ARS | Publication request: Genetic architecture of aluminum tolerance in rice (O. sativa) determined through genome-wide association analysis and QTL mapping

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 21, 2011
Publication Date: August 4, 2011
Citation: Famoso, A., Zhao, K., Clark, R.T., Tung, C., Wright, M.H., Bustamante, C., Mccouch, S.R., Kochian, L.V. 2011. Genetic architecture of aluminum tolerance in rice (O. sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genetics. 7(8):e1002221. DOI: 10.137/journal.pgen.1002221.

Interpretive Summary: Over 20 percent of the U.S. land area and approximately 50% of the world’s arable lands are acidic (pH < 5). On these acid soils, aluminum (Al) toxicity is the primary factor limiting crop production as Al is toxic to plant roots, leading to a damaged and stunted root system. As a large proportion of the acid soils are in the tropics/subtropics where many developing countries are located, Al toxicity limits crop production in the very areas where food security is most tenuous. Because of the importance of this problem to agriculture worldwide, there is considerable interest and research effort by researchers at universities, government agencies, and international agriculture organizations in identifying genes that provide tolerance to Al toxicity in order to improve crop Al tolerance via molecular breeding and biotechnology. It has been suggested that rice is the most Al tolerant in all cereals and thus may be a unique genetic research for novel tolerance genes and mechanisms. However, very little is known about the genetic diversity of rice Al tolerance. In this study, we used novel statistical genetic approaches in a large rice diversity panel to identify new regions of the rice genome involved in Al tolerance. We also identify Al tolerance QTL that were associated with candidate Al tolerance genes from other studies where no evidence of variation in these genes had been observed. The importance of these findings is that they open up new avenues and new candidate genes for rapidly improving the Al tolerance of rice and other cereals via molecular breeding approaches.

Technical Abstract: Aluminum (Al) toxicity is a primary limitation to crop productivity on acid soils and rice is significantly more Al tolerant than other cereals. However, mechanisms of rice Al tolerance are largely unknown and no genes underlying natural variation have been reported. We screened 383 diverse rice accessions for Al tolerance, and conducted genome-wide association (GWA) analysis as well as QTL mapping in two bi-parental populations. 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. Four of these regions co-localized with a priori candidate genes and 2 highly significant regions co-localized with previously identified QTLs. Three regions corresponding to Al sensitive rice mutants (ART1, STAR2, Nrat1) were identified to be involved in natural variation for Al tolerance. Haplotype analysis of the Nrat1 gene identified susceptible and tolerant haplotypes explaining 40% of the Al tolerance variation within the aus subpopulation. Nrat1 sequence analysis identified 3 non-synonymous mutations predictive of Al sensitivity. 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. Selectively introgressing alleles across subpopulations was shown to be an efficient approach for trait enhancement and demonstrates the fundamental importance of subpopulation in interpreting and manipulating the genetics of complex traits in rice.