Genome-wide characterization of the SHORT INTER-NODES/STYLISH and Shi-Related Sequence family in Gossypium hirsutum and functional identification of GhSRS21 under salt stress

Abstract

Saline stress is a significant factor that caused crop growth inhibition and yield decline. SHORT INTERNODES/STYLISH (SHI/STY) and SHI-RELATED SEQUENCE (SRS) transcription factors are specific to plants and share a conserved RING-like zinc-finger domain (CX2CX7CX4CX2C2X6C). However, the functions of SHI/STY and SRS genes in cotton responses to salt stress remain unclear. In this study, 26 GhSRSs were identified in Gossypium hirsutum, which further divided into three subgroups. Phylogenetic analysis of 88 SRSs from8 plant species revealed independent evolutionary pattern in some of SRSs derived from monocots. Conserved domain and subcellular location predication of GhSRSs suggested all of them only contained the conserved RING-like zinc-finger domain (DUF702) domain and belonged to nucleus-localized transcription factors except for the GhSRS22. Furthermore, synteny analysis showed structural variation on chromosomes during the process of cotton polyploidization. Subsequently, expression patterns of GhSRS family members in response to salt and drought stress were analyzed in G. hirsutum and identified a salt stress-inducible gene GhSRS21. The GhSRS21 was proved to localize in the nuclear and silencing it in G. hirsutum increased the cotton resistance to salt using the virus-induced gene silencing (VIGS) system. Finally, our transcriptomic data revealed that GhSRS21 negatively controlled cotton salt tolerance by regulating the balance between ROS production and scavenging. These results will increase our understanding of the SRS gene family in cotton and provide the candidate resistant gene for cotton breeding.

Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus

“…Additionally, some BnSRS genes contained stress-responsive, drought-inducibility, cell cycle regulation, and other related elements in the promoter region (Figure 6). These results suggest that BnSRS genes may play a crucial role in regulating hormone responses and in response to stresses, as well as growth and development, which is consistent with the SRS gene family in Cassava [61] and cotton [8].…”

“…Transcriptome data were obtained from the previous studies that included a total of 32 tissues containing bud, callus, leaf, stamen, new pistil, blossomy pistil, wilting pistil, stem, sepal, ovule, 11 time-course seeds and silique walls (0, 4,8,12,16,20,24,28,32,40,48), and five stress conditions (Sclerotinia sclerotiorum (S. sclerotiorum), dehydration, salt, cold, and abscisic acid) [45][46][47]. These data were aligned to the reference genome by software hisat2 with the following parameters: -t -p 40-min-intronlen 20-max-intronlen 20,000-dta [48], and the expression quantity based on the transcripts per kilobase million (TPM) normalization method was calculated by software Stringtie with the setting: -e -B -p 30 -f 0.1 [49].…”

“…To reveal the phylogenetic relationship of BnSRS, a maximum likelihood (ML) phylogenetic tree was constructed using protein sequences of the SRS gene from 34 BnSRSs, 10 AtSRSs, 6 OsSRSs [7], 26 GhSRSs [8], and 21 GmSRSs [9]. The results showed that all SRSs could be classified into four groups according to the clustering relationship, with varying numbers of gene members per group.…”

“…B. napus serves multiple purposes in our daily lives, including being used as edible oil, vegetable, high-quality protein animal feed, potential energy crop, and so on. SRS transcription factors play an important role in various biologic processes [2][3][4][5][6][7][8][9][10]. Nevertheless, their function in B. napus has not been extensively studied.…”

“…The number of SRS gene family members differs among different plants. Arabidopsis thaliana (Arabidopsis), for example, a popular model plant, contains 10 members including SHI, STY1(SRS1/STYlISH1), STY2(SRS2/STYlISH2), LRP1(LATERAL ROOT PRI-MORDIUM1), and SRS3-SRS8 (SHI-related sequence 3-8) [2,[4][5][6], 6 in rice [7], 26 in cotton [8], and 21 in soybean [9]. Extensive research has been conducted on SRS genes since their discovery in Arabidopsis.…”