Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.)

Wen Gui Yan, Yong Li, Hesham A. Agrama, Dagang Luo, Fangyuan Gao, Xianjun Lu, Guangjun Ren

Research output: Contribution to journalArticle

63 Citations (Scopus)

Abstract

Stigma and spikelet characteristics play an essential role in hybrid seed production. A minicore of 90 accessions developed from USDA rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 DNA markers, 108 SSRs plus an indel. Three major clusters were built upon Rogers' genetic distance, indicative of indicas, and temperate and tropical japonicas. A mixed linear model combining PC-matrix and K-matrix was adapted for mapping marker-trait associations. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role indicative of high regression with not only DStgE but also SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. The co-association should improve breeding efficiency because single marker could be used to assist breeding for multiple traits. Indica entry 1032 (cultivar 50638) and japonica entry 671 (cultivar Linia 84 Icar) with 80.65 and 75.17% of TStgE, respectively are recommended to breeder for improving stigma exsertion.

Original languageEnglish
Pages (from-to)277-292
Number of pages16
JournalMolecular Breeding
Volume24
Issue number3
DOIs
Publication statusPublished - 2009

Fingerprint

stigma
chromosome mapping
Breeding
Oryza sativa
Iron-Dextran Complex
inflorescences
rice
United States Department of Agriculture
Genetic Markers
Linear Models
Seeds
seed productivity
breeding
cultivars
USDA
genetic distance
linear models
Oryza
genetic markers
methodology

Keywords

  • Association mapping
  • Hybrid rice
  • Mixed linear model
  • Molecular marker
  • Stigma exsertion

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Agronomy and Crop Science
  • Genetics
  • Plant Science

Cite this

Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). / Yan, Wen Gui; Li, Yong; Agrama, Hesham A.; Luo, Dagang; Gao, Fangyuan; Lu, Xianjun; Ren, Guangjun.

In: Molecular Breeding, Vol. 24, No. 3, 2009, p. 277-292.

Research output: Contribution to journalArticle

Yan, Wen Gui ; Li, Yong ; Agrama, Hesham A. ; Luo, Dagang ; Gao, Fangyuan ; Lu, Xianjun ; Ren, Guangjun. / Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). In: Molecular Breeding. 2009 ; Vol. 24, No. 3. pp. 277-292.
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