A strategy on constructing core collections by least distance stepwise sampling

A strategy was proposed for constructing core collections by least distance stepwise sampling (LDSS) based on genotypic values. In each procedure of cluster, the sampling is performed in the subgroup with the least distance in the dendrogram during constructing a core collection. Mean difference percentage (MD), variance difference percentage (VD), coincidence rate of range (CR) and variable rate of coefficient of variation (VR) were used to evaluate the representativeness of core collections constructed by this strategy. A cotton germplasm collection of 1,547 accessions with 18 quantitative traits was used to construct core collections. Genotypic values of all quantitative traits of the cotton collection were unbiasedly predicted based on mixed linear model approach. By three sampling percentages (10, 20 and 30%), four genetic distances (city block distance, Euclidean distance, standardized Euclidean distance and Mahalanobis distance) combining four hierarchical cluster methods (nearest distance method, furthest distance method, unweighted pair-group average method and Ward’s method) were adopted to evaluate the property of this strategy. Simulations were conducted in order to draw consistent, stable and reproducible results. The principal components analysis was performed to validate this strategy. The results showed that core collections constructed by LDSS strategy had a good representativeness of the initial collection. As compared to the control strategy (stepwise clusters with random sampling strategy), LDSS strategy could construct more representative core collections. For LDSS strategy, cluster methods did not need to be considered because all hierarchical cluster methods could give same results completely. The results also suggested that standardized Euclidean distance was an appropriate genetic distance for constructing core collections in this strategy.     

中国芒(Miscanthus sinensis)初级核心种质的构建

以555份芒(Miscanthus sinensis)种质资源为研究对象,根据26个表型性状数据,按地理来源、植物区系和单一性状进行分组,分别采用简单比例法、平方根法和多样性指数法确定组内取样数,再根据聚类和随机2种方法进行组内个体选择。依照上述方案共构建出19个具有代表性的芒初选核心种质样本库。通过平均相似系数、性状符合度、数量性状变异系数和遗传多样性指数等4项检测指标对上述19种构建方案进行比较,最终确定了按"植物区划分组+多样性指数确定取样数+聚类选择个体"为芒初级核心种质构建的最佳方案。通过此方法建立起的芒初级核心种质资源共83份,占总资源的14.95%,且新构建的初级种质资源与总资源性状符合度达到100%。     

AFLP assessment of genetic diversity among Indian Mucuna accessions

Amplified fragment length polymorphism (AFLP) marker was used to assess diversity in germplasm collection of Mucuna species which has gained tremendous attention in the recent past due to its promising nutritional, agronomic and medicinal attributes. Twenty five accessions comprising five species, collected from seven states of India were evaluated with twelve AFLP primer combinations that generated a total of 1,612 fragments with an average of 134 fragments per primer combination. The values of polymorphic information content (PIC), marker index (MI) and the resolving power (Rp) demonstrated the utility of the primer combinations used in the present study for discriminating the Mucuna accessions. UPGMA and Principal coordinate analysis (PCoA) of the genotypic data revealed clustering of accessions as per phenetic and genetic relationships. The Jaccard’s similarity coefficient values suggested good variability among the M. pruriens accessions indicating their utility in breeding programs. Molecular diversity presented in this study combined with the datasets on other morphological/agronomic traits will be highly useful for selecting appropriate accessions for plant improvement through conventional as well as molecular breeding approaches and for evolving suitable conservation strategies.     

Developing a common bean core collection suitable for association mapping studies

Because of the continuous introduction of germplasm from abroad, some collections have a high number of accessions, making it difficult to explore the genetic variability present in a germplasm bank for conservation and breeding purposes. Therefore, the aim of this study was to quantify and analyze the structure of genetic variability among 500 common bean accessions to construct a core collection. A total of 58 SSRs were used for this purpose. The polymorphism information content (PIC) in the 180 common bean accessions selected to compose the core collection ranged from 0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500 accessions were clustered into 15 distinct groups and the 180 accessions into four distinct groups in the Structure analysis. According to analysis of molecular variance, the most divergent accessions comprised 97.2% of the observed genetic variability present within the base collection, confirming the efficiency of the selection criterion. The 180 selected accessions will be used for association mapping in future studies and could be potentially used by breeders to direct new crosses and generate elite cultivars that meet current and future global market needs.     

基于农艺性状指标的山西高粱地方品种核心种质构建

利用1285份山西省高粱地方品种18个农艺性状的历史数据,通过比较不同取样方法、取样比例和聚类方法组合的构建方法,确定了"多次聚类偏离度取样法+15％取样比例+欧氏距离+最长距离法"为山西省高粱地方核心种质构建的方法.192份初选核心种质和所有样本的均值差异百分率、方差差异百分率、极差符合率和变异系数变化率分别为0、8...     

Assessment of genetic diversity in three subsets constituted from the ICRISAT sorghum collection using random vs non-random sampling procedures A. Using morpho-agronomical and passport data

A large collection, such as the sorghum [Sorghum bicolor (L.) Moench] landrace collection held at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), represents a challenge for the maintenance of both the accessions of and the information documented for the germplasm collection. The accessibility and knowledge of the landrace collection are the essential factors for an efficient utilization of the genetic resources by both breeders and farmers. Different sampling strategies, either random or non-random, were proposed to obtain subsets of reduced size (core collection). Three subsets were established; a random sampling within a stratified collection (logarithmic strategy: L); a sample based upon morpho-agronomic diversity (principal component score strategy: PCS); and a sample based upon an empirical knowledge of sorghum (taxonomic strategy: T). Comparisons of these three samples for morpho-agronomic characterization and passport information were assessed to determine their impact on phenotypic diversity. For their overall diversity, the three subsets did not differ, as shown with the two-dimensional representation of the morpho-agronomic diversity and the Shannon-Weaver diversity indices. When comparisons for morpho-agronomic and passport data were considered, the PCS subset looked similar to the entire landrace collection. The L subset showed differences for characters associated with the photoperiod reaction that was considered in the stratification of the collection. The T subset was the most distinct from the entire landrace collection as it over-represented the landraces selected by farmers for specific uses and covered the widest range of geographical adaptation and morpho-agronomic characteristics. Received: 5 October 1999 / Accepted: 3 November 1999     

利用分子标记和数量性状基因型值构建作物核心种质库的研究

提出了一种基于分子标记数据及数量性状基因型值构建作物种质资源核心种质库的方法.采用包括基因型与环境互作的遗传模型及相应的混合线性模型统计分析方法,无偏预测各材料的基因型值,分别用基因型值和分子标记数据计算个体间的相似系数,加权得到最终的相似距离.采用不加权类平均法（UPGMA）进行系统聚类,用多次聚类随机取样法构建核心种质库.以水稻DH群体111个基因型8个农艺性状、175个分子标记位点的数据为实例,按四种抽样比率（25%,20%,15%,10%）构建了四个核心种质库,比较了核心种质库与整个群体的分子标记多样性及数量性状的遗传变异,评价了所用方法的有效性。     

Assessment of genetic diversity within and between pearl millet landraces

A minimum core subset of pearl millet [Pennisetum glaucum (L.) R. Br.], which comprised 504 landrace accessions, was recently established from the global pearl millet germplasm collection of ICRISAT. The accessions for this core were selected by a random proportional sampling strategy following stratification of the entire landrace collection (about 16,000 accessions) according to their geographic origin and morpho-agronomic traits. In this study RFLP probes were used to quantify the genetic diversity within and between landrace accessions of this minimum core using a subset comprising ten accessions of Indian origin. Twenty five plants per accession were assayed with EcoRI, EcoRV, HindIII and DraI restriction enzymes, and 16 highly polymorphic RFLP probes, nine associated with a quantitative trait loci (QTLs) for downy mildew resistance, and five associated with a QTL for drought tolerance. A total of 51 alleles were detected using 16 different probe-enzyme combinations. The partitioning of variance components based on the analysis of molecular variance (AMOVA) for diversity analysis revealed high within-accession variability (30.9%), but the variability between accessions was significantly higher (69.1%) than that within the accessions. A dendrogram based on the dissimilarity matrix obtained using Ward's algorithm further delineated the 250 plants into ten major clusters, each comprised of plants from a single accession (with the exception of two single plants). A similar result was found in an earlier study using morpho-agronomic traits and geographic origin. This study demonstrated the utility of RFLP markers in detecting polymorphism and estimating genetic diversity in a highly cross-pollinated species such as pearl millet. When less-tedious marker systems are available, this method could be further extended to assess the genetic diversity between and within the remaining accessions in the pearl millet core subset.     

Morphological diversity of Ethiopian barley (Hordeum vulgare L.) in relation to geographic regions and altitudes

A total of 199 germplasm accessions collected from 10 administrative regions of Ethiopia and four released cultivars, which were used for estimating of error variance, of barley in Ethiopia were field evaluated for nine agronomic traits at Holetta and Bekoji Agricultural Research Centers of Ethiopia during the 2006 main cropping season using non-replicated augmented design plots consisting of four incomplete blocks. The objectives were to assess the extent and pattern of morphological variation in the barley accessions with respect to regions and altitude of collection, to classify the genotypes tested into relatively homogenous groups and to identify the major traits contributing to the overall observed diversity in the germplasm. Genotype variance estimate of regions and altitudes indicated wide variation among accessions depending on the traits involved. The presence of high morphological variation within regions and altitudes particularly above 2000 m a.s.l. indicated the potential of each region and high altitude zones for barley improvement and conservation in the country. The clustering of accessions did not show grouping on the basis of regions of origin. Traits like thousand kernel weight, plant height, days to head and days to maturity accounted for most of the gross variance among the barley accessions and played role in differentiating accessions collected from different regions and altitude classes into principal components. In general because of environmental factors on the observed morphological variation future germplasm collection should consider to explore wide geographical and climatic differences within the country.     

Genetic Diversity of Soybean and the Establishment of a Core Collection Focused on Resistance to Soybean Cyst Nematode

Soybean cyst nematode （SCN; Heterodera glycines） Is one of the most Important pests affecting soybean production. The best method of control of SCN is through the development of resistant cultlvars. However, limited progress has been made in soybean breeding In China because most modern cultlvars have no resistance to SCN. The distribution and phenotype of 432 immune or highly resistant Chinese accessions were surveyed and a primary core collection was selected as a representative sample for further analyses. Using evenly distributed simple sequence repeat markers, five selection methods were applied to the primary core collection and the optimal method was chosen to establish a core collection, which consisted of 28 accessions. These encompassed 70.8% of the ailelic variation present in the overall resistant collection. The 28 accessions differed from the reference resistant accessions at the genomlc level, Indicating that Chinese resistant accessions are distinct from known resistant accessions. This applied core collection provides a rational framework for undertaking diversity surveys, using genetic variation for the investigation of complex traits and for the discovery of novel traits.     

利用表型数据构建陆地棉核心种质

以5963份陆地棉种质资源为材料,根据品种主要突变性状和品种类型分组成11组群,在分组的基础上利用21个表型性状,用非加权类平均聚类分析法,构建了281份陆地棉核心种质,占全部种质资源总量的4.71%。利用不同性状的均值t测验、方差F测验、变异系数、多样性指数t检验、均值、极差、表型方差、变异系数、均值差异百分率、方差差异百分率、极差符合率、变异系数变化率、主成分分析等参数进行核心种质代表性检验和评价。结果表明,所构建的陆地棉核心种质可以代表全部种质的遗传多样性。     

A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement

A core collection is a chosen subset of large germplasm collection that generally contains about 10% of the total accessions and represents the genetic variability of entire germplasm collection. The purpose of a core collection is to improve the use of genetic resources in crop improvement programs. In many crops the number of accessions contained in the genebank are several thousands, and a core subset consisting of 10% of total accessions would be an unwieldy proposition. In this article we have suggested a two-stage strategy to select a chickpea mini core subset consisting of only about 1% of the entire collection held in trust at ICRISAT’s genebank (16,991 accessions). This mini core subset still represents the diversity of the entire core collection. The first stage involves developing a representative core subset (about 10%) from the entire collection using all the available information on origin, geographical distribution, and characterization and evaluation data of accessions. The second stage involves evaluation of the core subset for various morphological, agronomic, and quality traits, and selecting a further subset of about 10% accessions from the core subset. At both stages standard clustering procedure was used to separate groups of similar accessions. A mini core subset consisting 211 accessions from 1,956 core subset accessions, using data on 22 morphological and agronomic traits, was selected. Newman- Keuls’ test for means, Levene’s test for variances, the chi-square test and Wilcoxon’s rank-sum non-parametric test for frequency distribution analysis for different traits indicated that the variation available in the core collection has been preserved in the mini core subset. The most important phenotypic correlations which may be under the control of coadapted gene complexes, were also preserved in the mini core. This mini core subset, due to its drastically reduced size, will prove to be a point of entry to proper exploitation of chickpea genetic resources. Received: 20 August 2000 / Accepted: 25 September 2000     

核心种质数量性状代表性评价指标的研究

对植物核心种质数量性状遗传多样性代表性的评价指标进行了系统的研究．以夏播菜用大豆154个品种为材料,采用马氏距离计算品种间的距离,并用不加权类平均法(UPGMA)进行聚类,根据树型图,采用逐步聚类随机取样法,构建了37个品种组成的核心种质．以此为例,通过方差F测验、均值t测验、极差符合率、表型频率分布、遗传多样性指数、表型相关分析等多个指标分析,来评价核心种质数量性状遗传多样性的代表性,结果表明构建的核心种质具有代表性,表明核心种质评价需包含评价遗传变异和遗传结构的指标．     

Methods of developing a core collection of annual Medicago species

A core collection is a subset of a large germplasm collection that contains accessions chosen to represent the genetic variability of the germplasm collection. The purpose of the core collection is to improve management and use of a germplasm collection. Core collections are usually assembled by grouping accessions and selecting from within these groups. The objective of this study was to compare 11 methods of assembling a core collection of the U.S. National collection of annual Medicago species. These methods differed in their use of passport and evaluation data as well as their selection strategy. Another objective was to compare core collections with sample sizes of 5%, 10% and 17% of the germplasm collection. Core collections assembled with evaluation data and cluster analysis better represented the germplasm collection than core collections assembled based solely on passport data and random selection of accessions, The Relative Diversity and the logarithm methods generated better core collections than the proportional method. The 5% and 10% sample size core collection were judged insufficient to represent the germplasm collection.     

Genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Zambia as revealed by simple sequence repeats (SSR)

Twenty seven accessions of sorghum conserved in the national gene bank of Zambia, representing two of the three agroecological regions of the country, were investigated using simple sequence repeats (SSR) markers in order to determine the extent and distribution of its genetic diversity. We used 10 microsatellite primer-pairs, which generated 2-9 alleles per locus and a total of 44 alleles across the 27 accessions. The observed heterozygosity (Ho(P) ) among the accessions ranged from 0 to 0.19 with an average of 0.04 whereas the average expected heterozygosity (He(P) ) among accessions was 0.07 in line with the fact that sorghum is predominately inbreeder. The analysis of molecular variance (AMOVA) revealed that 82% of the total genetic variation was attributable to the genetic variation among accessions (F(ST) = 0.824; p < 0.001) whereas the genetic variation within accessions accounted for 18% of the total genetic variation. AMOVA on sorghum accessions grouped based on four ethnic groups (Soli, Chikunda, Lozi and Tonga) associated with collection sites revealed a highly significant variation among groups (23%; p < 0.001). Although cluster analysis grouped most accessions according to their sites of collection, some accessions that originated from the same site were placed under different clusters. In addition to the extent and pattern of genetic diversity, consideration should also be given to other factors such as ecogeographic and ethnic differences when sampling sorghum genetic resources for rational and efficient conservation and utilization in the breeding program.     

基于穗形特征与分子标记进行中国节节麦核心种质的创建

节节麦是普通小麦D基因组供体,遗传多样性丰富,而我国节节麦资源是有别于中东节节麦资源的重要基因源。为了合理高效地管理、评价、保护和利用我国节节麦资源,本研究将野生采集的762份中国节节麦资源作为试验材料,基于SSR标记分组状况,利用小穗长、护颖长、护颖宽、外稃长、外稃宽、内稃长、内稃宽、穗宽、粒长和粒宽等10个穗形性状指标,在欧氏距离、马氏距离和4种取样比例下构建节节麦核心种质候选集。进而采用均值差异百分率、极差符合率、方差差异百分率及变异系数变化率4个指标对不同方法构建的核心种质候选集的可行性和有效性进行评价,并利用原种质和核心种质的主成分分析法进行验证,最终确定基于欧氏距离、10%取样比例下、采用最小距离逐步取样法构建的包含76个样品的节节麦核心种质能够以最小的资源份数、最大限度地代表我国节节麦的遗传多样性。     

贵州核桃核心种质筛选与构建研究北大核心CSCD

为了更好地构建贵州核桃核心种质,该研究以245份贵州核桃种质资源为试材,利用数量性状的遗传变异数据,对其构建方法进行了探索;采用随机取样策略、偏离度取样策略和位点优先取样策略,结合8个取样比例(5%、10%、15%、20%、25%、30%、40%和50%),进行多次聚类构建核心种质;将核心种质与原种质和保留种质进行t检验比较来评价核心种质,并用主成分分析法和表型性状对核心种质进行确认。结果表明:(1)选取偏离度取样策略,总体取样比例为50%,构建出131份贵州核桃核心种质资源。(2)对种质资源核心库13个数量性状进行主成分分析,其累计贡献率达到76.48%,主成分图中核桃核心种质与原种质的分布较为相似,表明核心种质有效地保存了核桃原种质的遗传结构,并有效避免了种质的冗余。(3)在欧氏距离结合组间联接法的聚类条件下,偏离度取样策略是构建贵州核桃核心种质的最佳方法。     

Optimal sampling strategy and core collection size of Andean tetraploid potato based on isozyme data - a simulation study

Selection of an appropriate sampling strategy is an important prerequisite to establish core collections of appropriate size in order to adequately represent the genetic spectrum and maximally capture the genetic diversity in available crop collections. We developed a simulation approach to identify an optimal sampling strategy and core-collection size, using isozyme data from a CIP germplasm collection on an Andean tetraploid potato. Five sampling strategies, constant (C), proportional (P), logarithmic (L), square-root (S) and random (R), were tested on isozyme data from 9,396 Andean tetraploid potato accessions characterized for nine isozyme loci having a total of 38 alleles. The 9,396 accessions, though comprising 2,379 morphologically distinct accessions, were found to represent 1,910 genetically distinct groups of accessions for the nine isozyme loci using a sort-and-duplicate-search algorithm. From each group, one accession was randomly selected to form a genetically refined entire collection (GREC) of size 1,910. The GREC was used to test the five sampling strategies. To assess the behavior of the results in repeated sampling, k = 1,500 and 5,000 independent random samples (without replacement) of admissible sizes n = 50(50)1,000 for each strategy were drawn from GREC. Allele frequencies (AF) for the 38 alleles and locus heterozygosity (LH) for the nine loci were estimated for each sample. The goodness of fit of samples AF and LH with those from GREC was tested using the L² test. A core collection of size n = 600, selected using either the P or the R sampling strategy, was found adequately to represent the GREC for both AF and LH. As similar results were obtained at k = 1,500 and 5,000, it seems adequate to draw 1,500 independent random samples of different sizes to test the behavior of different sampling strategies in order to identify an appropriate sampling approach, as well as to determine an optimal core collection size.     

Suppression of Rotylenchulus reniformis 122-cm Deep Endorses Resistance Introgression in Gossypium

Nine sources of resistance to Rotylenchulus reniformis in Gossypium (cotton) were tested by measuring population density (Pf) and root-length density 0 to 122 cm deep. A Pf in the plow layer less than the autumn sample treatment threshold used by consultants was considered the minimum criterion for acceptable resistance, regardless of population density at planting (Pi). Other criteria were ample roots and a Pf lower than on the susceptible control, as in pot studies. In a Texas field in 2001 and 2002, no resistant accessions had Pf less than the control but all did in microplots into which nematodes from Louisiana were introduced. An environmental chamber experiment ruled out nematode genetic variance and implicated unknown soil factors. Pf in field experiments in Louisiana, Mississippi, and Alabama were below threshold for zero, six and four of the accessions and above threshold in the control. Gossypium arboreum A2–87 and G. barbadense GB-713 were the most resistant accessions. Results indicate that cultivars developed from these sources will suppress R. reniformis populations but less than in pots in a single season.