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Title: A natural mutation led truncation in Ma1, one of the two aluminum-activated malate transporter like genes at the Ma locus, is associated with low fruit acidity in apple

item BAI, YANG - Cornell University
item DOUGHTERY, LAURA - Cornell University
item LI, MINGJUN - Cornell University
item Fazio, Gennaro
item CHENG, LAILIANG - Cornell University
item XU, KENONG - Cornell University

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/3/2012
Publication Date: 7/18/2012
Citation: Bai, Y., Doughtery, L., Li, M., Fazio, G., Cheng, L., Xu, K. 2012. A natural mutation led truncation in Ma1, one of the two aluminum-activated malate transporter like genes at the Ma locus, is associated with low fruit acidity in apple. Molecular Genetics and Genomics. 287:563-678.

Interpretive Summary: The level of tartness in apples is a major component of fruit flavor and eating preference. High tartness is associated with high levels of malic acid naturally present in apple fruit. High tartness is genetically inherited and one of the major genetic factors has been located on chromosome 16 of the apple genome in a region dubbed the Ma locus. In this study we identified two genes that may be responsible for the tart flavor of apples and associated a mutation in one of the genes to a premature stop of the gene product. In apple trees where the mutation is homozygous it leads to low tartness apples. We have used this information to create new genetic markers for breeding new apple varieties.

Technical Abstract: Acidity levels greatly affect fruit taste and flavor, thereby the consumer’s acceptance and market value. In mature apple fruit, malic acid is the nearly exclusive organic acid. Several studies have confirmed that the major quantitative trait locus Ma largely controls the variation of fruit acidity levels, and the Ma locus has recently been defined in a region of 150 kb that contains 44 predicted genes in the Golden Delicious genome (Xu et al. 2011). In this study, we identified two aluminum-activated malate transporter (ALMT) like genes, designated Ma1 and Ma2, as strong candidates of Ma by narrowing down the Ma locus to 65-82 kb containing of 12-19 predicted genes depending on the haplotypes. The Ma haplotypes were determined by sequencing two BAC clones from G.41 (an apple rootstock of genotype Mama) that cover two distinct haplotypes of the Ma locus. Gene expression profiling in 25 apple germplasm accessions suggested that Ma1 is the major determinant at the Ma locus controlling fruit acidity as Ma1 is expressed at much higher levels than Ma2 and the Ma1 expression is significantly correlated with fruit titratable acidity variation (R2=0.4543, P=0.0021). In the coding sequences of low acidity alleles of Ma1 and Ma2, sequence variations at the amino acid level between Golden Delicious and G.41were not detected. But the alleles for high acidity vary considerably between the two apples. The low acidity allele of Ma1, Ma1-1455A, is mainly characterized by a mutation at base 1455 in the open reading frame. The mutation leads to a premature stop codon that truncates the carboxyl terminus of Ma1-1455A by 84 amino acids compared with protein Ma1-1455G. A survey of 25 apple germplasm accessions using marker CAPS1455 that targets the SNP1455 in Ma1 found that the CAPS1455A allele completely associated with low acidity, suggesting that the natural mutation led truncation is most likely responsible for the abolished function of Ma1 for high acidity in apple.