Identification and Evolutionary Analysis of Cotton (<i>Gossypium hirsutum</i>) <i>WOX</i> Family Genes and Their Potential Function in Somatic Embryogenesis
WUSCHEL-related homeobox (WOX) proteins participate profoundly in plant development and stress responses. As the difficulty of somatic embryogenesis severely constrains cotton genetic modification, in this study, we identified and comprehensively analyzed <i>WOX</i> genes in cotton. As a...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-07-01
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| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/24/13/11077 |
| Summary: | WUSCHEL-related homeobox (WOX) proteins participate profoundly in plant development and stress responses. As the difficulty of somatic embryogenesis severely constrains cotton genetic modification, in this study, we identified and comprehensively analyzed <i>WOX</i> genes in cotton. As a result, 40 <i>WOX</i> genes were identified in the upland cotton genome. All these cotton <i>WOX</i> genes were classified into three clades, ancient, intermediate, and modern clades, based on the phylogenetic analysis of previous studies. The majority (24) of the cotton <i>WOX</i> genes belonged to the modern clade, in which all gene members contain the vital functional domain WUS-box, which is necessary for plant stem cell regulation and maintenance. Collinearity analysis indicated that the <i>WOX</i> gene family in cotton expanded to some degree compared to Arabidopsis, especially in the modern clade. Genome duplication and segmental duplication may greatly contribute to expansion. Hormone-response- and abiotic-stress-response-related cis-acting regulatory elements were widely distributed in the promoter regions of cotton <i>WOX</i> genes, suggesting that the corresponding functions of stress responses and the participation of development processes were involved in hormone responses. By RNA sequencing, we profiled the expression patterns of cotton <i>WOX</i> genes in somatic embryogenesis. Only about half of cotton <i>WOX</i> genes were actively expressed during somatic embryogenesis; different cotton <i>WOX</i> genes may function in different development stages. The most representative, <i>GhWOX4</i> and <i>GhWOX13</i>, may function in almost all stages of somatic embryogenesis; <i>GhWOX2</i> and <i>GhWOX9</i> function in the late stages of embryo patterning and embryo development during cotton somatic embryogenesis. Co-expression analysis showed that the cotton <i>WOXs</i> co-expressed with genes involved in extensive genetic information processing, including DNA replication, DNA repair, homologous recombination, RNA transport, protein processing, and several signaling and metabolism pathways, in which plant hormones signal transduction, MAPK signaling pathways, phosphatidylinositol signaling systems, and ABC transporters, as well as the metabolism of fatty acid; valine, leucine, and isoleucine biosynthesis; and cutin, suberine, and wax biosynthesis, were most significantly enriched. Taken together, the present study provides useful information and new insights into the functions of cotton <i>WOX</i> genes during somatic embryogenesis. The specific regulatory roles of some <i>WOX</i> genes in somatic embryogenesis are worthy of further functional research. |
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| ISSN: | 1661-6596 1422-0067 |