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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 #239431

Title: Association and linkage analysis of aluminum tolerance genes in maize

item KRILL, ALLISON - Cornell University
item KIRST, MATIAS - Florida State University
item Kochian, Leon
item Buckler, Edward - Ed
item Hoekenga, Owen

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/11/2010
Publication Date: 4/1/2010
Citation: Krill, A.M., Kirst, M., Kochian, L.V., Buckler Iv, E.S., Hoekenga, O. 2010. Association and linkage analysis of aluminum tolerance genes in maize. PLoS One. 5(4):e9958. DOI: 10.1371/journal.pone.0009958.

Interpretive Summary: More than 40% of the arable lands in the world have acidic soils. This largely natural agronomic problem is a major limitation to agricultural productivity, decreasing food security and increasing production costs. The most important facet of the “acid soil syndrome” is aluminum stress, where this highly abundant metal is solubilized in rhizotoxic forms due to low pH. Thus, we need to obtain a more complete understanding of the genetic, molecular and physiological mechanisms that underlie aluminum stress tolerance in order to improve crop production. In this study, we evaluated the importance of several candidate aluminum tolerance genes using association analysis, a statistical genetics technique that originated in human genetics research but has now been applied to plant genetics as well. Association analysis takes advantage of evolutionary time scales and can identify genes or portions of genes that are important for a trait of interest. We found five new genes that are responsible for improving aluminum stress tolerance in maize. This information will be highly useful to plant breeders, working to improve maize varieties for use in acidic soil regions, and to plant physiologists, working to understand the molecular and physiological bases of aluminum tolerance in maize.

Technical Abstract: Aluminum (Al) toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa. Al exclusion and intracellular tolerance have been suggested as two important mechanisms for Al tolerance in maize, but little is known about the underlying genetics. An association panel of 282 diverse maize inbred lines and three F2 linkage populations were used to study genetic variation in this complex trait. Al tolerance was measured as net root growth in nutrient solution under Al stress, which exhibited a wide range of variation between lines. Comparative and physiological genomics-based approaches were used to select 21 candidate genes for evaluation by association analysis. Six candidate genes had significant results from association analysis, but only four were confirmed by linkage analysis as new Al tolerance genes: Zea mays AltSB like (ZmASL), Zea mays aluminum-activated malate transporter2 (ALMT2), S-adenosyl-L-homocysteinase (SAHH), and Malic Enzyme (ME). These four candidate genes are high priority subjects for follow-up biochemical and physiological studies on the mechanisms of Al tolerance in maize. Immediately, elite haplotype-specific molecular markers can be developed for these four genes and used for efficient, allele specific marker-assisted selection of superior alleles in Al tolerance maize breeding programs.