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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic and Genetic Analysis of Crop Adaptation to Soil Abiotic Stresses

Location: Plant, Soil and Nutrition Research

Title: Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan)

item Guimaraes, Claudia
item Simoes, Christiano
item Lyza, Maron
item Pastina, Maria
item Magalhaes, Jurandir
item Vasconcellos, Renato C.c
item Guimaraes, Lauro J.m.
item Lana, Ubiraci G.p.
item Tinoco, Carlos F.s.
item Noda, Roberto
item Jardim-belicuas, Silvia
item Parentoni, Sidney
item Alves, Vera Mc
item Kochian, Leon

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/29/2014
Publication Date: 2/24/2014
Citation: Guimaraes, C.T., Simoes, C.C., Lyza, M.G., Pastina, M.M., Magalhaes, J.V., Vasconcellos, R., Guimaraes, L., Lana, U., Tinoco, C., Noda, R.W., Jardim-Belicuas, S.N., Parentoni, S.N., Alves, V., Kochian, L.V. 2014. Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan. Biomed Central (BMC) Genomics. 15:153. DOI:10.1186/1471-2164-15-153.

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. The release of organic acid from the root apex in response to Al-stress constitutes a widespread Al-tolerance mechanism by which plant roots are able to ameliorate the toxic levels of Al surrounding the growing root. We previously identified a major Al tolerance gene in maize, ZmMATE1, which encodes a root tip citrate efflux transporter. In the current study, we validated the use of ZmMATE1 for breeding for improved maize Al tolerance. We generated a pair of near isogenic lines (NIL) which have identical genomes from an Al sensitive line, except that in one of the NILs, the tolerant version of ZmMATE1 has been introgressed using marker-assisted breeding techniques. This resulted in a two-fold increase in Al tolerance compared with the other NIL carrying the sensitive version of ZmMATE1. We previously showed that very tolerant versions of this gene are rare in maize, so the approaches we used here are a very useful approach for improving maize growth and yield on acid soils that limit crop production around the world.

Technical Abstract: Aluminum (Al) toxicity is an important limitation to food security in the tropical and subtropical regions. High Al saturation in acid soils limits root development and its ability to uptake water and nutrients. In this study, we present a genome scan for Al tolerance loci with over 50,000 GBS-based SNP markers in a recombinant inbred line population, obtained by crossing two maize lines contrasting in Al tolerance. Five genomic regions were significantly associated with Al tolerance, including two quantitative trait loci (QTLs) co-localized with candidate genes that were further investigated. ZmNrat1, located close to qALT5, shares high amino acid sequence identity with OsNrat1, a specific transporter for Al3+ previously associated with Al tolerance in rice. We demonstrate that in maize, ZmNrat1 is preferentially expressed in root tips and is up-regulated by Al, in a similar pattern presented by OsNrat1. The other region was the main Al tolerance QTL on chromosome 6 (qALT6), previously shown to carry three copies of the Al tolerance gene ZmMATE1, also harbors a cis element controlling approximately 71% of ZmMATE1 expression. qALT6 was validated using near-isogenic lines (NILs), which presented a two-fold increase in Al tolerance, as well as high expression of ZmMATE1. Additionally, in contrast to the results obtained with the RILs and NILs, a new source of Al tolerance via ZmMATE1 was identified in a Brazilian elite line, which showed high expression of ZmMATE1 but carries a single copy of ZmMATE1. As qALT6 enhances Al tolerance, and superior alleles for ZmMATE1 expression are rare in maize, the introgression of this QTL region may be an important strategy to improve maize adaptation to acid soils worldwide.

Last Modified: 05/21/2017
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