ARS | Publication request: SNP-assisted development of interspecific CSSLs in rice

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 8, 2010
Publication Date: December 13, 2010
Citation: Kim, H., Eizenga, G.C., Ahn, S., Zhao, K., Ali, M., Akthur, K., Wright, M.H., Reynolds, A., Mccouch, S.R. 2010. SNP-assisted development of interspecific CSSLs in rice. Plant and Animal Genome Conference. http://www.intl-pag.org/19/abstracts/P05b_PAGXIX_266.html.

Technical Abstract: The objective of this study is to generate six libraries of chromosome segment substitution lines (CSSLs) using three diverse accessions of the wild Oryza sativa progenitor species, O. rufipogon/O. nivara as donors, and two elite O. sativa cultivars, Cybonnet (tropical japonica) and IR64 (indica) as recurrent parents. To facilitate the selection of lines carrying the desired introgressions in each backcross generation, two 384-plex SNP assays (visualized on an Illumina BeadXpress) were designed based on the individual recurrent parent and wild donors to detect polymorphisms between the three wild donors and the specific recurrent parent. Additional SNP markers providing denser coverage of specific regions were designed for the KASP system (KBioSciences). SNPs were selected from a larger dataset consisting of 44,000 SNPs (Affymetrix custom-array) × 400 O. sativa and 100 O. rufipogon/O. nivara accessions (rice diversity panel). The conversion rate across the three SNP detection platforms was 82%. We generated and genotyped 225-900 BC2F1 individuals per cross from ~25-50 BC1 founder lines carrying the full complement of wild introgressions. Further SNP-based selection is currently underway for the BC3 generation. Seeds from each generation, including BC2F1s and BC3F1s, are being conserved for further study. Our goal is to develop six BC3F2 libraries consisting of 96 homozygous CSSLs, with each line carrying a single, unique 4-5 Mb chromosomal segment from O. rufipogon/O. nivara. These CSSLs will be used to understand the genetic basis of transgressive variation, investigate allelic series coming from the wild donors, characterize G×G interaction between wild donors and divergent elite cultivated backgrounds, and broaden the gene pool of cultivated rice.