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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #260290

Title: Development Of Interspecific Cssls In Rice Using SNP-Based Selection

item KIM, HYUNJUNG - Cornell University
item Eizenga, Georgia
item AHN, SANG-NAG - Chungnam National University
item ZHAO, KEYAN - Cornell University
item WRIGHT, MARK - Cornell University
item REYNOLDS, ANDY - Cornell University
item MCCOUCH, SUSAN - Cornell University

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/30/2009
Publication Date: 12/11/2009
Citation: Kim HJ, Eizenga G, Ahn SN, Zhao K, Wright M, Reynolds A, McCouch SR. Development of interspecific CSSLs in rice using SNP-based selection. 2010. In: Proc. of the Plant & Animal Genomes XVIII Conf. 9-13 Jan. 2010. San Diego, California. Available at:

Interpretive Summary:

Technical Abstract: Six libraries of chromosome segment substitution lines (CSSLs) are being developed based on crosses between three diverse accessions of O. rufipogon (from China, Laos and Indonesia) and two O. sativa recurrent parents, IR64, an indica variety (from the Philippines), and Cybonnet, a tropical japonica variety (from the US). To select the three wild donors, a collection of 285 O. rufipogon and O. nivara accessions were evaluated for genetic diversity using both nuclear and cytoplasmic SSR, indel and SNP markers. The three wild donors were selected based on genetic divergence, phenotypic variation, fertility of crosses with both the indica and japonica recurrent parents and geographical origin. To facilitate marker-based selection of CSSLs, we developed two 384-SNP chips (to be run on Illumina’s BeadXpress station); one was optimized for the crosses with IR64 and the other for crosses with Cybonnet. The software package, CSSL Finder, was used to select lines in each backcross generation carrying introgressions of interest. Our goal is to develop six BC3 libraries consisting of 94 CSSLs per library, with each line carrying a single 4-5 Mb introgression from O. rufipogon. These CSSL libraries will be used to investigate the genetic basis of transgressive variation, to identify novel phenotypes of importance to breeding, to explore the potential for introducing allelic series from the wild ancestor, to characterize GxG interaction in the indica and japonica backgrounds and to broaden the gene pool of cultivated rice. Online reference for abstract: