Journal of Genetics

, 98:13 | Cite as

Genomewide analysis of homeobox gene family in apple (Malus domestica Borkh.) and their response to abiotic stress

  • Rong Li
  • Hongjuan Ge
  • Yaqing Dai
  • Li Yuan
  • Xin Liu
  • Qinghua SunEmail author
  • Xiaoyun WangEmail author
Research Article


Homeobox proteins (HOXs) comprise a large family in eukaryotes and share a highly conserved DNA-binding motif, the homeodomain (HD). HOXs play an important role in the regulation of plant growth, development and stress response. However, systematic analysis and expression profiling of these genes have not been reported in Malus domestica. In this study, a total of 207 HOXs of M. domestica (MdHOXs) were identified and classified into 11 distinct subfamilies, and an unclassified group according to their functional domains. The MdHOXs were localized in all 17 chromosomes with various densities and a majority of them tended to form gene clusters. Analysis of the \(K_{\mathrm{a}}/K_{\mathrm{s}}\) ratios suggested that the duplicated genes of MdHOXs mainly underwent purifying selection with restrictive functional divergence after the duplication events. The expression of MdHOXs has organ specific characteristics and were divided into seven different groups. Stress-related cis-acting elements were prevalent in the upstream sequence of MdHOXs by systematic analysis. To explore the response to abiotic stress, eight MdHOXs were randomly selected to investigate their expression using quantitative real-time polymerase chain reaction. Transcription levels of MdHOXs were upregulated in the leaves and roots under cold, osmotic, high salinity or exogenous ABA treatments, which suggested that they may take part in the plant response to abiotic stress. These results provided basic information of HOXs in apple and will further contribute to the functional research of MdHOXs, especially the response to abiotic stress.


homeobox apple expression pattern stress-related cis-acting element analysis abiotic stress 



This work was supported by the Special Research Fund of Public Welfare of China Agricultural Ministry (201303093) and China Natural Foundation (31872042).

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Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  1. 1.College of Life Science, State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianPeople’s Republic of China
  2. 2.Qingdao Academy of Agricultural ScienceQingdaoPeople’s Republic of China

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