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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: A Putative Gene sbe3-rs for Resistant Starch Mutated from SBE3 for Starch Branching Enzyme in Rice (Oryza sativa L.)

Authors
item Rang, Ruifang -
item Sun, Chunlong -
item Bai, Jianjiang -
item Luo, Zhixiang -
item Shi, Biao -
item Zhang, Jianming -
item Yan, Wengui
item Piao, Zhongze -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 17, 2012
Publication Date: August 24, 2012
Repository URL: http://handle.nal.usda.gov/10113/58032
Citation: Rang, R., Sun, C., Bai, J., Luo, Z., Shi, B., Zhang, J., Yan, W., Piao, Z. 2012. A putative gene sbe3-rs for resistant starch mutated from SBE3 for starch branching enzyme in rice (Oryza sativa L.). PLoS One. 7(8):Article e43026.

Interpretive Summary: Foods high in resistant starch (RS) are beneficial to prevent various diseases including diabetes, colon cancer, diarrhea and chronic renal or hepatic diseases. Since rice is a staple food for half of the world’s population, rice having elevated RS is important for public health. Breeding for RS in crops has been difficult due to the laborious analytical method required to determine the amount of RS. This study was conducted to understand the inheritance of RS in a segregating cross and to develop a genetic marker that could be used to breed for this trait in new rice cultivars. Using a japonica mutant ‘Jiangtangdao 1’ having a RS level of 11.67%, a mapping population was made by crossing this mutant with an indica cultivar having a RS level of 0.41%. Through QTL mapping and fine mapping the mutant gene sbe3-rs was identified on chromosome 2, which was responsible for the high RS due to a genetic change in the starch branching enzyme. A DNA marker was developed that closely tracks this gene. Results demonstrated that the marker could be used in marker-assisted breeding to develop rice cultivars with elevated RS, which is otherwise difficult to accurately assess in crops.

Technical Abstract: Foods high in resistant starch (RS) are beneficial to prevent various diseases including diabetes, colon cancer, diarrhea and chronic renal or hepatic diseases. Elevated RS in rice is important for public health since rice is a staple food for half of the world’s population. A japonica mutant ‘Jiangtangdao 1’ (RS=11.67%) was crossed with an indica cultivar ‘Miyang 23’ (RS=0.41%). The mutant sbe3-rs that explained 60.4% of RS variation was mapped between RM6611 and RM13366 on chromosome 2 (LOD=36) using 178 F2 plants genotyped with 106 genome-wide polymorphic SSR markers. Using 656 plants from four F3:4 families, sbe3-rs was fine mapped to a 573.3 kb region between InDel 2 and InDel 6 using one STS, five SSRs and seven InDel markers. SBE3 which codes for starch branching enzyme was identified as a candidate gene within the putative region. Nine pairs of primers covering 22 exons were designed to sequence genomic DNA of the wild type for SBE3 and the mutant for sbe3-rs comparatively. Sequence analysis identified a missense mutation site which changed Leu-599 in the wild type to Pro-599 in the mutant in the SBE3 coding region. Because the point mutation resulted in the loss of a restriction enzyme site, sbe3-rs was not digested by a CAPS marker for SpeI site while SBE3 was. Verification among F2 individuals segregating for RS demonstrated that the CAPS marker could be used in marker-assisted breeding to develop rice cultivars with elevated RS, which is otherwise difficult to accurately assess in crops.

Last Modified: 7/25/2014