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United States Department of Agriculture

Agricultural Research Service

Title: Microsatellites and a Single Nucleotide Polymorphism Differentiate Apparentamylose Classes in An Extended Pedigree of Us Rice Germplasm

Authors
item Ayres, N - TEXAS A&M UNIV
item McClung, Anna
item McClung, Anna
item Larkin, P - TEXAS A&M UNIV
item Bligh, H F - UNIV OF NOTTINGHAM
item Jones, C - UNIV OF NOTTINGHAM
item Park, W - TEXAS A&M UNIV

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 19, 1996
Publication Date: N/A

Interpretive Summary: The Waxy gene (Wx) codes for the granule bound starch synthase enzyme which is responsible for the synthesis of amylose. Amylose is the principle component controlling the cooking and nutritional properties of rice and thus is a very important breeding trait in the development of new rice cultivars. In this study, about 200 rice cultivars and progeny from a segregating cross were evaluated for differences in amylose content and variation in the length of a repeated sequence of DNA (microsatellite). Seven microsatellites were identified which together explained most of the genetic variation (ca 83%) in amylose content. This suggests that these microsatellites could be used as a breeding tool for improving amylose content in rice. Furthermore, evaluation of a subset of the genetic lines indicated that high and low amylose types could be differentiated based upon a single nucleotide difference located near the waxy gene. The use of such biotechnology methods (PCR) will greatly enhance the ability to selec for important grain traits in rice even at a young seedling stage and thus, will improve the efficiency of cultivar development.

Technical Abstract: The waxy gene (wx) encodes the granule bound starch synthase responsible for the synthesis of amylose. Recently, a polymorphic microsatellite sequence closely linked to the waxy gene was reported (Bligh et al., in press). To determine whether polymorphism in this sequence correlates with variation in apparent amylose content, we tested 86 rice varieties representing current and historical long and medium grain U.S. rice germplasm. Seven wx microsatellite alleles were identified which together explain 83.3 percent of the variation in apparent amylose content of the 84 nonglutinous rice varieties tested. Similar results were also obtained with 101 progeny of a cross between a low and an intermediate amylose variety. We sequenced a 200 bp PCR amplified fragment containing the microsatellite and the putative 5' splice site of the wx leader intron from a subset of 45 nonglutinous varieties representing all seven microsatellite alleles. All of the varieties with more than 19 percent amylose had the sequence AGGT a the putative 5' splice site, while all low amylose varieties had AGTT. Interestingly, two varieties in the (CT)17 microsatellite class that differed substantially in amylose content still showed the correlation between the AGGT/AGTT polymorphism and apparent amylose content. This single nucleotide substitution could explain more than 80 percent of the variation in the apparent amylose content of the 45 nonglutinous varieties tested and can be easily assayed by AccI digestion of the amplified fragment. Polymorphism at this site was not, however, able to explain the very low amylose contents of two glutinous varieties tested, both of which had the sequence AGTT at the putative 5' splice site and belonged to the (CT)17 wx microsatellite class.

Last Modified: 4/23/2014