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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #319898

Title: Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB


Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/24/2013
Publication Date: 1/20/2014
Citation: Caniato, F.F., Hamlin, M.T., Guimaraes, C.T., Zhang, Z., Schaffert, R.E., Kochian, L.V., Magalhaes, J.V. 2014. Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB. PLoS One. 9(1):e87438.

Interpretive Summary: Over 20% of the US 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 agricultural productivity, as toxic Al results in damaged and stunted plant root systems, ultimately resulting in a reduction of crop yields. Given that a large proportion of the acid soils are found in the tropics/subtropics regions where many developing countries are located, Al toxicity limits agricultural productivity 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. This research is a detailed genetic analysis of the variation in the major sorghum Al tolerance gene we previously discovered, SbMATE, which encodes the root transporter that mediates Al activated release of citric acid from the root. The released citric acid binds toxic Al ions in the soil and detoxifies them, conferring Al tolerance to the sorghum plant. We used a sophisticated genetic mapping approach called association mapping to identify changes in single nucleotide changes (SNPs) in and around the SbMATE DNA sequence that were statistically associated with the ability of the transporter to release citrate. In this way we were able to identify changes in SbMATE sequence that can be used as genetic markers to identify the most Al tolerant versions of SbMATE. This information is now being used in trial studies in Brazil and Africa to facilitate the molecular breeding of improved sorghum performance on acid soils.

Technical Abstract: Root damage caused by aluminum (Al) toxicity is a major cause of grain yield reduction on acid soils, which are prevalent in tropical and subtropical regions of the world where food security is most tenuous. In sorghum, Al tolerance is conferred by SbMATE, an Al-activated root citrate efflux transporter that underlies the major Al tolerance locus, AltSB, on sorghum chromosome 3. We used association mapping to gain insights into the origin and evolution of Al tolerance in sorghum and to detect functional variants amenable to allele mining applications. Linkage disequilibrium across the AltSB locus decreased much faster than in previous reports in sorghum, and reached basal levels at approximately 1000 bp. Accordingly, intra-locus recombination events were found to be extensive. SNPs and indels highly associated with Al tolerance showed a narrow frequency range, between 0.06 and 0.1, suggesting a rather recent origin of Al tolerance mutations within AltSB. A haplotype network analysis based on polymorphisms associated with Al tolerance suggested a single geographic and racial origin of Al tolerance mutations in primordial guinea domesticates in West Africa. This analysis of recombinant haplotypes suggests that causative polymorphisms are localized to a ~6 Kb region including intronic polymorphisms and a transposon (MITE) insertion, whose size variation has been shown to be positively correlated with Al tolerance. We show that the SNP with the strongest association signal, located in the second SbMATE intron, recovers 9 of the 14 highly Al tolerant accessions and 80% of all the Al tolerant and intermediately tolerant accessions in the association panel. Our results also demonstrate the pivotal importance of knowledge on the origin and evolution of Al tolerance mutations in molecular breeding applications. Allele mining strategies based on associated loci are expected to efficiently lead to the identification of Al tolerant accession in diverse sorghum germplasm, which should maintain grain yields under Al toxicity.