the PCA could be due to the common UK practice of breeding Irish Draught horses with Thoroughbreds to produce WB-like Irish Sports Horses predominantly for eventing. This could have affected the UK-based WB stock. The WB in the PCA that were located closest to CP did in fact have some Irish Sports Horses in their pedigrees. This reflects the historical influence of Irish Draughts on the CP, although such pedigree information was not available for all Anglo European and British WB to confirm this hypothesis. Furthermore, the historical reluctance of UK breeders to engage with the grading and registration procedures that are a core tenet of WB breeding and studbook registration in continental Europe  would liThe results of the LD patterns across all origin groups and within-breed genetic groups showed lower values than previously reported in Thoroughbreds , but simeb/Ne ratio was found between the W3 genetic group and the median of the CP genetic groups with similar sample size . A lower ratio can be indicative of a skewed ratio of breeding stallions to mares, indicating that popular sires are contributing to the gene pool to a greater degree. While some studies indicate that WB are affected by the choice of popular sires [Estimates of effective population size were carried out within specific genetic groups, and specifically those of similar sample size. A similar Nar sires , 101, thar sires , 102.ROH method in CP, so comparisons with previous studies based on pedigree estimates are difficult [ROH to be much higher than pedigree estimates. Specifically, in the study of Feely et al. [ROH does tend to be higher than pedigree estimates, or also a recent increase in inbreeding.In spite of the similar or greater degree of popular sire choice, registered CP tended to be, although not significantly, less inbred than WB, with the non-registered CP significantly less inbred than the CP of all groups but C4—most likely due to admixture. To our knowledge, our study is the first to estimate genomic inbreeding using the Fifficult , e.g.. sifficult , Norwegiifficult , and Sztifficult  found FRy et al. , estimatThe inbreeding values that we found for CP are not particularly high compared to those for rare North European breeds , but a rST analysis were reported in a previous study on exercising horses [Furthermore, differences in signatures of selection were identified between breeds as well as between within-breed genetic groups. The immune and inflammatory ontology terms identified in all within-breed genetic groups in the Fg horses  that alsg horses , 111 andg horses –115 relag horses . In a stg horses . Immune g horses , 119. Thg horses  may haveIn conclusion, the genetic characterisation of the CP and WB has identified several key findings. The genetic variation and population substructure in the WB is not well captured by subtype based on the registered studbook and it is likely that a similar genetic effect of popular sire choice is present in the CP as in the WB, which is thought to be considerable. We report the first estimates of inbreeding from ROH in CP, and found that CP have a similar or slightly lower average level of inbreeding than WB but with a greater degree of recent inbreeding. Hopefully, these findings will prompt further studies to better understand the population substructure in WB horses, and act as an early warning to breeders of CP that proactive changes in breed management are required to sustain genetic variation and overall breed health in this highly popular breed.Additional file 1: Methods S1. Additional methods: DNA extraction protocols. Protocols used for DNA extraction from equine muscle, blood and hair root samplesAdditional file 2:Table S1. Horse breed and sample type. Table indicating the breed, breed subtype, sample origin, sample type and genotyping platform of each sample. CP: Connemara pony; WB: Warmblood horse; KWPN: Koninklijk Warmbloed Paardenstamboek Nederland; M: male; F: female; WGS: whole genome sequencing; SNP: single nucleotide polymorphism array genotyping panel.Additional file 3: Figure S1. Elbow plot using within-sum of squares and silhouette plot for selection of appropriate number of clusters. Elbow plots (top) and silhouette plots (bottom) for selection of appropriate number of clusters (k) for k-means clustering analysis in WB (left) and CP (right). CP: Connemara pony; WB: Warmblood horse; WSS: within sum of squares; k: number of clusters.Additional file 4: Figure S2. Principal components (PCs) of the genetic relationship matrices for 116 WB  and 36 CP . Principal components of the genetic relationship matrices for 116 WB  and 36 CP . Upper and lower diagonal plots for CP and WB respectively, with colour designating the k-means assigned cluster and marker designating breed subtype: in CP B) principal component (PC) 1 by PC 2; C) PC 1 by PC 3; and F) PC 2 by PC 3; in WB D) PC 1 by PC 2; G) PC 1 by PC 3; and H) PC 2 by PC 3. Diagonal plots are kernel density estimator plots illustrating the distribution of the principal components, with distribution curves for each cluster: A) PC 1; E) PC 2; and I) PC 3. The first three PC in CP explained 4.7%, 4.2% and 3.7% of variance respectively, and in WB explained 2.5%, 2.2% and 1.7% of variance respectively. CP: Connemara pony; WB: Warmblood horse; UK: United Kingdom; EU: rest of Europe; US: United States; X: unregistered.Additional file 5: Table S2. Over-representation of breed subtypes and sample origin in CP and WB within-breed genetic groups. Breed subtypes and sample origins significantly associated with different genetic groups using Chi-square testing. CP: Connemara pony; WB: Warmblood horse; UK: United Kingdom; EU: rest of Europe; US: United States; X: unregistered.Additional file 6: Table S3. Significant terms associated with genes within 1 Mb of top 0.5% markers. Ontology terms identified as significantly over-represented in genes within 1 Mb of the top 0.5% SNPs between different groups using DAVID. CP: Connemara pony; WB: Warmblood horse; FST: Wright’s fixation index.Additional file 7: Table S4. Largest number of individuals and % of the group sharing a run of homozygosity (ROH) in CP and WB, and in within-breed genetic groups. CP: Connemara pony; WB: Warmblood horse; ROH: runs of homozygosity.Additional file 8: Table S5. Significant ontology terms associated with genes within ROH regions present in > 10% of horses belonging to a given genetic group, origin group or breed. Ontology terms identified as significantly over-represented in genes within 1 Mb of the ROH regions present in > 10% of horses belonging to a given genetic group, origin group or breed using DAVID. CP: Connemara pony; WB: Warmblood horse; ROH: runs of homozygosity.Additional file 9: Figure S3. Mean genomic inbreeding (as FROH) by chromosome, illustrated in within-breed genetic group. Mean genomic inbreeding (as FROH) by chromosome, illustrated in within-breed genetic group. CP: Connemara pony; WB: Warmblood horse; ROH: runs of homozygosity.


Arabidopsis or rice that have been in the spotlight for the past few decades, trees and tree genomes have received limited attention. Studying the biology of trees poses many challenges including long generation time , low and asynchronous seed germination rate, difficulty for genetic transformation, and absence of genomic data and mutants. Despite so many challenges, genomes of several tree species have been sequenced, comparative genomics will help us to understand the complexity of tree genetics and genomes.Trees contribute significantly to our economy. Unlike reference plants, such as Camellia sinensis (tea), Casuarina equisetifolia , Cunninghamia lanceolata (lamb.) hook (Chinese fir), Phyllostachs edulis (Moso bamboo), and Torreya grandis (Chinese Nutmeg Tree).The objective of this Research Topic was to update current research advances in tree genetics and genomics. A total of six articles were accepted into this Research Topic, which include Camellia sinensis) plants, An et al. identified 26 members from cultivar tea and 13 from ancient tea plants. Many OVATE family members were highly expressed in young leaves and shoots, but their expression levels decreased with the maturation of leaves. The authors also found a key gene associated with the development of leaf area. These findings may suggest that many OFPs could be implicated in the regulation of leaf development of woody plants.OVATE family proteins (OFPs) are a novel class of plant-specific transcription regulators modulating plant growth and development. Through genome-wide analysis of the OVATE gene family in tea (Casuarina equisetifolia) is a monoecious tree that is cultivated in tropical and subtropical regions for various purposes. An effective micropropagation method was developed by Ahmad et al. where nodal segments were cultured on Murashige and Skoog medium supplemented with BA and NAA. A maximum of 32 adventitious shoots were produced per explant. Scanning electron microscopy showed that shoots was directly regenerated from explants. RAPD and ISSR analyses showed that the regenerated plants were genetically uniform. This developed protocol could be used for large-scale multiplication and germplasm preservation of C. equisetifolia, thus meeting the growing demands of C. equisetifolia in the forest industry.Australian pine  markers and investigated genetic structure and diversity of 233 Chinese fir (Cunninghamia lanceolata) individuals derived from the fourth cycle of selection. Result showed that the genetic diversity in the fourth cycle was high with the nucleotide diversity (Pi) of 0.003, and Ho and He of 0.215 and 0.233, respectively, suggesting that the genetic base had increased in breeding population. This work provided a foundation for further marker-assisted breeding of Chinese fir and other coniferous trees.Population genetic structure and diversity are critical for marker-assisted breeding of tree species. Using RAD-Seq technology, Phyllostachys edulis) is a versatile plant species that is widely used as a construction material in many countries. Del Giudice et al. re-sequenced eight Phyllostachys species and 18 natural accessions of P. edulis and generated a large set of functionally annotated molecular markers (SNPs and InDels). Subsequent genome-wide association analysis identified several candidate genes that were correlated with a mechanical property, which is of highly interest to structural engineers: its tensile strength normal to its fibers . The splitting strength is strongly related to the structural performance of bamboo, and it was associated with genomic regions that included several important candidate genes. These genes could be used for population genetic studies and fine genetic association analyses. This study provides the genetic architecture of a complex structural property trait, the splitting strength, in bamboo.Scientifically speaking, bamboo is a member of the grass family Poaceae. However, from the forest view, bamboo is woody grass or bamboo tree. Moso bamboo  mapping strategy. Nearly 100 unrelated trees randomly chosen from the species’ natural distribution and their half-sib progeny were simultaneously genotyped. The authors reconstructed a high-density linkage map of 4,203 SNPs covering a total distance of 8,393.95 cM. They identified 13 QTLs for stem basal diameter growth and four QTLs for stem height growth in juvenile seedlings. The authors believed that those QTLs and their harboring genomic regions were evolutionarily relatively young, and the plants should better be utilized by clonal propagation rather than through seed propagation. Genetic results from the OP sampling strategy could provide guidance for genetic studies of other dioecious species.Ailanthus altissima, Saina et al. investigated the effects of anthropogenic disturbance on genetic variability in natural and disturbed forests. The genetic diversity and population structure of A. altissima was analyzed by nuclear and chloroplast microsatellite markers. The genetic diversity across the 34 study populations based on EST-SSRs was moderate to high (HE= 0.547-0.772) with a mean HE of 0.680 . Overall, genetic variation did not differ substantially across disturbed and undisturbed sites, there were small trends toward higher genetic diversity and population bottlenecks in disturbed forests. The authors concluded that disrupted ecosystems might display surprising genetic patterns that could be difficult to predict and should not be overlooked.How tree populations in the wild respond to anthropogenic disturbance has received increasing attention. Using Papers published in this Research Topic highlight some recent progress on tree genetics and genomics. Considering the majority of trees are economically important; more research is needed to explore their values through genetic and genomic analyses. Advancement in long read sequencing technology has enabled researchers to sequence large polyploid genomes and negate over-reliance on a limited, reference tree genome, such as Poplar or Eucalyptus. Yet, accurate analysis of large heterozygous tree genomes needs robust bioinformatics pipeline. It will further assist in understanding genotype and population-level genetic diversity, which is required to connect sequence diversity to phenotypic variations. Other areas where significant progress may be noticed in the next few decades include genome assisted selection and breeding to improve important woody traits, biodiversity conservation and effective forest management practices to tackle climate change.MD: Writing – review & editing. JC: Writing – original draft.