Genetic Diversity and Population Structure of the Brachiaria brizantha Germplasm

Brachiaria brizantha (Hochst. ex A. Rich.) Stapf. (syn. Urochloa brizantha (Hochst. ex A. Rich.) R.D. Webster) is a species used primarily as forage in tropical America and Southeast Asia. B. brizantha has been extensively researched since the 1980s with the initiation of the Tropical Forages Breeding Program conducted by the Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária; EMBRAPA), holding one of the largest germplasm collections in the world. This work has identified 15 new microsatellite markers for this species, which have been used in addition to five previously reported markers, to estimate the genetic similarities among 172 accessions and six cultivars of this species. Similarity index values ranged from 0.40 to 1.00. Two duplications were found in the germplasm. A Bayesian analysis performed using the STRUCTURE 2.3.3 program revealed the presence of three clusters with different allelic pools. This analysis is valuable for the performance of crosses to explore heterosis; however, the mode of reproduction of the accessions and ploidy barriers must be observed for effective exploration. A grouping analysis using the neighbor-joining method was consistent with the STRUCTURE analysis, and a combination approach suggested that this germplasm collection does not exhibit considerable genetic variability despite the presence of three distinct allelic pools. The lack of correlation between the genetic and geographic distances is also discussed.     

Genetic Diversity and Population Structure of Coffee Germplasm Collections in China Revealed by ISSR Markers

Plant Molecular Biology Reporter - Population genetics analysis is crucial for understanding the degree of linkage disequilibrium in a germplasm collection for association mapping and breeding...     

东南亚国家引进水稻种质的遗传多样性和遗传结构分析

用72对SSR引物对316份东南亚不同地理来源的水稻种质资源进行遗传多样性和遗传结构分析。结果表明,共检测到387个等位基因,平均每对引物检测到5.375个,变幅在2~12之间;其中频率5%的稀有等位基因有293个,占全部等位基因数的75.7%。Nei基因多样性指数(He)变化幅度在0.055~0.855之间,平均为0.623。He以菲律宾的种质资源最为丰富(He=0.619),其余国家的He大小依次是越南(He=0.515)老挝(He=0.467)柬埔寨(He=0.455);聚类分析显示分为籼粳稻两大群体,地理分组不是特别清晰。AMOVA分析表明,遗传变异主要来源于不同地理类群间,且遗传分化极显著。遗传结构分析结果显示K=2时,有相对明显的遗传结构。其次是K=5时,显示菲律宾群体分为了3个比较明显的小类群,存在较为明显的遗传分化结构。东南亚引进水稻种质资源丰富的遗传多样性和遗传结构为后期水稻育种的亲本选择提供依据。     

Genetic Diversity and Population Structure of Sitodiplosis mosellana in Northern China

The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups), broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F _ST = 0.117) between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F _ST = 0.116, Nm = 1.89) than those in the eastern group (F _ST = 0.049, Nm = 4.91). Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001). The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.     

Genetic Diversity and Population Structure Analysis in Indian Mustard Germplasm Using Phenotypic Traits and SSR Markers

Plant Molecular Biology Reporter - Indian mustard is an economically important oilseed crop in India; therefore, exploring the genetic diversity of various germplasm collections is quite relevant...     

中国绿豆种质资源遗传多样性研究

分析中国作物种质资源数据库中5072份国内绿豆资源的地理分布,并对14个性状(6个质量性状和8个数量性状)进行遗传多样性分析。结果表明:我国绿豆种质资源分布在约28个纬度、60个经度内,其中29~41°N×107~123°E范围内分布最多,占总材料数的75.99%。6个质量性状中荚色的遗传多样性指数最高,而8个数量性状中百粒重的遗传多样性指数最高。35~37°N×111~115°E、37~39°N×111~115°E、39~41°N×115~119°E、41~43°N×115~119°E几个小区遗传多样性指数较高,可初步推断中国绿豆资源遗传多样性中心在35~43°N×111~119°E范围内。     

Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of Agaricus bisporus by SSR Markers

Agaricus bisporus is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated A. bisporus strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected A. bisporus strains using simple sequence repeat (SSR) markers. Agaricus bisporus strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy–Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance A. bisporus breeding programs and support the protection of genetic resources.     

中国麻风树种质资源SSR遗传多样性的研究初报

麻风树（Jatropha curcas）是世界上最有潜力的能源植物之一。本研究针对来自全国6省区的219份麻风树种质资源,应用SSR分子标记对其进行了初步的遗传多样性分析。根据公共数据库中的所有序列设计出了20对SSR及4对eSSR引物,这些引物均能很好地扩增麻风树DNA片段。在上述24个SSR标记中,有8个（33.33%）探测到麻风树群体的DNA多态性。这24个SSR标记共扩增出36个位点,平均每个标记扩增1.5个位点,其中12个（33.33%）位点显现出多态性。这表明中国麻风树是一个具有中等SSR多态性水平的物种,其多态百分率为33.3%。     

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers

Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (F _st = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei’s genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These data provide comprehensive information for the development of conservation strategies of these valuable hazelnut resources.     

Genetic diversity of natural Miscanthus sinensis populations in China revealed by ISSR markers

Miscanthus sinensis is a typical perennial C₄ grass in Asia. In the present study, ISSR markers were used to evaluate the genetic variation within and among grass populations that were sampled from the Zhejiang and Guangdong Provinces of China. Based on nine ISSR primers, 206 clear and reproducible DNA fragments were generated. Relatively low levels of genetic diversity were determined among the populations. The coefficient of genetic differentiation among the populations was 0.52, which indicates that 52.3% of the total molecular variance exists among the populations. Such a high level of divergence present among the populations might be caused by the complex topography and variable climatic conditions present in the two provinces. AMOVA revealed that the majority of the genetic variation was within the populations (50.6%). The application of a novel method, which combines geographical coordinates and genetic differentiation to detect barriers for gene flow, allowed us to identify two zones of lowered gene flow.     

茄子种质遗传多样性及群体结构的SRAP分析

采用SRAP标记法对183份茄子(Solanum melongena)种质资源的遗传关系和群体结构进行分析。结果表明, 33对多态性SRAP引物组合共扩增出215条清晰稳定的多态性条带, 平均每对引物组合产生7条多态性条带。183份茄子种质的遗传相似系数介于0.276-0.813之间, 平均值为0.623, 表明茄子种质资源间遗传背景存在一定的差异。在遗传距离为0.345 6处可将183份茄子种质分为4组。通过群体结构分析可将种质划分为4个群体, 不同群体间的界限十分明显, 且群体间的基因渗透较高。     

Genetic diversity of Miscanthus sinensis in US naturalized populations

Miscanthus is increasingly gaining popularity as a bioenergy grass because of its extremely high biomass productivity. Many clones of this grass were introduced into United States over the past century from East Asia where it originated, and planted for ornamental and landscaping purposes. An understanding of the genetic diversity among these naturalized populations may help in the efficient selection of potential parents in the Miscanthus breeding program. Here, we report our study analyzing the genetic diversity of 228 MiscanthusDNA samples selected from seven sites in six states (Ohio, North Carolina, Washington D.C., Kentucky, Pennsylvania, and Virginia) across the eastern United States. Ten transferable DNA markers from other plant species were employed to amplify genomic DNA of Miscanthus because of the paucity of molecular markers in Miscanthus. There were significant genetic variations observed within and among US naturalized populations. The highest genetic diversity (0.3738) was found among the North Carolina genotypes taken from Biltmore Deer Park and Biltmore, Madison County, Cody Rd. The lowest genetic diversity (0.2776) was observed among Virginia genotypes that were diverged from those from other states, suggesting Virginia genotypes might be independently introduced into the United States from the different origin. By the cluster and structure analysis, 228 genotypes were categorized into two major groups that were further divided into six subgroups at the DNA level and the groups were generally consistent with geographic region.     

Analysis of Genetic Diversity and Population Structure of Rice Germplasm from North-Eastern Region of India and Development of a Core Germplasm Set

The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is a hot spot for genetic diversity and the most probable origin of rice. North-east rice collections are known to possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36 genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively. Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure. AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58% for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core set developed will be a valuable resource for future genomic studies and crop improvement strategies.     

内蒙古西伯利亚杏群体遗传多样性和遗传结构分析

利用27对SSR分子标记对内蒙古地区13个西伯利亚杏群体的遗传多样性和遗传结构进行分析,评价其遗传多样性水平和分化程度,为内蒙古西伯利亚杏资源的合理保护与利用提供理论依据。结果显示:(1)27对SSR引物共检测到512个等位基因(Na),各位点平均等位基因数(Na)和多态性信息含量(PIC)分别为19和0.84;物种水平上Shannons信息指数(I)和期望杂合度(He)分别为2.25和0.73。(2)群体水平上的等位基因(Na)、有效等位基因(Ne)、Shannons信息指数(I)、期望杂合度(He)和观察杂合度(Ho)分别为6.95、4.48、1.60、0.76和0.56;其中科左后旗群体遗传多样性最丰富,克什克腾旗群体遗传多样性最低。(3)基于F统计量分析的遗传分化系数(Fst)为0.12,基因流(Nm)为1.86;分子方差分析显示内蒙古西伯利亚杏群体大部分遗传变异来自群体内(92%),群体间的遗传变异仅占8%。(4)内蒙古西伯利亚杏群体遗传距离为0.04~0.67,遗传相似度为0.33~0.83;遗传相似度的聚类分析、遗传距离的主坐标分析和遗传结构分析(Structure)均将供试13个群体划分为4组。Mantel检测显示,内蒙古西伯利亚杏群体遗传距离与地理距离呈显著相关关系(r=0.453,P0.01)。研究表明,内蒙古西伯利亚杏资源具有丰富的遗传多样性,这一特性与其群体的大小、悠久的演化历史以及自身生物学特性相关;内蒙古西伯利亚杏群体间存在中等程度的遗传分化,这可能源于自然地理隔离以及近期人类活动引起的生境片段化。     

北沙柳群体遗传多样性和遗传结构分析

以内蒙古北沙柳(Salix psammophila)国家种质资源库内9个群体(P1~P9)288个无性系为实验材料,利用TP-M13-SSR技术,选取22对具有多态性EST-SSR北沙柳引物,采用毛细管电泳对PCR产物进行检测,分析北沙柳遗传多样性、分化程度和群体遗传结构,为北沙柳种质资源库遗传管理、无性系鉴定、品种选育、遗传改良和构建指纹图谱提供理论依据。结果显示:(1)22对EST-SSR引物共检测到222个等位基因,各位点平均等位基因数(A)为10,四倍体基因型丰富度(G)和特异基因型(G1)总和分别为1 460和802个,平均特异基因型比率(P1)和种质鉴别率(P2)分别为45.86%和13.21%。(2)9个群体平均等位基因数(A)为7.475,基因型丰富度(G)为15.586,观察杂合度(Ho)和期望杂合度(He)分别为0.577和0.638。以期望杂合度He为标准,北沙柳群体遗传多样性水平最低的是P1和P9。(3)北沙柳群体遗传分化系数仅为0.02,AMOVA分子变异分析显示,北沙柳群体大部分遗传变异来自群体内(97%),群体间变异仅为3%。(4)三维主成分、聚类和Structure群体遗传结构分析显示,9个群体被划分为2个组,Mantel检验表明北沙柳遗传距离与地理距离极显著相关(r=0.684 P0.001)。研究表明,北沙柳种质资源具有丰富的遗传多样性,这是其具有耐旱、耐寒、耐高温、耐沙埋和抗风蚀等适应性较强的分子基础;北沙柳的遗传变异集中在群体内;分布区群体呈现由中心向边缘群体扩张分化的趋势。     

Population Structure and Diversity in Finger Millet (Eleusine coracana) Germplasm

A genotypic analysis of 79 finger millet accessions (E. coracana subsp. coracana) from 11 African and five Asian countries, plus 14 wild E. coracana subsp. africana lines collected in Uganda and Kenya was conducted with 45 SSR markers distributed across the finger millet genome. Phylogenetic and population structure analyses showed that the E. coracana germplasm formed three largely distinct subpopulations, representing subsp. africana, subsp. coracana originating from Africa and subsp. coracana originating from Asia. A few lines showed admixture between the African and Asian cultivated germplasm pools and were the result of either targeted or accidental intercrossing. Evidence of gene flow was also seen between the African wild and cultivated subpopulations, indicating that hybridizations among subspecies occur naturally where both species are sympatric. The genotyping, combined with phylogenetic and population structure analyses proved to be very powerful in predicting the origin of breeding materials. The genotypic study was complemented by a phenotypic evaluation. The wild and cultivated accessions differed by a range of domestication-related characters, such as tiller number, plant height, peduncle length, seed color and grain yield. Significant differences in plant architecture and yield were also identified between the Asian and African subpopulations. The observed population structure within cultivated finger millet is consistent with the theory that, after the introduction of finger millet from Africa into India via the trade routes some 3000 years ago, the two germplasm pools remained largely isolated until recent times. The significantly lower diversity present within the Asian subpopulation also suggests that it arose from a relatively small number of founder plants.     

Genetic Diversity and Population Structure of Theileria annulata in Oman

Background

Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.

Methods

Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.

Results

We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise F_ST values being less than 0.03. Slightly higher F_ST values (G_ST’ = 0.075, θ = 0.07) were detected when the data for T. annulata parasites in Oman was compared with that previously generated for Turkey and Tunisia.

Conclusion

Genetic analyses of T. annulata samples representing four geographical regions in Oman revealed a high level of genetic diversity in the parasite population. There was little evidence of genetic differentiation between parasites from different regions, and a high level of genetic diversity was maintained within each sub-population. These findings are consistent with a high parasite transmission rate and frequent movement of animals between different regions in Oman.     

Genetic Diversity,Population Structure,and Resistance to Phytophthora capsici of a Worldwide Collection of Eggplant Germplasm

Eggplant (Solanum melongena L.) is an important solanaceous crop with high phenotypic diversity and moderate genotypic diversity. Ninety-nine genotypes of eggplant germplasm (species (S. melongena, S. incanum, S. linnaeanum and S. gilo), landraces and heirloom cultivars) from 32 countries and five continents were evaluated for genetic diversity, population structure, fruit shape, and disease resistance to Phytophthora fruit rot. Fruits from each line were measured for fruit shape and evaluated for resistance to two Phytophthora capsici isolates seven days post inoculation. Only one accession (PI 413784) was completely resistant to both isolates evaluated. Partial resistance to Phytophthora fruit rot was found in accessions from all four eggplant species evaluated in this study. Genetic diversity and population structure were assessed using 22 polymorphic simple sequence repeats (SSRs). The polymorphism information content (PIC) for the population was moderate (0.49) in the population. Genetic analyses using the program STRUCTURE indicated the existence of four genetic clusters within the eggplant collection. Population structure was detected when eggplant lines were grouped by species, continent of origin, country of origin, fruit shape and disease resistance.     

云杉矮槲寄生遗传多样性及其群体遗传结构分析

该研究采用CTAB法提取云杉矮槲寄生(Arceuthobium sichuanense)的基因组DNA,利用ITS1片段的序列信息对中国9个不同地理群体的62份云杉矮槲寄生样本的遗传多样性及群体遗传结构进行分析。结果表明:(1)62条ITS1序列共定义16个单倍型(H1~H16),表现出较低的遗传多样性水平(h=0.678 5,π=0.005 9),而群体间的遗传多样性水平则表现出较大差异(h=0~1.000 0,π=0~0.009 4);AMOVA分析显示云杉矮槲寄生群体内的遗传变异占到51.37%,群体间为48.63%。(2)Network单倍型网络分析表明,单倍型H1和H12较为古老,且所有群体对2种单倍型无共享现象;单倍型H1是广布单倍型,存在于青海和甘肃的6个群体中,单倍型H12仅在四川的2个群体中有分布。(3)基于最大似然法(ML)构建的群体聚类和中介邻接法构建的单倍型网络图均显示,四川的3个群体为独立类群,区别于青海、甘肃群体,且甘肃和青海的群体之间没有明显分化。该研究首次报道了云杉矮槲寄生遗传多样性和遗传结构,为进一步研究其进化及后续的病害防控提供了一定的参考。