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Title:   Author  item
                                            BAI, YANG - Cornell Universityitem
                                            DOUGHERTY, LAURA - Cornell Universityitem
                                            CHENG, LAILIANG - Cornell Universityitem
                                            Zhong, Gan-Yuanitem
                                            XU, KENONG - Cornell University
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 8/16/2015
                                    Publication  Date: 8/16/2015
                                    Citation: Bai, Y., Dougherty, L., Cheng, L., Zhong, G., Xu, K. 2015. Uncovering co-expression gene network regulating fruit acidity in diverse apples. Biomed Central (BMC) Genomics. 16(1):612. DOI:10.1186/s12864-015-1816-6.Interpretive Summary: Apple fruit can taste very differently. One of the attributes which contribute to taste is acidity. Apple acidity refers to the sensory intensity of tartness of fruit flesh tissues. The stronger the tartness taste, the higher the fruit acidity levels. Apples with different levels of acidity can serve different purposes of consumption. For example, for dessert apples, the acceptable range of fruit acidity was estimated of 3.0-10.0 mg/ml. Because of its importance in determining fruit quality, acidity has long been an important subject area of investigations in apple breeding and genetics. This study identified 672 genes that were expressed differentially between two groups of apples with high and low levels of fruit acidity. Discovery of these genes will help us understand the gene network controlling acidity in apples and ultimately breed apple cultivars with desirable levels of fruit acidity.
                                Technical Abstract: 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. In conjunction with the identification of other Ca2+ signaling related genes, a Ca2+ signal pathway based model was proposed to illustrate the network regulation.


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