Using genetic diversity information to establish core collections of Stylosanthes capitata and Stylosanthes macrocephala

Stylosanthes species are important forage legumes in tropical and subtropical areas. S. macrocephala and S. capitata germplasm collections that consist of 134 and 192 accessions, respectively, are maintained at the Brazilian Agricultural Research Corporation Cerrados (Embrapa-Cerrados). Polymorphic microsatellite markers were used to assess genetic diversity and population structure with the aim to assemble a core collection. The mean values of H_O and H_E for S. macrocephala were 0.08 and 0.36, respectively, whereas the means for S. capitata were 0.48 and 0.50, respectively. Roger’s genetic distance varied from 0 to 0.83 for S. macrocephala and from 0 to 0.85 for S. capitata. Analysis with STRUCTURE software distinguished five groups among the S. macrocephala accessions and four groups among those of S. capitata. Nei’s genetic diversity was 27% in S. macrocephala and 11% in S. capitata. Core collections were assembled for both species. For S. macrocephala, all of the allelic diversity was represented by 23 accessions, whereas only 13 accessions were necessary to represent all allelic diversity for S. capitata. The data presented herein evidence the population structure present in the Embrapa-Cerrados germplasm collections of S. macrocephala and S. capitata, which may be useful for breeding programs and germplasm conservation.     

利用分子标记分析高粱的遗传多样性及其在种质创新中的应用

分子标记由于能够反映DNA水平上的遗传变异而成为研究遗传多样性的重要方法。本文综述了利用分子标记分析高粱遗传多样性的研究进展,并阐述了遗传多样性分析在种质创新中的应用方向,提出了利用分子标记分析高粱遗传多样性研究中尚需进一步加强的研究内容。     

Genetic diversity analysis of 60 ginger germplasm core accessions using ISSR and SSR markers

Molecular techniques play a critical role in studies of phylogeny and, thus, have been applied to understand the distribution and extent of genetic variation within and between species. In the present study, a genetic analysis was undertaken using molecular markers (9 ISSR and 13 SSR) on 60 ginger cultivars from different regions of the eastern coast of India (Odisha). The data obtained with 22 polymorphic markers revealed moderate to high diversity in the collection. Both ISSR and SSR markers were efficient in distinguishing all the 60 ginger cultivars. A total of 42 and 160 polymorphic bands were observed with ISSR and SSR markers, respectively. However, SSR markers were observed to be better at displaying average polymorphism (63.29%) than ISSR markers (55%). Analysis of molecular variance results showed that 52 and 66% of the variation occurred among different ginger populations, whereas 48 and 34% of the variation was found within populations, respectively, using ISSR and SSR markers, indicating that ginger cultivars display significant genetic diversity at the population level. Principal coordinates analysis and the dendrogram constructed out of combined data of both markers showed grouping of ginger accessions to their respective area of collection, indicating geographical closeness due to genetic similarity irrespective of the relationship that exists at the morphological level.     

走马胎种质资源遗传多样性的ISSR分析

走马胎( Ardisia gigantifolia)是紫金牛科( Myrsinaceae)紫金牛属( Ardisia)多年生小灌木植物。走马胎作为我国传统中药材,已有多年的药用历史。目前,走马胎不再局限于临床药用,在食疗和保健方面的开发利用崭露头角,大大扩展了其应用范围。随着走马胎市场需求量的增大,野生走马胎植物被过度采挖,导致野生走马胎资源几乎枯竭。人工栽培走马胎逐渐成为供应药用市场的主力军,但是人工栽培走马胎种质、种子来源混杂,常会造成质量和疗效的不稳定,而利用分子标记技术可以从分子水平上对走马胎进行种质的区分和评价。该研究利用ISSR分子标记技术,对来自广西地区的36份走马胎种质资源进行了遗传多样性分析,采用POPGEN32软件进行数据分析,用UPGMA软件绘制聚类图。结果表明：14条ISSR引物共检测到136个清晰的扩增位点,多态性位点112个,多态位点百分率为82.35％;Nei’ s基因多样性指数( H)为0.2965,Shannon多样性指数(I)为0.4417,基因分化系数(Gst)为0.8558。个体间的遗传相似系数为0.6678~0.8382,平均为0.7391。基于聚类分析可知,所有的个体被划分为5类,其中绝大多数来自相同或者邻近地区的个体严格按照地理位置聚为相同的一类或者亚类,只有少数个体在归类上与地理位置相悖。研究证明ISSR分子标记技术在评价走马胎种质资源亲缘关系和遗传变异等方面有很好的适用。该研究结果为该药用植物的种质资源评估和引种栽培提供了科学依据。     

Genetic diversity estimation and core collection construction of Sinojackia huangmeiensis based on novel microsatellite markers

Sinojackia huangmeiensis is a critically endangered tree species in the Styracaceae endemic to China. To create tools to better evaluate the genetic diversity of this species, we used a modified genomic library enrichment method, the PETUER (Probe Extension and TEACl Universal EnRichment) method, to develop genetic markers. The resulting 18 microsatellite loci had high polymorphism with 3–12 alleles per locus and showed negligible stutter. Observed (H_O) heterozygosities were 0.057–0.724, and polymorphism information content (PIC) was 0.109–0.794. No significant linkage disequilibrium between pairs of loci was found. All 123 individuals found in the National Natural Reserve of Longgan Lake was genotyped at the 18 loci and used to estimate a UPGMA dendrogram. Using an iterative clustering method, a set of 18 individuals was established as a core collection to represent genetic diversity and would be useful to facilitate the conservation for S. huangmeiensis. In addition, we tested the 18 loci for cross-species amplification in three other Sinojackia species and the closely related Changiostyrax dolichocarpa. These polymorphic loci will be valuable for future population genetic and phylogenetic studies of S. huangmeiensis and congeneric species, as well as in closely related Styracaceae.     

Genetic differentiation analysis of African cassava (Manihot esculenta) landraces and elite germplasm using amplified fragment length polymorphism and simple sequence repeat markers

Molecular‐marker‐aided evaluation of germplasm plays an important role in defining the genetic diversity of plant genotypes for genetic and population improvement studies. A collection of African cassava landraces and elite cultivars was analysed for genetic diversity using 20 amplified fragment length polymorphic (AFLP) DNA primer combinations and 50 simple sequence repeat (SSR) markers. Within‐population diversity estimates obtained with both markers were correlated, showing little variation in their fixation index. The amount of within‐population variation was higher for landraces as illustrated by both markers, allowing discrimination among accessions along their geographical origins, with some overlap indicating the pattern of germplasm movement between countries. Elite cultivars were grouped in most cases in agreement with their pedigree and showed a narrow genetic variation. Both SSR and AFLP markers showed some similarity in results for the landraces, although SSR provided better genetic differentiation estimates. Genetic differentiation (Fst) in the landrace population was 0.746 for SSR and 0.656 for AFLP. The molecular variance among cultivars in both populations accounted for up to 83% of the overall variation, while 17% was found within populations. Gene diversity (H_e) estimated within each population varied with an average value of 0.607 for the landraces and 0.594 for the elite lines. Analyses of SSR data using ordination techniques identified additional cluster groups not detected by AFLP and also captured maximum variation within and between both populations. Our results indicate the importance of SSR and AFLP as efficient markers for the analysis of genetic diversity and population structure in cassava. Genetic differentiation analysis of the evaluated populations provides high prospects for identifying diverse parental combinations for the development of segregating populations for genetic studies and the introgression of desirable genes from diverse sources into the existing genetic base.     

广西地方稻种资源核心种质构建和遗传多样性分析

以丁颖分类体系分组原则与组内逐层聚类取样方法,对8609份广西地方栽培稻资源表型数据信息进行分析,通过对表型保留比例等评价指标的多重比较确定核心种质总体取样比例,构建出占总体样本5%(414份)的广西地方栽培稻资源初级核心种质。初级核心种质能代表总体遗传变异的89%。用34对SSR分子标记对初级核心种质进行遗传多样性分析,结果表明:广西地方栽培稻资源有较高的遗传多样性(等位基因数A为4.91,Nei’s多样性指数为0.574)。就Nei’s遗传多样性指数而言,粳稻高于籼稻,晚稻高于早稻,水稻高于陆稻,糯稻高于粘稻;来自桂中的稻种资源具有最高的遗传多样性。研究最终利用SSR数据,把414份初级核心种质压缩50%后形成209份核心种质,核心种质基因保留比例达到98%以上,有效代表了广西地方栽培稻资源多样性水平。     

Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system

Occurrence of intervarietal or interspecific natural crosses has been reported for many crop plants in traditional farming systems, underlining the potential importance of this source of genetic exchange for the dynamics of genetic diversity of crop plants. In this study, we use microsatellite loci to investigate the role of volunteer seedlings (plants originating from unmanaged sexual reproduction) in the dynamics of genetic diversity of cassava (Manihot esculenta Crantz), a vegetatively propagated crop, in a traditional farming system in Guyana. A previous field study showed that farmers incorporate such plants into the germplasm for vegetative propagation, and that many of them are likely to be assigned by farmers to recognized varieties. Under strict vegetative propagation clonality of varieties is expected. The high proportion of polyclonal varieties observed suggests that incorporation of seedlings into the germplasm for propagation is a frequent event. The molecular variability assessed with microsatellite markers shows that there is high differentiation among heterozygous varieties, whereas populations of seedlings do not depart from the proportions expected under Hardy-Weinberg assumptions. Assignment of seedlings to a recognized variety on the basis of morphological similarity greatly increases genetic diversity within the variety. We argue that recombination and gene flow play a major role in the dynamics of genetic diversity of cassava in traditional farming systems. Documenting unmanaged sexual reproduction and its genetic consequences is a prerequisite for defining strategies of in situ conservation of crop plant genetic resources.     

中国花生核心种质中高油酸材料的分布和遗传多样性

利用代表花生基础资源的核心种质分析花生高油酸资源的分布和遗传多样性,结果表明：在花生核心种质中油酸含量高于57%的种质40份,主要分布在密枝亚种（普通型25份和龙生型8份）,少数分布在疏枝亚种（珍珠豆型6份和中间型1份）; 除了10份资源来源于国外（ICRISAT 7 份,美国1份,日本1份和韩国1份,其他种质资源来源于中国12个省市。 同时发现高油酸种质中3份资源的含油量在55%左右,分别是Zh.h4094（油酸66.70%,含油量54.99%）, Zh.h4029（油酸63.50%,含油量55.58%）和Zh.h4319（油酸59.70%,含油量56.04%; 小区产量超过3000 kg/ha 有10 份种质,前三位分别是Zh.h0883 （4086.06kg/ha）, Zh.h1182（3955.00kg/ha）和 Zh.h2910 （3741.00kg/ha）。基于植物学和产量性状分析,前5个主成份（PC）可以解释81.17% 的变异。聚类分析,在域值为0.1942时,可分为6个组。 因此中国花生核心种质中高油酸种质存在丰富的遗传多样性,而且分布较广,高油酸种质的获得对花生高油酸育种提供基础材料。     

Using SSR markers to evaluate the genetic diversity of Lentinula edodes’ natural germplasm in China

In this study, microsatellite markers were utilized to reveal the genetic diversity of 56 strains of Lentinula edodes grown in China. A total of 224 DNA bands were detected through 25 primer pairs, of which, 223 bands (99.6%) were polymorphic between two or more strains. The variation in SSR (Simple Sequence Repeat) DNA band patterns and average genetic similarity among the wild strains of L. edodes obtained from the same region uncovered a vast genetic diversity in the natural germplasm found in China. Compared with L. edodes strains from other areas, the genetic diversity of those from the Yunnan Plateau, Hengduanshan mountains, Taiwan, and south China was significantly greater. Based on cluster analysis and principal coordinate analysis, the results indicated that all L. edodes strains could be divided into three major groups. These results effectively displayed the differences between the strains from North and South China, and those from the same or adjoining regions could cluster preferentially into small groups in most cases, suggesting the positive correlation between the cluster results and the geographical origin for the natural germplasm of Chinese L. edodes. To our knowledge, this is a pioneering report on the utilization of the SSR marker technique in analyzing L. edodes’ genetic diversity.