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United States Department of Agriculture

Agricultural Research Service

Title: Analysis of a Single Nucleotide Polymorphism That Controls the Cooking Quality of Rice Using a Non-Gel Bases Assay

Authors
item Bormans, Concetta - TX A&M UNIV
item Rhodes, Richard - PROMEGA CORP
item Kephart, Daniel - PROMEGA CORP
item McClung, Anna
item McClung, Anna
item Park, William - TX A&M UNIV

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 15, 2002
Publication Date: April 15, 2002
Citation: BORMANS,C.A., RHODES,R.B., KEPHART,D.D., MCCLUNG,A.M., PARK,W.D., ANALYSIS OF A SINGLE NUCLEOTIDE POLYMORPHISM THAT CONTROLS THE COOKING QUALITY OF RICE USING A NON-GEL BASES ASSAY, EUPHYTICA, 2002. p. 261-267.

Interpretive Summary: Development of technology which can rapidly screen for the presence of different genes in plants will help breeders to develop improved crops in a rapid and efficient manner. Research has been conducted which demonstrates a new method which detects small changes in a rice gene that controls the chemical composition of the grain. This method proved to be very accurate and will allow rapid screening of genetic materials for rice cooking quality. This technology can be used to discern the presence of other genes in plants and will expedite the development of improved cultivars for farmers to grow.

Technical Abstract: The waxy gene encoding granule-bound starch synthase (GBSS) is responsible for the synthesis of amylose in developing grain. Recent work has shown that a G-T polymorphism in the leader intron 5 prime splice site of GBSS plays a key role in determining the cooking and processing quality of rice. Cultivars with sequence AGGTATA at this location splice GBSS pre-mRNA efficiently and produce relatively large amounts of amylose. These varieties generally have a firm texture when cooked and the grains remain separate. In contrast, GBSS pre-mRNA splicing is temperature sensitive and generally less efficient in cultivars with the sequence AGTTATA. As a result, these cultivars generally have lower amylose content and produce soft and sticky cooked rice. We have used the READIT assay, a non-gel based assay that uses the ability of DNA polymerization, to screen the critical G-T polymorphism in more than 750 samples from U.S. and Asian germplasm. We observed complete concordance between the results obtained using DNA sequencing or restriction enzyme digestion and the READIT assay. It also gave accurate results with both heterozygous plants and with complex mixtures as might result when grain from generation plants is pooled to obtain larger samples.

Last Modified: 10/25/2014