Comparative analysis of SIMILAR to RCD ONE (SRO) family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development
Abstract Background SRO (Similar to RCD1) genes family is largely recognized for their importance in the growth, development, and in responding to environmental stresses. However, genome-wide identification and functional characterization of SRO genes from cotton species have not been reported so fa...
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | Journal of Cotton Research |
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| Online Access: | https://doi.org/10.1186/s42397-024-00165-2 |
| _version_ | 1797275973099454464 |
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| author | Muhammad Shaban Riaz Tabassum Iqrar Ahmad Rana Rana Muhammad Atif Muhammad Abubakkar Azmat Zubair Iqbal Sajid Majeed Muhammad Tehseen Azhar |
| author_facet | Muhammad Shaban Riaz Tabassum Iqrar Ahmad Rana Rana Muhammad Atif Muhammad Abubakkar Azmat Zubair Iqbal Sajid Majeed Muhammad Tehseen Azhar |
| author_sort | Muhammad Shaban |
| collection | DOAJ |
| description | Abstract Background SRO (Similar to RCD1) genes family is largely recognized for their importance in the growth, development, and in responding to environmental stresses. However, genome-wide identification and functional characterization of SRO genes from cotton species have not been reported so far. Results A total of 36 SRO genes were identified from four cotton species. Phylogenetic analysis divided these genes into three groups with distinct structure. Syntenic and chromosomal distribution analysis indicated uneven distribution of GaSRO, GrSRO, GhSRO, and GbSRO genes on A2, D5 genomes, Gh-At, Gh-Dt, Gb-At, and Gb-Dt subgenomes, respectively. Gene duplication analysis revealed the presence of six duplicated gene pairs among GhSRO genes. In promoter analysis, several elements responsive to the growth, development and hormones were found in GhSRO genes, implying gene induction during cotton growth and development. Several miRNAs responsive to plant growth and abiotic stress were predicted to target 12 GhSRO genes. Organ-specific expression profiling demonstrated the roles of GhSRO genes in one or more tissues. In addition, specific expression pattern of some GhSRO genes during ovule development depicted their involvement in these developmental processes. Conclusion The data presented in this report laid a foundation for understanding the classification and functions of SRO genes in cotton. |
| first_indexed | 2024-03-07T15:21:42Z |
| format | Article |
| id | doaj.art-3bb032088cca4ba49f5eb14b757e9669 |
| institution | Directory Open Access Journal |
| issn | 2523-3254 |
| language | English |
| last_indexed | 2024-03-07T15:21:42Z |
| publishDate | 2024-02-01 |
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| record_format | Article |
| series | Journal of Cotton Research |
| spelling | doaj.art-3bb032088cca4ba49f5eb14b757e96692024-03-05T17:34:48ZengBMCJournal of Cotton Research2523-32542024-02-017111310.1186/s42397-024-00165-2Comparative analysis of SIMILAR to RCD ONE (SRO) family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and developmentMuhammad Shaban0Riaz Tabassum1Iqrar Ahmad Rana2Rana Muhammad Atif3Muhammad Abubakkar Azmat4Zubair Iqbal5Sajid Majeed6Muhammad Tehseen Azhar7Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Sub-Campus BurewalaDepartment of Chemistry and Biochemistry, University of AgricultureCentre of Agricultural Biochemistry and Biotechnology, University of AgricultureDepartment of Plant Breeding and Genetics, University of AgricultureDepartment of Plant Breeding and Genetics, University of Agriculture Faisalabad, Sub-Campus BurewalaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural SciencesFederal Seed Certification and Registration Department, Ministry of National Food Security and ResearchDepartment of Plant Breeding and Genetics, University of AgricultureAbstract Background SRO (Similar to RCD1) genes family is largely recognized for their importance in the growth, development, and in responding to environmental stresses. However, genome-wide identification and functional characterization of SRO genes from cotton species have not been reported so far. Results A total of 36 SRO genes were identified from four cotton species. Phylogenetic analysis divided these genes into three groups with distinct structure. Syntenic and chromosomal distribution analysis indicated uneven distribution of GaSRO, GrSRO, GhSRO, and GbSRO genes on A2, D5 genomes, Gh-At, Gh-Dt, Gb-At, and Gb-Dt subgenomes, respectively. Gene duplication analysis revealed the presence of six duplicated gene pairs among GhSRO genes. In promoter analysis, several elements responsive to the growth, development and hormones were found in GhSRO genes, implying gene induction during cotton growth and development. Several miRNAs responsive to plant growth and abiotic stress were predicted to target 12 GhSRO genes. Organ-specific expression profiling demonstrated the roles of GhSRO genes in one or more tissues. In addition, specific expression pattern of some GhSRO genes during ovule development depicted their involvement in these developmental processes. Conclusion The data presented in this report laid a foundation for understanding the classification and functions of SRO genes in cotton.https://doi.org/10.1186/s42397-024-00165-2CottonSROmiRNAsGene duplicationsGene expressionOvule development |
| spellingShingle | Muhammad Shaban Riaz Tabassum Iqrar Ahmad Rana Rana Muhammad Atif Muhammad Abubakkar Azmat Zubair Iqbal Sajid Majeed Muhammad Tehseen Azhar Comparative analysis of SIMILAR to RCD ONE (SRO) family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development Journal of Cotton Research Cotton SRO miRNAs Gene duplications Gene expression Ovule development |
| title | Comparative analysis of SIMILAR to RCD ONE (SRO) family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development |
| title_full | Comparative analysis of SIMILAR to RCD ONE (SRO) family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development |
| title_fullStr | Comparative analysis of SIMILAR to RCD ONE (SRO) family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development |
| title_full_unstemmed | Comparative analysis of SIMILAR to RCD ONE (SRO) family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development |
| title_short | Comparative analysis of SIMILAR to RCD ONE (SRO) family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development |
| title_sort | comparative analysis of similar to rcd one sro family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development |
| topic | Cotton SRO miRNAs Gene duplications Gene expression Ovule development |
| url | https://doi.org/10.1186/s42397-024-00165-2 |
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