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     

Genetic Characterization of a Core Set of a Tropical Maize Race Tuxpe?o for Further Use in Maize Improvement

The tropical maize race Tuxpeño is a well-known race of Mexican dent germplasm which has greatly contributed to the development of tropical and subtropical maize gene pools. In order to investigate how it could be exploited in future maize improvement, a panel of maize germplasm accessions was assembled and characterized using genome-wide Single Nucleotide Polymorphism (SNP) markers. This panel included 321 core accessions of Tuxpeño race from the International Maize and Wheat Improvement Center (CIMMYT) germplasm bank collection, 94 CIMMYT maize lines (CMLs) and 54 U.S. Germplasm Enhancement of Maize (GEM) lines. The panel also included other diverse sources of reference germplasm: 14 U.S. maize landrace accessions, 4 temperate inbred lines from the U.S. and China, and 11 CIMMYT populations (a total of 498 entries with 795 plants). Clustering analyses (CA) based on Modified Rogers Distance (MRD) clearly partitioned all 498 entries into their corresponding groups. No sub clusters were observed within the Tuxpeño core set. Various breeding strategies for using the Tuxpeño core set, based on grouping of the studied germplasm and genetic distance among them, were discussed. In order to facilitate sampling diversity within the Tuxpeño core, a minicore subset of 64 Tuxpeño accessions (20% of its usual size) representing the diversity of the core set was developed, using an approach combining phenotypic and molecular data. Untapped diversity represents further use of the Tuxpeño landrace for maize improvement through the core and/or minicore subset available to the maize community.     

Genetic characterization of a core set of a tropical maize race Tuxpeño for further use in maize improvement

The tropical maize race Tuxpe?o is a well-known race of Mexican dent germplasm which has greatly contributed to the development of tropical and subtropical maize gene pools. In order to investigate how it could be exploited in future maize improvement, a panel of maize germplasm accessions was assembled and characterized using genome-wide Single Nucleotide Polymorphism (SNP) markers. This panel included 321 core accessions of Tuxpe?o race from the International Maize and Wheat Improvement Center (CIMMYT) germplasm bank collection, 94 CIMMYT maize lines (CMLs) and 54 U.S. Germplasm Enhancement of Maize (GEM) lines. The panel also included other diverse sources of reference germplasm: 14 U.S. maize landrace accessions, 4 temperate inbred lines from the U.S. and China, and 11 CIMMYT populations (a total of 498 entries with 795 plants). Clustering analyses (CA) based on Modified Rogers Distance (MRD) clearly partitioned all 498 entries into their corresponding groups. No sub clusters were observed within the Tuxpe?o core set. Various breeding strategies for using the Tuxpe?o core set, based on grouping of the studied germplasm and genetic distance among them, were discussed. In order to facilitate sampling diversity within the Tuxpe?o core, a minicore subset of 64 Tuxpe?o accessions (20% of its usual size) representing the diversity of the core set was developed, using an approach combining phenotypic and molecular data. Untapped diversity represents further use of the Tuxpe?o landrace for maize improvement through the core and/or minicore subset available to the maize community.     

A core collection and mini core collection of Oryza sativa L. in China

The extent of and accessibility to genetic variation in a large germplasm collection are of interest to biologists and breeders. Construction of core collections (CC) is a favored approach to efficient exploration and conservation of novel variation in genetic resources. Using 4,310 Chinese accessions of Oryza sativa L. and 36 SSR markers, we investigated the genetic variation in different sized sub-populations, the factors that affect CC size and different sampling strategies in establishing CC. Our results indicated that a mathematical model could reliably simulate the relationship between genetic variation and population size and thus predict the variation in large germplasm collections using randomly sampled populations of 700?C1,500 accessions. We recommend two principles in determining the CC size: (1) compromising between genetic variation and genetic redundancy and (2) retaining the main types of alleles. Based on the most effective scheme selected from 229 sampling schemes, we finally developed a hierarchical CC system, in which different population scales and genetic diversities allow a flexible use of genetic resources. The CC, comprising 1.7% (932) of the accessions in the basic collection, retained more than 85% of both the SSR and phenotypic variations. A mini core collection, comprising 0.3% (189) of the accessions in the basic collection, retained 70.65% of the SSR variation and 76.97% of the phenotypic variation, thus providing a rational framework for intensive surveys of natural variation in complex traits in rice genetic resources and hence utilization of variation in rice breeding.     

中国花生核心种质的建立

以中国花生种质资源数据库中记录的6390份花生资源为材料,以其基本数据、特征数据和评价数据为信息,采用分层、层内分组聚类以及随机取样与必选资源相结合的方法,构建了由576份资源组成的花生核心种质,占基础收集品的9.01%。对核心种质的植物学类型组成和遗传多样性指数的分析,以及对各性状特征值、符合率和包含的主要抗病资源抗性等级及重要农艺性状资源的检测结果表明,本研究建立的核心种质是有效的。基础收集品中各种性状的遗传变异在核心种质中均存在,所用15个性状的各种特征值符合率均在90%以上,其中绝大部分性状的符合率达96%以上。     

中国花生核心种质的建立

以中国花生种质资源数据库中记录的6390份花生资源为材料,以其基本数据、特征数据和评价数据为信息,采用分层、层内分组聚类以及随机取样与必选资源相结合的方法,构建了由576份资源组成的花生核心种质,占基础收集品的9.01%。对核心种质的植物学类型组成和遗传多样性指数的分析,以及对各性状特征值、符合率和包含的主要抗病资源抗性等级及重要农艺性状资源的检测结果表明,本研究建立的核心种质是有效的。基础收集品中各种性状的遗传变异在核心种质中均存在,所用15个性状的各种特征值符合率均在90%以上,其中绝大部分性状的符合率达96%以上。     

Molecular markers in management of ex situ PGR – A case study

Worldwide germplasm collections contain about 7.4 million accessions of plant genetic resources for food and agriculture. One of the 10 largest ex situ genebanks of our globe is located at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. Molecular tools have been used for various gene bank management practices including characterization and utilization of the germplasm. The results on genetic integrity of long-term-stored gene bank accessions of wheat (self-pollinating) and rye (open-pollinating) cereal crops revealed a high degree of identity for wheat. In contrast, the out-pollinating accessions of rye exhibited shifts in allele frequencies. The genetic diversity of wheat and barley germplasm collected at intervals of 40 to 50?years in comparable geographical regions showed qualitative rather than a quantitative change in diversity. The inter- and intraspecific variation of seed longevity was analysed and differences were detected. Genetic studies in barley, wheat and oilseed rape revealed numerous QTL, indicating the complex and quantitative nature of seed longevity. Some of the loci identified were in genomic regions that co-localize with genes determining agronomic traits such as spike architecture or biotic and abiotic stress response. Finally, a genome-wide association mapping analysis of a core collection of wheat for flowering time was performed using diversity array technology (DArT) markers. Maker trait associations were detected in genomic regions where major genes or QTL have been described earlier. In addition, new loci were also detected, providing opportunities to monitor genetic variation for crop improvement.     

Genomics of gene banks: A case study in rice

Only a small fraction of the naturally occurring genetic diversity available in the world's germplasm repositories has been explored to date, but this is expected to change with the advent of affordable, high-throughput genotyping and sequencing technology. It is now possible to examine genome-wide patterns of natural variation and link sequence polymorphisms with downstream phenotypic consequences. In this paper, we discuss how dramatic changes in the cost and efficiency of sequencing and genotyping are revolutionizing the way gene bank scientists approach the responsibilities of their job. Sequencing technology provides a set of tools that can be used to enhance the quality, efficiency, and cost-effectiveness of gene bank operations, the depth of scientific knowledge of gene bank holdings, and the level of public interest in natural variation. As a result, gene banks have the chance to take on new life. Previously seen as "warehouses" where seeds were diligently maintained, but evolutionarily frozen in time, gene banks could transform into vibrant research centers that actively investigate the genetic potential of their holdings. In this paper, we will discuss how genotyping and sequencing can be integrated into the activities of a modern gene bank to revolutionize the way scientists document the genetic identity of their accessions; track seed lots, varieties, and alleles; identify duplicates; and rationalize active collections, and how the availability of genomics data are likely to motivate innovative collaborations with the larger research and breeding communities to engage in systematic and rigorous phenotyping and multilocation evaluation of the genetic resources in gene banks around the world. The objective is to understand and eventually predict how variation at the DNA level helps determine the phenotypic potential of an individual or population. Leadership and vision are needed to coordinate the characterization of collections and to integrate genotypic and phenotypic information in ways that will illuminate the value of these resources. Genotyping of collections represents a powerful starting point that will enable gene banks to become more effective as stewards of crop biodiversity.     

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     

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%。     

Is It Still Necessary to Continue to Collect Crop Genetic Resources in the Mediterranean Area? A Case Study in Catalonia

Crop genetic resources have been extensively collected in Europe in the last century, creating large, publicly available ex situ collections. While this huge genetic diversity is often underutilized, in recent decades, several initiatives have emerged at the local level to collect germplasm cultivated on farm. Uncoordinated actors often carry out these collecting missions without considering previously collected data. To explore whether new collecting missions are likely to be worthwhile, we studied the crop genetic resources conservation network in Catalonia by analyzing the passport data and geographical distribution of germplasm stored in seed banks. Moreover, to determine whether this germplasm was representative of the diversity cultivated on farm, we performed new collecting missions in four randomly selected areas in the European Union’s Natura 2000 network and compared the results with the ex situ databases. Seed banks currently hold a large germplasm collection (2931 accessions), although most materials are conserved in private collections without regulated systems for seed regeneration and are not present as duplicates in the National Inventory. One important shortcoming of the ex situ network is that the germplasm conserved ex situ shows a low geographical coverage, representing only 35.3% of the municipalities in Catalonia. Our new missions allowed us to collect 234 accessions, mostly tomatoes (17.5%) and beans (16.2%). The ecological indicators’ richness (both at species (S) and variety (V) levels), total abundance (A), and the Shannon-Weaver diversity index calculated at species (H2, considering the different accessions of each variety as a single population) and variety levels (H3, considering the intra-varietal genetic diversity) were higher in the newly collected germplasm than in the ex situ collections, suggesting that seed banks do not accurately represent the genetic diversity still cultivated on farm. Moreover, some important landraces from each area were absent or underrepresented in the ex situ collections. Thus, it is necessary to continue to devote efforts to collecting germplasm; better organization between actors and targeting specific species/varieties can increase the efficiency of new collecting missions. As a conclusion, we propose different criteria to guide new missions and to improve the network’s conservation activities.     

Assessment of Genetic Diversity in <Emphasis Type="Italic">Secale cereale</Emphasis> Based on SSR Markers

The primary aim of this study was to estimate genetic diversity among Secale cereale L. accessions using 22 previously published simple sequence repeat (SSR) markers. The plant material included 367 rye accessions comprising historical and contemporary cultivars, cultivated materials, landraces, and breeding strains from the Polish breeding company Danko. The studied accessions represented a wide geographical diversity. Several methods were employed to analyze genetic diversity among the Secale cereale L. accessions and to determine population structure: principal coordinate analysis (PCoA), neighbor-joining (NJ), and Bayesian clustering. We also defined a core collection of 25 rye accessions representing over 93 % of SSR alleles. The results of these analyses showed that accessions from the rye gene bank are clearly divergent in comparison with materials received directly from European breeding companies. Our findings suggest also that the genetic pool of current rye cultivars is becoming narrower during breeding processes. The selected panel of SSR markers performed well in detection of genetic diversity patterns and can be recommended for future germplasm characterization studies in rye.     

A platform for soybean molecular breeding: the utilization of core collections for food security

Soybean is an important crop not only for human consumption but also for its addition of nitrogen to the soil during crop rotation. China has the largest collection of cultivated soybeans (Glycine max) and wild soybeans (Glycine soja) all over the world. The platform of soybean core, mini core and integrated applied core collections has been developed in the past decade based on systematic researches which included the sampling strategies, statistical methods, phenotypic data and SSR markers. Meanwhile, intergrated applied core collections including accessions with single or integrated favorite traits are being developed in order to meet the demand of soybean breeding. These kinds of core collections provide powerful materials for evaluation of germplasm, identification of trait-specific accessions, gene discovery, allele mining, genomic study, maker development, and molecular breeding. Some successful cases have proved the usefulness and efficiency of this platform. The platform is helpful for enhancing utilization of soybean genetic resources in sustainable crop improvement for food security. The efficient utilization of this platform in the future is relying on accurate phenotyping methods, abundant functional markers, high-throughput genotyping platforms, and effective breeding programs.     

Ex situ conservation of underutilised fruit tree species: establishment of a core collection for Ficus carica L. using microsatellite markers (SSRs)

Ex situ germ plasm collections of woody crops are necessary to ensure the optimal use of plant genetic resources. The fig tree (Ficus carica L.) germ plasm bank, consisting of 229 accessions, is located in Centro de Investigación ‘La Orden’. Despite great progress in conservation, ex situ collections face size and organization problems. Core collections obtained from structured samples of bigger collections are a useful tool to improve germ plasm management. In this work, we used simple sequence repeat (SSR) markers to establish a core collection in this underutilised Mediterranean fruit tree species. Four approaches have been carried out (random sampling, maximization, simulated annealing and stepwise clustering) to determine the best method to develop a core collection in this woody plant. The genetic diversity obtained with each subset was compared with that of the complete collection. It was found that the most efficient way to achieve the maximum diversity was the maximization strategy, which, with 30 accessions, recovers all the SSR alleles and does not show significant differences in allele frequency distribution in any of the loci or in the variability parameters (H _O, H _E) between the whole and core collections. Thus, this core collection, a representative of most fig diversity conserved in the germ plasm bank, could be used as a basis for plant material exchange among researchers and breeders.     

Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora

The management of diversity for conservation and breeding is of great importance for all plant species and is particularly true in perennial species, such as the coffee Coffea canephora. This species exhibits a large genetic and phenotypic diversity with six different diversity groups. Large field collections are available in the Ivory Coast, Uganda and other Asian, American and African countries but are very expensive and time consuming to establish and maintain in large areas. We propose to improve coffee germplasm management through the construction of genetic core collections derived from a set of 565 accessions that are characterized with 13 microsatellite markers. Core collections of 12, 24 and 48 accessions were defined using two methods aimed to maximize the allelic diversity (Maximization strategy) or genetic distance (Maximum-Length Sub-Tree method). A composite core collection of 77 accessions is proposed for both objectives of an optimal management of diversity and breeding. This core collection presents a gene diversity value of 0.8 and exhibits the totality of the major alleles (i.e., 184) that are present in the initial set. The seven proposed core collections constitute a valuable tool for diversity management and a foundation for breeding programs. The use of these collections for collection management in research centers and breeding perspectives for coffee improvement are discussed.     

中国绿豆应用型核心样本农艺性状的分析

为提高种质资源在育种中的利用效率,建立了我国绿豆（Vigna radiata）应用型核心样本。该样本既包括了资源库中具有特异性状的种质和曾经在生产上大面积种植的品种,也包括了在育种中使用频繁的亲本及苗头品系等。农艺性状变异分析表明,该核心样本具有丰富的表型变异,是绿豆种质资源的代表性样本。聚类分析可将核心样本分为4大类,但类别内种质与其地理来源相关性不明显。不同来源表型数据的分析发现,不同性状间的一致性存在差异。但产量相关性状的表现均与当前育种目标相接近,说明该核心样本具有较高的实用性。     

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。     

Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, <Emphasis Type="Italic">Helianthus annuus</Emphasis> L

Crop germplasm collections are valuable resources for ongoing plant breeding efforts. To fully utilize such collections, however, researchers need detailed information about the amount and distribution of genetic diversity present within collections. Here, we report the results of a population genetic analysis of the primary gene pool of sunflower (Helianthus annuus L.) based on a broad sampling of 433 cultivated accessions from North America and Europe, as well as a range-wide collection of 24 wild sunflower populations. Gene diversity across the cultivars was 0.47, as compared with 0.70 in the wilds, indicating that cultivated sunflower harbors roughly two-thirds of the total genetic diversity present in wild sunflower. Population structure analyses revealed that wild sunflower can be subdivided into four genetically distinct population clusters throughout its North American range, whereas the cultivated sunflower gene pool could be split into two main clusters separating restorer lines from the balance of the gene pool. Use of a maximum likelihood method to estimate the contribution of the wild gene pool to the cultivated sunflower germplasm revealed that the bulk of the cultivar diversity is derived from two wild sunflower population genetic clusters that are primarily composed of individuals from the east-central United States, the same general region in which sunflower domestication is believed to have occurred. We also identified a nested subset of accessions that capture as much of the allelic diversity present within the sampled cultivated sunflower germplasm collection as possible. At the high end, a core set of 288 captured nearly 90% of the alleles present in the full set of 433, whereas a core set of just 12 accessions was sufficient to capture nearly 50% of the total allelic diversity present within this sample of cultivated sunflower.