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.     

Genetic diversity in a world germplasm collection of tall fescue

Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.     

A comparative assessment of molecular marker assays (AFLP, RAPD and SSR) for white yam (Dioscorea rotundata) germplasm characterization

Several DNA‐based marker systems are available for genetic fingerprinting of plants but information on their relative usefulness for yam germplasm characterisation is lacking. The efficiency of RAPD, AFLP and SSR markers for the assessment of genetic relationships, and for cultivar identification and discrimination among 45 West and Central African white yam cultivars belonging to 22 morphotypes/cultivar groups was investigated. Dendrograms were produced based on band pattern scores using the UPGMA method. Results showed that each of the three techniques could unequivocably identify each cultivar, but that techniques differed in the mean number of profiles generated per primer (or primer pair) per cultivar, referred to as genotype index (GI). The order of merit based on this criterion in this study was AFLPs (GI = 2.56), SSRs (GI = 0.39) and RAPDs (GI = 0.35). Yam genotypes classified in the same cultivar group based on morphology were often genetically different, emphasising the need for molecular fingerprinting in yam germplasm characterisation. AFLPs showed the highest efficiency in detecting polymorphism and revealed genetic relationships that most closely reflected morphological classification.     

Genetic structure of Argentinean hexaploid wheat germplasm

The identification of genetically homogeneous groups of individuals is an ancient issue in population genetics and in the case of crops like wheat, it can be valuable information for breeding programs, genetic mapping and germplasm resources. In this work we determined the genetic structure of a set of 102 Argentinean bread wheat (Triticum aestivum L.) elite cultivars using 38 biochemical and molecular markers (functional, closely linked to genes and neutral ones) distributed throughout 18 wheat chromosomes. Genetic relationships among these lines were examined using model-based clustering methods. In the analysis three subpopulations were identified which correspond largely to the origin of the germplasm used by the main breeding programs in Argentina.     

Developing a common bean core collection suitable for association mapping studies

Because of the continuous introduction of germplasm from abroad, some collectionshave a high number of accessions, making it difficult to explore the geneticvariability present in a germplasm bank for conservation and breeding purposes.Therefore, the aim of this study was to quantify and analyze the structure of geneticvariability among 500 common bean accessions to construct a core collection. A totalof 58 SSRs were used for this purpose. The polymorphism information content (PIC) inthe 180 common bean accessions selected to compose the core collection ranged from0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500accessions were clustered into 15 distinct groups and the 180 accessions into fourdistinct groups in the Structure analysis. According to analysis of molecularvariance, the most divergent accessions comprised 97.2% of the observed geneticvariability present within the base collection, confirming the efficiency of theselection criterion. The 180 selected accessions will be used for association mappingin future studies and could be potentially used by breeders to direct new crosses andgenerate elite cultivars that meet current and future global market needs.     

57株毛头鬼伞遗传多样性分析

运用SRAP、RAPD、ISSR3种分子标记技术对来源不同地区的57株毛头鬼伞Coprinus comatus进行了遗传多样性分析,通过3种分子标记进行聚类分析,当相异系数D为0.48时,可以把57株毛头鬼伞分为4类:Ⅰ类包括Co0001;Ⅱ类包括Co0003;Ⅲ类包括Co0005;Ⅳ类包括其余54个菌种。供试的57个菌株间的相异系数范围从0–0.72,具有一定的遗传多态性。但其中有许多菌株两者之间的相异系数为0,说明毛头鬼伞菌种存在着比较严重的同种异名现象。     

广西部分地区野生茶树遗传关系EST-SSR标记分析

为了明确广西野生茶树种质资源的遗传背景,该研究从广西的宁明县、金秀县、苍梧县收集到14份地方野生茶树种质资源,以17个国家级茶树良种作为参照,采用EST-SSR分子标记技术,探讨了广西这三个地方野生茶树与国家级茶树良种间的亲缘关系以及广西地方茶树自身的遗传多样性。结果表明:15对EST-SSR引物共检测到68个等位基因,平均每个引物可扩增出4.53个,其中多态性位点为60个,多态性比率达88.2%。平均观测杂合度、平均期望杂合度、平均Shannon信息指数分别为0.42、0.55和0.97。PIC值在0.23~0.74之间,平均为0.52,多态性较好。遗传相似系数在0.53~0.9之间,平均值为0.71,31份供试材料在遗传相似系数为0.71分为5组群,76%参照品种聚在A组群,而广西本地的野生茶树资源则主要分布在B、C、D、E组群。利用该研究中的4对核心引物即可将31份供试材料全部区分开,挑选其中10个多态性较好的等位位点进行编码,构建31份供试种质的DNA分子指纹图谱。这表明广西野生茶树资源与国家级茶树良种间遗传差异较大、亲缘关系较远、遗传基础宽、多样性非常丰富,可作为茶树育种的亲本或开展茶树功能基因研究的材料。     

Characterization of microsatellite markers in mandarin orange (Citrus reticulata Blanco)

A dinucleotide-enriched genomic library was obtained from mandarin orange (Citrus reticulata Blanco). A subset of 101 positive clones was sequenced and primers were designed. The loci were screened for levels of variation using 26-29 wild mandarin oranges collected in Vietnam. Forty-three loci were polymorphic with the number of alleles ranging from two to 18. The observed heterozygosity (H(O) ) and expected heterozygosity (H(E) ) were from 0.03 to 0.96 and from 0.03 to 0.92, respectively.     

Uncovering the genetic diversity of yams (Dioscorea spp.) in China by combining phenotypic trait and molecular marker analyses

Yam is an important edible tuber and root plant worldwide; China as one of the native places of yams has many diverse local resources. The goal of this study was to clarify the genetic diversity of the commonly cultivated yam landraces and the genetic relationship between the main yam species in China. In this study, 26 phenotypic traits of 112 yam accessions from 21 provinces in China were evaluated, and 24 simple sequence repeat (SSR) and 29 sequence‐related amplified polymorphism (SRAP) markers were used for the genetic diversity analysis. Phenotypic traits revealed that Dioscorea opposita had the highest genetic diversity, followed by D. alata, D. persimilis, D. fordii, and D. esculenta. Among the 26 phenotypic traits, the Shannon diversity indexes of leaf shape, petiole color, and stem color were high, and the range in the variation of tuber‐related traits in the underground part was higher than that in the aboveground part. All accessions were divided into six groups by phenotypic trait clustering, which was also supported by principal component analysis (PCA). Molecular marker analysis showed that SSR and SRAP markers had good amplification effects and could effectively and accurately evaluate the genetic variation of yam. The unweighted pair‐group method with arithmetic means analysis based on SSR‐SRAP marker data showed that the 112 accessions were also divided into six groups, similar to the phenotypic trait results. The results of PCA and population structure analysis based on SSR‐SRAP data also produced similar results. In addition, the analysis of the origin and genetic relationship of yam indicated that the species D. opposita may have originated from China. These results demonstrate the genetic diversity and distinctness among the widely cultivated species of Chinese yam and provide a theoretical reference for the classification, breeding, germplasm innovation, utilization, and variety protection of Chinese yam resources.     

Classification of genetic diversity in Abelmoschus tuberculatus germplasm collection using morphometric data

Abelmoschus tuberculatus Pal & Singh is endemic to India and is the close relative of cultivated okra, A. esculentus. Data on 49 selected accessions of A. tuberculatus were used to study genetic diversity for a range of morphological characters through the use of multi-variate statistics. Epicalyx segments, shape, size and persistence; petal colour and petal blotch; stem and fruit pubescence; pigmentation of various plant parts; days to flowering; plant height; and the fruit yield/plant were the important components of variation and contributed significantly to the total variation in germplasm accessions under study. The accessions could be grouped into four distinct clusters. The grouping pattern, however, did not reflect relationship between geographic origin and genetic diversity. The potential use of the variability in okra improvement programmes is discussed.     

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.     

不同来源甜高粱种质资源的表型遗传多样性分析

通过对主要农艺性状的方差分析及聚类分析,对194份不同来源的甜高粱种质资源进行了表型性状的遗传多样性分析。结果表明,不同来源品种间的性状差异较大,与中国品种相比,国外品种具有植株高大、生物产量高及含糖量高等优异性状,可用于国内资源的种质创新及品种改良。遗传距离为0.66时将所有资源划分为6类,各类群主要按农艺性状进行了划分。研究结果将为杂交育种的亲本选择提供理论参考。     

Using microsatellites,isozymes and AFLPs to evaluate genetic diversity and redundancy in the cassava core collection and to assess the usefulness of DNA-based markers to maintain germplasm collections

The cassava core collection was selected to represent, with minimum repetitiveness, the potential genetic diversity of the crop. The core (630 accessions) was chosen from the base collection (over 5500 accessions) on the basis of diversity of origin (country and geographic), morphology, isozyme patterns and specific agronomic criteria. To asses the genetic diversity of the core, 521 accessions were typed with four microsatellite loci. Allele diversity and frequency, and size variance of dinucleotide repeats (Rst statistic) were estimated. Microsatellite allele numbers and frequencies varied among countries: Colombia and Brazil had the largest number of different alleles across all loci. Mexico also had a high number, ranking fifth after Peru, Costa Rica and Venezuela (which tied). Unique alleles were present in accessions from Brazil, Colombia, Guatemala, Venezuela and Paraguay. A small number (1.34%) of potential duplicates were identified through isozyme and AFLP profiles. Thus, the present results indicated that traditional markers have been highly effective at selecting unique genotypes for the core. Future selections of cassava germplasm sets can be aided by DNA-based markers to ensure genetically representative, non-redundant samples. This revised version was published online in June 2006 with corrections to the Cover Date.     

基于SSR分子标记的175份蜡梅种质遗传多样性分析和指纹图谱构建

理清蜡梅品种资源、构建指纹图谱是推动蜡梅科学研究和产业发展的重要基础。利用简单重复序列(simple sequence repeats, SSR)分子标记技术,对鄢陵地区175个蜡梅(Chimonanthus Praecox L.)品种(系)的遗传多样性进行了研究,使用NTSYSpc 2.1软件中的UPDM聚类方法分析品种间的遗传多样性。利用基于贝叶斯模型的Structure v2.3.3软件解析175份种质的遗传结构。通过一般线性模型(general linear model, GLM)对性状和标记进行关联分析。在遗传多样性分析中,平均等位基因数(number of alleles, Na)为6.857,平均期望杂合度(heterozygosity, He)为0.496 3,平均观测杂合度(observed heterozygosity, Ho)为0.503 7,蜡梅Nei’s平均基因多样性指数为0.494 9,平均Shannon信息指数为0.995 8,表明鄢陵地区蜡梅群体内具有较丰富的遗传多样性。群体结构和UPDM聚类分析均表明可将175个品种(系)分为7个类群。在GLM模型中有15个标记位点与8个表型性状显著(P<0.05)关联,表型变异解释范围为14.90%−36.03%。利用11对多态信息含量(polymorphic information content, PIC)最高的引物,构建175份蜡梅品种(系)资源SSR标记的指纹图谱。本研究综合分析了鄢陵地区蜡梅的遗传多样性与SSR分子标记,并构建了蜡梅核心种质资源库,为蜡梅新优品种选育、品种鉴定、资源保护与利用等工作提供理论支撑。     

基于遗传多样性构建金针菇的核心种质群体及分子身份证

金针菇Flammulina filiformis是我国产量最高的工厂化栽培食用菌.为提高优良工厂化栽培金针菇种质的育种效率,本研究以国内外收集的105份金针菇种质为材料,开展体细胞不亲和评价,并采用SSR分子标记的方法对所有种质进行遗传多样性分析和聚类分析.20对SSR引物在105份种质中共扩增得到209个等位基因位点...     

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.     

葡萄座腔菌科研究进展——鉴定,系统发育学和分子生态学

葡萄座腔菌科（Botryosphaeriaceae）真菌是农业和林业上重要的病原菌、内生真菌或潜在的致病菌,主要引起树木溃疡病。这类真菌种类繁多,寄主范围广,广泛分布于全球,在生态系统中占有重要的地位。本文综述了近年来国内外在葡萄座腔菌科的分子生态学研究方面取得的新进展。简要介绍了葡萄座腔菌科真菌物种鉴定及其研究方法方面的发展,并列出了2006年以来发现的6个新属和38个新种;概述了该科各个种、属之间的系统发育关系以及科内区分的18个群。在真菌种群遗传结构及其与寄主关系方面,已有研究表明葡萄座腔菌科真菌大体可分为寄主专化型和广谱寄生型两种类型,并已经揭示了无性型为Diplodia,Lasiodiplodia和Dothiorella等部分种群的遗传结构及它们与寄主之间的联系。在种内遗传多样性和基因流动研究方面,展示了利用ISSR、SSR等分子标记方法取得的一些重要结果,有些种群（如Lasiodiplodia theobromae）没有寄主专化性,它们在不同寄主间表现出很强的基因流动,但在不同区域内的基因交流却很有限。文章最后讨论了该科分子生态学研究有待进一步解决的问题。     

TETRASAT: a program for the population analysis of allotetraploid microsatellite data

Microsatellite markers are quite popular due to their degree of polymorphism and efficiency; however, the utility of such markers for analysing allotetraploid species is often hampered by an inability to determine allele copy number for partial heterozygotes. tetrasat is a program that uses an iterative substitution process to account for all probable combinations of allele copy numbers in populations with partial heterozygote samples. The program subsequently calculates allele frequencies, and mean Hardy–Weinberg expected heterozygosity (H_E), Shannon–Weiner Diversity Index (H′) and Nei's measure of population differentiation (G_ST) are reported for each locus and population. Of equal importance is the calculation of statistical variability generated by the missing data and allele substitution process, which allows for assessment of the strength of conclusions drawn from the statistics.