GENOMIC CHARACTERIZATION OF RICE GERMPLASM
Location: Dale Bumpers National Rice Research Center
Title: Molecular Characterization of the Recombinant Inbred Line Population of the Cross of Lemont with Jasmine 85
Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 15, 2008
Publication Date: March 1, 2008
Citation: Liu, G., Jia, Y., Jia, M.H., McClung, A.M., Correll, J.C. 2008. Molecular characterization of the recombinant inbred line population of the cross of Lemont with Jasmine 85. In: Proceedings of the 32nd Rice Technical Working Group Meetings, February 18-21, 2008, San Diego, CA. 2008. CDROM.
Recombinant inbred line (RIL) populations of rice are an essential genetic resource for the construction of molecular genetic linkage maps and map-based identification of quantitative trait loci (QTL). The RIL F5 population derived from a cross of the United Stated tropical japonica rice cultivar Lemont (LMNT) and Jasmine 85 (JSMN) was used to tag QTLs for rice sheath blight (RSB) resistance which is one of the most severe diseases of rice in the world. JSMN, an aromatic indica cultivar co-developed by scientists at the International Rice Research Institute and USDA, is known to possess significant resistance to RSB in greenhouse and field conditions.
The objective of this study, as part of USDA-NRI funded RiceCAP project, was to characterize the 256 F5 RILs population of LMNT/JSMN using 196 polymorphic simple sequence repeat (SSR) markers for QTL analysis. A genetic linkage map was constructed having markers every 10 cm across all rice chromosomes. One hundred ninety-three SSR markers were mapped on 12 rice chromosomes representing a total of 1634.8 cM of the genetic distance. Seven markers (3.6%) on chromosomes 3, 4 and 12 favored the LMNT allele; 19 markers (9.7%) on chromosomes 3, 7, 9 and 12 favored the JSMN allele. Twelve (4.7%) and 24 (9.2%) RILs were skewed towards LMNT and JSMN, respectively. As expected from F5 progeny, the average frequencies of overall genome heterozygous and non-parental alleles per RIL were 9.7% (0.0%-45.4%) and 0.4‰ (0.0%-2.6%), respectively. These results demonstrate that the LMNT/JSMN F5 RIL population is an excellent mapping population with the low percentages of skewed markers and RILs, low frequencies of non-parental alleles, and the expected frequencies of heterozygosity. This will be useful for identifying QTL for a wide diversity of traits in addition to RSB that are segregating in this population.