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United States Department of Agriculture

Agricultural Research Service

Research Project: USING FUNCTIONAL AND APPLIED GENOMICS TO IMPROVE STRESS AND DISEASE RESISTANCE IN FRUIT TREES

Location: Appalachian Fruit Research Laboratory: Innovative Fruit Production, Improvement and Protection

Title: Genome-wide identification and analysis of the SBP-box family genes in apple (Malus x domestica Borkh)

Authors
item Li, Jun -
item Hou, Hongmin -
item Li, Xiaoqin -
item Xiang, Jiang -
item Yin, Xiangjing -
item Gao, Hua -
item Zheng, Yi -
item Bassett, Carole
item Wang, Xiping -

Submitted to: Plant Physiology and Biochemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 15, 2013
Publication Date: August 23, 2013
Citation: Li, J., Hou, H., Li, X., Xiang, J., Yin, X., Gao, H., Zheng, Y., Bassett, C.L., Wang, X. 2013. Genome-wide identification and analysis of the SBP-box family genes in apple (Malus x domestica Borkh). Plant Physiology and Biochemistry. 70:100-114.

Interpretive Summary: Genes determine important apple traits, such as fruit development and quality, disease resistance and survival under adverse weather conditions. In order to improve desirable physical traits in apple, it is imperative that we understand how the genes controlling these traits are regulated. The SBP family of genes in plants encode transcript factors that regulate the expression of many different genes. This paper describes how different members of this family are regulated and the impact this has on response to various plant hormones. Information derived from these studies can be used in breeding programs to select desirable cultivars with improved characteristics.

Technical Abstract: SQUAMOSA promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors and play many crucial roles in plant development. In this study, 27 SBP-box gene family members were identified in the apple (Malus × domestica Borkh.) genome, 15 of which were suggested to be putative targets of MdmiR156. Plant SBP proteins were classified into eight groups according to the phylogenetic analysis of SBP-domain proteins. Gene structure, gene chromosomal location and synteny analysis of MdSBP genes within the apple genome demonstrated that tandem and segmental duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of the SBP-box gene family in apple. Additionally, synteny analysis between apple and Arabidopsis indicated that several paired homologs of MdSBP and AtSPL genes were located in syntenic genomic regions. Tissue-specific expression analysis of MdSBP genes in apple demonstrated their diversified spatiotemporal expression patterns. Most MdmiR156-targeted MdSBP genes, which had relatively high transcript levels in stems, leaves, apical buds and some floral organs, exhibited a more differential expression pattern than most MdmiR156-nontargeted MdSBP genes. Finally, expression analysis of MdSBP genes in leaves upon different plant hormone treatments showed that many MdSBP genes were responsive to different plant hormones, indicating that MdSBP genes may be involved in responses to various plant hormones signaling during stress or in apple development. The results obtained provide basic information about the apple MdSBP gene family, which should facilitate further research aimed at revealing the potentially important function of MdSBP genes in apple.

Last Modified: 9/22/2014