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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 Title: Using minimum DNA marker loci for accurate population classification in rice (Oryza sativa L.)

Authors
item Agrama, Hesham -
item McClung, Anna
item McClung, Anna
item Yan, Wengui

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 21, 2011
Publication Date: March 15, 2011
Citation: Agrama, H.A., McClung, A.M., Yan, W. 2011. Using minimum DNA marker loci for accurate population classification in rice (Oryza sativa L.). Molecular Breeding. 29:413-425.

Interpretive Summary: Using few DNA markers to classify genetic background of a germplasm pool will help breeders make a quick decision while saving time and resources. WHICHLOCI is a computer program that selects the best combination of loci for population assignment through empiric analysis of molecular marker data. This program has been used in plant barcoding, fish population assignment and human ancestry analysis, and this is the first time for being used in rice. We used WHICHLOCI to rank discriminatory power of 72 DNA markers in genotyping 1,604 accessions of the USDA rice core collection, and develop panels with minimum markers for population assignment with 99% or higher accuracy in rice. Reliability for applying the marker panel in population assignment was proved using correlation and regression of the resultant populations between the panel of few marker loci and the complete set of 72 marker loci. These markers panels could be used by rice geneticists and breeders to understand ancestry background in a quick and economical way.

Technical Abstract: Using few DNA markers to classify genetic background of a germplasm pool will help breeders make a quick decision while saving time and resources. WHICHLOCI is a computer program that selects the best combination of loci for population assignment through empiric analysis of molecular marker data. This program has been used in plant barcoding, fish population assignment and human ancestry analysis. Using WHICHLOCI, we ranked discriminatory power of 72 DNA markers in genotyping 1,604 accessions of the USDA rice core collection, and developed panels with minimum markers for population assignment with 99% or higher accuracy in rice. Tropical japonica panel included RM11, RM489 and RM555 with 99.8% of correct assignments. The panel of RM489, RM171 and RM145 for Temperate japonica had 99.5% of correct assignments. The panel of RM125, RM536 and RM555 had 99.6% of correct assignments for indica; RM178, RM551 and RM1339 had 99.8% of correct assignments for aus; and RM551, RM169 and RM408 had 99.3% of correct assignments for aromatic. Four marker panel, RM551, RM11, RM224 and RM44, assigned germplasm accessions to one of the five populations with 99.4% accuracy. Reliability for application of the marker panel in population assignment was proved using correlation and regression of the resultant populations between the panel of few marker loci and the complete set of 72 marker loci. These markers panels could be used by rice geneticists and breeders to understand ancestry background in a quick and economical way.

Last Modified: 11/28/2014
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