Genetic diversity of Chinese summer soybean germplasm revealed by SSR markers

There are abundant soybean germplasm in China. In order to assess genetic diversity of Chinese summer soybean germplasm, 158 Chinese summer soybean accessions from the primary core collection of G max were used to analyze genetic variation at 67 SSR loci. A total of 460 alleles were detected, in which 414 and 419 alleles occurred in the 80 Huanghuai and the 78 Southern summer accessions, respectively. The average number of alleles per locus was 6.9 for all the summer accessions, and 6.2 for both Huanghuai and Southern summer accessions. Marker diversity (D) per locus ranged from 0.414 to 0.905 with an average of 0.735 for all the summer accessions, from 0.387 to 0.886 with an average of 0.708 for the Huanghuai summer accessions, and from 0.189 to 0.884 with an average of 0.687 for the Southern summer accessions. The Huanghuai and Southern summer germplasm were different in the specific alleles, allelic-frequencies and pairwise genetic similarities. UPGMA cluster analysis based on the similarity data clearly separated the Huanghuai from Southern summer soybean accessions, suggesting that they were different gene pools. The results indicate that Chinese Huanghuai and Southern summer soybean germplasm can be used to enlarge genetic basis for developing elite summer soybean cultivars by exchanging their germplasm.     

Genetic diversity and construction of core collection in Chinese wheat genetic resources

Genetic diversity among 5029 accessions representing a proposed Chinese wheat core collection was analyzed using 78 pairs of fluorescent microsatellite （SSR） primers mapped to 21 chromosomes. A stepwise hierarchical sampling strategy with priority based on 4×10^5 SSR data-points was used to construct a core collection from the 23090 initial collections. The core collection consisted of 1160 accessions, including 762 landraces, 348 modern varieties and 50 introduced varieties. The core accounts for 23.1% of the 5029 candidate core accessions and 5% of the 23090 initial collections, but retains 94.9% of alleles from the candidate collections and captures 91.5% of the genetic variation in the initial collections. These data indicate that it is possible to maintain genetic diversity in a core collection while retaining fewer accessions than the accepted standard, i.e., 10% of the initial collections captured more than 70% of their genetic diversity. Estimated genetic representation of the core constructed by preferred sampling （91.5%） is much higher than that by random sampling （79.8%）. Both mean genetic richness and genetic diversity indices of the landraces were higher than those of the modern varieties in the core. Structure and principal coordinate analysis revealed that the landraces and the modern varieties were two relatively independent subpopulaUons. Strong genetic differentiation associated with ecological environments has occurred in the landraces, but was relatively weak in the modern culUvars. In addition, a mini-core collection was constructed, which consisted of 231 accessions with an estimated 70% representation of the genetic variation from the initial collections. The mini-core has been distributed to various research and breeding institutes for detailed phenotyping and breeding of genetic introgression lines.     

Genetic diversity, geographic differentiation and evolutionary relationship among ecotypes of Glycine max and G. soja in China

The knowledge of origin and evolution of cultivated soybeans is one of the basic issues in both biology and agronomy of the crop. In order to investigate the nuclear and cytoplasmic genetic diversity, geographic differentiation and genetic relationship among geographic ecotypes of cultivated （Glycine max） and wild （G. soja） soybeans, the allelic profiles at 60 nuclear simple-sequence repeat （nuSSR） loci and 11 chloroplastic SSR （cpSSR） loci evenly distributed on whole genome of 393 landraces and 196 wild accessions from nation-wide growing areas in China were analyzed. （i） The genetic diversity of the wild soybean was obviously larger than that of the cultivated soybean, with their nuSSR and cpSSR alleles as 1067 vs. 980 and 57 vs 44, respectively. Of the 980 nuclear alleles detected in the cultivated soybean, 377 new ones （38.5%） emerged, while of the 44 chloroplastic alleles in the cultivated soybean, seven new ones （15.9%） emerged after domestication. （ii） Among the cultivated geographic ecotypes, those from southern China, including South-Central China, Southwest China and South China possessed relatively great genetic diversity than those from northern China, while among the wild geographic ecotypes, the Middle and Lower Changjiang Valleys wild ecotype showed the highest genetic diversity. （iii） The analysis of molecular variance, association analysis between geographic grouping and molecular marker clustering and analysis of specific-present alleles of ecotypes demonstrated that the geographic differentiation of both cultivated and wild soybeans associated with their genetic differentiation, or in other words, had their relevant genetic bases. （iv） The cluster analysis of all accessions clearly showed that the wild accessions from Middle and Lower Changjiang Valleys and South-Central ＆ Southwest China had relatively small genetic distances with all cultivated accessions. The UPGMA dendrogram among geographic ecotypes further showed that the genetic distances between all cultivated ecotypes and the Middle and Lower Changjiang Valleys wild ecotype were smaller than those with other wild ones, including their local wild counterparts. Therefore, it is inferred that the wild ancestors in southern China, especially those from Middle and Lower Changjiang Valleys might be the common ancestor of all the cultivated soybeans.     

Characterization of root architecture in an applied core collection for phosphorus efficiency of soybean germplasm

In the present study, we constructed an “applied core collection“ for phosphorus (P) efficiency of soybean germplasm using a GIS-assisted approach. Systematic characterization and comparative analysis of root architecture were conducted to evaluate the relationship between root architecture and P efficiency and its possible evolutionary pattern. Our results found that: i) root architecture was closely related to P efficiency in soybean. Shallow root architecture had better spatial configuration in the P-rich cultivated soil layer hence higher P efficiency and soybean yield; ii) there was a possible co-evolutionary pattern among shoot type, root architecture and P efficiency. The bush cultivated soybean had a shallow root architecture and high P efficiency, the climbing wild soybean had a deep root architecture and low P efficiency, while the root architecture and P efficiency of semi-wild soybean were intermediate between cultivated and wild soybean; iii) P availability regulated root architecture. Soybean roots became shallower with P addition to the topsoil, indicating that the co-evolutionary relationship between root architecture and P efficiency might be attributed to the long-term effects of topsoil fertilization. Our results could provide important theoretical basis for improving soybean root traits and P efficiency.     

Further molecular evidence for the Hordeum vulgare ssp. spontaneum in Tibet as ultimate progenitor of Chinese cultivated barley

106 aeeessions of Tibetan wild barley, including 50 accessions of the two-rowed wiht barley Hordeum vulgare ssp. sopntaneum （HS）, 27 accessions of the six-rowed bottle-shaped wild barley H. lagunculiforme （HL） and 29 accessions of the six-rowed wiht barley H. agriocrithon （HA） that separately represent different agrigeographical regions of Tibet, were used to study the genetic diversity and genetie differentiation using SSR markers selected from seven barley linkage groups. 229 allelic variants were identified with an average of 7.6 alleles/locus. The average of total number of alleles per locus in HA （6.4） is much higher than that in HS （3.9） and HL （3.4）. The genetie diversity and its standard deviation among the three subspecies were in the order of HS〉HL〉HA. Very significant genetic differentiation was observed among the three subspecies of wild barley. Comparisons of the results fiom this and previous studies showed a strong Oriental-Occidental differentiation of barley, and that Shannan region of Tibet might be the center of origin of the Tibetan two-rowed wild barley, thus supporting not only the hypothesis of a mono-phyletie origin of cultivated barley but also the proposition that the Tibetan two-rowed wild barley as ultimate progenitor of Chinese cultivated barley.     

RAPD analysis of genetic variability among Stylosanthes guianenesis accessions of resistant and susceptible to the stylo anthracnose

Stylosanthes guianenesis Sw. is an important tropical forage legume grown and utilized in the tropics and the subtropics of South China. Anthracnose, caused by Colletotrichum gloeosporioides (Penz.) Sacc., is a major constraint to the extensive use of Stylosanthes. Forty-five accessions of S. guianensis were assessed with RAPD for genetic diversity and for resistance to anthracnose. RAPD analysis was performed using twenty primers screened from 200 arbitrary oligonucleotides, and a 71.5% level of polymorphism was found. The dendrogram obtained with unweighted pair group method of averages (UPGMA) based on the RAPD data showed genetic similarity from 50% to 94% among all stylo accessions, and fourteen clusters were defined at 66.5% genetic similarity. Two strains of C. gloeosporioides from stylo in China were used for anthracnose resistance screening. All plant accessions showed variation in the reaction to two strains and the correlation of resistance had a value of 0.904. Multiple correspondence analysis displayed a random distribution of the resistance or susceptibility response with respect to the genetic diversity measured by RAPD analysis except one group. Mean distance was also calculated to determine the diversity within clusters. From our results, the RAPD analysis is an effective and efficient technique of providing quantitative estimates of genetic similarity among stylo accessions.     

Relationships of Aegilops tauschii revealed by DNA fingerprints: the evidence for agriculture exchange between China and the West

Genetic diversity and relationships of wild goat grass (Aegilops tauschii Cosson) from Iran and Xinjiang, west China, as well as its weedy type from the Yellow River region of Shaanxi and Henan provinces in China were analyzed by simple sequence repeat (SSR) fingerprinting. A high level of genetic diversity in Aegilops tauschii accessions from Iran was observed, and the richness of genetic diversity was followed by accessions from Shaanxi, Henan, and Xinjiang. The weedy type of Aegilops tauschii showed a close genetic relationship with the wild type from different regions in Iran. The results indicated that the weedy Aegilops tauschii found in the Yellow River region was most likely introduced from Iran—the diversity center of Aegilops tauschii. The weedy Aegilops tauschii populations found in the Yellow River region may be brought into the central part of China as a weed species together with common wheat (Triticum aestivum L.) from the west during various periods of time in history. This finding has provided strong evidence for the introduction of common wheat from the West into China via the Silk Road, and also demonstrated the important role of the Silk Road in the exchange of agriculture and other relevant technologies between China and the West.     

Genetic structure and eco-geographical differentiation of cultivated Hsien rice (Oryza sativa L. subsp. indica) in China revealed by microsatellites

Indica is not only an important rice subspecies widely planted in Asia and the rest of the world,but it is also the genetic background of the majority of hybrid varieties in China.Studies on genetic structure and genetic diversity in indica germplasm resources are important for the classification and utilization of cultivated rice in China.Using a genetically representative core collection comprising 1482 Chinese indica landraces,we analysed the genetic structure,geographic differentiation and diversity.Model-based structure analysis of varieties within three ecotypes revealed nine eco-geographical types partially accordant with certain ecological zones in China.Differentiation of eco-geographical types was attributed to local ecological adaption and physical isolation.These groups may be useful for developing heterotic groups of indica.To facilitate the identification of different ecotypes and eco-geographical types,we identified characteristic SSR alleles of each ecotype and eco-geographical type and a rapid index of discrimination based on characteristic alleles.The characteristic alleles and rapid discrimination index may guide development of heterotic groups,and selection of hybrid parents.     

Genetic diversity in Penaeus chinensis shrimp as revealed by RAPD technique

The random amplified polymorphic DNA analysis was used to estimate genetic diversity in one successively cultivated stock and three wild stocks of Penaeus chinensis shrimp, two of which were collected from the spawning and wintering grounds in the west coast of Korean Peninsula, and one from the feeding ground in the China coast of the Yellow Sea. A random primer kit was employed to scan the genomic DNA in 20 individuals of each index stock. A total of 110 reproducible RAPD markers were obtained, 68.2 % of which showed a sound eonformability within all the individuals detected, implying that the genetic variability in P. chinensis is relatively low. The proportions of polymorphic loci among these four stocks ranged from 20% to 33.3%, while the degrees of genetic polymorphisms varied from 0.0093 to 0.0307. The genetic variability of inter-stocks was higher than that of intra-stock. The genetic diversity in different stocks differed from each other; that is, a less genetic differentiation in the spawning and wintering stocks from the west coast of Korean Peninsula was revealed and their genetic diversities were higher than that of the spawning stock in the Bohai Sea and the China coast of the Yellow Sea. As detected, the genetic diversity in the successively cultivated stock was the lowest among these four stocks. Through genetic distance analysis between a random pair of individuals, a dendrogram of the above-mentioned four stocks was constructed by unweighted pair group method with arithmetic mean. The results based on cluster analysis well fitted with the geographical distribution of P. chinensis in the Bohai and Yellow Seas.     

Geographical genetic diversity and divergence of common wild rice (O. rufipogon Griff.) in China

Using 36 SSR markers and 889 accessions of common wild rice in China, the genetic diversity and the divergence among different geographical populations are investigated. Guangdong Province has the largest number of alleles, which account for 84% of the total alleles detected in the study, followed by Guangxi Province. The Nei's gene diversity indices, from high to low, are in the sequence of Hainan, Guangdong, Guangxi, Fujian, Hunan, Jiangxi, and Yunnan provinces. Two genetic diversity centers of Chinese common wild rice are detected on the basis of geographic analysis, i.e., the region covering Boluo, Zijin, Lufeng, Haifeng, Huidong and Huiyang counties of Guangdong Province and the region covering Yongning, Longan, Laibin and Guigang counties of Guangxi Province. The common wild rice in Yunnan, Hunan, Jiangxi, and Fujian provinces are diverged into respectively independent populations with relatively large genetic distances, whereas, those in Hainan, Guangdong and Guangxi provinces have relatively low genetic divergence. Under the condition of geographic separation, natural selection is considered as one of the primary forces contributing to the divergence of common wild rice in China.     

基于表型性状的菠菜核心种质构建

以483份菠菜种质为材料,基于20个表型性状数据,根据2种遗传距离、3种取样方法、8种系统聚类方法、3种取样比例构建了144份菠菜核心种质.应用均值差异百分率、方差差异百分率、极差符合率和变异系数变化率4个参数来检验各取样策略的优劣.通过比较核心种质和原始种质的变异系数、方差、多样性指数、符合率和主成分,对构建的核心种...     

西藏石榴野生群体的SSR遗传多样性分析

【目的】调查西藏地区野生石榴种质资源,分析西藏野生石榴群体的遗传多样性和遗传结构,为野生石榴资源的保护和利用提供理论依据。【方法】使用13对SSR引物对3个自然群体共42份西藏地区野生石榴种质资源材料DNA进行PCR扩增,毛细管电泳检测扩增片段长度,使用GenAlEx和Arlequin等软件对SSR数据进行分析。【结果】13对引物共检测到44个等位基因,平均3.385个,引物的平均有效等位基因数(N_e)、香农信息指数(I)、期望杂合度(H_e)和多态信息量(PIC)分别为1.971、0.771、0.481和0.393。3个野生群体的平均有效等位基因数(N_e)、平均香农信息指数(I)和平均期望杂合度(H_e)分别为1.867、0.646和0.421,林芝b(LZb)群体的遗传多样性水平高于其他2个群体。AMOVA分析表明,群体内遗传变异高达88.43%,3个群体间的遗传分化系数(F_st)为0.116。种质聚类分析将供试种质划分为3个亚群,结果与种质地理来源具有一定关联性。遗传结构分析显示西藏野生石榴有4个可能的基因库来源。【结论】13对SSR引物可用于西藏野生石榴种质的遗传多样性等研究。西藏野生石榴种质的遗传变异主要存在于群体内;林芝b(LZb)群体遗传多样性最高,遗传结构复杂,且含有最多的野生种质采样点,可予以优先保护。     

基于荧光SSR标记的紫薇遗传多样性分析

【目的】以收集的239份紫薇属(Lagerstroemia)种质和1份黄薇属(Heimia)种质为材料,开展种质种间特征分析和紫薇种内资源的遗传多样性分析,为进一步优化紫薇种质资源收集保存及合理利用提供科学依据。【方法】基于16对荧光引物鉴定样品基因型,利用GeneMarker软件进行基因型数据的读取;对239份紫薇属种质和1份黄薇属种质进行特征位点分析;并利用Popgene、Cervus、NTSYS和GenAlEx软件对227份紫薇种质进行遗传多样性参数估算、聚类分析和主成分分析。【结果】紫薇(L.indica)种内的特征位点信息最为丰富,其中15个引物所体现出的特征位点信息中,紫薇都有其独特的位点区别于其他6个种,而在福建紫薇(L.limii)、川黔紫薇(L.excelsa)和尾叶紫薇(L.caudata)中也有部分特异的特征位点是紫薇中没有的;16对紫薇SSR荧光引物共检测出143个等位基因,平均每个位点有8.938个等位基因,平均有效等位基因数(N_e)为3.600,Shannon’s信息指数(I)均值为1.459,观测杂合度(H_o)均...     

基于ISSR标记的稻属AA基因组遗传多样性分析

为了确定稻属AA基因组物种间的遗传差异和系统进化关系,62份来自广泛地理分布的水稻品系被用于ISSR标记分析。这些品系包含有6个野生稻种(O.nivara,O.rufipogon、O.barthi,O.longistaminata,O.glumaepatula,和O.meridionalis)和2个栽培稻种(O.sativa和O.glaberrima)。21条能产生良好重复性条带模式的ISSR引物被筛选出,并在62个水稻品系中揭示出非常好的多态性。全部样品的基因多样性为0.527,同时显示出ISSR标记在稻属物种遗传多样性研究中具有强大的作用。根据ISSR条带模式,利用Jaccard配对相似系数构建的一致性树状图,显示出具有良好自展支持率的稻属AA基因组遗传多样性关系。结果表明,来自不同大陆的稻属物种具有较近的亲缘关系,尤其是亚洲野生稻物种与Vaughan1989年建立的稻属分类系统具有良好的一致性。研究结果将对稻属AA基因组野生稻在水稻育种实践中的有效利用具有非常重要的意义。     

Estimating genetic diversity and sampling strategy for a wild soybean （Glycine soja） population based on different molecular markers

With the rapid development of the global economy and continued increase in world population, natural environments face serious deterioration and change, which has led to the extinction or severe endangerment of many plant species including important crops…     

烟草种质资源研究进展

烟草种质资源是烟草遗传育种工作的物质基础,本文从烟草种质资源的搜集保存、鉴定和评价、遗传多样性研究及利用等方面综述了烟草种质资源研究成果,并对烟草种质资源研究战略进行了展望。     

基于遗传多样性和空间遗传结构的野生大豆居群采样策略

筛选了17对SSR引物对山东省垦利黄河口自然保护区野生大豆(G.sojaSieb.etZucc.)居群892份材料的遗传多样性及其随样本量变化而变化的规律进行了分析,同时以SSR的多态性为参照对该居群内的小尺度空间遗传结构进行了研究.发现该种群的平均每位点的等位基因数(A)为2.88,预期杂合度(He)为0.431,Shannon多样性指数(I)为0.699,多态位点比率(P)为100%.以计算机模拟方法随机抽取该居群不同个体组成的抽样样本,并计算各样本的多样性指数与样本量变化的回归关系,发现27~52个样本即可达到居群总体多样性水平的95%.通过空间自相关分析,得出该居群遗传结构的斑块大小约为18 m.该研究为野生大豆居群的合理取样提供了科学依据.