ARS | Publication request: MOLECULAR CHARACTERIZATION OF RICE RECOMBINANT INBRED LINE POPULATION DERIVED FROM A JAPONICA-INDICA CROSS

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 11, 2006
Publication Date: May 27, 2007
Citation: Liu, G., Bernhardt, J., Jia, M.H., Wamishe, Y., Jia, Y. 2007. Molecular characterization of rice recombinant inbred line population derived from a japonica-indica cross. Euphytica. 159:73-82.

Interpretive Summary: Recombinant inbred line (RIL) populations of rice can be used to facilitate the mapping of genes that may segregate in a population. A population of 269 F10-11 RIL lines from a cross between Kaybonnet lpal-1 (KBNT1pa) and Zhe733 was characterized using 109 polymorphic simple sequence repeat (SSR) markers. These SSR markers were distributed on 12 rice chromosomes representing a total of 1016.3 cM of genetic distance. The markers were used to determine that the chromosomes showed a good mixture of alleles from both parents. However, about 10% of the RIL population was genetically skewed toward the Zhe733 parent. On average, only 1.3% of alleles per RIL were still heterozygous indicating continued segregation and less than 1% of the alleles per RIL were non-paentals, indicating outcrossing. Thus compared to other mapping populations, the KBNTlpa X Zhe733 F10-11 RIL population has low percentage of heterozygosity, non-parent alleles and skewed markers. We believe that this RIL population has an excellent potential for mapping QTL.

Technical Abstract: Recombinant inbred line (RIL) populations of rice represent a permanent genetic source usable for the construction of molecular genetic linkage maps and map-based identification of quantitative trait loci (QTL). The objective of this study was to characterize a population of 269 F10-11 RILs from a cross between Kaybonnet lpa1-1 (KBNTlpa) and Zhe733 using 109 polymorphic simple sequence repeat (SSR) markers. SSR markers (107) were mapped on 12 rice chromosomes representing a total of 1016.3 cM of genetic distance. Ten markers (9.2%) on chromosomes 3, 6,7, and 11 favored Zhe733 allele and three markers (2.7%) on chromosome 6 favored KBNTlpa allele. Twenty-six RILs (10.2%) were skewed (x2 greater than 15.7, P less than or equal to 0.01) towards Zhe733. The average frequencies of overall genome heterozygous and non-parental alleles per RIL were 1.3% (ranging 0.0%-38.9%) and 0.4% (ranging 0.0%-15.0%), respectively. Thirteen RILs that were heterozygous at more than 5 marker loci and nine RILs with more than 5 non-parental alleles were identified representing 5.1% and 3.5%, respectively, in the population of 255 RILs. Two hundred and thirty-five RILs were clustered into seven sub-groups based on Nei's (1972) genetic distance. These results demonstrate that the KBNTlpa X ZHE733 F10-11 population is an excellent mapping population characterized by low frequencies of heterozygosity and non-parental alleles, and by low percentages of skewed markers and RILS.