Identification and Expression Analysis of Homeobox Gene Family in Potato (Solanum tuberosum)
YE Ming-Hui1, ZHAO Peng1, NIU Yang1, WANG Dong-Dong1,*, CHEN Qin2,*
1 State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling 712100, China; 2 College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
Abstract：Homeobox (HB) genes play an important role in diverse physiological and developmental processes of plants. The HB genes of many plants have been identified. However, the complete identification and classification of potato HB genes is still lacking. In this study, a total of 35 HB genes in the potato (Solanum tuberosum) were identified. The physicochemical properties, phylogenetic relationships, chromosome locations, gene and protein structure, and potential functions were analyzed in detail by bioinformatics. The tissue-specific expression patterns of potato HB genes were also analyzed with qRT-PCR. According to the Neighbor-joining phylogenetic tree and domain architecture, 35 potato HB genes were classified into 6 subfamilies. An analysis of the exon-intron structures and conserved motifs provided further insight into the evolutionary relationships between these genes. Synteny analysis of potato, Arabidopsis and tomato genomes provided a reference for the potential functional relevance of these HB genes. All of the potato HB genes were distributed on 12 chromosomes. Through the RNA sequencing (RNA-Seq) and qRT-PCR analyses, many potato HB genes including StBEL35 (S. tuberosum bell-type homeobox 35), StKNOX1 (S. tuberosum KNOTTED1-like homeobox 1) and StKNOX9 showed a relatively higher expression levels on storage organs (including stolon and tuber). Most of these genes showed higher expression levels in mature tubers, indicating that they may play a role in the later stages of tuber development. Combined with previous studies, these genes may be involved in gibberellins (GA) biosynthesis, thereby affecting tuber formation. This study will facilitate the functional analysis of these genes and provide comprehensive information for further analyses of the molecular functions of the potato HB gene family, and provide a theoretical basis for further molecular breeding in potato.
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