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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS

Location: Dale Bumpers National Rice Research Center

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

Authors
item Yan, Wengui
item Li, Yong - SICHUAN ACAD. OF AGR. SCI
item Agrama, Hesham - UNIV. OF AR RREC
item Luo, Dagang - SICHUAN ACAD. OF AGR. SCI
item Gao, Fangyuan - SICHUAN ACAD. OF AGR. SCI
item Ren, Guangjun - SICHUAN ACAD. OF AGR. SCI

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 24, 2009
Publication Date: October 1, 2009
Citation: Yan, W., Li, Y., Agrama, H.A., Luo, D., Gao, F., Ren, G. 2009. Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). Molecular Breeding. 24(3):277-292.

Interpretive Summary: Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core sample from the USDA rice core collection was phenotyped for nine traits of stigma and spikelet and genotyped with 109 DNA markers. A mixed linear model combining PC-matrix and K-matrix was adapted for marker-trait association mapping. 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 a major role and explained 35% of phenotypic variation for DStgE and 17% for 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 was associated with all three correlated spikelet traits. These correspondences between trait-trait correlation and trait-marker association provide further confirmation to the mapped associations.

Technical Abstract: Hybrid rice exhibits a yield advantage of 15 to 20 percent (or more than one ton of paddy rice per hectare) over the best traditional varieties. Because rice plants are self-pollinating, commercial production of hybrid seed plays a key role in successful implementation of hybrid rice. Stigma exsertion and associated spikelet traits are important to increase pollination opportunity for a higher yield of hybrid seed because the exserted stigmas remain viable up to six days. A mini-core sample from the USDA rice core collection was phenotyped for nine traits of stigma and spikelet and genotyped with 109 DNA markers. As a result, 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 a major role and explained 35% of the phenotypic variation for DStgE and 17% for SStgE. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 was associated with all three correlated spikelet traits. These correspondences between trait-trait correlation and trait-marker association confirmed the associations. These identified associations could be used in marker-assisted breeding to improve stigma exsertion in rice.

Last Modified: 7/30/2014