Development of an RFLP-based Rice Diversity Research Set of Germplasm

Abstract

A rice diversity research set of germplasm (RDRS) was developed based on a genome-wide RFLP polymorphism survey of 332 accessions of cultivated rice (Oryza sativa L.). The accessions used in the initial survey were selected based on the passport data from the whole collection maintained at the Genebank of the National Institute of Agrobiological Sciences (NIAS). These accessions were analyzed using 179 nuclear RFLP markers. A total of 554 alleles were detected, and the number of alleles per locus ranged from 2 to 8 (mean 3.1). Principal coordinate analysis using RFLP data enabled to classify the accessions into three major groups, one Japonica and other two Indica. To develop a rice diversity research set of germplasm, the RFLP data on the 332 accessions were subjected to cluster analysis and 67 groups were recognized at a similarity index of 0.915. A single accession from each of the 67 groups was selected. These 67 accessions retained 91% of the alleles detected in the original 332 accessions, and covered the variation of the initial set of accessions in terms of several agro-morphological traits. The 69 accessions including varieties from 19 countries and the reference varieties, Nipponbare and Kasalath, were selected for the development of a rice diversity research set of germplasm. This collection which is presently well characterized at the molecular level will be used for the detailed genetic studies and rice improvement.

Bayesian QTL mapping for multiple families derived from crossing a set of inbred lines to a reference line

“…In some crop species such as maize, rice and wheat, germplasm collections that include accessions consisting of traditional landraces, modern cultivars and wild species have recently been established (Flint-Garcia et al, 2005;Kojima et al, 2005;Crossa et al, 2007), and used for evaluation of the genetic diversity present in a species. Such collections are also useful as stocks of genes for breeding programs.…”

Comparative Analysis of Rice Genome Sequence to Understand the Molecular Basis of Genome Evolution

“…There are geographic, physiological, and genetic diversities among Oryza species, including among rice varieties, landraces, and wild accessions. In recognition of the fact that this variation is indispensable for maintaining the vast genetic resources that should help in developing a sustainable future for the human race, rice is collected, evaluated, and stored in either national or international gene banks (e.g., NIAS Genebank, http://www.gene.affrc.go.jp/ about_en.php; [18]; Japanese National Bioresource Project, http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp; International Rice Research Institute; Genetic Resource Center, http://www.irri.org/GRC/GRChome/Home.htm). Global genome and information resources for the investigation of genome evolution among Oryza species have been facilitated by The Oryza Map Alignment Project (OMAP, http://www.omap.org/; [17]).…”

The copy number of rice CACTA DNA transposons carryingMIR820does not correlate withMIR820expression

“…We used 45 cultivars from the Japanese Rice Core Collection (JRC) and 56 cultivars from the World Rice Core Collection (WRC) ( Tables 1 and 2). 8,9 Among the JRC cultivars, the average copy number of MIR820 was 4.5 (minimum: 2; maximum: 6). Among the WRC cultivars, the average copy number was 6.3 (minimum: 3; maximum: 11) ( Fig.…”