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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #313102

Title: Construction of six Oryza sativa x O. rufipogon Chromosome Segment Substitution Line (CSSL) Libraries

item SHAKIBA, EHSAN - University Of Arkansas
item Eizenga, Georgia
item SINGH, NAMRATA - Cornell University
item ALI, MD LIAKAT - University Of Nebraska
item KIM, HYUNJUNG - Cornell University
item DECLERCK, GENEVIEVE - Cornell University
item WRIGHT, MARK - Cornell University
item AHN, SANG-NAG - Chungnam National University
item MCCOUCH, SUSAN R - Cornell University

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 11/14/2014
Publication Date: 1/5/2015
Citation: Shakiba E., Eizenga G.C., Singh N., Ali M.L., Kim H.J., Wright M., Ahn S.N., McCouch S. 2014. Construction of six Oryza sativa x O. rufipogon chromosome segment substitution line (CSSL) libraries. International Plant & Animal Genome XXIII. San Diego, CA. 10-14 Jan. 2015. Available at:

Interpretive Summary:

Technical Abstract: Transgressive variation has been observed in rice (Oryza sativa) as an increase in grain yield and attributed to the ancestral parent, O. rufipogon, in mapping populations developed from several adapted rice varieties crossed with a single O. rufipogon accession. To explore this phenomenon of transgressive variation, six chromosome segment substitution line (CSSL) libraries were developed. Two adapted rice varieties, IR64 (indica subpopulation) and Cybonnet (tropical japonica subpopulation), were selected as recurrent parents to represent the rice subspecies Indica and Japonica, respectively. Based on previous phylogenetic analyses, the two O. rufipogon donor parent accessions clustered with the Indica (IRGC106148) and Japonica (W1944) O. sativa subspecies, and one (IRGC105567) was independent of these. Marker assisted backcrossing was used to select the individual CSSLs to advance each generation. Most recently, an Infinium 6,000 SNP array was used for high-resolution genotyping and provided between 1,069 to 1,916 (˜1 SNP/cM) polymorphic genome-wide SNPs per library. Currently, the CSSL libraries with IRGC106148 and IRGC105567 as donors, are being advanced to the BC4F3 or BC5F3 generation and the two with the W1944 donor, are being backcrossed to the BC4. Once complete, each CSSL library will consist of 60-90 lines, with each line having a target a single wild donor segment. The six CSSL libraries will provide complete coverage of the three divergent O. rufipogon genomes in the recurrent parent background, and will be among the most densely genotyped CSSL libraries. These libraries will be used to understand the genetic basis of transgressive variation, identify novel genes/alleles from wild donors, and characterize genetic interactions between donors and recurrent parents.