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

Hesham A. Agrama, Anna M. McClung, Wen Gui Yan

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Because of the rich diversity among rice accessions grown around the world in distinct environments, traditional methods using morphology, cross compatibility and geography for classifying rice accessions according to different sub-populations have given way to use of molecular markers. Having a few robust markers that can quickly assign population structure to germplasm will facilitate making more informed choices about genetic diversity within seedbanks and breeding genepools. WHICHLOCI is a computer program that selects the best combination of loci for population assignment through empirical analysis of molecular marker data. This program has been used in surveys of plant species, for fish population assignment, and in human ancestry analysis. Using WHICHLOCI, we ranked the discriminatory power of 72 DNA markers used to genotype 1,604 accessions of the USDA rice core collection, and developed panels with a minimum number of markers for population assignment with 99% or higher accuracy. A total of 14 markers with high discriminatory power, genetic diversity, allelic frequency, and polymorphic information content were identified. A panel of just four markers, RM551, RM11, RM224 and RM44, was effective in assigning germplasm accessions to any of five sub-populations with 99. 4% accuracy. Panels using only three markers were effective for assignment of rice germplasm to specific sub-populations, tropical japonica,temperate japonica,indica, aus, and aromatic. Assignment to tropical japonica,temperate japonica, or indica sub-populations was highly reliable using 3-4 markers, demonstrated by the high correlation with assignment using 72 markers. However, population assignment to aus and aromatic groups was less reliable, possibly due to the smaller representation of this material in the USDA core collection. More reference cultivars may be needed to improve population assignment to these two groups. This study demonstrated that a small number of DNA markers is effective for classification of germplasm into five sub-populations in rice. This will facilitate rapid screening of large rice germplasm banks for population assignment at a modest cost. The resulting information will be valuable to researchers to verify population classification of germplasm prior to initiating genetic studies, maximizing genetic diversity between sub-populations, or minimizing cross incompatibility while maximizing allelic diversity within specific sub-populations.

Original languageEnglish
Pages (from-to)413-425
Number of pages13
JournalMolecular Breeding
Volume29
Issue number2
DOIs
Publication statusPublished - Feb 2012

Fingerprint

Genetic Markers
Oryza sativa
taxonomy
rice
loci
genetic markers
Population
germplasm
United States Department of Agriculture
Oryza
USDA
genetic variation
aromatic compounds
Geography
geography
gene frequency
Breeding
population structure
ancestry
researchers

Keywords

  • Discriminatory power
  • Molecular marker
  • Population assignment
  • Rice structure
  • WHICHLOCI

ASJC Scopus subject areas

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

Cite this

Using minimum DNA marker loci for accurate population classification in rice (Oryza sativa L.). / Agrama, Hesham A.; McClung, Anna M.; Yan, Wen Gui.

In: Molecular Breeding, Vol. 29, No. 2, 02.2012, p. 413-425.

Research output: Contribution to journalArticle

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