Identification and Bioinformatics Analysis of <i>KNOX</i> Gene Family in Wheat (<i>Triticum aestivum</i> L.)

Abstract

KNOTTED-like homeodomain (KNOX) gene family is a transcription factor encoding homeobox protein, which plays an important role in plant growth and morphogenesis. However, little information is available on the KNOX gene family in wheat (Triticum aestivum L.). In this study, 36 KNOX genes with KNOX1 or KNOX2 domain distributed on 18 chromosomes were identified from wheat genome using bioinformatics methods. The phylogenetic evolution, gene structure, protein domains, cis-acting elements and gene expression patterns were analyzed in the present study. Based on the phylogenetic tree, the 36 TaKNOX genes were divided into two major subclasses, Class I and Class II, and the two subclasses were further divided into five evolutionary branches. Most TaKNOX genes contain four typical conserved protein domains: KNOX1, KNOX2, ELK and HOX. Some cis-acting elements are associated with hormonal, plant development and stress in TaKNOX promoters. The analysis result of transcriptome data from wheat different tissue showed that Class I KNOX genes had obvious tissue specificity, while Class II KNOX genes expressed widely in different wheat tissues. The study results provide important information for future analysis of the regulation and functions of the TaKNOX gene family. Keywords Wheat; KNOX gene family; Gene structure; Gene expression KNOX (KNOTTED1-like homeobox) transcription factor family is a subfamily of the homeobox gene TALE (Three amino acid loop extension) protein superfamily, which is widely involved in the regulation of plant growth and development (Hamant and Pautot, 2010). Most KNOX proteins contain four typical conserved domains:

Genome-Wide Classification and Evolutionary Analysis of the KNOX Gene Family in Plants

“…The first KNOX gene (KN1 or ZmKNAT1) was cloned and characterized in Zea mays [7,8]. Until now, the KNOX gene has been characterized in most species, such as 8 members in A. thaliana [6], 23 members in Brassica juncea [9], 20 members in Brassica napus [10], 9 members in Brassica oleracea [11], 12 members in Brassica rapa [9], 8 members in Cardamine hirsute [12], 8 members in Citrus clementina [13], 11 members in Cucumis sativus [14], 8 members in Fragaria vesca [15], 28 members in Glycine max [16], 8 members in Lactuca sativa [17], 17 members in Malus domestica [18], 10 members in Medicago truncatula [19], 7 members in Prunus persica [20], 7 members in Solanum lycopersicum [21], 8 members in Solanum tuberosum [22], 9 members in Triticum aestivum [23], and 9 members in Vitis vinifera [24]. These studies will provide a rich resource for further analysis of the function and evolution of the KNOX family gene in plants.…”