Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

Abstract

<jats:title>Abstract</jats:title> <jats:p><jats:bold>Background: </jats:bold>The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton. <jats:bold>Results:</jats:bold> In this study, 108, 55, and 52 <jats:italic>PHD</jats:italic> genes were identified in <jats:italic>G. hirsutum</jats:italic>, <jats:italic>G. raimondii</jats:italic>, and <jats:italic>G. arboreum</jats:italic>, respectively. A total of 297 <jats:italic>PHD</jats:italic> genes from three cotton species, <jats:italic>Arabidopsis</jats:italic>, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for <jats:italic>GhPHD</jats:italic> genes. <jats:italic>GhPHD</jats:italic> genes were unevenly distributed on each chromosome, however, more <jats:italic>GhPHD</jats:italic> genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and <jats:italic>GhPHD</jats:italic> genes exhibiting similar gene structure were clustered together. Further, whole genome duplication analysis indicated that purification selection greatly contributed to the functional maintenance of <jats:italic>GhPHD</jats:italic> gene family. Expression pattern analysis based on RNA-seq data showed that most <jats:italic>GhPHD</jats:italic> genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of <jats:italic>GhPHDs</jats:italic> in plant growth and development. Moreover, analysis of <jats:italic>cis</jats:italic>-acting elements revealed that <jats:italic>GhPHDs</jats:italic> may respond to a variety of abiotic and phytohormonal stresses. In this regard, some <jats:italic>GhPHD</jats:italic> genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that <jats:italic>GhPHDs</jats:italic> are essential for plant growth and development, while <jats:italic>GhPHD</jats:italic> genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions. <jats:bold>Conclusion:</jats:bold> This study will provide useful information to facilitate further research related to the vital roles of <jats:italic>GhPHD</jats:italic> gene family in plant growth and development.</jats:p>

Genome-wide identification and expression analysis of GL2-interacting-repressor (GIR) genes during cotton fiber and fuzz development

“…The gain or loss of key motifs as species evolved may have resulted in changes to protein functions that altered plant development. Phytohormones and abiotic stresses might affect fiber development through signal transduction pathways (Chen et al 2019;He et al 2019;Cheng et al 2020;Wang et al 2020a, b;Zhang et al 2020;Tian and Zhang 2021;Wu et al 2021). We identified numerous cisacting elements responsive to light, phytohormones, defense processes, and stress as well as multiple TF-binding sites upstream of transcriptional start sites.…”

PHD-finger family genes in wheat (Triticum aestivum L.): Evolutionary conservatism, functional diversification, and active expression in abiotic stress

“…Since Schinder first discovered and identified PHD proteins in plants (Schindler et al, 1993), an increasing number of PHDs have been reported. To date, 59 Oryza stiva members (Sun et al, 2017), 108 Gossypium hirsutum members (Wu et al, 2021), 72 Solanum tuberosum members (Qin et al, 2019), 60 Phyllostachys edulis members (Gao et al, 2018), and 67 Zea mays members (Wang et al, 2015a) have been identified. It is known that PHD proteins not only participate in the regulation of plant growth and development but also play an important role in stress response, especially to abiotic stresses such as salt, hightemperature, low-temperature, and drought stress.…”

“…Wei et al also found that Arabidopsis thaliana transgenic plants overexpressing soybean GmPHD2 exhibited higher salt resistance, possibly because overexpression of GmPHD2 enhanced the scavenging of oxidative substances (Wei et al, 2009). Furthermore, under abiotic stress, genes in the PHD-finger family in maize, cotton, and poplar show differential expression under salt, drought, and cold stress (Wang et al, 2015a;Wu et al, 2016;Wu et al, 2021). Thus, it can be seen that the PHD family genes play a crucial role in regulating plant resistance to stress.…”

RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum

“…Cotton is an important economic crop of the world and contributes largely to the textile industry. Different gene families such as GGPPS [ 23 ], LOG [ 24 ], BES1 [ 25 ], GH3 [ 26 ], GSK [ 27 ], GATL [ 28 ], GhPHD [ 29 ] and GhAA1 [ 30 ] have been identified in cotton, but there is no published research about RAD gene family in cotton. Previous studies reported that RAD51 participate in DNA repair, homologous recombination and genome stability.…”