ARS | Publication request: Molecular characterization of a population of backcross introgression lines derived from crossing the US japonia rice cultivar Lemont as the recurrent parent withthe Chinese indica cultivar TeQing

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: November 1, 2006
Publication Date: January 13, 2007
Citation: Liu, G., Jia, Y., Jia, M.H., Fjellstrom, R.G., Sharma, A., Li, Z., Pinson, S.R. 2007. Molecular characterization of a population of backcross introgression lines derived from crossing the US japonia rice cultivar Lemont as the recurrent parent withthe Chinese indica cultivar TeQing. Plant and Animal Genome Conference Proceedings.

Technical Abstract: The complete genome sequences of both indica and japonica rice present a unique opportunity for assessing rice genes in different genomic content. A set of 269 backcross introgression lines were developed at IRRI, being derived from a cross of ‘Lemont’ by ‘TeQing’ followed by two to four backcross cycles using Lemont as the recurrent parent, and finished with three to five generations of selfing. This set of TeQing-into-Lemont introgression lines (TILs) was created to determine the biological functions of rice genes of indica origin in the japonica background. The 269 TILs were analyzed using 104 polymorphic simple sequence repeat (SSR) markers. The rates of successful amplification per locus/TIL were 62.7%-100.0%. As expected for backcross lines having Lemont as the recurrent parent, the majority of the lines (85%, or 231 TILs) contained a preponderance of Lemont SSR alleles (Lemont at ÿ 66% SSR loci). Among the 269 TILs evaluated, 6% (17) lines were found to contain a preponderance ( 66%) of TeQing alleles, and 8% (21) contained 37%-65% TeQing alleles. Nineteen (7%) of the TILs remained heterozygous at 5 SSR loci and 30 (11%) were found to contain non-parental alleles at 5 loci, presumably from outcrossing during the developmental process. Molecular characterization of the introgressed regions in the 269 TILs allows us to carry on detailed comparative genomic analysis of rice genes.