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United States Department of Agriculture

Agricultural Research Service

Title: Confirmation of Red Rice Hybrids from Crosses with Rice in Grower Fields Using Ssr Analysis

Authors
item Gealy, David
item Estorninos, Leopoldo - UNIV ARK

Submitted to: Weed Science Society of America Meeting Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: February 9, 2004
Publication Date: February 9, 2004
Citation: Gealy, D.R., Estorninos, L. 2004. Confirmation of red rice hybrids from crosses with rice in grower fields using SSR analysis. Weed Science Society of America Meeting. 44:65.

Interpretive Summary: Abstract only - interpretive summary not required.

Technical Abstract: In the past few years, the land area planted to herbicide-resistant cultivars in the southern U.S. has increased rapidly. Growers, extension advisors, and industry representatives have become increasingly cognizant of the need to accurately identify rice-red rice hybrids in these areas. Thus, we evaluated more than 150 SSR markers on numerous rice and red rice entries using a microcapillary, automated DNA sequencer. Using cluster analysis, we established genetic distances (GD) among rice cultivars, putative red rice hybrid derivatives, red rice ecotypes, and known hybrids. Rice and red rice lines obtained from US collections were included as standards. We visualized GD on multidimensional scaling (MDS) plots in which close proximity of data points equates to close genetic relationship of genotypes. Used in combination with a large database of standard genotypes, the analysis can identify potential rice and red rice parents, and in some cases, the generation of the putative hybrid plant. Genetic distances between both of the known parents and their known F1 hybrids are identical. Thus, data points from true F1 hybrids will lie midway between their parents on the MDS graph, and all markers will produce fragment sizes that are consistent with both the male and female parents. These will be heterozygous for each marker at which allele sizes of the parents differed. MDS data points for F2 and later generation hybrid derivatives also lie at or near the midpoint between the parents, but the genetic distances to each parent will usually not be identical and will have a smaller fraction of heterozygous alleles than was the case for F1 hybrids. Hybrids derived from blackhull awned red rice types were easily distinguished from those derived from strawhull awnless types because of the large genetic separation between these two main groups of red rice. We are also employing allele frequency analysis and using DNA marker data available on public databases to further characterize and establish probable identities of red rice hybrid derivatives and their parents. This information may be useful to the rice seed industry in its quest to confirm or reject claims of contamination from red rice ecotypes or their hybrid derivatives.

Last Modified: 10/23/2014
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