Genetic diversity of wild soybean (<Emphasis Type="Italic">Glycine soja</Emphasis> Sieb. et Zucc.) and Japanese cultivated soybeans [<Emphasis Type="Italic">G. max</Emphasis> (L.) Merr.] based on microsatellite (SSR) analysis and the selection of a core collection

Wild soybeans, Glycine soja, are a source of genetic variation to improve soybeans. To improve the efficiency evaluation of conserved germplasm a core or mini-core collection approach that maximizes allelic diversity in a proportion of the whole collection has frequently been advocated. The genetic diversity of a wild soybean collection (1,305 accessions) plus Japanese cultivated soybeans (53 accessions) were analyzed at 20 SSR marker loci. Higher levels of allelic diversity were found in wild soybeans (28 alleles per locus) than Japanese cultivated soybean (five alleles per locus). The genetic distance between wild soybeans from different regions reflected their proximity. Accessions from Russia consisted of a diverse array of alleles resulting in accessions being spread further apart in a PCA plot than accessions from other regions. Accessions of wild soybean from Korea included many rare alleles and thus had a high representation in the core collection. The two core collections developed here, traditional and mini, consisted of 192 accessions with 97% of the allelic diversity (14% of the whole collection) and 53 accessions with 62.4% of the allelic diversity (5% of the whole collection), respectively.     

SSR Diversity of Vegetable Soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.]

Edamame [Glycine max (L.) Merr.] is a type of soybean selected for fresh or frozen vegetable use at an immature stage. Since edamame has a similar protein content, milder flavor, nuttier texture, and is easier to cook when compared to grain soybean, it is being promoted as a new vegetable for global consumption. Global production will require breeding programs for local adaptation; however, limited research has been published on genetic diversity of edamame varieties for the assessment of genetic resources. Simple sequence repeats (SSRs) were used to study the genetic diversity among 130 accessions, including edamame cultivars and landraces from Japan, China and the US, and also the new breeding lines in the US. Although it is assumed that elite edamame cultivars would have narrow genetic diversity, seventeen SSRs detected polymorphism to distinguish 99 of the 130 accessions. The cluster analysis generated nine clusters and 18 outliers. Genetic diversity within Japanese edamame was lower than that within Chinese vegetable soybean accessions (maodou), even though only 10 Chinese maodou were analyzed compared to 107 Japanese edamame. Cluster analysis revealed that the patterns of SSR diversity in edamame can generally distinguish maturity classes and testa color. We concluded that Japanese edamame have a narrow genetic base different from others and that SSRs can describe the patterns of genetic diversity among the elite vegetable soybean.     

Genetic diversity and population structure of vegetable soybean (Glycine max (L.) Merr.) in China as revealed by SSR markers

Vegetable soybean is a kind of value-added specialty soybean serving as vegetable or snacks. Understanding the genetic structure of vegetable soybean is a key point for further utilization in breeding programs. In the present study, the genetic structure and diversity of 100 vegetable soybean accessions planted in China was analyzed using 53 simple sequence repeat (SSR) markers. A total of 296 alleles were detected with an average of 5.6 alleles per SSR locus. The polymorphism information content (PIC) values of SSR markers ranged from 0.074 to 0.831, with an average of 0.573. Nei’s genetic distance between accessions ranged from 0 to 0.9434 with an average of 0.6286. These vegetable soybean germplasms could be divided into 8 subgroups based on STRUCTURE analysis, or 11 subgroups based on unweighted pair group method with arithmetic average (UPGMA) cluster. Further comparison showed that the UPGMA subgroups and STRUCTURE subgroups were in fact highly consistent. Germplasms in each classified groups showed great consistency with their origins, seed coat colors or pedigrees. Genetic relationships among germplasm panels that initially came from different geographical regions were also analyzed. Germplasm panels from China Mainland, Taiwan Island and Japan were highly similar to each other with the similarities of over 98 %. Molecular data and cluster analysis also showed that germplasms from China Mainland are more diverse than those from other areas. These results gave us a deep insight into the genetic structure of vegetable soybeans in China and will help us to improve the breeding strategies.     

A wide range of genetic diversity in pear (<Emphasis Type="Italic">Pyrus ussuriensis</Emphasis> var. <Emphasis Type="Italic">aromatica</Emphasis>) genetic resources from Iwate,Japan revealed by SSR and chloroplast DNA markers

Iwateyamanashi (Pyrus ussuriensis var. aromatica) is one of the Pyrus species which grows wild in Japan. The number of Iwateyamanashi trees has been decreasing, so conservation and evaluation is urgently needed. Over 500 accessions of Pyrus species collected from Iwate in northern Tohoku region are maintained at Kobe University as an Iwateyamanashi germplasm collection. In order to investigate the genetic diversity, five SSR (simple sequence repeat) markers, developed from Japanese and European pear were examined for 86 Pyrus individuals including 58 accessions from Iwate. These SSR loci could discriminate between all the Iwate accessions except for 10 that bear seedless fruit, as well as determine the genetic diversity in Iwateyamanashi germplasms. High levels of variation were detected in 41 alleles and the mean observed heterozygosity across 5 loci was 0.50 for the Iwate accessions. Seedless accessions sharing identical SSR genotype with the local pear variety “Iwatetanenashi” were supposed to have been propagated vegetatively via grafting. In an UPGMA phenogram, Japanese pear varieties (P. pyrifolia) were clustered into two groups with some Iwate accessions including seedless ones. Another 38 Iwate accessions were not clustered clearly, and there was no clear relationship between these accessions and geographical distribution or morphological characters. Allele frequency revealed that the Iwate accessions were genetically more divergent than the Japanese pear varieties. Most Japanese pears possessed a 219 bp deletion at a spacer region between the accD and psaI genes in the chloroplast DNA (cpDNA), but other Pyrus species and two Iwateyamanashi trees did not. In the Iwate accessions, 79.3% had a deletion type cpDNA and others had a standard type cpDNA without deletion. These results are indicative of the wide range of genetic diversity in the Iwate accessions which include Japanese pear varieties. A combination of SSR and cpDNA analyses revealed high heterogeneity in Iwateyamanashi and coexistence of Iwateyamanashi and hybrid progeny with P. pyrifolia. These could be reasons for the wide range of continuous morphological variation described previously.     

Genetic structure of the Japanese soybean population

The genetic structure of the Japanese soybean population was evaluated based on the variation at 16 isozyme and seed protein loci for 781 landraces and pure line selections. A relatively high diversity was found in the Japanese population, compared with 158 Korean accessions and 94 Chinese accessions that were tested for comparison. The average gene diversity in the Japanese population was 0.248, being comparable to the estimate obtained for the Chinese population (0.249) but higher than that for the Korean population (0.209). There were a number of alleles that differentiated the Japanese population from either of the Korean or Chinese populations or both. The presence of the alleles which are characteristic of the Japanese population suggests that the Japanese population is not solely a part of the population of China, which is considered as the place of origin of soybean. Only 11% of the total variation was attributable to the differences among seven regional groups, which occurred mainly between Hokkaido or Okinawa and the other regions. A test of two-locus associations revealed that the variation was itself highly structured despite the high level of variation at each of the polymorphic loci. In addition, Aco1, Aco4, Dia1, Enp and Idh1 varied with maturity or seed size. The Japanese soybean population may consist of different cultivar groups that had been established independently as the result of adaptation to different environmental conditions and/or diversification of food culture. The origins of the cultivar groups are discussed.     

Detection of genetic integrity of conserved maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) germplasm in genebanks using SNP markers

Twenty maize landrace accessions regenerated and conserved in five maize genebanks were investigated for genetic integrity using 1,150 Single Nucleotide Polymorphisms (SNPs) and 235 SNP haplotypes. The genetic diversity of three accessions changed significantly in terms of the average number of alleles per locus. Ten out of twenty accessions had significantly different SNP allelic frequencies, either after regeneration or in the same accession held in different genebanks. The proportion of loci with significant changes in SNP allelic frequency was very low (37/1,150). Changes in the major allelic frequency (MAF) for the majority of SNP loci (60.2–75.2%) were less than 0.05. For SNP haplotypes, the genetic diversity of four accessions changed significantly in terms of average number of haplotype alleles and polymorphic information content (PIC) per locus. The proportion of SNP haplotype alleles lost in the later generations ranged between 0 and 22.6%, and at the same time 0–19.9% of the SNP haplotype alleles appeared in later generations, however, these were absent in the earlier generations. Dynamic changes in genetic integrity, in terms of presence and absence of genes (alleles), by both SNP and SNP haplotype analysis were detected during regeneration. A suboptimum number of ears harvested in one generation can be combined with those from another, repeated regeneration to capture the diversity of the previous generation. Use of molecular markers during regeneration of accessions can help in understanding the extent of genetic integrity of the maize accessions in ex situ genebanks and in recommending the best practice for maintaining the original genetic diversity of the genebank accessions.     

利用SSR分析小豆种质遗传多样性

摘要：小豆是一类重要的食用豆,本研究利用45对SSR引物对小豆基因组DNA进行了SSR标记的筛选鉴定,共筛选出多态性良好、扩增效果稳定的SSR引物18对。利用筛选出的18个SSR标记,分析了来自我国栽培小豆优异种质53份和日本引进种质27份,旨在阐明其遗传多样性特点,为育种利用提供理论依据。结果表明,在所有参试的80份小豆种质中共鉴定出等位变异92个,平均每个位点为5.1个;其中53份国内小豆和27份日本小豆的等位变异数分别为89个和74个,平均每个位点分别为4.9个和4.1个。所有供试小豆平均每个位点的多态信息含量（PIC）为0.64,变化范围为0.23～0.83,其中国内小豆的平均PIC值为0.63,变化范围为0.23~0.86;日本小豆平均PIC值为0.61,变化范围为0.20~0.81。国内栽培小豆和日本小豆在等位变异数、多态信息含量（PIC）、遗传相似性系数均存在差异,UPGMA聚类分析将参试的80份小豆明显分为五大类,聚类结果与小豆种质地理起源呈现出一定的相关性。试验表明,在小豆遗传育种中,可以通过种质资源相互利用来拓宽育成品种的遗传基础,同时这些SSR标记对于小豆资源DNA指纹图谱构建、遗传作图、基因型鉴定及分子标记辅助育种具有重要意义。     

Analysis of Genetic Diversity in the Brassica napus L. Gene Pool Using SSR Markers

Genetic diversity throughout the rapeseed (Brassica napus ssp. napus) primary gene pool was examined by obtaining detailed molecular genetic information at simple sequence repeat (SSR) loci for a broad range of winter and spring oilseed, fodder and leaf rape gene bank accessions. The plant material investigated was selected from a preliminary B. napus core collection developed from European gene bank material, and was intended to cover as broadly as possible the diversity present in the species, excluding swedes (B. napus ssp. napobrassica (L.) Hanelt). A set of 96 genotypes was characterised using publicly available mapped SSR markers spread over the B. napus genome. Allelic information from 30 SSR primer combinations amplifying 220 alleles at 51 polymorphic loci provided unique genetic fingerprints for all genotypes. UPGMA clustering enabled identification of four general groups with increasing genetic diversity as follows (1) spring oilseed and fodder; (2) winter oilseed; (3) winter fodder; (4) vegetable genotypes. The most extreme allelic variation was observed in a spring kale from the United Kingdom and a Japanese spring vegetable genotype, and two winter rape accessions from Korea and Japan, respectively. Unexpectedly the next most distinct genotypes were two old winter oilseed varieties from Germany and Ukraine, respectively. A number of other accessions were also found to be genetically distinct from the other material of the same type. The molecular genetic information gained enables the identification of untapped genetic variability for rapeseed breeding and is potentially interesting with respect to increasing heterosis in oilseed rape hybrids.     

Genetic diversity and similarity of pear (<Emphasis Type="Italic">Pyrus</Emphasis> L.) cultivars native to East Asia revealed by SSR (simple sequence repeat) markers

Simple sequence repeat (SSR) markers were used to assess genetic diversity and relationship of Pyrus L. cultivars native mainly to East Asia. A total of 168 putative alleles were generated from six primer-pairs (BGA35, KU10, BGT23b, NH004a, NH011b and NH015a). All the SSR markers showed a high level of genetic polymorphism with a mean of 28 putative alleles per locus and the heterozygosity of 0.63. The Dice’s similarity coefficient between cultivars ranged from 0.02 to 0.98 and Occidental pears generally had low affinities to Asian pears. Ten major groups were generated from all the accessions by UPGMA clusters analysis. Chinese sand pears consisted of four groups with Chinese white pears and Japanese pears, of which Chinese sand pears occurred in all four groups, presenting a large genetic diversity, Chinese white pears were included in three groups, and Japanese pears only fell into one group. In the dendrogram, Chinese sand pears and Chinese white pears did not form discrete group, even subgroups. Some Japanese pear cultivars had high affinities to Chinese sand pear cultivars. These findings supports the authors’ previous viewpoints of Chinese white pears as a variety or an ecotype of Chinese sand pears (P. pyrifolia var. sinensis (Lindley) Y. Teng et K. Tanabe) and the progenitor of Japanese pears coming from China. Cultivars of P. ussuriensis Maxim. were clustered together with one clone of P. hondoensis Nakai et Kikuchi, a relative species of P. ussuriensis. Cultivars of P. communis L. and other Occidental species formed three independent groups and were distant from most Asian pears, except for P. betulaefolia Bge.     

A Preliminary Comparative Evaluation of Genetic Diversity between Chinese and Japanese Wild Soybean (<Emphasis Type="Italic">Glycine soja</Emphasis>) Germplasm Pools using SSR markers

The wild soybean, an annual self-pollinating plant, is the progenitor of soybeans and is extensively distributed in the Far East of Russia, the Korea peninsula, China and Japan. Geographically, Japan is surrounded by sea and insulated from China. We preliminarily evaluate whether the Japanese and Chinese wild soybean germplasm pools are genetically differentiated from each other using SSR markers. The results showed that the two pools have great genetic differentiation. Some loci presented obvious differences in mean genetic divergence (G_ST) value between the two pools. The G_ST among the geographic regions in China was higher than that in Japan. The average within-geographic region gene diversity values (H_S) in the two pools were completely identical and thus the genetic difference between the two pools was mostly attributed to the relatively high level of between-geographic region gene diversity (D_ST) in China. We suggest that Japanese and Chinese wild soybeans should be comparatively independently evolving in phylogeny.     

Genetic differentiation and diversity of phenotypic characters in Chinese wild soybean (<Emphasis Type="Italic">Glycine soja</Emphasis> Sieb. et Zucc.) revealed by nuclear SSR markers and the implication for intraspecies phylogenic relationship of characters

Genetic diversity is reduced from wild soybean to cultivars and from landraces to modern varieties. However, intraspecies genetic diversity loss between characters or phenotypes also existed in wild soybean. We revealed the phylogenic relationship of character types in Chinese wild soybean using 42 SSR markers. We conjectured that white flower, no-seed bloom, grey pubescence, and four seed coat colours were evolutionarily acquired phenotypes. There were a small decrease (∆H = 0.1–6.46%) of gene diversity and a moderate reduction (∆Na = 10.81–53.54%) of number of alleles but a violent loss (80.74–98.59%) of unique alleles in the acquired phenotypes. Our results seemed to suggest that ovoid and elliptic leaves were differentiated at the earliest and subsequently lanceolate leaf appeared before the domestication of soybeans within wild soybean, and that G. gracilis type was another earliest type, maybe emerged since the appearance of soybeans or it was concomitant with the domestication of soybean.     

东北地区水稻品种与日本引进品种遗传多样性比较

利用20个表型性状和40个SSR标记,对我国东北18份水稻选育品种和13份日本引进品种的遗传多样性,共检测到82个表型变异和108个SSR等位基因,其中中国东北水稻品种表型变异数和SSR等位基因数分别为72和103个（平均2.54个）,日本引进品种表型变异数和等位基因数分别为63和94个（平均2.32个）。遗传变异主要...     

Genetic Diversity of Japanese Melon Cultivars (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) as Assessed by Random Amplified Polymorphic DNA and Simple Sequence Repeat Markers

The genetic diversity among 67 melon (C. melo L.) cultivars from five Japanese seed companies was assessed using 25 10-mer RAPD primers (56 bands) and nine SSR (36 alleles) markers. These cultivars belong to three horticultural varieties (synom. Groups) spanning eight melon market classes: Group Cantalupensis (market classes Earl’s, House, Galia, Charentais, and Ogen), Group Inodorus [Honeydew and Casaba melons (market classes Amarillo, Piel de Sapo, Rochet, Negro, Crenshaw, and Tendral)], and Group Conomon (market class Oriental). Genetic variation among these cultivars was compared to variation in a reference array (RA) consisting of 34 selected melon accessions from previous studies. Cluster analysis resulted in 11 of 15 Japanese Oriental accessions forming a group with South African RA accessions. The remaining Group Conomon Japanese accessions grouped either with Casaba or with Honeydew cultivars. Japanese Group Conomon accessions and South African RA accessions formed a genetic group that was distinct from all other accessions studied, and suggests either an Asiatic origin for the South African melon germplasm examined or an independent domestication involving similar ancestors. The majority of Japanese House and Earl market class accessions shared genetic affinities, and were genetically different from the Japanese Group Inodorus accessions examined. These Japanese accessions were most similar to Casaba RA accessions. Japanese Galia accessions were similar to either House and Earl’s market classes or to Galia, Ogen, Casaba, and Honeydew RA accessions. Genetic differences exist between melon types that were domesticated from wild, ‘free-living’ subspecies agrestis and from melo. Mention of trade name, proprietary products, or specific equipment does not costitute a guarantee or warranty by the USDHA and does not imply its approval to the exclusion of other products that may be suitable.     

Genetic Survey of Chinese and Swedish Oilseed Rape (Brassica napus L.) by Simple Sequence Repeats (SSRs)

Eleven Chinese and twelve Swedish rapeseed (Brassica napus) genotypes were analysed by PCR with 41 microsatellite primers, generating a total of 50 loci. For these 50 loci, the number of alleles ranged from 1 to 14, and the average number of alleles per loci was 2.7. As an example of simple sequence repeat (SSR) scoring in Metaphor agarose gel, a single marker could distinguish 14 different DNA profiles. Based on cluster analysis (UPGMA), the dendrogram clearly distinguished three clusters, a cluster with exclusively Swedish genotypes, and two clusters with Chinese genotypes. The genetic diversity within the Chinese genotypes was broad compared to the genetic diversity within the Swedish material. The genetic similarity within the Swedish breeding lines ranged from 69.5 to 95.6%, while that of Chinese genotypes ranged from 57.1 to 81.6%. The results in this report will permit to establish a set of microsatellite primers that can be used for selecting appropriate parents for Brassica napus hybrids and for monitoring hybridity level.     

Genetic diversity of carrot (<Emphasis Type="Italic">Daucus carota</Emphasis> L.) cultivars revealed by analysis of SSR loci

Polymorphism of simple sequence repeat (SSR) loci was assessed in a collection of 88 carrot (Daucus carota L. subsp. sativus Hoffm.) accessions. The collection comprised cultivars and landraces mainly from Asia, Europe, and North America. Plants were grown in the glasshouse and characterized for root color and shape. Thirty SSR loci were fully characterized using parameters derived from allele frequencies, i.e. the number of total, effective and rare alleles, the observed and expected heterozygosity, and fixation index. Using a Bayesian approach, two clusters of 17 and 61 accessions were distinguished, which comprised the Asian and Western type accessions, respectively. Genetic diversity of the Asian gene pool was higher than that of the Western gene pool. The results of SSR analysis were supported by morphological characterization, and are congruent with current knowledge on the history of carrot domestication and breeding.     

Genetic diversity and population structure of worldwide eggplant (<Emphasis Type="Italic">Solanum melongena</Emphasis> L.) germplasm using SSR markers

Two hundred and eighty-seven worldwide eggplant accessions were examined for genetic diversity and population structure analysis with 45 SSR markers. The results resolved 242 alleles across all the accessions. Gene diversity ranged from 0.104 to 0.832 with an average of 0.558. Polymorphic information content ranged from 0.102 to 0.815 with an average of 0.507. The genetic diversity analysis classified all accessions into four groups, and the data showed that gene exchanges occurred in two groups during germplasm introduction, domestication, and improvement; however, the frequency was low. Population structure analysis classified 269 accessions into two subgroups, and the remaining 18 accessions were defined as admixed. The accessions from the same geographic origin tend to be clustered into same group. These results provide new insights into the exploitation of genetic diversity of germplasm for eggplant breeding program.     

Genetic analysis of wheat (Triticum aestivum L.) and related species with SSR markers

Genetic diversity among 19 Triticum aestivum accessions and 73 accessions of closely related species was analyzed using simple sequence repeat (SSR) markers. Forty-four out of 497 SSR markers were polymorphic. In total 274 alleles were detected (mean 6.32 alleles per locus). The polymorphic information content (PIC) of the loci ranged from 0.3589 to 0.8854 (mean 0.7538). The D genome contained the highest mean number of alleles (6.32) followed by the A and B genomes (6.13 and 5.94, respectively). The correlation between PIC and allele number was significant in all genome groups (0.7540, 0.7361 and 0.7482 for A, B and D genomes, respectively). Among the seven homologous chromosome groups, genetic diversity was lowest in group 7 and highest in group 5. In cluster and principal component analyses, all accessions grouped according to their genomes were consistent with their taxonomic classification. Accessions with the A and D genomes were clustered into two distinct groups, and AABB accessions showed abundant genetic diversity and a close relationship. Triticum durum and T. turgidum were clustered together, consistent with their morphological similarity. Cluster analysis indicated emmer is closely related to hexaploid wheat. Compared with common wheat, higher genetic variation was detected in spelt, T. aestivum subsp. yunnanense and subsp. tibetanum. In addition, a close genetic relationship between T. polonicum and T. macha was observed. The results of the clustering and principal component analyses were essentially consistent, but the latter method more explicitly displayed the relationships among wheat and closely related species.     

黄淮麦区部分小麦种质资源的SSR聚类分析

利用79对SSR引物对黄淮麦区129份种质资源进行了分析。结果表明, 79对引物共检测到335个等位变异，每个引物检测到的等位变异数目2～8个，平均4.240个，变异最大的位点主要位于B组染色体上。79个SSR位点的遗传多态性信息含量在0.015～0.820之间，平均0.498。种质资源间的遗传相似系数在0.253～0.909之间，平均0.492。聚类分析把这些种质资源分为4大类和7个亚类。聚类结果与地域并不吻合，但能较好地反映出亲本的特性和其间的亲缘关系。关键词：黄淮麦区；小麦；种质资源；遗传多样性；SSR标记；聚类分析     

黄淮麦区部分小麦种质资源的遗传差异分析

利用79对SSR引物对黄淮麦区129份种质资源进行了分析。结果表明,79对引物共检测到335个等位变异,每个引物检测到的等位变异数目2～8个,平均4.240个,变异最大的位点主要位于B组染色体上。79个SSR位点的遗传多态性信./010.015～0.820之间,平均0.498。种质资源间的遗传相似系数在0.253～0.909之间,平均0.492。聚类分析把这些种质45674大类和7个亚类。聚类结果与地域并不吻合,但能较好地反映出亲本的特性和其间的亲缘关系。