Aluminum tolerance in maize is associated with higherMATE1gene copy number

Abstract

Genome structure variation, including copy number variation and presence/absence variation, comprises a large extent of maize genetic diversity; however, its effect on phenotypes remains largely unexplored. Here, we describe how copy number variation underlies a rare allele that contributes to maize aluminum (Al) tolerance. Al toxicity is the primary limitation for crop production on acid soils, which make up 50% of the world's potentially arable lands. In a recombinant inbred line mapping population, copy number variation of the Al tolerance gene multidrug and toxic compound extrusion 1 (MATE1) is the basis for the quantitative trait locus of largest effect on phenotypic variation. This expansion in MATE1 copy number is associated with higher MATE1 expression, which in turn results in superior Al tolerance. The three MATE1 copies are identical and are part of a tandem triplication. Only three maize inbred lines carrying the three-copy allele were identified from maize and teosinte diversity panels, indicating that copy number variation for MATE1 is a rare, and quite likely recent, event. These maize lines with higher MATE1 copy number are also Al-tolerant, have high MATE1 expression, and originate from regions of highly acidic soils. Our findings show a role for copy number variation in the adaptation of maize to acidic soils in the tropics and suggest that genome structural changes may be a rapid evolutionary response to new environments. abiotic stress | selection

Duplicate and Conquer: Multiple Homologs ofPHOSPHORUS-STARVATION TOLERANCE1Enhance Phosphorus Acquisition and Sorghum Performance on Low-Phosphorus Soils

“…Lehti-Shiu et al (2009) found that RLKs present in tandem repeats were more likely than nontandem RLKs to be up-regulated by biotic stress factors and UV-B light in Arabidopsis, suggesting that the SbPSTOL1 homologs close together at position 60 Mb on chromosome 3 may constitute a functional module controlled by common regulatory elements. If so, similar to the case for maize aluminum tolerance (Maron et al, 2013), tandem duplication events may provide an additional level of regulation, leading to enhanced gene expression and increased P acquisition controlled by PSTOL1 homologs in sorghum.…”

Recent advances towards understanding and managing Kenyan acid soils for improved crop production

“…A major physiological mechanism of plant aluminum tolerance involves aluminum activation of membrane transporters that mediate organic acid release from the root apex, the site of aluminum phytotoxicity, with the released organic acids forming stable, nontoxic complexes with Al 3+ in the rhizosphere (Magalhaes et al, 2007). In sorghum a multidrug and toxic compound extrusion (MATE) gene that transport citric acid was found to confer Al tolerance (Magalhaes et al, 2007) and in maize a similar gene, ZmMATE1, (Maron et al, 2013) was also found. The introgression of such genes into Al sensitive cultivars have been shown to improve grain yield performance in acid soils.…”

The genome of the stress-tolerant wild tomato species Solanum pennellii

“…Stress tolerance has frequently been associated with allelic polymorphisms 12 , copy number variation 13 and constitutive or inducible differential expression of numerous genes involved in regulatory or metabolic pathways 14 . To specifically target stress-related mechanisms, we identified 389 potential stress-related genes by mining the literature (Supplementary Table 22).…”