Identification and Tissue Expression Pattern Analysis of KNOX Gene Family in Setaria italica
SHI Wei-Ping1, ZHANG Xin1, ZHAO Yuan1,3, LIU Min1,3, DAI Ke-li1, ZHANG Ai-Ying3, GUO Er-Hu3, SHI Guan-Yan1,2,*, GUO Jie1,*
1 College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong 030801, China; 2 Industrial Crop Institute, Shanxi Agricultural University, Taiyuan, 030031, China; 3 Millet Research Institute, Shanxi Agricultural University, Changzhi 046011, China
Abstract：Knotted1-like homeobox (KNOX) is a transcription factor unique to plants, characterized by its homologous domain, and is widely involved in plant growth and development. To explore the potential function of the foxtail millet (Setaria italica) KONXs, bioinformatic methods were used to identify and analyze the SiKNOX gene family at the whole-genome level of foxtail millet, and the expression patterns of SiKNOXs in different tissues were also detected using RT-qPCR. The results showed that a total of 11 SiKNOXs were identified in the S. italica genome. Phylogenetic analysis classified them into 2 groups, classⅠ and classⅡ. ClassⅠ contained 5 SiKNOXs and classⅡ contained 6 SiKNOXs. Subcellular localization prediction revealed that all SiKNOX proteins were predicted to be nuclear. Chromosomal localization analysis showed that they were unevenly distributed among the 7 chromosomes of S. italica. Duplication analysis showed that there were 5 SiKNOXs forming 4 segmental duplication gene pairs. Gene structure analysis revealed that all 11 SiKNOXs consisted of 5~6 exons. Protein conserved domain analysis indicated 10 motifs in SiKNOXs. Motifs 2, 3, 5, and 6 corresponded to the KNOX1, KNOX2, ELK, and HD domains, respectively. The promoter region of the SiKNOXs harbored numerous cis-acting elements that were closely associated with various biological processes. Expression pattern analysis revealed that all SiKNOXs were detected in different tissues (including roots, stems, leaves, tassels, and seeds), and most of them showed tissue-specific expression. This study lays the foundation for further research on KNOX genes family in the growth and development of S. italica.
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