ARS | Publication request: A population of ‘TeQing’-into-‘Lemont’ chromosome segment substitution lines supports QTL discovery, fine-mapping, and determination of breeding values

Submitted to: International Rice Genetics Symposium
Publication Type: Proceedings
Publication Acceptance Date: October 16, 2009
Publication Date: November 16, 2009
Citation: Pinson, S.R., Liu, G., Jia, M.H., Jia, Y., Fjellstrom, R.G., Sharma, A., Yang, Y., Tabien, R.E., Li, Z. 2009. A population of ‘TeQing’-into-‘Lemont’ chromosome segment substitution lines supports QTL discovery, fine-mapping, and determination of breeding values. 6th International Rice Genetics Symposium on Nov. 16-18, 2009, Manilla, Philippines. P9-1 Page 215.

Technical Abstract: Genetic maps and populations are important tools for gene/QTL mapping, and for functional genomics research. One of the most phenotypically characterized rice mapping populations is a set of 280 ‘Lemont’/‘TeQing’ recombinant inbred lines (LT-RILs) in which more than 250 agronomically important loci have been identified. While randomly segregating populations (i.e. F2s and RILs) allow QTL identification using small populations, such mapping is often imprecise, locating loci to chromosomal regions 5 to 20 cM in length. To provide an efficient avenue for verifying, fine-mapping, and incorporating desired TeQing QTL into improved tropical japonica rice varieties, a subsequent population of TeQing-into-Lemont backcross introgression lines (TILs) was developed. Backcrossing was accomplished at IRRI; final selfing and selection for homozygosity based on data from 166 SSRs was accomplished in Beaumont, TX, where tropical japonicas are better adapted. The resulting set of 123 TILs contains every molecularly tagged segment of the indica TeQing genome now introgressed into Lemont’s genetic background within two or more TILs. As a set of molecularly characterized chromosome segment substitution lines (CSSLs), the population of 123 TILs can support de novo mapping of genes, and fine-mapping of targeted genomic regions can be accomplished with molecularly-selected subsets of TILs. The TILs contain foreign QTL regions now introgressed into a tropical japonica genetic background, and as such, can serve as improved gene donors. They also allow researchers to directly measure the agronomic utility, or breeding value, of the various indica QTLs after actual introgression into a sub-tropical semi-dwarf japonica rice genetic background.