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United States Department of Agriculture

Agricultural Research Service


Location: Dale Bumpers National Rice Research Center

Title: Marker-assisted NIL development of an Oryza sativa x Oryza rufipogon cross using SSRs, InDels and SNPs)

item Imai, Ize
item Kimball, Jennifer
item Moon, Shannon
item Mcclung, Anna
item Mcclung, Anna
item Mccouch, Susan

Submitted to: Symposium Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 9/30/2009
Publication Date: 11/15/2009
Publication URL: www://
Citation: Imai, I., Kimball, J.A., Moon, S., Mcclung, A.M., Mccouch, S.R. 2009. Marker-assisted NIL development of an Oryza sativa x Oryza rufipogon cross using SSRs, InDels and SNPs. Symposium Proceedings. P9-20.

Interpretive Summary:

Technical Abstract: A set of near isogenic lines (NILs) with introgressions from O. rufipogon (IRGC 105491) in the genetic background of an elite US variety, cv Jefferson, were developed to confirm the performance of six yield-enhancing QTLs identified in a previous study. Approximately 200 SSRs were used to evaluate the genotypes of 50-60 BC2F3 individuals from each of 14 families (~700 plants) to identify individuals containing homozygous O. rufipogon introgressions across the target regions and as few background introgressions as possible. An average of six background introgressions (2-9 introgressions) ranging from 2Mb to 16Mb in size, were detected in each of the families. 50 lines containing the smallest number of background introgressions were selected for evaluation in standard yield plots at four locations and compared with three commercial inbred cultivars, Jefferson (recurrent parent), Cocodrie, Trenasse, and one hybrid, XL723. The 13 top performing BC2F4 lines from the field were then genotyped with an Illumina 1,536 SNP assay to provide a higher resolution definition of the size and location of donor introgressions in each NIL. Based only on genotypic data, 1-2 plants/family were simultaneously selected for an additional round of backcrossing to Jefferson and selfing. These BC3F2 lines were screened with SSRs and InDel markers for selecting individuals with no or minimum background, and recombination within the target QTL regions as the basis for fine mapping. NIL status was confirmed using the 384 SNP assay prior to sending select lines to a winter nursery for seed amplification in preparation for multi-location field trials in summer 2010.

Last Modified: 8/24/2016
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