Title: SSR marker analysis of atypical U.S red rice phenotypes: indications of prior gene flow in rice fields? Authors
Submitted to: Weed Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 28, 2012
Publication Date: July 1, 2012
Citation: Gealy, D.R., Agrama, H., Jia, M.H. 2012. SSR marker analysis of atypical U.S red rice phenotypes: Indications of prior gene flow in rice fields? Weed Science. 60:451-461. Interpretive Summary: Weedy red rice is a troublesome weed problem in rice fields of the southern U.S. Because it is the same species as rice, red rice has traditionally been difficult to control in the rice crop, and has the added problem that its flowers can intercross with those on rice plants. Although outcrossing between rice and red rice occurs at low frequencies (usually less than 0.5%) a large array of plant types may develop within a few years once outcrossing has occurred. This phenomenon adds to the complexity of red rice identification and management. We used DNA markers, which are located on each of the 12 chromosomes of rice and red rice, to reveal key information about the differences in genetic backgrounds of rice varieties and red rice biotypes from the southern U.S. Various analytical procedures revealed that relatively uncommon red rice biotypes (5% of total) with plant heights as much a foot shorter than normal biotypes were closely genetically related to their normal-sized counterparts, and thus probably of the same origin as the two most common biotypes (awned and awnless). However, an equally uncommon biotype (4% of total) with extremely short awns and intermediate height was shown to be genetically distinct from all of the other red rice biotypes and rice, and apparently had resulted from intercrossing between awned and awnless red rice biotypes at some earlier time. These findings show for the first time that an established red rice biotype in U.S. rice fields was derived from two distinctly different weedy rice biotypes. The combined weedy traits contributed by the two different red rice biotypes appear to have been great enough for this short-awned biotype to overcome the natural limitations caused by its relatively small plant size.
Technical Abstract: Red rice is a troublesome weed problem in rice fields of the southern U.S. Outcrossing between rice and red rice occurs at low rates, resulting in a broad array of plant types. SSR markers were used to evaluate the genetic backgrounds of atypical red rice types obtained from rice farms in comparison to standard red rice types and rice cultivars. Principal coordinate analysis (PCA) and population structure analysis of atypical red rice accessions suggested that short-stature awnless (LhtsA-) and awned (LhtsA+) types, each representing about 5% of the total accessions, usually were closely genetically related to their normal-sized counterparts, and not with cultivated rice. A short-awned, intermediate height type, 'Sawn', representing about 4% of the accessions was genetically distinct from all of the other types. Key alleles in Sawn types appeared to be shared by both standard awnless (StdRRA-) and awned (StdRRA+) red rice, suggesting that Sawn types could have arisen from gene flow between awned and awnless red rice types.