Allozyme Diversity and Population Genetic Structure of Three Medicinal Epimedium Species from Hubei

Three Epimedium species, E. pubescens Maxim., E. sagittatum （Sieb. ＆ Zucc.） Maxim., and E. wushanense T. S. Ying, which are sympatrically distributed in the western Hubei Province, have been used in traditional Chinese medicine （TCM） for about 2,000 years. Genetic variability and population genetic structure of 11 natural populations of these Epimedium species were investigated using isoelectric focusing in thin-layer polyacrylamide slab gels. Of the 22 enzyme systems prescreened, six coding for 13 loci and 45 alleles were resolved, which were used for analyzing genetic diversity and population structure at both intraspecific and interspecific levels. The results showed that： l） high levels of genetic diversity were observed in all three species （A = 2.6-3.2, P = 69.2%-84.6%, Ho= 0.274-0.377, HE= 0.282-0.369）, which were higher than that of other herbaceous and aulmal-pollinated species with similar life-history characteristics; 2） there was significant deviation from Hardy-Weinberg Equilibrium, with one half of the loci showing heterozygote excess and the other homozygote excess, in all populations, suggesting the complicated breeding system of Epimedium species; 3） the low level of intraspecific and interspecific genetic differentiation （GST= 0.0246-0.0409 and 0.0495-0.1213, respectively） indicated a high level of gene flow among populations and close genetic relationship among the three species; and 4） UPGMA cluster analysis further showed that E. pubescens was more closely related to E. sagittatum than to E. wushanense, which was in good agreement with the morphological characters and the recent phylogenetic analysis of these species. On the basis of these results, it was concluded that the mixed breeding system, long-lived perennial life form, ancient evolutionary history, and seed dispersal by ants in Epimedium are responsible for the genetic variation and population structure of these species.

Genetic diversity and genetic structure of the Daurian Partridge(Perdix dauuricae) in China,assessed by microsatellite variation

The Daurian Partridge(Perdix dauuricae) is a kind of hunting bird with high economic value.Genetic diversity and structure in the Daurian Partridge were studied by analyzing eight microsatellite loci in 23 populations found throughout the range of the species in China.The objectives were to evaluate the consequences on genetic diversity and differentiation of Daurian Partridge populations and to obtain a profound genetic insight for future management decisions and for effective measures to protect and exploit Daurian Partridges.The results showed that microsatellites were polymorphic in all Daurian Partridge populations,with a high level of genetic diversity over all the loci,especially in the Qaidam Basin populations which have the highest level of diversity.Significant genetic divergence was observed among different groups as well as between populations within the same group;most pairwise FST values were highly significant.Both phylogenetic trees and Bayesian clustering analyses revealed clear differentiation among the 23 populations of the Daurian Partridge,which were classified into two genetically differentiated groups.A bottleneck analysis indicated that Daurian Partridge populations have experienced a recent bottleneck.Our study argues that the Qaidam populations,North China populations,JN population,ZJC population,and Liupan Mountain populations should be paid special attention in order to retain adequate population sizes for maintaining genetic diversity.

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.

Comparative Analysis of Genetic Diversity and Structure in Rice Using ILP and SSR Markers

Genetic diversity of 36 rice entries from the United States Department of Agriculture （USDA） rice collection was assessed using 103 ILP （intron length polymorphism） and 54 SSR （simple sequence repeats） markers. A total of 236 and 332 alleles were detected by the ILP and SSR markers, respectively. On average, the SSR markers produced higher polymorphism information content value and number of alleles than the ILP markers. Whereas the Nei＇s genetic distance measured using the SSR markers was much higher than that measured using the ILP markers. Manters test indicated that there was a statistically significant correlation （r=0.827, P〈0.001 ） between the two marker systems. UPGMA clustering based on the ILP and SSR markers resulted in consensus dendrograms. The cophenetic correlation coefficient （r=0.918, 0.878 and 0.924, P〈0.001 for the ILP, SSR and combined markers, respectively） showed a highly accurate dendrogram represented the genetic distance among these entries. The 36 entries were divided into four groups. Four African Oryza glaberrima accessions were clustered within a distinct group （I）, and the remaining entries were separated into three groups （11, III and IV）. All the entries could be also clustered into two main groups： One was composed of III and IV, considered as indica group, and the other was composed of I （O. glaberrima） and II （japonica-like）. Model-based cluster analysis revealed that the japonica-like group maintained very pure ancestry while the indica group shared mixed ancestry, especially for group III, which had seven admixtures sharing from 19.5% to 30.0% of ancestry with group IV （based on SSR markers）. It is suggested that ILP and SSR markers could be very useful for the genetic study and breeding in rice.

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.

Analysis of Genetic Diversity and Population Structure of Maize Landraces from the South Maize Region of China

Understanding genetic diversity and population structure of landraces is important in utilization of these germplasm in breeding programs. In the present study, a total of 143 core maize landraces from the South Maize Region （SR） of China, which can represent the general profile of the genetic diversity in the landraces germplasm of SR, were genotyped by 54 DNA microsatellite markers. Totally, 517 alleles （ranging from 4 to 22） were detected among these landraces, with an average of 9.57 alleles per locus. The total gene diversity of these core landraces was 0.61, suggesting a rather higher level of genetic diversity. Analysis of population structure based on Bayesian method obtained the samilar result as the phylogeny neighbor-joining （N J） method. The results indicated that the whole set of 143 core landraces could be clustered into two distinct groups. All landraces from Guangdong, Hainan, and 15 landraces from Jiangxi were clustered into group 1, while those from the other regions of SR formed the group 2. The results from the analysis of genetic diversity showed that both of groups possessed a similar gene diversity, but group 1 possessed relatively lower mean alleles per locus （6.63） and distinct alleles （91） than group 2 （7.94 and 110, respectively）. The relatively high richness of total alleles and distinct alleles preserved in the core landraces from SR suggested that all these germplasm could be useful resources in germplasm enhancement and maize breeding in China.

Genetic Diversity Analysis of Wild Tea Plants in Yunnan Province Using EST-SSR Markers

In this study, 27 pairs of EST-SSR primers were employed to analyze the genetic diversity and genetic relationship of 100 wild tea plant germplasm re- sources and 22 cultivars, according to the results, a total of 88 polymorphic bands were amplified with 27 pairs of primers; the variation of effective alleles accounted for 69.01% ; a total of 183 genotypes were detected, with a variation range of 4 -11 ; averagely 6.78 genotypes were amplified with each primer pair; Shannon index （I） of 27 primer pairs ranged from 0.32 to I. 35, with an average of 0.88 ; the observed heterozygosity （0.52） was basically consistent with the expected het- erozygosity （0.52） ; the average polymorphism heterozygosity was 0.48, which was very close to 0.50 ; the average Nei＇s index was 0.51, which was higher than 0. 50 ; the average polymorphism information content （PIC） was 0.52, which was higher than 0.50, indicating high genetic diversity among wild tea germplasm resources in Yuunan Province. According to the clustering results, based on geographical origins and genetic backgrounds, 122 materials were clustered into 14 categories. Dendrogram based on Nei＇s genetic distance revealed complex genetic relationships among wild tea germplasm resources in Yunnan Province. This study provided certain reference for subsequent preservation, development and research of wild tea germplasm resources in China.

Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers

To better understand the genetic diversity and population structure of broccoli cultivars planted in China,a total of 161 representative broccoli cultivars in the past 25 years were collected and analysed based on single nucleotide polymorphism(SNP)markers.Ten pairs of primers with good polymorphism and high resolution were screened from 315 pairs of SNP primers by 3 broccoli accessions(inbred lines)with different phenotypes and maturity.The 10 pairs of SNP primers were selected,producing 78 alleles.The diversity analysis indicated that the polymorphism information content(PIC)of SNP primer ranged from 0.64 to 0.90.The observed number of alleles(Na)was 2.00,the effective number of alleles(Ne)was 1.11–2.00,the Nei’s gene diversity(H)was 0.10–0.50,and Shannon information index(I)was 0.20–0.70 using PopGene32 software.The clustering results showed that the 161 broccoli cultivars could be divided into 4 major subgroups(A,B,C and D),foreign cultivars were all assigned to subgroup A,and domestic cultivars were assigned to 3 subgroups of B,C,and D.This study indicated that some domestic cultivars and foreign cultivars were similar in genetic background,but most domestic cultivars were still different from the Japanese cultivars.When K=2,the population structure result presented that 161 broccoli cultivars could be divided into 1 simple group(2 groups)and 1 mixed group.When Q≥0.6,143(88.82%)broccoli cultivars belonged to the simple groups.In simple groups 68(42.24%)broccoli cultivars of group 1 were derived from Japan,the United States,Switzerland,the Netherlands,China-Taiwan,and China-Mainland;75(46.58%)broccoli cultivars belonged to group 2;when Q<0.6,18(11.18%)broccoli cultivars belonged to the mixed groups.This study is helpful to understand the diversity and resolution of broccoli cultivars from worldwide,which is beneficial to plant breeding and materials innovation.And meanwhile,this result is also used for construction of broccoli fingerprint serving for cultivar identification.

Genetic diversity and population structure of Eleutheronema rhadinum in the East and South China Seas revealed in mitochondrial COI sequences

Eleutheronema rhadinum is a potential commercial fisheries species and is subject to intense exploitation in China. Knowledge on the population structure of E. rhadinum in Chinese coastal waters, which is important for sustainable exploitation and proper resource management, is lacking. In the present study, the genetic diversity and population structure of E. rhadinum were evaluated using a 564-base pair fragment of the mitochondrial cytochrome c oxidase subunit I （COl） gene. A total of 76 specimens were collected from three localities around the East （Qidong and Zhoushan） and South China Seas （Zhuhai）. Among these individuals, nine polymorphic sites were detected and 1 l distinct haplotypes were defined. High levels ofhaplotype diversity （h=0.759i0.035） and low levels of nucleotide diversity （re=0.001 98i0.003 26） were observed in these populations, Hierarchical analysis of molecular variance （AMOVA） indicated that 96.72% of the genetic variation occurred within the populations, whereas 3.28% occurred among populations. No significant genealogical branches or clusters were recognized on the neighbor-joining tree. Intra-group variation among populations was significant （~0~t=0.032 85, P〈0.01）. These results suggest that E. rhadinum populations in the East and South China Seas have developed divergent genetic structures. Tests of neutral evolution and mismatch distribution suggest that E. rhadinum may have experienced a population expansion. The present study provides basic information for the conservation and sustainable exploitation of this species.

Genetic diversity and population structure of 288 potato(Solanum tuberosum L.) germplasms revealed by SSR and AFLP markers

Potato （Solanum tuberosum L.） is an important staple food and economic crop in many countries. China has led world potato production in recent years. To understand the genetic diversity of potato germplasms and to enrich the current gene pool for potato improvement, we made a global collection consisted of 288 potato germplasms from eight countries and the International Potato Center （CIP）. Using SSR and AFLP techniques, we evaluated the genetic diversity and population structure of these 288 potato accessions. A total of 190 alleles on 20 SSR loci were detected and all of the SSR alleles were polymorphic among these potato germplasms with an average of 9.5 alleles per SSR locus ranging from 2 to 23. The effective number of alleles per locus （Ne＊）, Nei＇s genetic diversity （H＊）, and Shannon＇s information index （I＊） was from （0.1709＋0.3698） to （1.6166＋0.3414）, （0.076＋0.1388） to （0.3812＋0.1886）, and （0.1324＋0.1970） to （0.5347＋0.1440）, respec- tively, and the mean polymorphic information content （PIC） value was 0.7312. A total of 988 AFLP alleles were detected by 10 AFLP primer combinations with 983 polymorphic alleles, and 99.49% alleles was polymorphic with an average of 98.3 polymorphic alleles per primer combination ranging from 91 to 116. The values of Ne＊, H＊ and/＊ were from （1.5162＋0.311 ） to （1.6423＋0.3278）, （0.3114＋0.145） to （0.3675＋0.1121）, and （0.4761＋0.1792） to （0.547＋0.1322）, respectively, and the average PIC value was 0.9871. Bayesian analysis discriminated the accessions into seven subgroup and an admix group. The majority of accessions from CIP and China were assigned into SG1, SG5, SG6, SG7 and admix group. Accessions in SG3 were mainly from CIP and two small groups SG2 and SG4 were mainly from northeastern China. In general, the results obtained from Bayesian statistical analysis, cluster analysis and principal coordinate analysis consistently revealed the lack of geographical differentiation among country-wide collections, indicating germplasm introduction was common for the countries out of potato origin center. The poiymorphic markers and the differentiate genetic lineages found in this study provide useful information for potato improvement and conservation programs.

Genetic structure associated with diversity and geographic distribution in the USDA rice world collection

Cultivated rice (Oryza sativa L.) is structured into five genetic groups, indica, aus, tropical japonica, temperate japonica and aromatic. Genetic characterization of rice germplasm collections will enhance their utilization by the global research community for improvement of rice. The USDA world collection of rice germ-plasm that was initiated in 1904 has resulted in over 18,000 accessions from 116 countries, but their ancestry information is not available. A core subset, including 1,763 accessions repre-senting the collection, was genotyped using 72 genome-wide SSR markers, and analyzed for genetic structure, genetic relationship, global distribution and genetic diversity. Ancestry analysis proportioned this collection to 35% indica, 27% temperate japonica, 24% tropical japonica, 10% aus and 4% aromatic. Graphing model-based ancestry coefficients demon-strated that tropical japonica showed up mainly in the American continents and part of the South Pacific and Oceania, and temperate japonica in Europe and the North Pacific far from the equator, which matched the responses to tem-perature. Indica is adapted to the warm areas of Southern Asia, South China, Southeast Asia, South Pacific and Central Africa and around the equator while aus and aromatic are special types of rice that concentrates in Bangladesh and India. Indica and aus were highly diversified while temperate and tropical japonicas had low diversity, indicated by average alleles and pri-vate alleles per locus. Aromatic has the most polymorphic information content. Indica and aromatic were genetically closer to tropical ja-ponica than temperate japonica. This study of global rice has found significant population stratification generally corresponding to major geographic regions of the world.

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 Population Structure of North China Mountain Walnut Revealed by ISSR

North China Mountain Walnut (NCMW) is one of the ancestors of extant cultivated species, and a valuable gene resource for resistance breeding of walnut in China. Inter-Simple Sequence Repeat (ISSR) primers were designed to evaluate the level and pattern of genetic diversity in eight populations of NCMW. Nine ISSR primers yielded 91 amplification products with different sizes, of which 84 (92.31%) were polymorphic. A high species-level genetic diversity was detected with Nei’s (H = 0.2592) and Shannon’s diversity (I = 0.4003). In contrast, the population-level genetic diversity was relatively lower (PPB = 43.27%, H = 0.1347, I = 0.1862). Coefficient of populations differentiation (GST) was 0.5066, indicating that inter-population and intra-population variation contributed 50.66% and 49.34% respectively to the total genetic variability. This relative level of variation was further supported by AMOVA analysis. Limited gene flow (Nm = 0.5133.), habitat fragmentation and geographical isolation might be responsible for the population structure of NCMW. UPGMA cluster analysis classified the eight populations into three groups which showed no significant relationship between the genetic similarity coefficient and geographic origin but showed remarkable association with morpho-physiological characters, particularly nut traits. The results of the study provide species-level and population-level genetic profiles for further exploitation and conservation of genetic diversity of NCMW.

Genetic diversity and a population structure analysis of accessions in the Chinese cowpea [Vigna unguiculata(L.)Walp.]germplasm collection

Cowpea(Vigna imguicuiata) is an important legume crop with diverse uses. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, a total of 200 genic and 100 genomic simple sequence repeat(SSR) markers were developed from cowpea unigene and genome sequences, respectively. Among them, 27 genic and 27 genomic SSR markers were polymorphic and were used for assessment of genetic diversity and population structure in 105 selected cowpea accessions. A total of 155 alleles and 2.9 alleles per marker were identified, and the average polymorphic information content(PIC) value was 0.3615. The average PIC of genomic SSRs(0.3996) was higher than that of genic SSRs(0.3235), and most of the polymorphic genomic SSRs were composed of di-and trinucleotide repeats(51.9% and 37.0% of all loci, respectively). The low level of detected genetic diversity may be attributed to a severe genetic bottleneck that occurred during the cowpea domestication process. The accessions were classified by structure and cluster analysis into four subgroups that correlated well with their geographic origins or collection sites. The classification results were also consistent with the results from principal coordinate analysis and can be used as a guide during future germplasm collection and selection of accessions as breeding materials for cultivar improvement. The newly developed genic and genomic SSR markers described in this study will be valuable genomic resources for the assessment of genetic diversity, population structure, evaluation of germplasm accessions, construction of genetic maps, identification of genes of interest,and application of marker-assisted selection in cowpea breeding programs.

Evaluation of Population Structure, Genetic Diversity and Origin of Northeast Asia Weedy Rice Based on Simple Sequence Repeat Markers

Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 simple sequence repeat markers. The results showed that weedy rice in Northeast Asia had a high genetic diversity, with Shannon＇s diversity index （I） of 0.748 and the heterozygosity （He） of 0.434. In each regional population, I value varied widely. The widest range of I （0.228-0.489） was observed in the weedy rice of Eastern China, which was larger than that of Northeast China and Korea （0.168-0.270）. The F-statistics of regional populations （Fis, Fit and Fst） also showed higher values in the weedy rice of Eastern China than those of Northeast China and Korea All weedy rice accessions were grouped into two clusters in the unweighted pair group method with arithmetic mean cluster analysis dendrogram, namely Eastern China branch and Northeastern China plus Korea branch. There was significant differentiation in genetic characteristics in weedy rice of northeastern and eastern Asia, especially in Eastern China.

Genetic Diversity and Population Structure in Landraces and Improved Rice Varieties from India

A set of 50 rice genotypes comprising landraces, local selections, and improved varieties were characterized using simple sequence repeat（SSR） and inter simple sequence repeat（ISSR） markers to study genetic diversity and population structure. Following unweighted pair group method with arithmetic mean based clustering using binary data of polymorphic markers, the genotypes were grouped into 5 clusters and 11 sub-clusters, whereas population structure analysis separated 50 rice genotypes into 5 sub-populations. Grouping of rice genotypes showed better resemblance with the pedigree information of the genotypes. Both genetic diversity and population structure analysis separated majority of the improved varieties from landraces and local selections. Some of the SSR markers amplified unique alleles which were specific to a particular genotype and could distinguish them from the rest. The results indicate that these rice genotypes exhibit a higher genetic diversity and can be very useful in rice improvement program.

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.