Genetic analysis of atypical U.S. red rice phenotypes: Indications of prior gene flow in rice fields?

David H. Gealy*, Hesham Agrama, Melissa H. Jia

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

23 Citations (Scopus)


Weedy red rice is a troublesome weed problem in rice fields of the southern United States. Typically, red rice plants are much taller than rice cultivars, and most biotypes are either awnless with straw-colored hulls (strawhull) or have long awns with black-colored hulls (blackhull). Outcrossing between rice and red rice occurs at low rates, resulting in a broad array of plant types. Simple sequence repeat (SSR) markers were used to evaluate the genetic backgrounds of atypical red rice types obtained from rice farms in Arkansas, Louisiana, Missouri, and Mississippi, in comparison to standard red rice types and rice cultivars. Principal coordinates analysis (PCoA) and population structure analysis of atypical red rice accessions suggested that short-stature awnless (LhtsA-) and awned (LhtsA+) types, each representing a total of about 5% of a 460-accession collection, 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.

Original languageEnglish
Pages (from-to)451-461
Number of pages11
JournalWeed Science
Issue number3
Publication statusPublished - Jul 2012


  • Oryza sativa L.
  • Weedy red rice
  • blackhull red rice
  • genetic diversity
  • rice (Oryza sativa L.)
  • rice-red rice hybrid
  • simple sequence repeat (SSR)
  • strawhull red rice
  • tropical japonica rice

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Plant Science


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