Uncovering a Major Ma1 Associated Co-Expression Gene Network Governing Apple Fruit Acidity

Acidity is a major contributor to fruit quality. Several organic acids are present in apple fruit, but malic acid is predominant and determines fruit acidity. The trait is largely controlled by the Malic acid (Ma) locus, underpinning which Ma1 that encodes an Aluminum-activated Malate Transporter1 (ALMT1) like protein is a strong candidate gene. To understand the transcriptional control of Ma1 and its associated gene network, we analyzed the transcriptomes of mature fruit from two genotype groups Ma_ (MaMa or Mama) and mama of contrasting acidity using RNA-seq approach. The analysis identified 672 genes (including Ma1) that were expressed differentially between the two groups. Network inferring revealed a major Ma1 associated co-expression network of 501 genes, where Ma1 had eight primary and 54 secondary neighbor genes. Analyzing the major network uncovered two parallel cores with the first core of five genes being directly associated with Ma1. Revealing the putative identity of three genes that are not only part of the first core but also the Ma1 primary neighbors showed that two are calcium (Ca²⁺) signaling related protein encoding genes, i.e. M140330 (A. thaliana calmodulin like 3 –AtCML3 like) and M319170 (a calmodulin binding protein AtIQD2 like), and one is a transcription factor M423596 (AtHB13 like). This indicated that calcium signaling is likely a crucial mechanism regulating Ma1 and the Ma1 associated network governing fruit acidity.