Genome-wide identification and expression analyses of homeodomain-leucine zipper family genes reveal their involvement in stress response in apple(Malus×domestica)

The homeodomain-leucine zipper(HD-Zip)family has been shown to perform amultitude of functions during plant development and stress responses;however,the familymembers and functions have not been identified in apple(Malus×domestica).In this study,83 HD-Zips(MdHDZs)were identified in the apple genome.They were assembled into four subgroups according to the classification in Arabidopsis,where MdHDZs in the same subgroup had similar gene structures and conserved protein motifs.Putative cis-element analysis of MdHDZs promoter regions uncovered numerous elements related to the response of stress and plant hormones.In addition,twelve transcripts of the MdHDZs showed different expression patterns under salt,drought,low temperature and ABA stresses by quantitative reverse transcription-PCR(qRT-PCR)assay.To further explore the function of MdHDZs in apple,MdHDZ3 was selected to verify its function under salt,low temperature and ABA stresses;and genetic transformation was used to obtain MdHDZ3 transgenic apple calli.The results demonstrated that MdHDZ3 increased sensitivity to salt,low temperature and abscisic acid in apple calli,suggesting that MdHDZ3 plays an important role in response to stresses.Subcellular localization and three-dimensional structural analysis revealed that MdHDZ3 was a nuclear-localized protein.Taken together,these findings provide potential information for further identification of HD-Zip proteins in apple.

Unraveling a genetic roadmap for improved taste in the domesticated apple

Although taste is an important aspect of fruit quality, an understanding of its genetic control remains elusive in apple and other fruit crops. In this study, we conducted genomic sequence analysis of 497 Malus accessions and revealed erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size, but not for fruit sugar content, were detected during the processes of both domestication and improvement. Furthermore, we found that single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate, and sorbitol accumulation, respectively, and correspond to important domestication events. Interestingly, Ma1 was identified to have pleiotropic effects on both organic acid content and sugar:acid ratio, suggesting that it plays a vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. Collectively, our study provides new insights into the genetic basis of fruit quality and its evolutionary roadmap during apple domestication, pinpointing several candidate genes for genetic manipulation of fruit taste in apple.