Association mapping of straighthead disorder induced by arsenic in Oryza sativa

H. A. Agrama, W. G. Yan

Research output: Contribution to journalArticlepeer-review

26 Citations (Scopus)


Straighthead is a physiological disorder in rice (Oryza sativa L.) resulting in sterile florets, poorly developed panicles and yield loss. Because of its sporadic nature and unidentified causes for the disorder, molecular marker assisted selection is essential for resistance improvement in breeding programmes. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association mapping to identify genetic regions associated with straighthead disorder using 547 accessions of germplasm from the USDA rice core collection. Straighthead was evaluated in arsenic treated soil and genotyping was conducted with 75 molecular markers covering the entire rice genome about every 25 cM. A mixed-linear model approach combining the principal component assignments with kinship estimates proved to be particularly promising for association mapping. The extent of linkage disequilibrium, was described among the markers. Six markers were found to be significantly associated with straighthead, explaining 35% of the total, phenotypic variation. However, only two SSR markers, RM413 and RM277 on chromosome 5 and 12, respectively, have a significant association with low rating indicating straighthead resistance. Confirmation of the marker-straighthead association using segregating populations is necessary before markerassisted selection can be applied.

Original languageEnglish
Pages (from-to)551-558
Number of pages8
JournalPlant Breeding
Issue number6
Publication statusPublished - Dec 2009


  • Genetic diversity
  • Linkage disequilibrium
  • Oryza
  • Population structure
  • Principal component
  • Straighthead disorder
  • Unified mixedmodel

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science


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