Eupsittula canicularis) is the Mexican psittacine that is most captured for the illegal pet trade. However, as for most wildlife exploited by illegal trade, the genetic diversity that is extracted from species and areas of intensive poaching is unknown. In this study, we analyzed the genetic diversity of 80 E. canicularis parakeets confiscated from the illegal trade and estimated the level of extraction of genetic diversity by poaching using the mitochondrial DNA sequences of cytochrome b (Cytb). In addition, we analyzed the genealogical and haplotypic relationships of the poached parakeets and sampled wild populations in Mexico, as a strategy for identifying the places of origin of poached parakeets.The Orange-fronted Parakeet (Poached parakeets showed high haplotype diversity (Hd = 0.842) and low nucleotide diversity (Pi = 0.00182). Among 22 haplotypes identified, 18 were found exclusively in 37 individuals, while four were detected in the remaining 43 individuals and shared with the wild populations. A rarefaction and extrapolation curve revealed that 240 poached individuals can include up to 47 haplotypes and suggested that the actual haplotype richness of poached parakeets is higher than our analyses indicate. The geographic locations of the four haplotypes shared between poached and wild parakeets ranged from Michoacan to Sinaloa, Mexico. However, the rare haplotypes detected in poached parakeets were derived from a recent genetic expansion of the species that has occurred between the northwest of Michoacan and the coastal region of Colima, Jalisco and southern Nayarit, Mexico.Poached parakeets showed high genetic diversity, suggesting high extraction of the genetic pool of the species in central Mexico. Rarefaction and extrapolation analyses suggest that the actual haplotype richness in poached parakeets is higher than reflected by our analyses. The poached parakeets belong mainly to a very diverse genetic group of the species, and their most likely origin is between northern Michoacan and southern Nayarit, Mexico. We found no evidence that poachers included individuals from Central American international trafficking with individuals from Mexico in the sample.The online version contains supplementary material available at 10.1186/s40850-021-00080-y. Illegal exploitation of natural resources is the third most profitable criminal business in the world . Within Eupsittula and Aratinga genera remained in second place in parrot trafficking detected through international customs , su, su21], On the other hand, the H1 haplotype was found mainly distributed in wild populations of Sinaloa, with lower proportions in Nayarit, Jalisco, and Michoacan and was not detected in the localities of Guerrero . HoweverThe H3 haplotype was detected in nine poached parakeets, previously showing a distribution only in the wild population of Sinaloa . HoweverIn addition, no shared haplotypes were detected between poached parakeets and wild population located in Guerrero, where a second genetic group of the species was detected . Since pOn the other hand, genealogical analysis showed that the EcNCBI haplotype is the ancestor of the rest of the analyzed haplotypes Fig. , corroboCantú-Guzmán et al.  describeDatabases provided by molecular analysis after sampling constitute one of the most valuable sets of information for conservation purposes. Estimates of genetic diversity could be applied for genetic restoration and the establishment of the captive-bred colonies. For example, if the goal is to release individuals to strengthen wild populations, the organisms evaluated are suitable if they show high genetic diversity. On the other hand, when designing a captive breeding program, the genotypes of individuals should be considered with the aim of increasing genetic diversity –46.E. canicularis parakeets showed high genetic diversity, suggesting high extraction from the genetic pool of the species in central Mexico. Rarefaction and extrapolation analyses suggest that the actual haplotype richness in poached parakeets is higher than our analyzes indicate. The poached parakeets belong mainly to a quite diverse genetic group of the species and their most likely origin is between northern Michoacan and southern Nayarit, Mexico. We found no evidence that poachers included individuals from Central American international trafficking with individuals from Mexico in the sample.Poached E. canicularis chicks. In addition, 53 Cytb sequences (GenBank Access: MF441334-MF441390) of parakeets from wild populations distributed on the Pacific slope of Mexico from Sinaloa to Guerrero were used [We used the Cytb gene sequences of 80 poached parakeets previously reported by Padilla-Jacobo et al.  GenBank. In testere used  Fig. 1)E. canicuAlignment and construction of data matrices were carried out with PhyDE . NumbersWe used rarefaction and extrapolation to calculate the richness of the haplotypes in the species using the individual-based method (Coleman method). The application of rarefaction and extrapolation curves is especially useful in the area of ecology and conservation biology to estimate the richness of species in an area –53. MoreTo review frequencies of haplotypes and their relationships, a haplotype network was constructed by the median-joining method with NETWORK v5 software . In totaE. canicularis (EcNCBI hereinafter) (GenBank Access: KJ142251.1). A sequence of Eupsittula pertinax was included as an outgroup (GenBank Access: HM640208.1). Molecular evolution models were constructed using jModelTest 2.1.1 [The inference of genealogic relationships was accomplished under the criteria of maximum likelihood (ML) and Bayesian inference (BI). The matrix included the 36 haplotypes with 931 characters from this study and a Cytb sequence reported for a specimen identified as st 2.1.1  and selest 2.1.1 . The besst 2.1.1 . The ML st 2.1.1  and MrBast 2.1.1 .Additional file 1 Haplotypes and variable sites in 931 pb of the Cytb gene from 133 samples of poached and wild E. canicularis individuals. Number of haplotypes; alignment site; frequency (n) in wild population, in poached, and total sample; locality of natural distribution; poached.


The aim of the study is to evaluate the suitability of STRs for molecular characterization and forensic applications in unrelated Brahmins of Rajasthan and Haryana states, India.® PCR Amplification Kit. Allelic frequencies and different forensic parameters like PD, PE, PIC, PM, Ho, He, UHe, and TPI were calculated with different software.A total of 203 male DNA samples from various districts of Haryana (n=104) and Rajasthan (n=99) were genotyped using the GlobalFilerMore than 200 alleles were present in both populations, ranging from 6.0 to 35.2 and SE33 was the most polymorphic marker. The combined power of discrimination was 1. To know the relatedness with other Indian Brahmin populations, the UPGMA dendrogram and principal component analysis plot were visualized to show that both populations are close to each other and in nearby Saraswat Brahmins of Himachal Pradesh. This study showed a genetic relationship and forensic examination in the Haryana and Rajasthan Brahmin populations and various ethno-linguistically diverse populations of India.The results imply that the highly polymorphic 21 autosomal STR loci might be applied for individuals’ forensic identification and parentage testing. This study also suggests that the kit having both autosomal and Y-STR markers is appropriate for a better understanding of the genetic and forensic examination in the Brahmin population of Haryana and Rajasthan. Genetic diversity is essential for the evolution of a species, and it offers the genetic make-up of a species based on the total number of gene distinctiveness features. Diversity reasonably determines population or human social organization in language, ethnicity, culture, geography, social aspect, and communities worldwide. These characteristics are common in the alpine environment, where people frequently live in separate communities far from developed areas .Some traditions emerged due to the assimilation of varied cultures and others died over a period of time. On the other hand, certain cultures have remained steadfast and persistent in demonstrating their presence over time . India hBy the mid-1990s, multiple STR markers were added in single multiplexed reactions in forensic DNA testing. Several studies have been used with autosomal STR markers to investigate genetic relationships among Indian groups. The caste system in India is supported by four primary groups or varna: Brahmin, Kshatriya, Vaishya, and Sudra. The castes are further divided into sub-castes and individuals belonging to these sub-castes practice endogamy, a system in which an individual marries inside a specific group .The aim of the study was to investigate the molecular characterization and forensic applications of Brahmins who practice endogamy i.e. they marry within the same caste, practice gotras (clan) system, and do not marry in the same gotras.Present study was conducted on stored DNA samples in lab G-22, Department of Genetics, Maharshi Dayanand University  . A total® PCR Amplification Kit  according to the manufacturer’s instructions. Throughout the reactions, positive and negative controls were employed. Capillary electrophoresis was used to separate and detect amplified products using an ABI 3500xL Genetic Analyzer . GeneMapper IDX version 1.6  was utilized for manual allele calling.1.2-mm punch of the FTA card containing the DNA samples was used for amplification . Twenty-sw distance determined by POPTREE2 software [To calculate the allelic frequency distribution, as well as forensic parameters like polymorphism information content (PIC), probability of match (PM), typical paternity index (TPI), observed heterozygosity (Ho), expected heterozygosity (He), and unbiased heterozygosity (UHe) for 21 autosomal STR loci, STRAF  online software  and GenAsoftware  to examisoftware  to evalu.A positive control DNA template (2800 M), provided along with the kit, and negative controls were used throughout the study. The experimental work was carried out in an accredited laboratory conforming to ISO/IEC 17025 standard. Further, the authors have also qualified International DNA Proficiency Test In the Haryana Brahmin population, a total of 61 distinct alleles were detected in the Haryana Brahmin community, ranging from 6.0 to 34.2 and 229 alleles with an average of 10.409. In the Rajasthan Brahmin population, 62 distinct alleles were detected, ranging from 6.0 to 35.2 and a total of 222 alleles with an average of 10.091 allelesper locus were discovered. sw genetic distance revealed that the Brahmin community shared a genetic affinity with Himachal Pradesh’s Saraswat Brahmin  and Brahmin of Haryana (HR), was compared to the previously reported Indian Brahmin population, namely, Saraswat Brahmin of Kashmir (KS), Rajasthan (RJ), Punjab (PB), Jammu (JM) and Himachal Pradesh (HP) , Kanyaku Brahmin .The PCA result of 10 populations was found to be consistent with the UPGMA dendrogram, indicative of the genetic relatedness of the Brahmin population of Haryana and Rajasthan with other Indian populations .This has been a pilot study to bring the genetic characteristics of the Haryana and Rajasthan Brahmin population together and demonstrating the utility of a panel of specific markers in the disputed forensic cases. The genetic data from the present study could be helpful in population genetics and forensics. We suggest further extending this study encompassing a greater more number of samples. It can be conducted by using the representative samples belonging to varied castes/ ethnic groups while keeping the immigration routes of the human population in Haryana and Rajasthan states under consideration. In addition, the fine scale understanding of population assignment can be aided by application of genomic data using next generation sequencing. In addition, based on the DNA technology, Regulation bill was enacted by the Ministry of Science and Technology of the Indian Government in Lok Sabha (2019). The presently conducted study would aid in the development of DNA Data Banks at national, as well as state, levels.


Echinococcus granulosus sensu lato is a group of tapeworm species known to cause cystic echinococcosis. Within this group, the Echinococcus canadensis cluster includes genotypes G8 and G10 that have a predominantly sylvatic life cycle – transmission occurs between wild cervids and wolves. Relatively few studies have explored the genetic variation of the elusive G8 and G10, and their extent of genetic variation is yet to be investigated at the complete mitochondrial (mt) genome level. The aim was to explore the genetic variation of these 2 genotypes in Europe using complete mtDNA sequences and provide a high-quality reference dataset for future studies. Sequences of complete mt genomes were produced for 29 samples of genotype G8 and G10 from wolves, moose, reindeer and roe deer, originating from Finland, Sweden, Russia, Poland, Latvia and Estonia. Genetic variation was explored based on phylogenetic network analysis, revealing marked differences between G8 and G10 (over 400 mutations), and more detailed patterns of variability within the 2 genotypes than previously observed. Understanding the mt genetic composition of a species provides a baseline for future studies aiming to understand whether this mt distinctiveness is mirrored in the nuclear genome and whether it has any impact on any phenotypic traits or parasite transmission. Echinococcus canadensis cluster  belongs to a group of cestode species called Echinococcus granulosus sensu lato (s.l.)  as definitive hosts harbouring adult worms, and wild cervids such as moose , elk/wapiti (Cervus canadensis) and roe deer (Capreolus capreolus) as intermediate hosts harbouring larvae  and dogs, and a semi-synanthropic life cycle involving wild cervids and free-roaming and/or hunting dogs are also known to occur  is more prone to establish infection in the lungs, with a more benign CE pathology than CE infections caused by other Echinococcus spp.  and NADH dehydrogenase subunit 1  gene fragments, 10 genotypes, i.e. G1–G10 (formerly known as strains), were originally defined within E. granulosus s.l.  together with G6/G7  cytochrome c oxidase subunit 1 (E. canadensis (G8/G10) is circumpolar and limited to North America , Fennoscandia , continental north-eastern Europe  and Russia   in European wildlife has been documented rather sporadically, while human infections are considered rare but have likely been underreported  is known to be present in wildlife, human CE infections are known to occur, but are not molecularly characterized. Data on E. canadensis (G8/G10) prevalence in wild mammals in Europe have shown that e.g. 0.8% of moose (16 of 2038) and 3.8% of wolves (1 of 26) in Estonia harbour E. canadensis  is considerably lower and less complex than within other Echinococcus species or genotypes, such as E. granulosus sensu stricto  and G6/G7 of the E. canadensis cluster , particularly as surveillance of the parasite infection in wildlife is not regularly performed and the detection and collection of E. canadensis (G8 and G10) specimens originating from the main distribution range of the parasite in Europe and provide a high-quality reference dataset for future genetic studies.The aim of the current study was to explore the extent of genetic variation based on complete mtDNA sequence data of Echinococcus cyst or adult worm per host animal was analysed. Echinococcus cyst samples (n = 22) were obtained from three intermediate host species  from four countries , whereas adult worms were collected from a definitive host species  from three countries  (A single  Poland) ; Table 1et al. , 0.2 mm dNTP , 1 U Advantage 2 Polymerase mix (BD Biosciences) and <1 μg of template DNA. Touchdown PCRs were carried out as described in Laurimäe et al. , and subsequent incubation at 37°C for 30 min, followed by 80°C for 15 min in order to inactivate the enzymes. Sequencing was performed at the Core Facility of Genomics  using the same set of primers as for the initial PCR. Both forward and reverse strands were sequenced.Genomic DNA was extracted from parasite material using a High Pure PCR Template Preparation Kit , according to the manufacturer's instructions. PCRs and amplification were carried out as described in Laurimäe et al. b. Briefle et al. b, with iet al., Consensus sequences were assembled in Codon Code Aligner v.6.0.2 and each polymorphic position was verified by eye using ‘raw’ chromatogram data. Sequence alignment using Clustal W was performed in BioEdit v.7.2.5 (Thompson E. granulosus s.l. species were retrieved from the GenBank database (Table S1) and aligned with the sequences produced in this study, to assess the extent of genetic variation between and among distinct genotypes . For this, median-joining phylogenetic networks were constructed using Network v.4.6.1.6  software, with both indels and point mutations considered. As the commonly applied mtDNA markers had been developed at a time when the extent of mtDNA variation was largely unknown (particularly for G8 and G10), we also aimed to assess and compare the degree of inter- and intra-genotypic phylogenetic resolution provided by other commonly used markers  or G10 (n = 15). For each specimen, the complete mt genome sequence was produced (13 550–13 552 bp). All sequences were deposited in the GenBank database , Latvia  and Poland . The G10 samples were from Estonia , Finland , Sweden  and Russia .All 29 samples analysed here were identified as Echinococcus ortleppi (G5) is separated from G10 and G8 by more than 800 and 1200 mutations, respectively  revealed a total of eight haplotypes, with G8 isolates represented by three haplotypes, and G10 isolates by five (n = 12) were identical (haplotype HAP2), with HAP2 comprising samples from Estonia (n = 6), Latvia (n = 4) and Poland (n = 2), obtained from wolves, roe deer and moose. The remaining two G8 haplotypes originated from moose from Estonia (EST2 and EST3) and were separated from HAP2 by one and two mutations, respectively. The intra-genotypic variability within G10 appeared more complex than that of G8. Interestingly, the single G10 sample from Estonia from a moose was highly diverged, with 24–28 mutations separating it from the rest of the G10 samples from Sweden, Finland and Russia. The samples from the latter three countries revealed eight samples with an identical mt genome sequence; these samples originated from Sweden , Finland  and Russia (moose n = 4). The remaining samples from Finland were grouped into three separate haplotypes (FIN1–FIN3), with 1–3 mutations apart from HAP1. Similar to HAP1, haplotype FIN2 was identified from both reindeer and moose.The phylogenetic network analysis of dataset B , the complete nad1 (894 bp) and its fragment (471 bp) and the complete 12S rRNA (726 bp) gene sequences are able to distinguish between G8 and G10 , they lack sufficient resolution to reveal detailed patterns of genetic variation within the two genotypes. An analysis based on a fragment of 12S rRNA (117 bp) revealed that G10 was indistinguishable from genotypes G6 and G7.An assessment of phylogenetic resolution provided by commonly used markers showed that while both the complete gene sequence and the widely used gene fragment of et al., et al., E. ortleppi (genotype G5) having only twice the distance to E. canadensis genotype G10 (~800 mutations). Echinococcus ortleppi has been firmly established as a distinct species and is predominantly transmitted through a cattle–dog cycle and has a distribution range distinct from the cervid genotypes  between the two cervid genotypes G8 and G10 . AlthougE. granulosus s.s. , particularly due to the low prevalence of E. canadensis G8 and G10 and its predominant perpetuation through a wildlife cycle. However, it could be hypothesized that the lower intraspecific variation could possibly be to some extent also explained by the small population size due to low prevalence and density of the parasite, as well as the rather restricted host spectrum (wild cervids and wolves) compared to other Echinococcus taxa e.g. E. granulosus s.s. G1  is an obligatory parasite that relies on wild animals (wolves and moose) to maintain its life cycle. For example, genetic analyses of moose and wolf populations across Europe have suggested limited dispersal between Fennoscandia  and continental Europe , while dispersal within both regions, as well as between Finland and Russia (Arkhangelsk region) appears to be continuous (Niedziałkowska et al., et al., Interestingly, the pattern of mt genetic variation within G8 and G10 appeared to some extent reflect the dispersal pattern of their wild host animals. This is somewhat expected given that Echinococcus taxa (Kinkar et al., et al., Echinococcus taxa, whereas single mtDNA genes or gene fragments are better suited for species/genotype identification in instances where sequencing of complete mtDNA is not feasible.Finally, an assessment of phylogenetic resolution provided by the widely applied mtDNA markers highlighted the importance of selecting a genetic marker in accordance with the aim of the analysis, as also discussed in previous studies for other E. canadensis G8 and G10 genotypes based on complete mt genome data, highlighting marked mt genetic divergence between G8 and G10, and higher levels of intra-genotypic genetic variation than previously observed. Understanding the mt genetic composition of a species provides a baseline for future studies exploring the nature and extent of nuclear genomic variation, which might lead to an enhanced understanding of the molecular epidemiology of the E. canadensis cluster.The current study provides insight into the genetic variation of the elusive


Numerous articles have recently studied the involvement of the gut microbiota in neurological diseases. Aging is associated with changes in the microbiome, which implies a reduction in microbial biodiversity among other changes. Considering that the consumption of a fermented-food diet improves intestinal permeability and barrier function, it seems of interest to study its participation in the prevention of neurodegenerative diseases. This article reviews existing studies to establish whether the consumption of fermented foods and fermented beverages prevents or ameliorates neurodegenerative decline in old age.The protocol used was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Details of the protocol for this systematic review are registered on PROSPERO (CRD42021250921).Out of 465 articles identified in the Pubmed, Scopus, and Cochrane Library databases, a total of 29 that examined the relationship of the consumption of fermented products with cognitive impairment in old people were selected . The results suggest that low-to-moderate alcohol consumption and daily intake of coffee, soy products, and fermented-food diets in general are associated with a lower risk of dementia and Alzheimer's disease.Daily consumption of fermented foods and beverages, either alone or as part of a diet, has neuroprotective effects and slows cognitive decline in old people.https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=250921, identifier: CRD42021250921. A healthy gut microbiota is responsible for synthesizing vitamins and essential amino acids and has an important role in the structural integrity of the intestinal mucosa producing neuromodulators, including bacteria-derived choline, tryptophan, intestinal-released hormones–such as ghrelin or leptin–and short-chain fatty acids (SCFA)–such as butyrate, acetate, and propionate. These metabolites are an energy and trophic-factors source for the intestinal epithelial cells, and thus strengthen the mucosal barrier –4, but aRecently, the role of the gut microbiota in the central nervous system, through the microbiota gut-brain axis, has been revealed , 3, 5–21Dysbiosis and some microbial metabolites are involved in a variety of diseases, such as inflammatory bowel disease, type 1 and type 2 diabetes mellitus, fatty liver, metabolic syndrome, obesity, cardiovascular disease, colorectal and breast cancer, hepatocellular carcinoma, asthma, osteoporosis, sarcopenia, atherosclerotic stroke, and nervous inflammatory disorders, and in neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, vascular dementia, fibromyalgia, autism spectrum disorder, and depression , 23, 24.It is proposed that systematic inflammatory processes may effect inflammation in the central nervous system by microglial activation, cytokines, astrocytes, neurotransmitters , and altered short-chain fatty acids (SCFA) secreted by bacteria, or changes in enteric neuron activity detected by the vagus nerve , 22, 28.Lipid accumulation in glia is a pathological characteristic of Alzheimer's disease . The APOConsidering the role of microbiome balance in neurological diseases and that numerous pathological processes require much time of performance before cognitive decline appears, it seems essential to protect its stability. There are several strategies to counteract gut dysbiosis, such as fecal microbiota transplant . HoweverFermentation is traditionally used as a biological method of food preservation. Fermented foods and beverages are defined as those prepared using microorganisms—bacteria, yeasts, and fungi- and enzymatic action to transform their components into various fermentation end-products. The type of fermentation depends on the final product. Due to their health benefits, fermented foods are considered functional foods. The process of microbial fermentation converts food substrates into nutritionally and functionally richer products, resulting in functional micro-organisms (probiotics), substrates that enhance the growth of beneficial bacteria in the gut (prebiotics) and bioactive components (biogenics). These substances act in the gastrointestinal tract by modifying the microbiota, influencing exogenous endotoxin translocation and subsequent immune activation, and promoting host nutrition .Lactobacilli, Enterococci, Bifidobacteria, yeasts and bacterial mixtures  derived from various crops or sucrose, and galactooligosaccharides (GOS). These substrates are present in various fermented foods, making them symbiotic foods (with probiotic and prebiotic effect), such as cheddar, gouda and parmesan cheeses, sauerkraut (fermented cabbage), kimchi (Korean pickle made from radish and cabbage), kefir, yogurt, kombucha, tempeh (made from fermented soybeans), miso (fermented soybean paste), soy sauce and apple cider vinegar .Acetobacter, Leuconostoc, Lactobacillus, Streptococcus, etc.), we find various types of fermented foods and beverages  guidelines . DetailsD=250921 .The articles included in this review were selected from PUBMED, SCOPUS, and Cochrane Library databases, limited to Spanish and English languages and published from 16 March 1991 to 16 June 2022. Several searches were performed in March, May, and June 2021, and in June 2022 . We also include articles from manual searches.We used Medical Subject Headings (Mesh) terms for the PUBMED search and Boolean operators for all the databases. The search followed the PICO strategy: population (Aged); intervention (Beer OR Cheese OR Koumiss OR Buttermilk OR Kefir OR Yogurt OR “Cultured milk products” OR “Soy foods” OR “Wine” OR “Fermented foods and beverages” OR “Kombucha tea” OR “Fermented beverages” OR “Fermented foods” OR “Cultured food” OR “Fermented dairy products”); and outcome .The studies included in this review were cross-sectional, cohort, and case-control studies, which passed the Newcastle-Ottawa Scale (NOS) , 49.Inclusion criteria were available full-text articles, conducted in elderly individuals (65 years or older) with preserved cognition at the initial cognitive evaluation, that investigated the relationship between consumption of fermented foods or beverages ; fermented dairy products; Kombucha, fermented or semi-fermented tea; soy-based foods; and coffee and cocoa, but not supplements) and cognitive dysfunction (dementia or Alzheimer's disease) as first outcome.Exclusion criteria applied to works done in animals or in people who were cognitively impaired at the start of the study and under 65 years old. We also excluded articles in languages other than English and Spanish, those published before 16 March 1991, and those that did not achieve 7 points or more on the Newcastle-Ottawa Scale (NOS) , 49.The authors independently selected and removed the duplicate studies, using Mendeley as database. The titles and the abstracts (in a first step) and the full text (in a second) of the remaining studies were screened according to the inclusion criteria. The authors extracted data from the included studies independently. The number of included and excluded studies and the selection process are illustrated in From the included documents, the authors extracted the number, sex, and age of participants, the characteristics and the duration of the intervention, the outcome measures, and the results obtained.The authors independently carried out the selection of the papers, the extraction of the data, and their analysis. We used the Newcastle-Ottawa Scale  to assesThe articles included in this review were collected from PUBMED , SCOPUS The studies included analyzed the association between cognitive impairment and consumption of alcohol , 50–77, Of the 29 selected studies, 22 were cohort studies , 68–75, The possibility of doing a meta-analysis was rejected because of the high heterogeneity of the data. We found many differences in the included articles in clinical aspects ; methodology (design of the studies and the risk of bias); and statistical processes .To evaluate the quality of these articles, we used the Newcastle-Ottawa Scale , 49. AllInformation about the design, quality, and intervention of the included studies is shown in To determine the cognitive performance, the outcome measures were examined neuropsychologically and clinically, including brain MRI scans , 52—takiThe effect of the consumption of fermented products either as individual items –71, 77 oThe consumption of alcohol–particularly wine and beer–was examined by most of the articles included in this review –71, 77. To facilitate the comparison between the different results, we have converted the alcohol intake quantities to grams of ethanol. In those articles where the ethanol intake was not specified in g, the conversion was made so that 1 drink  is equivalent to 14 g of alcohol .The reviewed articles have found some beneficial cognitive effect after low-moderate alcohol consumption (1 drink/month-4 drinks/day) –71, 77. When stratifying by gender, some controversies were revealed. While some found a protective effect of alcohol in general , 66, 68,Specific analysis of the effects of wine consumption has shown that moderate consumption (from 1 drink per day up to 4) may reduce the risk of dementia and/or Alzheimer's disease and enhance cognitive functions , 68, 71 In relation to white wine, a higher intake (≥1 drink/day) was significantly associated with a higher incidence of Alzheimer's disease in APOE4 allele carriers .Although some results are not statistically significant, moderate beer consumption (1–3 drinks/day) was related with a larger brain volume  and a trMany of the articles reviewed also found cognitive benefits following consumption of low-moderate amounts of liquors , 63, 68,The effects of the intake of coffee , 68, 77 Where data allowed, and to facilitate comparison between the different results, we estimated caffeine content (milligrams/standard unit) as 115 mg for regular coffee and 6 mg for chocolate .p < 0, 05) and cerebral blood flow in cognitively stable elderly subjects  was also observed on MRI, with increasing consumption up to 5–6 cups  = 0.45 (0.25–0.81);  < 0.01] . The sam < 0.01] , 73, 76 p = 0.01]  = 1.33 ;  = 0.01] .p = 0.0004;  = 0.18 (0.02–0.33); p = 0.03] with a dietary pattern rich in fermented foods :0, 17-0, 65;  < 0.001 ] and agap = 0.03 ]. Logicaed foods .p = 0.016; AD: HR (95% CI) = 0.54 (0.32–0.93); p = 0.045]  that includes various fermented products  .Moreover, studying the relationship of diet-related metabolites with cognitive impairment showed two of the three biomarkers of coffee intake were inversely associated (atractyligenin glucuronide [OR = 0.72] and cyclo (leucyl-prolyl) [OR = 0.68]), but not that of the caffeine biomarker [OR = 1.75]. Cyclo —a metabolite found in chocolate and other fermented foods, e.g., beer, bread, cheddar cheese, cocoa, coffee, wine, Greek yogurt —and an uDiet is increasingly used as a method of preventing disease and delaying aging. The use of fermented foods dates to prehistoric times, but findings on the benefits of this diet on the gut microbiota are relatively recent. The relationship between gut microbiota and the immune and nervous systems has been widely studied, and the implications of fermented food for mental processes performance, such as in dementia or Alzheimer's disease, are starting to be analyzed. For this reason, and considering that these are foods of daily consumption, it seems necessary to compile and analyze all the existing information on the elderly.The main limitation encountered in conducting this review was the difference in information provided by the articles. It was difficult to compare results obtained in different populations, by different covariates, and using different methodologies. An attempt was made to solve this problem by converting fermented beverage intakes  to a standard measure (mg/day or g/day). Furthermore, the covariates for the different elements are diverse and may become very significant; for example, in the case of tobacco, which is associated not only with altered gut microbiota but also with gut inflammation . The varThe definition used of an elderly subject was a person aged 65 years or older –81, but In relation to the risk of bias, this review followed the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines  and the This work comprises a comprehensive review of current knowledge on the neuroprotective use of fermented foods and beverages. An important strength is that the protocol used to carry it out was registered and approved by the International Prospective Register of Systematic Reviews (PROSPERO) as CRD42021250921 .The gut microbiota is essential to maintain the structural integrity of the intestinal mucosa and the immune system (see Section 1), but some diseases can disrupt the microbiota composition , 12, 82.The changes in microbiome during aging involve a reduction in microbial biodiversity and metabolites, leading to a chronic inflammatory reaction and changes in the immune system . These pA correlation has been found between an unhealthy gut microbiota and some nervous inflammatory and neurodegenerative diseases, such as some types of dementias and Alzheimer's disease (see Section 1).Lately, the inflammatory hypothesis of Alzheimer's disease etiology is receiving attention , 84–89. Firmicutes was significantly reduced, whereas that of Proteobacteria, Gammaproteobacteria, Enterobacteriales, and Enterobacteriaceae was increased, showing a progressively enriched prevalence from healthy individuals to mildly cognitive-impaired ones and patients with Alzheimer's disease  depended on the severity of the neurodegeneration. In individuals with Alzheimer's disease, the proportion of  disease .The group of Harach generated germ-free mice using APPPS1 mice as an animal model of Alzheimer's disease (a double transgenic mice expressing mutated forms of the genes for human amyloid protein (APP) and presenilin 1) and found a drastic reduction of cerebral amyloid pathology when compared with control APP mice with intestinal microbiota. Furthermore, these amyloid deposits increased when germline mice were colonized with microbiota from APP transgenic mice more than when they were colonized with microbiota from wild-type mice .In another mouse model of Alzheimer's disease, a dysregulated gut microbiota associated with the onset and progression of Alzheimer's disease was also observed, indicating that dysbiosis may occur before significant clinical signs appear, as evidenced by early alterations in short-chain fatty acids, compatible with intestinal inflammation .The inefficiency of the microglia in reducing the amyloid deposits could explain the relationship between Alzheimer's disease and neuroinflammation , 15. Furin vitro and even in human APOE4 astrocytes , gamma-aminobutyric acid (GABA), and serotonin, which are involved in learning and memory processes . The stuBifidobacterium, Prevotella, and Lactobacillus , and phenolic acids. These bioactive compounds are being analyzed for their antioxidant properties and their possible role in intestinal permeability –38, 110 bacillus , 120.In any case, not all fermented foods contain polyphenols, such as dairy products. The concentration of polyphenols and their gastrointestinal absorption vary depending on the fermentation process; they are not useful if the intestinal microbiota is not healthy and is not able to break them down properly; and not all of them affect the colonic microflora and its fermentative capacity .Most of the reviewed articles found cognitive benefits in old adults following low-moderate alcohol consumption –71, 77. Some authors claim vascular benefits after moderate alcohol consumption because it increases high-density lipoprotein (HDL) and decreases triglycerides and low- and very low-density lipoprotein  levels, thus reducing the risk of vascular lesions , 61. ThaThis hypothesis is supported by the results of the articles included in this review that analyzed moderate consumption of liquor (not shown), which indicated a positive effect on memory performance in men  and on cOn the other hand, the health benefits of alcohol consumption may be due not only to the fermentation process itself, but also to the food matrix, fermentation process and microorganisms, and to the content of polyphenols , vitamins, and other metabolites (see Section 4.3). That this occurs especially in the case of red wine could be explained by the fact that red wine is richer in resveratrol than white wine due to the different production processes, although the concentration varies according to climate, soil, and fermentation time of the wine , 122. ThFischer found differences in the effect of wine consumption in women and men, probably due to gender variations in alcohol metabolism. Women are more susceptible to alcohol toxicity, perhaps due to their smaller volume of distribution for ethanol, decreased first-pass metabolism or more rapid absorption, and more rapid metabolism of ethanol , 123. Fuin vitro study, which showed that natural compounds, including resveratrol, could modify the structure of APOE4 forms and thus ameliorate the pathogenic effects associated with Alzheimer's disease , which exert an anti-inflammatory and antioxidant effect and inhibit the effects of mitochondrial apoptosis –141, eleOn the other hand, sweet dairy products were associated with higher odds of cognitive impairment  in line Dietary patterns including fermented foods and beverages—such as soy products, alcoholic beverages, coffee, etc.—showed some benefits regarding cognitive function , 72–75, The neuroprotective effects after consumption of fermented products are mainly due to a decrease in inflammatory processes , 104 andThese benefits could be due not only to the fermentation process itself, but also to a synergistic effect of the joint consumption of fermented products and to their concentrations of polyphenol compounds and vitamins . All theDue to the aging of the population, dementias and cognitive impairment are becoming an increasingly important public health problem. This carries a significant economic and psychological cost for which there is no etiological treatment, so the most effective approach is an early detection and prevention.Eurostat predicts the population of the European Union in 2040 will be 524 million, of which the estimate of patients with Alzheimer's disease will be 13.1 million. By 2080, this figure is calculated to increase to 13.7 million individuals with Alzheimer's disease out of a total population of 520 million persons .Of the total global burden of diseases, 23% is attributed to disorders in people aged 60 years and over. Of this expenditure, neurological and mental disorders in the elderly accounted for 6.6% in 2010 . PrimaryWe have already mentioned the importance of a healthy gut flora in inflammatory reactions and to the immune system (see Sections 1 and 4.2). The involvement of the microbiota in pathologies, including neurodegenerative diseases, is increasingly accepted. Therefore, one strategy to prevent cognitive decline could be to take care of the composition of this microbiota through diet.Lactobacillus and Bifidobacterium, and a decrease in Clostridium and Enterobacterium, among others, in the gut microbiota, providing anti-inflammatory effects and cardiovascular and brain protection  are related to better preservation of bilateral deep white matter and cerebral blood flow.5. An improvement in cognitive function following the daily intake of soy products has been observed.6. Dietary patterns that include fermented foods and beverages have been shown to decrease the rates of cognitive decline, even in carriers of the APOE4 allele.7. Due to the fermentation process itself and to the polyphenolic compounds and other antioxidants and vitamins in fermented products, the fermented-food diet could become an effective, safe, and inexpensive preventive or cognitive enhancement strategy.The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author.EP-G: literature search and data analysis and writing. IF-E: literature search and data analysis. JG-G and JF-G: data analysis and writing—review and editing. All authors contributed to the study conception and design.


The dramatic fluctuations of climate conditions since the late Tertiary era have resulted in major species range shifts. These movements were conditioned by geographic barriers and species dispersal capacities. In land plants, gene flow occurs through the movement of male gametes , which carry nDNA, and diaspores , which carry both cpDNA and nDNA, making them an ideal model to compare the imprints of past climate change on the spatial genetic structures of different genomic compartments. Based on a meta-analysis of cpDNA and nDNA sequence data in western Europe, we test the hypotheses that nDNA genetic structures are similar in bryophytes and spermatophytes due to the similar size of spores and pollen grains, whereas genetic structures derived from the analysis of cpDNA are significantly stronger in spermatophytes than in bryophytes due to the substantially larger size of seeds as compared to spores.Sequence data at 1-4 loci were retrieved for 11 bryophyte and 17 spermatophyte species across their entire European range. Genetic structures between and within southern and northern populations were analyzed through F and N statistics and Mantel tests.Gst and Nst between southern and northern Europe derived from cpDNA were significantly higher, and the proportion of significant tests was higher in spermatophytes than in bryophytes. This suggests that in the latter, migrations across mountain ranges were sufficient to maintain a homogenous allelic structure across Europe, evidencing the minor role played by mountain ranges in bryophyte migrations. With nDNA, patterns of genetic structure did not significantly differ between bryophytes and spermatophytes, in line with the hypothesis that spores and pollen grains exhibit similar dispersal capacities due to their size similarity. Stronger levels of genetic differentiation between southern and northern Europe, and within southern Europe, in spermatophytes than in bryophytes, caused by higher long-distance dispersal capacities of spores as compared to seeds, may account for the strikingly higher levels of endemism in spermatophytes than in bryophytes in the Mediterranean biodiversity hotspot. In land plants, assessing dispersal is a challenging issue that can be approached either directly or indirectly . Direct In spermatophytes, variations in dispersal capacities are intimately linked to morphological traits of diaspores related to particular dispersal vectors, referred to as dispersal syndromes . In anemThe massive species distribution range shifts that took place due to fluctuations of climate conditions since the late Tertiary era  offer anThese movements have been hampered by East-West oriented mountain ranges, limiting genetic exchange between populations located South and North of the barrier and resulting in differences in allele frequencies among populations . When diHere, we performed a meta-analysis of the spatial genetic structures of bryophytes and spermatophytes across Europe to address the following questions and test the following hypotheses:- To what extent have mountain ranges hampered post-glacial colonization of the continent in bryophytes and spermatophytes? We hypothesize that genetic divergence between southern and northern populations is higher in spermatophytes than in bryophytes (H1). We further hypothesize that these differences are reflected by the presence of a phylogeographical signal in spermatophytes, wherein sister alleles are more likely to occur in sympatry, whereas in bryophytes, dispersal rates would exceed mutation rates, breaking the phylogenetic structure of genetic variation across the continent (H2).- To what extent have differences in dispersal capacities between bryophytes and spermatophytes shaped differences in their spatial genetic structure on both sides of the mountain barriers? We hypothesize that the slope of the regression between genetic similarity and geographic distance is significantly higher in spermatophytes than in bryophytes and that distance is a better predictor of genetic similarity in spermatophytes than in bryophytes due to faster recolonization by random long-distance dispersal events since the last glacial maximum in the latter (H3).- These differences vary depending on the analysis of cpDNA vs nDNA variation. We hypothesize that H1, H2 and H3 apply using cpDNA markers, whereas the spatial genetic structure derived from the analysis of nDNA markers are similar between bryophytes and spermatophytes due to similar sizes of spores and pollen grains (H4).This study focused on Western Europe, as circumscribed eastwards by the easternmost margin of the Alps, i.e., ~15.00 decimal degrees of longitude. The area was divided into South and North, delimited by the Pyrenees and the Alps Figure 1Individual sequences were retrieved from GenBank and aligned with the ‘muscle’ algorithm  as impleTo test the impact of geographic barriers on genetic structure, Gst and Nst were computed between the northern and southern areas. A standard deviation was computed for multilocus datasets by a Jackknife test, wherein Gst and Nst were recalculated after successively pruning one locus from the data at a time as implemented by Spagedi . PresencWe sought for phylogeographic signal in the data by testing the hypothesis that Nst > Gst (H2). Nst is a measure of genetic differentiation among populations analogous to Gst but taking into account the phylogenetic relationships among alleles . An inte2 of the Mantel test by comparing the r2 obtained using linear and log-transformed distances using a paired t-test. Significance of the slope was tested by 1000 random permutations of individuals among localities (Mantel test). We further estimated the standard deviation of the slope by implementing a Jackknife test as described above.To test our third hypothesis (H3) that the slope of the regression between genetic similarity and geographic distance is significantly higher in spermatophytes than in bryophytes and that distance is a better predictor of genetic similarity in spermatophytes than in bryophytes, we regressed pairwise kinship coefficients Fij  between Arabidopsis thaliana and Beta vulgaris), leaving only four spermatophyte species with nDNA data available for this comparison.To test the hypothesis that the spatial genetic structures of bryophytes and spermatophytes differ with cpDNA due to the larger size of seeds as compared to spores, but not with nDNA due to the similar size of spores and pollen grains (H4), all analyses were performed for cpDNA, nDNA, and both markers combined, except the Mantel tests between geographic distance and Fij derived from nDNA due to missing geographic coordinates for individuals in two spermatophyte species (Pulvigera lyellii (Hook. & Taylor) Plášek, Sawicki & Ochyra due to the very clear segregation of alleles, see Gst between populations of northern and southern Europe ranged in bryophytes between 0 and 0.17 , 0 and 0.37, and 0 and 0.34 with cpDNA markers, nDNA markers, and both combined, respectively  was found in 1 and 2 of the bryophyte and spermatophytes species investigated, respectively Table 1.2 as compared to linear distances . The average (± SD) slope of the regression between Fij derived from cpDNA markers and geographic distance was about four times steeper in spermatophytes than in bryophytes in the South , but did not significantly differ in the North   (Log-transforming geographic distances in Mantel tests did not improve the r p=0.49) Table S2While differences in long-distance dispersal capacities between bryophytes and spermatophytes have long been discussed in terms of community assembly rules  Crantz in the Italian peninsula , evidence for phylogeographical signal in the data was virtually absent for both bryophytes and spermatophytes. While in bryophytes, absence of a phylogeographical signal in the data was expected due to the large contribution of migrants of extra-European origin , therebyeninsula , Salvia  Balkans , the abs Balkans .Pulvigera lyellii due to the almost complete allele segregation between northern and southern Europe  T.J. Kop., did not display the same levels of spatial structure in cpDNA. Alternatively, the high cpDNA structure in P. lyellii could be explained in terms of selection. Recent evidence suggests that thermal adaptation may occur even in species with high gene flow  Hedenäs (Rhynchostegium riparioides (Hedw.) Cardot and Radula lindenbergiana Gottsche ex C. Hartm., respectively , the slope of the regression between kinship coefficients derived from cpDNA variation and geographic distance in southern Europe was about four times higher in spermatophytes than in bryophytes, and geographic distance was a significantly better predictor of this relationship, as evidenced by significantly higher r of time . In bryo of time , as furt Hedenäs , Fst=0.1ectively ). In theectively . In bryoectively  out of 1ectively , resultiectively  is endemIn agreement with our fourth hypothesis, the spatial genetic structure of spermatophytes was significantly stronger than those of bryophytes based on the analysis of cpDNA, but not nDNA. Seeds, which carry cpDNA, are in fact several orders of magnitude larger than bryophyte spores. The latter typically measure 10-20 µm on average  and are The comparative analysis of the genetic structure between northern and southern Europe in bryophytes and spermatophytes presented here suggests that mountain ranges of the Alps and the Pyrenees were a significantly more severe impediment for post-glacial migrations in the latter than in the former. The higher genetic structures found in European spermatophytes as compared to bryophytes offers an appealing explanation for the strikingly lower rates of endemism that characterize bryophytes, especially in areas recognized as biodiversity hotspots such as the Mediterranean. A lower dispersal capacity of spermatophytes has also implications for their ability to migrate as a response to ongoing climate change. The results presented here must, however, be interpreted with caution, as our review revealed a quite limited number of phylogeographic studies for plant species distributed across southern and northern Europe based on DNA sequence variation. In particular, the number of phylogeographic studies for bryophytes in the Mediterranean is extremely limited. Nevertheless, our results reveal intriguing patterns regarding the relative dispersal capacities of pollen grains, spores and seeds, opening the door to a large-scale comparative analysis based on large numbers of markers that can now relatively easily be generated with NGS techniques.https://doi.org/10.1111/j.1095-8339.2007.00775.x; https://doi.org/10.1111/ele.13254; https://doi.org/10.1111/j.1469-8137.2006.01870.x; https://doi.org/10.1111/j.1365-294X.2005.02848.x; https://doi.org/10.1111/mec.13348; https://doi.org/10.1111/j.1469-8137.2010.03328.x; https://doi.org/10.1111/j.1365-294X.2007.03615.x; https://doi.org/10.1002/ece3.3774; https://doi.org/10.1111/j.1365-294X.2009.04449.x ;https://doi.org/10.1111/jbi.13726; https://doi.org/10.1093/botlinnean/boab043; https://doi.org/10.1093/botlinnean/boab043 ;https://doi.org/10.1111/j.1365-294X.2007.03228.x; https://link.springer.com/article/10.1007/s00606-016-1299-1#Sec12; https://doi.org/10.1093/botlinnean/boy025; https://doi.org/10.1093/botlinnean/boy032; https://doi.org/10.1016/j.flora.2019.02.012; https://pbsociety.org.pl/journals/index.php/asbp/article/view/asbp.89313;https://doi.org/10.1371/journal.pone.0179961; https://doi.org/10.1016/j.ppees.2018.10.003.Publicly available datasets were analyzed in this study. This data can be found here: TF: Writing – original draft, Writing – review & editing. AL: Writing – review & editing. FC: Writing – review & editing. AV: Writing – original draft, Writing – review & editing, Conceptualization.


A collection of native farm animal breeds can be considered as a gene pool and a national heritage. Long-term artificial selection in domesticated animals has certain effects on their genomes, which can be investigated using genome-wide screens for DNA sequence variation, that is, so-called single nucleotide polymorphism (SNP) screens. Here, we looked at the genomes of 19 Russian chicken gene pool breeds, both native and imported, evaluating the contrasting egg, meat and dual-purpose types. Based on genetic diversity statistics, we identified differences between the breeds using many DNA markers (SNPs) that may represent genomic regions that are being selected for, either within a specific breed or shared between breeds. Our research will be helpful for further understanding the genomic diversity and demographic history of Russian domestic chickens. This would be essential for their successful breeding.A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th–19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool. Gallus gallus ; GGA; ; (3) WL, PC, RIR, AS, RW1 and RC, Ne = ; and (4) UshF, LMF, NH, AoB, Ush and RBB, Ne =   were characterized by higher Ne values (217–290) and three more breeds  significantly outperformed the others by this indicator (317–803). If we look at an even earlier demographic history of populations , while CW and YC had the largest Ne . Remarkably, there was a sharp Ne reduction in YC (from 2279 to 141), suggesting that this breed went through a severe genetic bottleneck, as confirmed by the fact that YC was almost extinct by the end of World War II. It can be assumed that breeds with a low Ne, both at present and 50–500 generations ago, apparently descended from a limited number of ancestors or were under significant selection pressure in a number of generations. However, it should be noted that, as a rule, a majority of the studied breeds were developed by hybridization of several breeds, as well as by “blood refreshing” , which could generally be reflected in similar dynamics patterns of their demographic history and Ne changes in a series of generations.The assessment results of demographic history in terms of he breed . Based o a. This pions ago a, most bears ago b, WL hadNSe method [Ne curves  as assessed using the SNP-based genome-wide analysis, the patterns of breed distribution by LD were also obtained (Ne (three generations ago) and taking into account the three parameters of LD between SNP markers made it possible to identify four clusters using PCA  was identified in the WL population, which, along with the lowest diversity indices, evidenced a severe selection pressure in this line of laying hens.Based on the performed analysis of the biodiversity of a large sample of native and foreign breeds, we can suggest the presence of very specific patterns of variability and genetic structure in the surveyed populations. For example, WL chickens were different from other breeds that are basically synthetic by origin. This appears to indicate a stronger and longer selection for egg production traits, which this line and the WL breed as a whole were subjected to, and, possibly, a narrower structural variability in the genomes of its ancestral forms. The greatest FST = 0.125 in the YC–RC pair to 0.525 in WL–NH). WL was characterized by less genetic variability than the other breeds (FROH inbreeding coefficient (0.551), and YC and CW the lowest ones . This may be an indication that WL descended from a small number of founders , whereas , and ofJudging from the biodiversity analysis of this large sample of native and foreign breeds, we noted very specific patterns of variability and genetic structure of the surveyed breeds, with WL being especially different from other breeds of synthetic origin. This, apparently, may indicate a stronger and longer selection for egg-laying traits, which this line and the WL breed as a whole were subjected to, and, possibly, a narrower structural variation in the genomes of its ancestral stocks. The phylogenetic analysis results did not contradict the available data on the origin and breeding history of the breeds. For example, WL and RW are typical specialized ETBs selected for egg production; moreover, WL roosters were used for the creation of RW. Ush and RBB are old indigenous breeds that are tolerant to cold, have a brooding instinct and are also used for fancy purposes. RIR was an original breed for developing NH, and both were supposedly involved in the creation of PC. One of the initial breeds in the development of AS was Pm; in addition, when creating both breeds, YC was also used. ZS was used to produce Kt, and both breeds descended from NH and RW among other parent breeds. This historical breed information was in line with the present whole genome screening study.In general, using the results of a multilateral survey of this sample of breeds, it can be argued that phylogenetic relationships based on their genetic structure and variability reflect the known, previously postulated and discovered patterns of evolution and selection in chickens ,106,107.


Castanea species, 16 phenotypic traits were measured, simple sequence repeat (SSR) markers were analyzed, and molecular identity cards (IDs) were constructed for 118 Castanea materials using fluorescent capillary electrophoresis. The coefficient of variation values of the 16 morphological traits of the test materials ranged from 11.11% to 60.38%. A total of 58 alleles were detected using six pairs of SSR core primers, with an average number of 9.7 alleles per locus. The average number of valid alleles per locus was 3.9419 and the proportion of valid alleles was 40.78%. A total of 105 genotypes were detected, and the number of genotypic species that could be amplified per primer pair ranged from 8 to 26. The mean value of the observed heterozygosity was 0.4986. The variation in the He, H, and PIC values was similar; the size of I value was approximately 2.21 times larger, and its mean number of variations was 0.7390, 0.7359, 0.6985, and 1.6015, respectively. The classification of 118 Castanea species was performed using three analytical methods: structure analysis, neighbor-joining (NJ) cluster analysis, and principal coordinate analysis (PCoA), and the results of the three methods were in high agreement. Six pairs of SSR core primers with high polymorphism and strong discriminatory properties were used to identify 118 Castanea plants, and a unique molecular ID card was constructed for each material. These results provide insight into the genetic diversity and population structure of Castanea plants and a theoretical basis for improving the phenomenon of mixed varieties and substandard plants in the Castanea plant market.To understand the genetic relationships of  Castanea, which is cross-pollinated, includes seven major species: Castanea mollissima Bl., Castanea henryi (Skam) Rehd. et Wils., Castanea seguinii Dode, Castanea crenata S. et Z., Castanea dentata (Marsh.) Brokh, Castanea sativa Mill., and Castanea pumila Mill. Among them, the Chinese chestnut (C. mollissima Bl.) exhibits superior disease resistance traits, such as exhibiting resistance to two major pathogens, Cryphonectria parasitica and Phytophthora cinnamomic [Castanea plants and has a crucial role. Castanea has comparatively high nutritional value due to its essential amino acids, fatty acids, vitamins, minerals, dietary fiber, and other nutrients. Additionally, cooked Castanea can strengthen the spleen, tone the kidneys, and nourish the stomach. It also has beneficial preventive and therapeutic effects on coronary heart disease, hypertension, and atherosclerosis [Castanea, such as hybridization of varieties and homonyms; this has led to a rise in imitation and inferior varieties and caused losses to breeders, farmers, and consumers. Therefore, there is an urgent need to establish an accurate, rapid, and efficient method for breed identification.The nnamomic . Chineseclerosis ,3. HowevWith the rapid development of molecular biology, a variety of molecular marker technologies, such as randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR) and single nucleotide polymorphism (SNP), have been widely used in the analysis of genetic diversity and plant variety identification. SSR molecular marker technology involves tandem repeat sequence consisting of 1–6 nucleotides as repeat units, which has excellent characteristics such as co-dominant inheritance, high polymorphism, good reproducibility, and stable and accurate results. It has emerged as a key molecular marker technology for plant genetic diversity analysis, population structure research, variety identification, and molecular ID construction ,5,6,7,8.Castanea plants, there are few reports on the construction of molecular ID cards for Castanea plants.The construction of various molecular ID cards is a highly efficient method for identifying germplasm resources and has been widely used for the identification and authentication of a variety of plants ,10. MoleCastanea were analyzed and systematically described using SSR molecular markers and fluorescence capillary electrophoresis; an exclusive molecular ID card was constructed for each material and used to identify the 118 distinct materials. The results of this study provide a molecular basis for understanding the genetic diversity and population structure of germplasm resources of Castanea and will serve as a reference for solving the problems of homonymy and synonymy.In this study, the genetic diversity and population structure of 118 materials from four species of Castanea plant materials into four groups  test, and the observed purity of each locus was determined to be within the 95% confidence interval of the respective expected purity , which wHe, H, and PIC values were similar, and the size of I value was approximately 2.15 times larger, with the smallest variation at primer P4 and the largest variation at primer P82, and the average number of variances were 0.7236, 0.7203, 0.6793 and 1.5203, respectively. The results indicated that 112 Chinese chestnut resources had high genetic diversity.The genetic diversity of the 112 Chinese chestnut cultivars was analyzed and evaluated using six chestnut SSR markers . A totalCastanea variety resources was analyzed and evaluated by adding six resources of other Castanea species to 112 Chinese chestnut cultivar resources using six Chinese chestnut SSR markers , the largest variation at primer P82 , and the average variation numbers were 0.7390, 0.7359, 0.6985, and 1.6015, respectively. Genetic diversity analysis and evaluation of the 118 Castanea resources at the genomic level using six Chinese chestnut SSR markers were generally slightly higher than those containing only Chinese chestnut cultivars, indicating that the six Castanea resources of other species also displayed higher genetic diversity and were valuable resources in the Castanea.The genetic diversity of 118  markers . A totalCastanea materials was performed using Structure software, and the optimal grouping was determined by ∆K based on the optimal grouping method. The results showed that ∆K reached its highest peak value when K = 3 (Castanea plant samples were divided into three groups (Castanea crenata Sieb. et Zucc.), Henry chestnut (Castanea henryi (Skam) Rehd. et Wils.), and European chestnut (Castanea sativa Mill.), and Taxon C consisted of 38 Chinese chestnut species. According to the major color ratio  in each variety, a Q value ≥ 0.6 indicated that the test materials were relatively single in kinship and genetic background, and a Q value < 0.6 indicated that the test materials had mixed kinship origin and a more complex genetic background. Of the measured materials, 93.2% had a Q value ≥ 0.6, and most of the test materials exhibited a relatively single kinship and genetic background with less gene penetration; 6.8% of the materials with Q value < 0.6 were Chinese chestnut cultivars, namely ‘Xin Zhuang No. 2’, ‘Tai Shan Hong Li’, ‘Chui Zhi Li’, ‘Long An No. 1’, ‘Yue You No. 9’, ‘Qing Mao Ruan Zha’, ‘No. 6’, and ‘No. 15’, which each revealed more complex kinship and genetic background. Thus, we can conclude that these materials have complex kinship and genetic backgrounds, and there is some germplasm gene penetration.Population structure analysis of 118 en K = 3 a. Therefe groups b: Taxon Castanea and plant species. The distance between species is related to genetic similarity. Proximity refers to a high genetic similarity and close kinship. Distance indicates low genetic similarity, long kinship, and large genetic differences. A PCoA of 118 Castanea plant species was performed using the first and second principal components as the horizontal and vertical coordinates, respectively , Taxon II (green), Taxon III (blue), and Taxon IV (red). Taxon I included 13 materials, Taxon II included 26 materials, and Taxon III included 15 materials. All materials clustered into Taxon I, Taxon II, and Taxon III were Chinese chestnut species. Taxon IV included Chinese chestnut, Japanese chestnut, Henry chestnut, and European chestnut, with a total of 64 materials.The NJ clustering diagram  was consCastanea plant materials were identified by combining multiple pairs of primers. By gradually increasing the number of primers, the purpose of identifying all materials was finally achieved. Primer P4 could only identify three parts of the material, but after adding primer P82, 35 parts of the material could be identified and gradually increasing the number of primers up to six pairs of highly polymorphic primers (P4 + P82 + P106 + P108 + P127 + P138) allowed all 118 materials to be distinguished ) was used to encode the desired variety with information such as variety name, germplasm type, botanical classification, phenotypic traits, and string molecular ID card, which well combines phenotypic traits and molecular information. Taking the Chinese chestnut variety ‘Jiu Jia Zhong’ as an example, On the basis of phenotypic trait data and molecular data, the online software forage QR code generator  [Castanea plants, Chinese chestnut, Japanese chestnut, and European chestnut. Nie et al. (2021) [MAF, Ho, and PIC as 0.420, 0.622, and 0.652, respectively, indicating that the 18 SSR markers were highly polymorphic. In this study, six pairs of highly polymorphic primers were screened from 153 pairs of SSR primers that were developed and designed based on the whole Chinese chestnut genome. In 112 Chinese chestnut cultivars, 51 alleles and 91 genotypes were detected, and the mean values of I, Ho, He, H, PIC, and MAF were 1.5203, 0.5134, 0.7236, 0.7203, 0.6793, and 0.4018, respectively, indicating high heterozygosity, polymorphism, and rich genetic diversity. An important reason for the high heterozygosity of Chinese chestnuts is that they are cross-pollinated plants [The genetic diversity of . (2009)  reported. (2021)  screenedd plants . The SSRCastanea species, Japanese chestnut, Henry chestnut, and European chestnut, were added to 112 Chinese chestnut species. The SSR molecular markers developed from the Chinese chestnut genome were successfully and efficiently amplified across species in Japanese chestnut, Henry chestnut, and European chestnut, indicating that the developed SSR molecular markers were highly versatile in the Castanea and can be used for genetic diversity analysis, species identification, and molecular ID construction of the Castanea.In addition, six resources of three Castanea plants. For example, Jiang et al. (2017) [Castanea for structural analysis, the present study involved Chinese chestnut, Japanese chestnut, Henry chestnut, and European chestnut.Population structure, NJ cluster analysis, and principal coordinate analysis are effective means to study the genetic diversity, kinship, and genetic background of plant germplasm resources and are critical bases for protecting and utilizing plant germplasm resources. Many studies have been conducted on the population structure of plants ,22,23,24. (2017)  analyzed. (2017)  classifi. (2017)  used 24 Castanea. A total of 118 Castanea plants were classified using three analytical methods: structural analysis, NJ clustering analysis, and PCoA analysis. The classification results of the three methods were highly consistent. Taxon A of the structure analysis results contained all the materials in Taxon I of the NJ cluster analysis except for the Chinese chestnut cultivar ‘Shi Men Zao Shuo’. All the remaining 32 materials in Taxon A except for the nine materials of ‘Jiao Zha’, ‘Jian Ding You Li’, ‘Yue Yao No. 8’, ‘Jie Jie Hong’, ‘Long An No. 1’, ‘Mei Gui Hong’, ‘Qing Mao Ruan Zha’, ‘ZA’, and ‘No. 15′ were clustered into Taxon P3 of the PCoA analysis. The remaining 36 materials in the B Taxon of the structure analysis were clustered into the P1 Taxon of the PCoA analysis, except for ‘Mao Pu’, ‘Chui Zhi Li’, and ‘No. 6’; the remaining 48 materials in the P1 Taxon were clustered into the IV Taxon of the NJ clustering analysis, except for ‘Shi Men Zao Shuo’. The P3 Taxon of the PCoA analysis included all materials from Taxon II of the NJ clustering analysis; six materials, including Japanese chestnut, Henry chestnut, and European chestnut, were grouped into the same taxon by structure analysis, NJ cluster analysis, or PCoA analysis. Although there was a high degree of agreement and similarity in the classification results among structure analysis, NJ clustering analysis, and PCoA analysis, there were also differences, with different clusters on select branches. The structural analysis and PCoA analysis divided the 118 materials into three broad categories, and the NJ clustering analysis divided the 118 materials into four broad categories.In this study, six pairs of highly polymorphic SSR markers were used to analyze the structure of 118 Q value of less than 0.6, indicating a certain frequency of gene exchange and infiltration among the participating material species. However, due to the lack of clarity regarding the origin and genetic background of certain resources, it was not possible to link taxonomy to geographic origin for analysis. In future studies, we will attempt to track the origin and genetic background information of each material to explore the genetic structure, genetic diversity, and affinity between different geographic resources.In the population structure analysis, 6.8% of the materials had a Castanea plants. Currently, however, there are many substandard phenomena, which are not conducive to market development. As an example, consider the fried Chinese chestnut market in Nanjing, Jiangsu Province, the market survey revealed that most of Nanjing’s fried Chinese chestnuts are made from Yanshan Chinese chestnuts produced in Qianxi, Hebei Province, which are soft and sweet and liked by consumers. However, most operators and consumers of fried Chinese chestnut are not able to distinguish between Yanshan Chinese chestnut and other varieties. The presence of mixed varieties in the market and the phenomenon of using the substandard as a good is endangering the legitimate rights and interests of both operators and consumers. Therefore, it will be necessary and meaningful to construct molecular ID cards to standardize the management of Castanea plants.Molecular identification is an effective method to solve the problems of species mixing, tautology, and synonyms and is an important guide for species identification. To date, many studies on molecular ID have been reported ,31,32,33Castanea plants using six pairs of SSR core primers, and were able to completely distinguish 118 materials, which not only provided a reference for the identification and authentication of the Castanea plants, but will also contribute to the development of the Castanea plant market.Nie et al. (2021)  construcCastanea plant resources in detail and comprehensively.Fruit phenotypic morphological traits have significant economic value and discriminatory ability, and are widely used in the identification of different plant varieties. However, due to environmental factors and plant growth cycles, phenotypic traits are somewhat unstable, and some varieties have very similar phenotypic traits. Therefore, it is difficult to identify all varieties using phenotypic traits alone. At present, rapid development and increasing sophistication of molecular marker technologies will help overcome the limitations of phenotypic traits. The combination of phenotypic and molecular-based methods will help to identify varieties more accurately and comprehensively ,36,37,38In addition, phenotypic trait clustering analysis and genetic distance clustering analysis showed that although the 118 materials were grouped into four groups by the two methods, the clustering results were different between the two methods. Genetic distance of varieties with similar phenotypic traits may be distant, for example, the cultivar ‘Duan Zha’ and the cultivar ‘Gui Hua Xiang’; phenotypic traits of varieties with similar genetic distance may have large differences, for example, the cultivar ‘Shi Men Zao Shuo’ and the cultivar ‘Cen Kou Da Li’. However, some of the materials were grouped together in both phenotypic and genetic distance clusters, for example, the cultivar ‘Chu Shu Hong’ and the cultivar ‘Bo Ke Chi Li’, the cultivar ‘Shu He No.1′ and the cultivar ‘Shu He No.7’, indicating that their genes and relatives may be very similar.Castanea were collected from Jiangsu Province, China. We collected 10–15 young leaves, marked them, placed them in self-sealing bags, brought back to the laboratory in ice boxes, and stored at −20 °C in a refrigerator.From April to October 2021, 118 materials  from 4 sCastanea germplasm resources were measured for three consecutive years from 2020 to 2022, and the appearance characteristics were photographed in a varietal box plot. A vernier caliper was used to measure the phenotypic data of 16 traits, including Single cone weight, Cone diameter, Cone length, Cone thickness, Spine length, Cone shell thickness, Single nut weight, Nut diameter, Nut length, Nut thickness, Fruit shape index, Stigma length, Single kernel weight, Kernel diameter, Kernel length, Kernel thickness. Each species has at least 3 replications. The maximum, minimum, mean, standard deviation and coefficient of variation were calculated for each trait. Cluster analysis of phenotypic traits was performed using RStudio software.The phenotypic traits of different varieties of the Leaf genomic DNA was extracted using a modified cetyltrimethylammonium bromide (CTAB) method . Two perPIC > 0.5) were selected from 153 pairs of primers developed and synthesized based on published chestnut genome sequence data [Six pairs of primers with high polymorphism , 1 μL template DNA (50 ng/μL), 0.3 μL of 10 μM fluorescence-modified upstream primer, 0.3 μL of 10 μM downstream primer, and 5.9 μL ddHThe PCR amplification reaction procedure was as follows: pre-denaturation at 94 °C for 3 min; denaturation at 94 °C for 30 s, annealing at 57 °C for 30 s, extension at 72 °C for 45 s and a total of 35 cycles; full extension at 72 °C for 10 min; and storage at −20 °C protected from light. Capillary electrophoresis detection was performed using an ABI 3730 XL DNA Sequencer , and Gene Mapper 4.1 software was used for data collation and image analysis.Na), the number of effective alleles (Ne), Shannon’s information index (I), observed heterozygosity (Ho), expected heterozygosity (He), Nei’s genetic diversity index (H) [PIC), Number of genotypes (NG) and master allele frequency (MAF) were calculated using PowerMarker V3.25 [https://itol.embl.de/ accessed on 26 February 2023).The data format was converted using DataFormater software , and POPndex (H) , and Eweer V3.25 . AdditioQ). Evanno’s method [Population genetic structure analysis was performed using Structure software ,47,48, as method  and the s method  were uses method ,52,53. Ps method ,55.https://cli.im/ accessed on 26 February 2023) to generate a two-dimensional code molecular identity card.The allelic genotypic fragments amplified by each primer pair were ranked from smallest to largest and numbered 1, 2, 3…9, A, B, C, etc., and the primer pair used P4, P82, P106, P108, P127, and P138. The sequence was arranged to construct fingerprint feature codes to obtain the molecular information of each material. The botanical taxonomic information of the materials was combined with molecular information using 2D code online generation technology (Castanea plants were analyzed using SSR molecular markers; the results showed that the test materials had rich genetic diversity. The molecular ID cards of 118 Castanea plant materials were successfully constructed using six pairs of core SSR primers, which can completely differentiate all participating materials and have important implications for the conservation, utilization, and management of Castanea plant resources.In this study, 16 phenotypic traits were measured and analyzed; among them, the coefficient of variation of five phenotypic traits such as single cone weight was greater than 30%, and the coefficient of variation of fruit shape index was the smallest, which was a relatively stable trait. The genetic diversity and population structure of 118


China is the largest producer of sweet potato in the world, accounting for 57.0% of the global output. Germplasm resources are the basis for promoting innovations in the seed industry and ensuring food security. Individual and accurate identification of sweet potato germplasm is an important part of conservation and efficient utilization.In this study, nine pairs of simple sequence repeat molecular markers and 16 morphological markers were used to construct genetic fingerprints for sweet potato individual identification. Combined with basic information, typical phenotypic photographs, genotype peak graphs, and a two-dimensional code for detection and identification were generated. Finally, a genetic fingerprint database containing 1021 sweet potato germplasm resources in the “National Germplasm Guangzhou Sweet Potato Nursery Genebank in China” was constructed. Genetic diversity analysis of the 1021 sweet potato genotypes using the nine pairs of simple sequence repeat markers revealed a narrow genetic variation range of Chinese native sweet potato germplasm resources, and Chinese germplasm was close to that from Japan and the United States, far from that from the Philippines and Thailand, and the furthest from that from Peru. Sweet potato germplasm resources from Peru had the richest genetic diversity, supporting the view that Peru is the center of origin and domestication of sweet potato varieties.Overall, this study provides scientific guidance for the conservation, identification, and utilization of sweet potato germplasm resources and offers a reference to facilitate the discovery of important genes to boost sweet potato breeding.The online version contains supplementary material available at 10.1186/s12870-023-04329-1. Ipomoea batatas (L.) Lam.) is a hexaploid annual or perennial dicotyledonous root plant of the Ipomoea genus in the Convolvulaceae family. Sweet potato has the valuable characteristics of high yield, strong adaptability, and rich nutritional value [4 ha, accounting for 30.4% of the global planted area and 55% of the worldwide output [Sweet potato  [Archaeological, historical, and biological studies have shown that Latin America is the key diversity center of sweet potato germplasm resources, also considered the most likely origin center of sweet potato , 18. Claby land)  or the PSweet potato propagates vegetatively and is thus, mainly preserved in the form of vegetative bodies, such as root tubers, seedlings, and test-tube seedlings. Resource identification has long been based on traditional phenotypic characteristics, which are susceptible to variation owing to environmental and subjective factors and thus, have low reliability. Furthermore, China’s collection methods and sources of sweet potato germplasm are diverse, with little standardization. Germplasm exchange and independent naming schemes among sweet potato planting operators or conservation organizations also result in the repeated introduction of germplasm, different names assigned to the same variety, and different varieties assigned under the same name, leading to unclear genetic relationships among germplasm accessions. This situation poses a challenge to cataloging and preserving sweet potato germplasm resources, selecting breeding parents, and promoting high-quality cultivars.Many methods are available for biological species identification and genetic diversity analysis. Phenotypic markers remain important research tools owing to their advantages of intuitiveness and convenience . The comTo determine the genetic structure and diversity of sweet potato resources in China and provide a standardized guide to the available resources, we analyzed the population structure and genetic diversity of 1021 sweet potato genotypes from natural populations and a full-sib population of 55 clones using SSR molecular marker technology. Subsequently, we constructed a fingerprint database with a combination of phenotypic and molecular markers to provide evidence and references for variety identification, research, and further utilization of sweet potato germplasm resources in China. This work should also provide technical support for the in-depth exploration and utilization of sweet potato germplasm resources, including their collection, identification, cataloging, conservation, and selection of appropriate breeding parents.Using 1021 sweet potato germplasm resources as a data set, 20 phenotypic traits were analyzed by factor analysis. In our Kaiser-Meyer-Olkin   were detected by the nine pairs of SSR primers in the 1021 germplasm samples  at the nearest location (0.4619) to the mean value (0.4648) Fig. a. Group The full-sib families with 55 clones clustered together completely in Group P, with an average genetic distance of 0.2277. These results further demonstrate the high discrimination efficiency of the primer combinations selected in this study for sweet potato resources.PCA results also showed that the 1021 sweet potato germplasms were not clustered together according to their regions Fig. , but theFinally, we constructed a unique genetic fingerprint database for sweet potato germplasm, including genotypic  and aid in dispelling cultivar confusion. If the genetic fingerprint data of two materials are consistent at both the phenotypic and genotypic levels, they will be considered the same variety. Thus, establishing genetic fingerprints of sweet potato germplasm resources will improve the efficiency and accuracy of variety identification, providing a theoretical foundation for future identification, protection, and breeding of sweet potato germplasm resources. The fingerprint database of sweet potato germplasm resources constructed in this study represents the largest such resource in the world to date.A genetic fingerprint database containing 1021 sweet potato germplasm resources was constructed with nine molecular markers and 16 morphological markers as core indicators. The genetic variation of native Chinese sweet potato germplasm resources was found to be narrow, demonstrating a closer relationship to those from Japan and the United States and the furthest relationship with resources from Peru. This study provides further scientific and technical support for the conservation, identification, research, and utilization of sweet potato germplasm resources.A total of 1021 sweet potato germplasm resource materials Table S and a fu−1 and stored at −20 ℃ for future use. The DNA stock solution was stored at −80 ℃. Sampling and DNA extraction were completed in 2018 and 2019.The experimental materials were planted in the Guangzhou Baiyun base of the Guangdong Academy of Agricultural Sciences, and DNA was extracted from the young leaves 45–50 d after planting. Genomic DNA was extracted using the ionic detergent cetyltrimethylammonium bromide, and DNA quality was examined by 2.0% agarose gel electrophoresis. The concentration of DNA was determined on a NanoDrop 2000 ultraviolet spectrophotometer. The DNA was then diluted to 50 ng μLTwenty-three pairs of sweet potato SSR primers were used in the experiment Table , of whicFour sweet potato resources  were selected from the experimental materials to screen the 23 pairs of SSR core primers by polyacrylamide gel electrophoresis (PAGE)-silver staining, with three replicates for each primer. The primers exhibiting high polymorphism and good repeatability were selected as core primers for genetic diversity analysis and genetic fingerprint construction of sweet potato germplasm resources.−1), 0.2 μL TaqDNA polymerase, 0.3 μL each of the upstream and downstream primer (20 μM), 0.4 μL dNTPs, 2 μL buffer, and 14.8 μL ddH2O. The following PCR cycling program was used: pre-denaturation at 94 ℃ for 5 min, denaturation at 94 ℃ for 30 s, annealing at 54 ℃ (varied according to primer) for 35 s, and extension at 72 ℃ for 40 s for a total of 35 cycles. The final product was extended at 72 ℃ for 3 min. The products were separated and visualized by PAGE-silver staining on a 6% gel, and fluorescence capillary electrophoresis was carried out on a 3730XL DNA analyzer .The total volume used for polymerase chain reaction (PCR) was 20 μL, including 2 μL of DNA template  was performed using Origin 2021. The KMO test was used to assess correlations and partial correlations between variables; a test outcome of < 0.5 indicates that each variable is independent and unsuitable for factor analysis.The genetic parameters of SSR typing from the raw capillary electrophoresis data were analyzed using Fragment (plant) analysis software in Genemaker. The labeled molecular weight in each lane was compared with the position of the peak value of each sample; the amplified band at the same migration position was marked as 1, and the non-amplified band was marked as 0 to construct a binary data matrix of 0 s and 1 s. The NTSYSpc 2.11 software package was used to calculate the genetic distance between materials. The number of alleles (Na), allele frequency, and genotype frequency were statistically analyzed. Shannon’s information index (I), number of effective alleles (Ne), and PIC were calculated according to the 0/1 data matrix using the following formulae:pi represents the gene frequency of the ith allele at a given locus.Two parameters were used to evaluate the individual recognition ability of nine pairs of SSR markers, PI, and PIsibs, representing the average probability of two random individuals with the same genotype, in the natural (1021 germplasm samples) and sibling (55 full-sib clones) population, respectively, calculated using the following equations:http://192.168.3.177), which was ultimately used to build genetic fingerprints and the two-dimensional code database of sweet potato germplasm resources.Molecular markers combined with phenotypic markers were used to construct the genetic fingerprint of sweet potato germplasm. The selected genotypic marker combinations were labeled with uppercase letters , and the genotypes were sorted and labeled with Arabic numerals; similarly, different phenotypic markers were labeled with lowercase letters , and the phenotypes were assigned Arabic numerals. Using this method, a series of numbers composed of uppercase or lowercase letters plus Arabic numerals were formed for each resource, providing genetic and phenotypic fingerprints of the germplasm. We combined the genotypic and phenotypic fingerprints with basic information, phenotype photographs, and molecular marker scanning peaks graph to develop a two-dimensional code of each germplasm resource using Golang on the local server  primers. Figure S2. Scanning peak graphs of all 943 genotypics.Additional file 2: Table S1. Genomic positons of core simple sequence repeat (SSR) primers. Table S2. Basic information of 1021 sweet potato germplasm resources. Table S3. Genotypics of 1021 sweet potato germplasm resources. Table S4. Phenotypics of 1021 sweet potato germplasm resources.