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PMID: 21829395 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping.

PLoS genetics ·Vol. 7 ·No. 8 ·2011-08-00 ·Pages e1002221

Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV, McCouch SR

Abstract

Aluminum (Al) toxicity is a primary limitation to crop productivity on acid soils, and rice has been demonstrated to be significantly more Al tolerant than other cereal crops. However, the mechanisms of rice Al tolerance are largely unknown, and no genes underlying natural variation have been reported. We screened 383 diverse rice accessions, conducted a genome-wide association (GWA) study, and conducted QTL mapping in two bi-parental populations using three estimates of Al tolerance based on root growth. Subpopulation structure explained 57% of the phenotypic variation, and the mean Al tolerance in Japonica was twice that of Indica. Forty-eight regions associated with Al tolerance were identified by GWA analysis, most of which were subpopulation-specific. Four of these regions co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified QTLs. Three regions corresponding to induced Al-sensitive rice mutants (ART1, STAR2, Nrat1) were identified through bi-parental QTL mapping or GWA to be involved in natural variation for Al tolerance. Haplotype analysis around the Nrat1 gene identified susceptible and tolerant haplotypes explaining 40% of the Al tolerance variation within the aus subpopulation, and sequence analysis of Nrat1 identified a trio of non-synonymous mutations predictive of Al sensitivity in our diversity panel. GWA analysis discovered more phenotype-genotype associations and provided higher resolution, but QTL mapping identified critical rare and/or subpopulation-specific alleles not detected by GWA analysis. Mapping using Indica/Japonica populations identified QTLs associated with transgressive variation where alleles from a susceptible aus or indica parent enhanced Al tolerance in a tolerant Japonica background. This work supports the hypothesis that selectively introgressing alleles across subpopulations is an efficient approach for trait enhancement in plant breeding programs and demonstrates the fundamental importance of subpopulation in interpreting and manipulating the genetics of complex traits in rice.

MeSH Terms
Aluminum/toxicity Chromosome Mapping Chromosomes, Plant/genetics Crosses, Genetic Genes, Plant/genetics Genome-Wide Association Study Haplotypes Oryza/drug effects,genetics Polymorphism, Single Nucleotide/genetics Quantitative Trait Loci/genetics
Chemicals
Aluminum
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Famoso Adam N
Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, USA.
Zhao Keyan
Clark Randy T
Tung Chih-Wei
Wright Mark H
Bustamante Carlos
Kochian Leon V
McCouch Susan R
Conflict of Interest

The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1002221
Published
2011-08-00
Epub
2011-00-04
Pages
e1002221
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC3150440
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pgen.1002221 PMC Full Text View journal details
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