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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

Location: Dale Bumpers National Rice Research Center

Title: Development of genetic markers linked to straighthead resistance through fine mapping in rice (Oryza sativa L.)

Authors
item Pan, Xuhao -
item Zhang, Qijun -
item Yan, Wengui
item Jia, Melissa
item Jackson, Aaron
item Li, Xiaobai -
item Jia, Limeng -
item Xu, Peizhou -
item Correa-Victoria, Fernando -
item Li, Shigui -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 15, 2012
Publication Date: December 28, 2012
Repository URL: http://handle.nal.usda.gov/10113/58044
Citation: Pan, X., Zhang, Q., Yan, W., Jia, M.H., Jackson, A.K., Li, X., Jia, L., Xu, P., Correa-Victoria, F., Li, S. 2012. Development of genetic markers linked to straighthead resistance through fine mapping in rice (Oryza sativa L.). PLoS One. 7(12):e52540.

Interpretive Summary: Straighthead is a physiological disorder in rice that is characterized by spikelet sterility resulting in blank panicles which remain upright at maturity. Straighthead can result in almost complete loss of grain yield, and is occurring with increasing frequency in Arkansas where about 50% of USA rice is produced. Cultivar resistance is regarded as the most efficient, economical, and environmentally friendly strategy for straighthead prevention. We mapped QTL (quantitative trait loci) for straighthead resistance using two RIL (recombined inbred line) F9 populations phenotyped over two years using MSMA (monosodium methanearsonate) to induce the symptoms. One population had 170 RILs genotyped with 136 SSR (simple sequence repeat) markers and the other had 91 RILs genotyped with 159 SSRs. A major QTL qSH-8 was identified in an overlapping region from both populations, fine mapped from 1.0 Mbp to 340 kb using 7 SSRs and further mapped to 290 kb in the populations. SSR AP3858-1 and InDel 11 (insertion and deletion marker) were within the fine mapped region, and significantly co-segregated with straighthead resistance in both RIL populations and a collection of diverse global accessions. These results demonstrate that AP3858-1 and InDel 11 can be used to efficiently develop straighthead resistant cultivars through marker-assisted breeding which is especially important because there is no effective way to directly evaluate straighthead.

Technical Abstract: Straighthead, characterized by sterile florets and distorted spikelets, results in significant yield losses in rice and occurs in many countries. The current prevention method of draining paddies early in the season stresses plants, is costly and wastes water. We mapped QTL for straighthead resistance using two RIL F9 populations phenotyped over two years using MSMA to induce the symptoms. One population had 170 RILs genotyped with 136 SSRs and the other had 91 RILs genotyped with 159 SSRs. A major QTL qSH-8 was identified in an overlapping region from both populations, and explained 46% of total variation in one and 67% in another population for straighthead resistance. qSH-8 was fine mapped from 1.0 Mbp to 340 kb using 7 SSR and further mapped to 290 kb in the populations between RM22573 and InDel 27 using 4 InDel markers. SSR AP3858-1 and InDel 11 were within the fine mapped region, and significantly co-segregated with straighthead resistance in both RIL populations and a collection of diverse global accessions. These results demonstrate that AP3858-1 and InDel 11 can be used to efficiently develop straighthead resistant cultivars through marker-assisted breeding which is especially important because there is no effective way to directly evaluate straighthead.

Last Modified: 4/19/2014
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