Genome-wide Identification, Phylogeny And Expression Analysis Of Aldehyde Dehydrogenase(ALDH) And TIFY Gene Families In Apple

Apple (Malus×domestica Borkh.) is economically one of the most important fruit cropsworldwide and the main fruit crop in the temperate regions of the world. The completion ofthe apple genome sequencing has paved the way for novel gene discovery and functionalanalysis. Aldehyde dehydrogenases (ALDHs) represent a protein superfamily encodingNAD(P)+-dependent enzymes that oxidize a wide range of endogenous and exogenousaliphatic and aromatic aldehydes. TIFY transcription factors comprise a plant-specific familyinvolved in the regulation of diverse developmental processes and responses tophytohormones. These two gene families are very important for plant stress tolerance.Although ALDHs and TIFYs have been systematically investigated in model plantArabidopsis, little attention has been paid to these genes in other plants. In this study, allmembers of apple ALDH and TIFY genes were identified in apple genome by bioinformaticsapproaches. Synteny analysis, phylogenetic and comparisons of exon-intron and proteinstructures were used to investigate the evolutionary relationships and their putative functionsof these two familes. In addition, we investigated their tissue-specific expression analysis andtheir response to abiotic stress and various hormone treatments in leaf tissue usingsemi-quantitative RT-PCR and quantitative real-time RT-PCR. The major findings were asfollowing:1. Genome-wide identification and annotation of ALDH and TIFY gene families in apple.39putative apple ALDH genes and30apple TIFY genes were identified in apple genome. Theidentified apple ALDH proteins were annotated using the criteria established by the ALDHGene Nomenclature Committee (AGNC). The39ALDH genes were grouped into ten familiesaccording to the criteria. The nomenclature of TIFY genes were carried out based on theirgenome location and chromosome orders.2. Gene duplications have played crutial roles in the expansion of apple ALDH and TIFYgene families. Gene chromosomal location and synteny analysis of apple ALDH and TIFYgenes within the apple genome demonstrated that tandem and segmental duplications, as well as whole genome duplications, have likely played critical roles in the expansion of the ALDHand TIFY gene families in apple.3. Synteny of apple and Arabidopsis ALDH and TIFY genes. The analyses of thecomparative synteny map between apple and Arabidopsis indicated that several pairedhomologs of ALDH and TIFY genes were located in syntenic genomic regions, indicatingthese syntenic orthologs likely share a common ancestor and have similar biological roles.Thus we could confidently infer the functions of apple ALDH and TIFY genes based on theirArabidopsis homologs.4. Tissue-specific expression profiles of apple ALDH and TIFY genes. Apple ALDH andTIFY genes exhibited diversified spatiotemporal expression patterns in various appletissues/organs, suggesting their likely crucial function in development of apple.5. Apple ALDH and TIFY genes were responsive to several abiotic stresses. All testedapple ALDH and TIFY genes were regulated by at least one abiotic stress (dourght andsalinity), indicating these genes are likely to be involved in plant abiotic stress tolerance.6. Apple ALDH and TIFY genes were responsive to various plant hormones. Expressionanalysis of apple ALDH and TIFY genes in leaves upon different plant hormone (abscisic acid,salicylic acid, methyl jasmonate and ethylene) treatments showed that many apple ALDHgenes were responsive to various plant hormones, indicating that apple ALDH genes may beinvolved in the responses to various plant hormones signaling in stress responses or in appledevelopment. Apple TIFY genes are regulated by ABA and MeJA, but not SA and Eth.