Development and Evaluation of a Core Subset of the USDA Rice Germplasm Collection

Abstract

A valuable core collection that is a subset of a whole germplasm collection should capture most of the variation present in the whole collection, while allowing for more efficient evaluation and management due to smaller size. The United States Department of Agriculture (USDA) rice (Oryza sativa L.) core subset (RCS), assembled by stratified random sampling, consists of 1790 entries from 114 countries and represents approximately 10% of the 18412 accessions in the rice whole collection (RWC). Data for this study were obtained from the USDA germplasm system at http://www.ars-grin.gov for the RWC and from an evaluation conducted in 2002 for the RCS. Comparative analysis for frequency distributions of 14 descriptors demonstrated that the RCS was highly correlated with the RWC (r = 0.94, P < 0.0001). Thus, information drawn from the RCS could be effectively used to assess the RWC with 88% certainty. Correlation coefficients between the RCS and the RWC for eight descriptors were ≥ 0.9, indicating that the RCS was highly representative of the RWC. Correlation coefficients for the other six descriptors were lower (0.65–0.88), but still significant.

Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.)

“…Analyses of molecular markers have also detected a considerable number of sequence variations in diverse cultivars (Sun et al 2002, Wang et al 1992, Yan et al 2007, Zeng et al 2007. Recent progress in rice genomics has enhanced our understanding of these natural variations, which are potential sources of useful genes for improving rice cultivars (Yamamoto et al 2009).…”

“…To assess and explore such variations effectively using genetic analyses, a collection of diverse germplasms consisting of a relatively small number of accessions representative of the variation in the natural rice population should be assembled. For this purpose, the United States Department of Agriculture has developed a core rice germplasm collection (Yan et al 2007). Moreover, the National Institute of Agrobiological Sciences (NIAS) have established two mini-core collections, each consisting of a small number of accessions that together cover more than 90% of the phenotypic and genotypic variation in rice accessions , Kojima et al 2005.…”

Identification of Blast Resistance in a Core Collection of Foxtail Millet Germplasm

“…To overcome these problems, Frankel and Brown (8) proposed the establishment of a core collection (10% of the total) that could be selected from the existing collection of crop species resources in a gene bank. Core collections based on phenotypic data have been reported in several crops (3,27,28,32). Using passport information and data on 23 morphological descriptors, Upadhyaya et al (29) developed a core collection consisting of 155 foxtail millet accessions.…”

Development of Core Set of Wheat (Triticum spp.) Germplasm Conserved in the National Genebank in India

“…M-Strat (Gouesnard et al 2001), Genetic distance sampling (Jansen and Van Hintum 2007), Power Core (Kim et al 2007) and Core Hunter (Thachuk et al 2009). Similarly core has been developed using several kinds of data ranging from genealogical data in the Czech spring wheat (Stehno et al 2006), agronomic data in groundnut (Upadhyaya 2003;Upadhyaya et al 2003) and molecular data or integration of data in bread wheat (Balfourier et al 2007) and in rice (Borba et al 2009;Yan et al 2007). PowerCore is a new and a faster approach for developing core collection, which effectively simplifies the generation process of a core set with reduced number of core entries but maintaining high percent of diversity compared to other methods used.…”