▪ Abstract Acid soils significantly limit crop production worldwide because approximately 50% of the world's potentially arable soils are acidic. Because acid soils are such an important constraint to agriculture, understanding the mechanisms and genes conferring tolerance to acid soil stress has been a focus of intense research interest over the past decade. The primary limitations on acid soils are toxic levels of aluminum (Al) and manganese (Mn), as well as suboptimal levels of phosphorous (P). This review examines our current understanding of the physiological, genetic, and molecular basis for crop Al tolerance, as well as reviews the emerging area of P efficiency, which involves the genetically based ability of some crop genotypes to tolerate P deficiency stress on acid soils. These are interesting times for this field because researchers are on the verge of identifying some of the genes that confer Al tolerance in crop plants; these discoveries will open up new avenues of molecular/physiological inquiry that should greatly advance our understanding of these tolerance mechanisms. Additionally, these breakthroughs will provide new molecular resources for improving crop Al tolerance via both molecular-assisted breeding and biotechnology.

Aluminum (Al) tolerance in Arabidopsis is a genetically complex trait, yet it is mediated by a single physiological mechanism based on Al-activated root malate efflux. We investigated a possible molecular determinant for Al tolerance involving a homolog of the wheat Al-activated malate transporter, ALMT1 . This gene, named AtALMT1 (At1g08430), was the best candidate from the 14-member AtALMT family to be involved with Al tolerance based on expression patterns and genomic location. Physiological analysis of a transferred DNA knockout mutant for AtALMT1 as well as electrophysiological examination of the protein expressed in Xenopus oocytes showed that AtALMT1 is critical for Arabidopsis Al tolerance and encodes the Al-activated root malate efflux transporter associated with tolerance. However, gene expression and sequence analysis of AtALMT1 alleles from tolerant Columbia (Col), sensitive Landsberg erecta (Ler), and other ecotypes that varied in Al tolerance suggested that variation observed at AtALMT1 is not correlated with the differences observed in Al tolerance among these ecotypes. Genetic complementation experiments indicated that the Ler allele of AtALMT1 is equally effective as the Col allele in conferring Al tolerance and Al-activated malate release. Finally, fine-scale mapping of a quantitative trait locus (QTL) for Al tolerance on chromosome 1 indicated that AtALMT1 is located proximal to this QTL. These results indicate that AtALMT1 is an essential factor for Al tolerance in Arabidopsis but does not represent the major Al tolerance QTL also found on chromosome 1.

Advances in “omics” technologies have revolutionized the collection of biological data. A matching revolution in our understanding of biological systems, however, will only be realized when similar advances are made in informatic analysis of the resulting “big data.” Here, we compare the capabilities of three conventional and novel statistical approaches to summarize and decipher the tomato metabolome. Principal component analysis (PCA), batch learning self-organizing maps (BL-SOM) and weighted gene co-expression network analysis (WGCNA) were applied to a multivariate NMR dataset collected from developmentally staged tomato fruits belonging to several genotypes. While PCA and BL-SOM are appropriate and commonly used methods, WGCNA holds several advantages in the analysis of highly multivariate, complex data. PCA separated the two major genetic backgrounds (AC and NC), but provided little further information. Both BL-SOM and WGCNA clustered metabolites by expression, but WGCNA additionally defined “modules” of co-expressed metabolites explicitly and provided additional network statistics that described the systems properties of the tomato metabolic network. Our first application of WGCNA to tomato metabolomics data identified three major modules of metabolites that were associated with ripening-related traits and genetic background.

Malate transporters play a critical role in aluminum (Al) tolerance responses for some plant species, such as Arabidopsis (Arabidopsis thaliana). Here, we further characterize AtALMT1, an Arabidopsis aluminum-activated malate transporter, to clarify its specific role in malate release and Al stress responses. Malate excretion from the roots of accession Columbia was sharply induced by Al, which is concomitant with the induction of AtALMT1 gene expression. The malate release was specific for Al among rhizotoxic stressors, namely cadmium, copper, erbium, lanthanum, sodium, and low pH, which accounts for the specific sensitivity of a null mutant to Al stress. Al-specific malate excretion can be explained by a combined regulation of AtALMT1 expression and activation of AtALMT1 protein, which is specific for Al. Although low pH treatment slightly induced gene expression, other treatments did not. In addition, malate excretion in Al-activated seedlings was rapidly stopped by removing Al from the solution. Other rhizotoxic stressors were not effective in maintaining malate release. Protein kinase and phosphatase inhibitor studies indicated that reversible phosphorylation was important for the transcriptional and posttranslational regulation of AtALMT1. AtALMT1 promoter-β-glucuronidase fusion lines revealed that AtALMT1 has restricted expression within the root, such that unnecessary carbon loss is likely minimized. Lastly, a natural nonsense mutation allele of AtALMT1 was identified from the Al-hypersensitive natural accession Warschau-1.