ARS | Publication request: Aluminum tolerance is associated with higher MATE1 gene copy-number in maize

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 7, 2013
Publication Date: N/A

Interpretive Summary: Over 20% of the US land area and approximately 50% of the world’s arable lands are acidic (pH Technical Abstract: Genome structure variation, including copy-number (CNV) and presence/absence variation (PAV), comprise a large extent of maize genetic diversity but their effect on phenotypes remains largely unexplored. Here we describe how copy-number variation in a major aluminum (Al) tolerance locus contributes to this agronomically important trait. In a recombinant inbred line (RIL) mapping population, copy-number variation of the Al tolerance gene multidrug and toxic compound extrusion1 (MATE1) underlies the QTL of largest effect on phenotypic variation. While the Al-tolerant parent carries three copies of MATE1, the sensitive parent carries only one. RILs segregate in a 1:1 ratio for MATE1 copy-number; individuals with three gene copies are significantly more Al-tolerant and show higher MATE1 expression than those inheriting a single copy. Sequencing of a BAC clone from the Al-tolerant parental line revealed that the three MATE1 copies, which are identical, are part of a tandem triplication. CNV for MATE1 is rare, as only two additional maize inbred lines carrying the three-copy haplotype were identified; these lines are also Al-tolerant, have high MATE1 expression, and share the same geographic origin froma region of highly acidic soils. Our findings indicate that greater MATE1 copy-number drives higher MATE1 expression that results in superior Al tolerance, and suggest a role for structural variation in the broad adaptation of maize to acidic soils in the tropics.