AUTHOR=Zhou Xiaoke , Li Yun , Wang Jian , Zhao Yuxue , Wang Huimin , Han Yucui , Lin Xiaohu 

TITLE=Genome-wide identification of U-box gene family and expression analysis in response to saline-alkali stress in foxtail millet (Setaria italica L. Beauv)

JOURNAL=Frontiers in Genetics

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1356807

DOI=10.3389/fgene.2024.1356807

ISSN=1664-8021

ABSTRACT=<p>E3 ubiquitin ligases are central modifiers of plant signaling pathways that regulate protein function, localization, degradation, and other biological processes by linking ubiquitin to target proteins. E3 ubiquitin ligases include proteins with the U-box domain. However, there has been no report about the foxtail millet (<italic>Setaria italica</italic> L. Beauv) <italic>U-box</italic> gene family (<italic>SiPUB</italic>) to date. To explore the function of <italic>SiPUBs</italic>, this study performed genome-wide identification of <italic>SiPUBs</italic> and expression analysis of them in response to saline-alkali stress. A total of 70 <italic>SiPUBs</italic> were identified, which were unevenly distributed on eight chromosomes. Phylogenetic and conserved motif analysis demonstrated that <italic>SiPUBs</italic> could be clustered into six subfamilies (I–VI), and most <italic>SiPUBs</italic> were closely related to the homologues in rice. Twenty-eight types of <italic>cis</italic>-acting elements were identified in <italic>SiPUBs</italic>, most of which contained many light-responsive elements and plant hormone-responsive elements. Foxtail millet had 19, 78, 85, 18, and 89 collinear <italic>U-box</italic> gene pairs with <italic>Arabidopsis</italic>, rice, sorghum, tomato, and maize, respectively. Tissue specific expression analysis revealed great variations in <italic>SiPUB</italic> expression among different tissues, and most <italic>SiPUBs</italic> were relatively highly expressed in roots, indicating that <italic>SiPUBs</italic> may play important roles in root development or other growth and development processes of foxtail millet. Furthermore, the responses of 15 <italic>SiPUBs</italic> to saline-alkali stress were detected by qRT-PCR. The results showed that saline-alkali stress led to significantly differential expression of these 15 <italic>SiPUBs</italic>, and <italic>SiPUB20/48/70</italic> may play important roles in the response mechanism against saline-alkali stress. Overall, this study provides important information for further exploration of the biological function of <italic>U-box</italic> genes.</p>