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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS Title: Validation of yield enhancing QTLs from a low-yielding wild ancestor of rice

Authors
item Imai, Ize -
item Kimball, Jennifer -
item Conway, Benjamin -
item Yeater, Kathleen
item Mccouch, Susan -
item McClung, Anna
item McClung, Anna

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 6, 2013
Publication Date: April 28, 2013
Repository URL: http://handle.nal.usda.gov/10113/57983
Citation: Imai, I., Kimball, J.A., Conway, B., Yeater, K.M., McCouch, S.R., McClung, A.M. 2013. Validation of yield enhancing QTLs from a low-yielding wild ancestor of rice. Molecular Breeding. 32(1):101-120.

Interpretive Summary: Cultivated rice in the USA comes from the genus/species Oryza sativa. However there are wild relatives of rice that come from several other species. Although these wild relatives of rice are very weedy-like and have no obvious agronomic value, research has shown that these materials can resistance to diseases, pests, and other plant stress factors. This study was conducted to determine if a wild relative, Oryza rufipogon, may possess yield enhancing genes that could be used to improve cultivated rice. Crosses were made between the USA rice cultivar Jefferson with the rufipogon wild relative. Progeny of the cross were developed that primarily had a Jefferson genetic background except for DNA insertions from the wild relative at six different chromosomal regions. The objective of the study was to determine if any of these DNA insertions would have a positive impact on yield. Fifty of these progeny lines were evaluated at four southern US locations over two years in replicated yield trials using flooded field paddies. Two of the families possessing DNA insertions on chromosomes 2 and 6 were found to have over a 25 percent yield increase as compared to the Jefferson parent. The same materials were grown using less water than the flooded management system at two field locations. The family with the DNA insertion on chromosome 2 was also one of the highest yielding lines under the water stressed conditions. Subsequently, the two families with the chromosome 2 and 6 insertions were evaluated in a multi-state yield trial and were found to have stable high yields comparable to some current commercial cultivars. Additional crossing was performed to remove any other background insertions from the wild relative so that the progeny would be essentially all Jefferson except for these specific chromosomal insertions on chromosomes 2 and 6. This was done using genetic markers which tracked the wild relative DNA through the crossing process. These new materials were tested along with the original materials and the Jefferson parent in replicated yield trials at three sites. It was found that the additional background wild relative insertions had no negative impact on yield and actually offered some additional yield enhancement. These results demonstrate the breeding value of incorporating genes from wild relatives of rice into US cultivars. These materials are being made available to the breeding community to help in further varietal development.

Technical Abstract: A set of introgression lines (ILs) containing chromosomal segments from O. rufipogon (IRGC 105491), a wild relative of O. sativa, in the genetic background of an elite U.S. variety, cv. Jefferson, was developed to confirm the performance of six yield-enhancing quantitative trait loci (QTLs). Fifty BC3F3 ILs containing homozygous O. rufipogon introgressions across each of the target QTL regions, and as few background introgressions as possible, were selected for evaluation of yield and 14 yield-related traits in field studies conducted over two years at four locations in the southern U.S. Performance of the IL families was compared with three commercial inbreds and one hybrid variety. IL families carrying introgressions from the low yielding wild parent at the QTLs, yld2.1 and yld6, yielded 27.7% and 26.1% more than Jefferson. IL yld2A also performed well under alternate wetting and drying conditions in two field locations, and had greater levels of resistance to four diseases. After the first year of field trials, 10 of the top-performing BC3F4 families, representing five of the QTL targets, were genotyped with an Illumina 1,536 assay to define the size and location of the wild introgressions. BC3F4 families with the fewest background introgressions were backcrossed to Jefferson and selfed. The resulting BC4F2 families were screened with targeted SNP assays to identify individuals carrying homozygous introgressions across the target QTLs. Twelve ILs, representing each of the six QTL targets, have been submitted to the Genetic Stocks Oryza Collection for studies on transgressive variation and as interspecific pre-breeding lines.

Last Modified: 10/25/2014
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