Comparative Study of Genetic Structure and Genetic Diversity betweenWild and Cultivated Populations of Taxus cuspidata,Northeast China

Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(p<0.001),this suggested that the genetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T.cuspidata species.These developed SNP markers can provide a molecular foundation for T.cuspidata breeding,construction of genetic maps,variety identification,and association analysis of agronomic traits.

A Discussion on Possible Indicators Related to Genetic Structure Changes in Plant Germplasm Conservation

The purpose of the present paper is to study and develop indicators and procedures for the evaluation of genetic structure changes in germplasm conservation due to social and natural environment reasons. Some basic concepts in germplasm study were introduced at first. Then, six kinds of indicators for genetic diversity as a measure of genetic potential of a germplasm collection were presented, i.e., numbers of different entities at certain level, evenness of the entity distribution, genetic similarity and genetic distance, genetic variance and genetic coefficient of variation, multivariate genetic variation indices, and coefficient of parentage. It was pointed out that genetic dispersion did not provide a complete concept of genetic diversity if without any information from genetic richness. Based on the above, the indicators for genetic erosion as the genetic structure changes of germplasm conservation due to social reasons, the indicators of genetic vulnerability as the genetic structure changes of germplasm conservation due to environmental stresses, the measurement of genetic drift and genetic shift as the genetic structure changes of germplasm collection during reproduction or seed increase were reviewed and developed. Furthermore, the estimation procedures of the indicators by using molecular markers were suggested. Finally, the case studies on suitable conservation sample size of self-pollinated and open-pollinated populations were given for reference.

Analysis of genetic diversity and population structure in sweetpotato using SSR markers

Sweetpotato, Ipomoea batatas(L.) Lam., is an important food crop worldwide. Large scale evaluation of sweetpotato germplasm for genetic diversity is necessary to determine the genetic relationships between them and effectively use them in the genetic improvement. In this study, the genetic diversity of 617 sweetpotato accessions, including 376landraces and 162 bred varieties from China and 79 introduced varieties from 11 other countries, was assessed using 30 simple sequence repeat(SSR) primer pairs with high polymorphism. Based on the population structure analysis,these sweetpotato accessions were divided into three groups, Group 1, Group 2 and Group 3, which included 228, 136and 253 accessions, respectively. Consistent results were obtained by phylogenic analysis and principal coordinate analysis(PCoA). Of the three groups, Group 2 showed the highest level of genetic diversity and its accessions were mainly distributed in low-latitude regions. The accessions from South China exhibited the highest level of genetic diversity, which supports the hypothesis that Fujian and Guangdong were the first regions where sweetpotato was introduced to China. Analysis of molecular variance(AMOVA) indicated significant genetic differentiations between the different groups, but low levels of genetic differentiation existed between the different origins and accession types.These results provide valuable information for the better utilization of these accessions in sweetpotato breeding.

Genetic Structure and Diversity Study of Cassava (Manihot esculenta) Germplasm for African Cassava Mosaic Disease and Fresh Storage Root Yield

A better understanding of population structure and genetic diversity among cassava germplasm for African cassava mosaic disease and fresh root yield traits is useful for cassava improvement programme. Phenotype-based selection for these traits is cumbersome due to phenotypic plasticity and difficulty in screening of phenotypic-induced variations. This study assessed quantitative trait loci (QTL) regions associated with African cassava mosaic disease (ACMD) and fresh storage root yield (FSRY) in 131 cassava (Manihot esculenta) genotypes using a genome-wide association study (GWAS). The single nucleotide polymorphism (SNP) loci and associated candidate genes, when validated, would be a valuable resource for marker-assisted selection in the breeding process for development of new cassava genotypes with improved resistance to ACMD and desirable high root yield. Population structure analysis using 12,500 SNPs differentiated the 131 genotypes into five distinct sub-groups (K = 5). Marker-trait association (MTA) analysis using the generalized linear model identified two QTL regions significant for ACMD and three for FSRY. This study demonstrated that DArTseq markers are useful genomic resources for genome-wide association studies of ACMD and FSRY traits in cassava for the acceleration of varietal development and release.

Large scale genetic landscape and population structure of Ethiopian sesame (Sesamum indicum L.) germplasm revealed through molecular marker analysis

Sesame(Sesamum indicum L.) plays a crucial role in Ethiopian agriculture,serving both subsistence and commercial purposes.However,our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited.To address this knowledge gap,we genotyped 368 Ethiopian sesame germplasms,categorizing into four distinct breeding groups:Accessions,landraces,improved varieties,and wild types,using a comprehensive set of 28 polymorphic markers,including 23 simple sequence repeat(SSR) and five Insertion-Deletion(InDel) markers.These markers ensured robust genomic representation,with at least two markers per linkage group.Our results unveiled substantial genetic diversity,identifying a total of 535 alleles across all accessions.On average,each locus displayed 8.83 alleles,with observed and expected heterozygosity values of 0.30 and 0.36,respectively.Gene Diversity and Polymorphic Information Content(PIC) were recorded at 0.37 and 0.35.The percentage of polymorphic loci varied significantly among breeding groups,ranging from8.00% to 82.40%,indicating high diversity in accessions(82.4%),moderate diversity in improved varieties(31.20%) and landraces(29.60%),and limited diversity in wild types(8.00).Analysis of Molecular Variance(AMOVA) results emphasized significant genetic differentiation among populations,with substantial diversity(P<0.001) within each population.Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations,while the larger proportion of genetic diversity(92%) resided within each individual sesame population,showcasing heightened diversity within each group.Our study’s findings received support from both Bayesian clustering and Neighbor-joining(NJ) analysis,reaffirming the credibility of our genetic structure insights.Notably,Population structure analysis at its highest Δk value(k=2) revealed the existence of two primary genetic clusters,further subdivided into four sub-populations at k=4.Similarly,NJ analysis identified two prominent clusters,each displaying additional sub-clustering.In conclusion,our research provides a comprehensive understanding of genetic groups,subpopulations,and overall diversity within Ethiopian sesame populations.These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections.This genetic richness holds promise for breeding and conservation efforts,highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.

Genetic Diversity,Population Structure,and Genome-Wide Association Study of Seven Agronomic Traits in 273 Diverse Upload Cotton Accessions

Upland cotton(Gossypium hirsutum)is the most important plant producing natural fibers for the textile industry.In this study,we first investigated the phenotypic variation of seven agronomic traits of 273 diverse cotton accessions in the years 2017 and 2018,which were from 18 geographical regions.We found large variations among the traits in different geographical regions and only half of the traits in either years 2017 or 2018 followed a normal distribution.We then genotyped the collection with 81,612 high quality SNPs.Phylogenetic tree and population structure revealed a diverse genetic structure of the core collection,and geographical diversification was an important factor,but account for part of the variances of genetic diversification.We then performed genome-wide association study for the seven traits in the years 2017 and 2018,and the average values of each trait in the two years,respectively.We identified a total of 19 significant marker-trait associations and found that Pollen Ole e 1 allergen/extension could be the candidate gene associated with the fall-off cotton bolls from the last three branches.In addition,large variations were observed for the heritability of traits in the years 2017 and 2018.These results provide new potential candidate genes for further functional validation,which could be useful for genetic improvement and breeding of new cotton cultivars with better agronomic performances.

Analysis of genetic diversity and structure across a wide range of germplasm reveals genetic relationships among seventeen species of Malus Mill,native to China

China is a center of diversity for Malus Mill,with 27 native species including 21 wild species and six domesticated species.We applied a set of 19 simple sequence repeat markers to genotype 798 accessions of 17 species(12 wild species and five cultivated species)of Malus originating from 14 provinces in China.A total of 500 alleles were detected.Diversity statistics indicated a high level of genetic variation as quantified by the average values of the effective allele number(N_(e)).expected heterozygosity(H_(e)),and Shannon's Information Index(I)(10.309,0.886,and 2.545,respectively).Malus sieversii(MSR;H_(e)=0.814,I=2.041,N_(e)=6.054),M.baccata(MBB;H_(e)=0.848,/=2.350,N_(e)=8.652),M.toringoides(MTH;He=0.663,I=1.355,N_(e)=3.332),and M.hupehensis(MHR;H_(e)=0.539,I=0.912,N_(e)=0.579)showed a higher level of genetic diversity in this study than the previous studies.MSR and MBB contributed to the origin and evolution of some accessions of M.domestica subsp.chinensis(MDC).However,other accessions of MDC showed a closer genetic distance with MBB and cultivated species,especially M.robusta(MRB),M.asiatica(MAN),and M.prunifolia(MPB).Not all accessions of MDC were descended from MSR in Xinjiang Uygur Autonomous Region of China.This research provides novel insights into the genetic relationships of Malus native to China,which will be useful for genetic association studies,germplasm conservation,and breeding programs.

Genetic diversity and structure of the endemic and endangered species Aristolochia delavayi growing along the Jinsha River

The traditional medicinal plant,and endangered species Aristolochia delavayi(Aristolochiaceae)is an endemic species in China and occurs in the warm and dry areas along the Jinsha river.It is also a specific host of the larvae of Byasa daemonius,a vulnerable butterfly.In this study,15 pairs of polymorphic microsatellite primers of A.delavayi were designed and screened based on the Simple Sequence Repeats(SSR)loci found by using the results of genome skimming.Based on these 15 SSR markers,the genetic diversity and structure of 193 individuals from ten natural populations were analyzed in detail.In comparison to other endemic and endangered plants in the region,the population of A.delavayi possess a relatively high genetic diversity(He=0.550,I=1.112).AMOVA analysis showed that 68.4%of the total genetic diversity was within populations and 31.6%of the variation occurred among populations.There was a significant genetic differentiation among natural populations of A.delavayi detectable,with low gene flow(Nm=0.591).This might be attributed to geographical barriers and limited seed dispersal.To test the isolation by distance(IBD),we performed Mantel test,which showed a significant correlation between the geographic and genetic distances.In order to cope with the possible biases caused by IBD,we additionally performed Bayesian genetic cluster analyses and principal coordinate analysis(PCoA).The final cluster analysis revealed three groups with distinct geographical distribution.Habitat fragmentation and limited gene flow between these populations may be the main reasons for the current genetic structure.For conservation of this species,we suggest to divide its populations into three protection management units,with subsequent focus on the Yongsheng and Luquan populations which experienced a genetic bottleneck event in the past.

Genetic Diversity and Genetic Structure of Maize Inbred Lines from Yunnan Revealed by SNP Chips

[Objectives]The genetic diversity and population genetic structure of 107 inbred lines of maize in Yunnan were analyzed,in order to provide technical support for maize germplasm innovation,genetic improvement of germplasm resources,variety management,and lay a solid foundation for exploring genes related to fine traits in the future.[Methods]The 107 maize inbred lines generalized in Yunnan were selected,and 45 backbone inbred lines commonly used in China were used as reference for heterotic group classification.On Axiom Maize 56K SNP Array platform,maize SNP chips(56K)were used to scan the whole maize genome,and the NJ-tree model of Treebest was used to construct a phylogenetic tree.Principal component analysis(PCA)was conducted by GCTA(genome-wide complex trait analysis)to reveal the genetic diversity and population genetic structure.[Results]In the 107 Yunnan local inbred lines,5533 uniformly distributed high-quality SNP marker sites were finally detected.Based on the analysis of these SNP marker sites,Nei s gene diversity index(H)of 107 maize germplasm genes was 0.2981-0.5000 with an average value being 0.4832,and polymorphism information content(PIC)values were 0.2536-0.3750 with an average value being 0.3662.The minimum allele frequency value was 0.5000-0.8178 with an average value being 0.5744.The analysis of population genetic structure showed that when K=6,the maximum value of△K was the maximum,which meant that the inbred lines used in this study could be divided into six groups.They were Tangsi Pingtou blood relationship group,PB blood relationship group,335 female blood relationship group,Zi 330 and the Lüda Honggu blood relationship group,unknown group 1 and unknown group 2.No inbred lines were divided into other heterotic groups.Among them,37 inbred lines from the 2 unknown groups could not be classified into the same group as the 10 known heterotic groups in China.The results of principal component analysis showed that the 107 maize inbred lines generalized in Yunnan could be clearly distinguished from the backbone maize inbred lines commonly used in China.Most of the maize inbred lines in Yunnan were concentrated near the reference backbone inbred lines.But some Yunnan inbred lines were far away from the reference inbred lines commonly used in China.[Conclusions]The maize germplasm resources in Yunnan area were rich in genetic diversity,including multiple heterotic groups,and there was a rich genetic basis of breeding parents.They could be clearly distinguished from the backbone inbred lines commonly used in China,and some of them had a long genetic distance from the backbone inbred lines.The resources which have good application potential can be used to create new heterotic groups.

Genetic Structure of Native Sheep Populations in East and South Asia

Variations of structural loci among 4 sheep populations in China were examined by the method of multiloci electrophoresis, and similar data from 11 sheep populations were taken as basic references to analyze the genetic structure of the native sheep populations in East and South Asia. The results showed that the average heterozygosity and effective number of alleles among 15 populations were 0.2746 and 1.559, respectively. Mongolian sheep possessed the largest average heterozygosity and effective number of alleles. Genetic diversity of sheep populations in Mongolia, China, Vietnam, Bangladesh and Nepal was reduced in this order. The coefficients of genetic differentiation were between 0.0126 and 0.3083, with the average of 0.148, demonstrating that genetic variations lay mainly in populations with 85.2% of the total variations. There exists no correlation between geographical distances and genetic distances. Gene flow was smooth among most populations, which led to inconsistency between geographical distances and genetic distances. The 15 native sheep populations in East and South Asia could be divided into two groups： One group included part populations of China and Mongolia, and the other included Yunnan populations of China, and part populations of Nepal and Bangladesh. Other populations did not cluster together and divide into the above-mentioned two groups. Tills study indicated genetic differentiation of the 15 native sheep populations in East and South Asia was relatively low, geographical isolation was not the main reason affecting genetic differentiation, and the fifteen sheep populations could be divided into two groups according to phylogenetic relationships.

Genetic Structure and Genetic Differentiation of Tibetan Mastiff Populations

[ Objective] To analyze the genetic structure and genetic differentiation of Tibetan Mastiff populations and provide a theoretical basis for the protection and rational development and utilization of the Tibetan Mastiff breed resources. [ Method] A total of 86 blood samples were collected from two populations of Hequ Tibetan Mastiff （HTM） and Qinghai Tibetan Mastiff （QTM）. The genetic structure and genetic differentiation of nine blood protein loci of ＂If, Po, Es-1, Es-2, S（alpha）2, Hb, AIb, Pr and Amy between these two populations were examined by vertical polyacrylam- ide gel electrophoresis with discontinuous buffer system. [ Result] The effective number of alleles （Ne）, Shannon genetic diversity index （I） and Nei average expected gene heterozygosity （H） of the HTM were respectively 1.690 7, 0.485 5 and 0.295 9, and these were higher than those of QTM. The Nei＇s standard genetic distance （D） between HTM and QTM was 0.012 3, and the degree of genetic similarity was 0.987 8. The gene flow （Nm） of these two Tibetan Mastiff populations was 14.543 7. [ Conclusion] The genetic variability of intra-population of HTM was higher than that of QTM, and the genetic differentiation of inter-population was very low （ GsT = 0.018 7）. Thereby, the great gene flow （ Nm = 14.543 7） is the main factor leading to the low genetic differentiation of the inter-population in different geographical groups.

Genetic diversity and population structure of Robinia pseudoacacia from six improved variety bases in China as revealed by simple sequence repeat markers

Robinia pseudoacacia is an important afforesta-tion tree introduced to China in 1878.In the present study,we examined the genetic diversity among 687 strains rep-resenting four improved varieties and two secondary prov-enances,comprising 641 clones and 46 seedlings.Ninety-one simple sequence repeats(SSRs)were selected through segregation analysis and polymorphism characterization,and all sampled individuals were genotyped using well-characterized SSR markers.After excluding loci with non-neutral equilibrium,missing locus data and null alleles,we used 36 primer pairs to assess the genetic diversity of these germplasm resources,revealing vast genetic differentiation among the samples,with an average of 8.352 alleles per locus and a mean Shannon′s index of 1.302.At the popula-tion level,the partitioning of variability was assessed using analysis of molecular variance,which revealed 93%and 7%variation within and among collection sites,respectively.Four clusters were detected using structure analysis,indi-cating a degree of genetic differentiation among the six populations.Insights into the genetic diversity and structure of R.pseudoacacia provide a theoretical basis for the con-servation,breeding and sustainable development in China.

Genetic diversity and population structure of Camellia huana(Theaceae),a limestone species with narrow geographic range,based on chloroplast DNA sequence and microsatellite markers

Camellia huana is an endangered species with a narrow distribution in limestone hills of northern Guangxi and southern Guizhou provinces,China.We used one chloroplast DNA(cpDNA)fragment and 12 pairs of microsatellite(simple sequence repeat;SSR)markers to assess the genetic diversity and structure of 12 C.huana populations.A total of 99 alleles were detected for 12 polymorphic loci,and eight haplotypes and nine polymorphic sites were detected within 5200 bp of cpDNA.C.huana populations showed a low level of genetic diversity(n=8,Hd=0.759,Pi=0.00042 for cpDNA,NA=3.931,HE=0.466 for SSRs),but high genetic differentiation between populations(FST=0.2159 for SSRs,FST=0.9318 for cpDNA).This can be attributed to the narrow distribution and limestone habitat of C.huana.STRUCTURE analysis divided natural C.huana populations into two groups,consistent with their geographical distribution.Thus,we suggest that five natural C.huana populations should be split into two units to be managed effectively.

Genetic Diversity and Population Structure of Three Strains of Indigenous Tswana Chickens and Commercial Broiler Using Single Nucleotide Polymormophic (SNP) Markers

The Tswana chicken is native to Botswana and comprises strains such as the naked neck, normal, dwarf, frizzled, and rumples. The origins of the different strains of Tswana chicken remain unknown and it is not yet clear if the different strains represent distinct breeds within the large Tswana chicken population. Genetic characterization of different strains of Tswana chickens using SNP arrays can elucidate their genetic relationships and ascertain if the strains represent distinct breeds of Tswana chicken population. The aim of this study was therefore to investigate population structure and diversity and to estimate genetic distances/identity between the naked neck, normal and dwarf strains of Tswana chickens. A total of 96 chickens (normal strain (n = 39), naked neck strain (n = 32), dwarf strain (n = 13) and commercial broiler (n = 12)) were used in the study. SNP genotyping was carried out using the Illumina chicken iSelect SNP 60 Bead chip using the Infinium assay compatible with the Illumina HiScan SQ genotyping platform. The observed heterozygosity (Ho) values were 0.610 ± 0.012, 0.611 ± 0.014, 0.613 ± 0.0006 for normal, naked neck and dwarf strains of Tswana chickens respectively and averaged 0.611 ± 0.016 across the three strains of Tswana chickens compared to Ho of 0.347 ± 0.023 in commercial broiler chicken. The expected heterozygosity (He) values were 0.613 ± 0.00012, 0.614 ± 0.00013, 0.608 ± 0.00021 for normal, naked neck and dwarf strains of Tswana chickens respectively and averaged 0.612 ± 0.00015 across the three strains of Tswana chickens compared to He of 0.577 ± 0.00022 in commercial broiler chicken. Principal component analysis (PCA) was used to get an insight into the population structure of indigenous Tswana chickens. The first two principal components revealed a set of three clusters. The normal strain of Tswana chicken and commercial broiler clustered together in one group. The dwarf strain clustered separately in one group and the naked neck and normal strains clustered together in the last group. The separate clustering of the dwarf strain from the rest of Tswana chicken strains suggests significant genetic uniqueness of the dwarf strain and very close genetic similarities between the normal and naked neck strains. The clustering pattern was confirmed by less genetic differentiation and less genetic distances between the naked neck and normal strains of Tswana chicken than between the two strains and the dwarf strain of Tswana chicken.

High levels of genetic diversity and an absence of genetic structure among breeding populations of the endangered Rufous-backed Bunting in Inner Mongolia,China:implications for conservation

Background:The Rufous-backed Bunting,Emberiza jankowskii,is an endangered species that is primarily distributed in Inner Mongolia,China.The main threats to the continued persistence of this species are habitat loss and degradation.However,the impact of population loss on genetic diversity remains unclear.To support future conservation and management efforts,we assessed the genetic diversity and population structure of E.jankowskii using mitochondrial DNA and microsatellites.Methods:Blood samples were collected from 7-8-day-old nestlings in Inner Mongolia,China between May and August of 2012 and 2013.Mitochondrial DNA sequences and microsatellite markers were used to assess the genetic diversity,genetic structure and inbreeding of E.jankowskii.The results of genetic diversity and inbreeding were compared to other avian species.Results:We found an unexpectedly high level of genetic diversity in terms of mitochondrial DNA and microsatellite compared to other avian species.However,there were high levels of gene flow and minimal genetic structuring,among the fragmented breeding populations of E.jankowskii in Inner Mongolia.These findings suggest that E.jankowskii in Inner Mongolia is a metapopulation.Despite the high genetic diversity of E.jankowskii,local populations in each small patch remain at risk of extinction due to habitat loss.In addition,the E.jankowskii population has a high risk of inbreeding.Conclusions:To minimize further loss of genetic diversity of this endangered species,we suggest that the E.jankowskii in Inner Mongolia should be considered as a protected species for management purposes.Conservation efforts should concentrate on E.jankowskii habitat management.This may be most effectively achieved by protecting the current breeding habitats and prohibiting over-grazing.

Microsatellite analysis of genetic diversity and population structure of Chinese mitten crab (Eriocheir sinensis)

Chinese mitten crab （Eriocheir sinensis） has higher commercial value as food source than any other species of Eriocheir in China. To evaluate the germplasm resources and characterize the genetic diversity and population structure of the crabs in different water systems, two stocks and two farming populations were assessed with 25 polymorphic microsallite loci available in public GenBank. Basic statistics showed that the average observed heterozygosity （Ho） amongst populations ranged from 0.5789 to 0.6824. However, a remarkable presence of inbreeding and heterozygote deficiencies were observed. To analyze population structure, pairwise FST coefficients explained only -10.3% variability from the subdivision of mitten crab populations, the remaining variability stems from the subdivision within subpopulations. Although the four populations had slight differentiation, different allelic frequencies resulted in distinct population structures. Two stocks and one farming population were clustered together to the phylogenetic branch of Yangtze crab, with an approximate membership of 95%. Whereas, another farming population was clustered singly to the phylogenetic branch of the Liaohe crab, with a membership of 97.1%. The tests for individual admixture showed that Yangtze crab had probably been contaminated with individuals from other water systems. Genetic relationships between populations also supported the conclusion that Yangtze crab and Liaohe crab had different gene pools in spite of the origins of the same species.

Molecular diversity and genetic structure of 380 sweetpotato accessions as revealed by SSR markers

Sweetpotato, Ipomoea batatas（L.） Lam., is an important food crop widely cultivated in the world. Evaluation of genetic relationships among diverse cultivars and landraces is necessary for efficient exploitation of genetic diversity in the existing germplasm resources. In the present study, a collection of 380 sweetpotato accessions assembled from different agro-climatic zones of China and other countries were genotyped using 30 SSR primer pairs. Model-based structure analysis separated the germplasm into three populations, P1, P2 and P3, containing 228, 133 and 19 accessions, respectively, which was consistent with the results of phylogenic and principal component analysis（PCA）. Analysis of molecular variance（AMOVA） revealed significant genetic differentiation among inferred populations, accounting for 16.47% of the total molecular variance, however, the differences between the regions were not significant, the total variation were due to the differences between the genotypes within the population. Pairwise fixation index（F ST） suggested that populations P1 and P3 had the highest differentiation, while populations P1 and P2 had the lowest differentiation. The diversity among populations was wide, which confirmed the genetic distinction of populations. Through comparing model-based structure and domestication-based classification, it was found that the accessions of population P1 mainly belonged to modern cultivars, and the accessions of populations P2 and P3 basically corresponded to landraces, by which we suggest that modern cultivars maybe had experienced a two-step domestication history. Our results illustrated clear genetic relationships among 380 sweetpotato accessions, exhibiting the potential of accelerating the process of future sweetpotato breeding program by molecular marker based parental selection.

Analysis of genetic diversity and population structure of Chinese yak breeds (Bos grunniens) using microsatellite markers

Nine Chinese yak breeds （Maiwa, Tianzhu White, Qinghai Plateau, Sibu, Zhongdian, Pali, Tibetan High Mountain, Jiulong, and Xinjiang） and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations, genetic relationship between populations, and population structure for each breed. A total of 206 microsatellite alleles were observed. Mean F-statistics （0.056） for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds. The Neighbor-Joining phylogenetic tree was constructed based on Nei＇s standard genetic distances and two clusters were obtained. The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together. The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one cluster includes yaks from Tibet Autonomous Region and Qinghai Province, one cluster combines Zhongdian, Maiwa, and Tianzhu White, and Jiulong and Xinjiang come into the third cluster. Pali was mainly in the first cluster （90%）, Jiulong was mainly in the second cluster （87.1%）, Zhongdian was primarily in the third cluster （83%）, and the other yak breeds were distributed in two to three clusters. The Gayal was positively left in the fourth cluster （99.3%）.

Genetic Structure and Diversity of Parental Cultivars Involved in China Mainland Sugarcane Breeding Programs as Inferred from DNA Microsatellites

To understand genetic structure and diversity of parental cultivars involved in China Mainland sugarcane breeding programs, 92 elite parents and 4 wild relatives were genotyped with 18 microsatellite DNA markers. The genetic similarity （GS） values among the cultivars ranged from 0.346 to 0.960 with an average of 0.533. Among the introduced cultivars, India accessions had the closest genetic distance to China Mainland accessions （0.447）, while Australia accessions have the furthest distance （0.503）. A comparison of allelic diversity among geographical origins showed that there were 22 China Mainland specific alleles, of which 28% were derived from native S. spontaneaum germplasm in China. Model-based genetic structure, clustering, and principal components analyses consistently revealed there were five groups within the 96 accessions. Groups 1, 2, 4, and 5 consisted of all cultivars and group 3 only contained wild germplasm. Group 2 was characterized as the Introduction group with 46 cultivars predominantly introduced from Australia, Taiwan of China, India, and USA. Groups 1, 4, and 5 consisted of cultivars mostly originated from China Mainland, defined as the Complex group, Yacheng lines group, and F134/CP72-1210 group, respectively, upon their pedigree. By understanding the genetic relationships among the parental cultivars, breeders can gain a rational basis for expanding the gene pool and select the best parental accessions for crossing.

Fine-scale genetic structure of Eremosparton songoricum and implication for conservation

Eremosparton songoricum (Litv.) Vass. is a clonal shrub that reproduces both asexually by under-ground rhizomes and sexually by seeds. It is now a rare species with a narrow distribution in fragmented habitat patches in the Gurbantunggut Desert of Xinjiang, China. The objective of this study was to determine the spatial pattern or structure of genetic variation within population. The within-populations genetic structure of E. songoricum in a plot (10 m×10 m) was analyzed using inter simple sequence repeats (ISSR) markers. Correlograms of Moran’s I showed significant positive value was about 7 m, but changed into a negative correlation with the increase of distance, indicating strong genetic structure. The natural character of clonal reproduction, restricted seed and pollen dispersal were the main factors of influencing the spatial pattern. The knowledge of clonal structures within populations was crucial for understanding evolutionary processes and ecological adaptation. This study provided basic data for the conservation and management of E. songoricum, especially for sampling strategies for ex situ conservation.