Genome-wide identification and expression analysis of the <italic>SMXL</italic> gene family in cotton

Abstract

<p indent="0mm">Strigolactones (SLs) is a novel plant hormone, which plays an important role in plant growth and development. At present, there are still few studies on SL in cotton. Therefore, it is necessary to explore the function and mechanism of SL on cotton growth and fiber quality. <italic>SMXL</italic>s (<italic>SUPPRESSOR OF MAX2 1-like</italic>s) are key genes of the SL pathway and act as repressors of SL signal transduction. Until now, there are no studies about <italic>SMXL</italic>s gene in cotton. In this study, 16 <italic>GhSMXL</italic>s, 16 <italic>GbSMXL</italic>s, 8 <italic>GaSMXL</italic>s, and 8 <italic>GrSMXL</italic>s were identified in <italic>G. raimondii</italic>,<italic> G. arboreum</italic>, <italic>G. hirsutum</italic>, and <italic>G. barbadense</italic>. Phylogenetic analysis revealed that SMXLs were divided into four subfamilies: SMXL-I (SMXL1, 2), SMXL-II (SMXL6, 7, 8), SMXL-III (SMXL3), and SMXL-IV (SMXL4, 5). The evolutionary characteristics showed that <italic>SMXL</italic> members located in the same subgroup had similar gene and protein structures. Fragment replication was the main reason for SMXL member expansion in cotton. Tissue expression profile analysis showed that <italic>GhSMXL1-A</italic>, <italic>GhSMXL1-D</italic>, <italic>GhSMXL7-1-A</italic>, <italic>GhSMXL7-1-D</italic>, <italic>GhSMXL8-1-A</italic>, and <italic>GhSMXL8-1-D</italic> were dominant expressions in roots, stems, leaves, fibers and ovules. <italic>GaSMXL8-1</italic>, <italic>GaSMXL1</italic>, and <italic>GaSMXL7</italic> were mainly expressed in roots, stems, leaves and ovules. Interestingly, most of the dominant genes were located in the SMXL-I and SMXL-II subfamilies, indicating that these genes might be the key genes in root, stem, leaf and ovule development. Stress expression profile analysis showed that the SMXL-II and SMXL-III subfamily genes (<italic>GhSMXL8-1-A</italic>, <italic>GhSMXL8-1-D</italic>, <italic>GhSMXL8-2-A</italic>, GhSMXL8-2-D, <italic>GhSMXL3-1-A</italic>,<italic> GhSMXL3-1-D</italic>, <italic>GhSMXL3-2-A</italic>, <italic>GhSMXL3-3-A</italic>, and <italic>GhSMXL3-3-D</italic>) have different expression patterns under different salt, drought, low temperature and high temperature treatment. Furthermore, some genes respond to different stress treatment, for example, <italic>GhSMXL8-1-A</italic> responds to both low temperature stress and salt stress, implying that these genes may regulate the response of abiotic stress in cotton. This study lays the foundation for further study of cotton <italic>SMXL</italic>s gene function.