Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Feb 3:14:1123745.
doi: 10.3389/fpls.2023.1123745. eCollection 2023.

Genomic identification of cotton SAC genes branded ovule and stress-related key genes in Gossypium hirsutum

Ma Shuya  1   2 , Liu Le  2 , Shi Huiyun  2 , Gu Yu  2   3 , Li Yujun  2   4 , Ghulam Qanmber  1   2
Affiliations

Genomic identification of cotton SAC genes branded ovule and stress-related key genes in Gossypium hirsutum

Ma Shuya et al. Front Plant Sci. .

Abstract

SAC genes have been identified to play a variety of biological functions and responses to various stresses. Previously, SAC genes have been recognized in animals and Arabidopsis. For the very first time, we identified 157 SAC genes in eight cotton species including three diploids and five tetraploids with 23 SAC members in G. hirsutum. Evolutionary analysis classified all cotton SAC gene family members into five distinct groups. Cotton SAC genes showed conserved sequence logos and WGD or segmental duplication. Multiple synteny and collinearity analyses revealed gene family expansion and purifying selection pressure during evolution. G. hirsutum SAC genes showed uneven chromosomal distribution, multiple exons/introns, conserved protein motifs, and various growth and stress-related cis-elements. Expression pattern analysis revealed three GhSAC genes (GhSAC3, GhSAC14, and GhSAC20) preferentially expressed in flower, five genes (GhSAC1, GhSAC6, GhSAC9, GhSAC13, and GhSAC18) preferentially expressed in ovule and one gene (GhSAC5) preferentially expressed in fiber. Similarly, abiotic stress treatment verified that GhSAC5 was downregulated under all stresses, GhSAC6 and GhSAC9 were upregulated under NaCl treatment, and GhSAC9 and GhSAC18 were upregulated under PEG and heat treatment respectively. Overall, this study identified key genes related to flower, ovule, and fiber development and important genetic material for breeding cotton under abiotic stress conditions.

Keywords: SAC genes; abiotic stresses; cotton; flower; multiple synteny; ovule; phylogenetic analysis.

PubMed Disclaimer

Conflict of interest statement

The AE MA declared a shared affiliation with the Authors MS, LL, SH at the time of review. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic analysis of cotton SAC genes. Phylogenetic tree among 157 SAC genes from three diploids (G. herbaceum, G. arboreum, and G. raimondii) and five tetraploids (G. hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii) cotton species. The prefixes Ghe. Ga, Gr, Gh, Gb, Gt, Gm, and Gd represents G. herbaceum, G. arboreum, G. raimondii, G. hirsutum, G. barbadense, G. tomentosum, G. mustelinum and G. darwinii respectively.
Figure 2
Figure 2
Multiple synteny analysis among cotton SAC genes. Multiple synteny analysis was used to show the orthologous relationship among G. herbaceum, G. arboreum, G. raimondii, G. hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii SAC genes. Chromosomes of different cotton species were represented with different colors.
Figure 3
Figure 3
Collinearity analysis of G. hirsutum and G. barbadense SAC genes. (A) Collinearity analysis of G. hirsutum SAC genes. (B) Collinearity analysis of G. barbadense SAC genes. A01 to A13 represents A-subgenome chromosomes while D01 to D13 represents D-subgenome chromosomes. Homologous gene pairs between A- to A-subgenome were represented with blue lines, homologous gene pairs between A- to D-subgenome were represented with red lines, and homologous gene pairs between the D- to D-subgenome were represented with green lines.
Figure 4
Figure 4
Promoter cis-element analysis of GhSAC genes. G. hirsutum SAC genes promoter region (2kb upstream from start codon) was used to explore cis-elements related to plant growth, abiotic stresses, and phytohormonal responses.
Figure 5
Figure 5
Expression pattern analysis of GhSAC genes. qRT-PCR analysis was performed to observe the relative expression patterns of GhSAC genes in vegetative, ovule, and fiber tissue of the cotton plant. Each experiment was conducted in three biological repeats and the error bar represents the standard deviation among repeats.
Figure 6
Figure 6
Responses of GhSAC genes under abiotic stresses. qRT-PCR analysis was performed to observe the relative expression patterns of GhSAC genes under cold, heat, NaCl, and PEG treatment. Each experiment was conducted in three biological repeats and the error bar represents the standard deviation among repeats.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Ali F., Qanmber G., Li F., Wang Z. (2021). Updated role of ABA in seed maturation, dormancy, and germination. J. Adv. Res. 35:199–214. doi: 10.1016/j.jare.2021.03.011 - DOI - PMC - PubMed
    1. Ali F., Qanmber G., Wei Z., Yu D., Li Y., Gan L., et al. . (2020). Genome-wide characterization and expression analysis of geranyl geranyl diphosphate synthase genes of cotton (Gossypium spp.) in plant development and abiotic stresses. BMC Genomics 21:1–15. doi: 10.1186/s12864-020-06970-8 - DOI - PMC - PubMed
    1. Bailey T. L., Williams N., Misleh C., Li W. W. (2006). MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34, W369–W373. doi: 10.1093/nar/gkl198 - DOI - PMC - PubMed
    1. Chen C., Chen H., Zhang Y., Thomas H. R., Frank M. H., He Y., et al. . (2020). TBtools: An integrative toolkit developed for interactive analyses of big biological data. Mol. Plant 13, 1194–1202. doi: 10.1016/j.molp.2020.06.009 - DOI - PubMed
    1. Crooks G. E., Hon G., Chandonia J.-M., Brenner S. E. (2004). WebLogo: A sequence logo generator. Genome Res. 14, 1188–1190. doi: 10.1101/gr.849004 - DOI - PMC - PubMed

LinkOut - more resources