Transcriptome dynamics along with expression analysis of key genes involved in fiber development between Gossypium barbadense and Gossypium darwinii
Abstract The transcriptome profiling for underpinning the role of key genes controlling formation of fiber in cultivated Gossypium barbadense compared to wild allotetraploid cotton Gossypium darwinii which remained less investigated. Owing to excellent fiber quality of both Gossypium barbadense and...
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2025-05-01
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| Online Access: | https://doi.org/10.1186/s12870-025-06697-2 |
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| author | Allah Ditta Xiaoyan Cai Muhammad Shehzad Sajid Fiaz Yanchao Xu Yuqing Hou Zunaira Anwar Aqsa Ijaz Najla B. S. Al-Saud Fang Liu Kunbo Wang Baohua Wang Baohong Zhang Ahmed M. Ramadan Muhammad Kashif Riaz Khan Zhongli Zhou |
| author_facet | Allah Ditta Xiaoyan Cai Muhammad Shehzad Sajid Fiaz Yanchao Xu Yuqing Hou Zunaira Anwar Aqsa Ijaz Najla B. S. Al-Saud Fang Liu Kunbo Wang Baohua Wang Baohong Zhang Ahmed M. Ramadan Muhammad Kashif Riaz Khan Zhongli Zhou |
| author_sort | Allah Ditta |
| collection | DOAJ |
| description | Abstract The transcriptome profiling for underpinning the role of key genes controlling formation of fiber in cultivated Gossypium barbadense compared to wild allotetraploid cotton Gossypium darwinii which remained less investigated. Owing to excellent fiber quality of both Gossypium barbadense and Gossypium darwinii and information obtained via Simple Sequence Repeat (SSR) markers, two lines: Xh-18 and darwinii 5–7 were selected for transcriptome sequencing during developmental stages i.e., fiber initiation, elongation, and secondary cell wall (SCW) biosynthesis followed by 0 day after anthesis (DPA), 5DPA, 10DPA, 15DPA and 25DPA, respectively. Twelve libraries of RNA-seq were generated and sequenced individually generating approximately 818 million clean reads of Gossypium darwinii. However, for Gossypium barbadense more than 844 million clean reads were recorded. The Pearson Correlation Coefficient (PCC) analysis results indicated that gene expressions for both Gossypium barbadense and Gossypium darwinii indicated more than 90% of the commonalities at the same stage of fiber growth. However, genes found among Gossypium darwinii at 5, 6 and 7 DPA and XH-18 at 10 and 25 DPA were found disimilar. The expression quantity of RNA sequencing data, 31 genes were found common throughout all stages of DPAs in Gossypium darwinii 5–7 whereas, 377 genes were common in Gossypium barbadense XH-18 at 0, 5, 10, 15, 20, and 25 DPA stages of fiber development. Three genes XLOC_080616 (LTPG2_ARATH/ NLTL2_ARATH; GPI-anchored 2 non-specific lipid transfer protein, similar to At2 g13820), XLOC_065471 (LPAT2_ARATH/LPAT2_BRAOL 1-acyl-sn-glycerol-3-phosphate acyltransferase2), and XLOC_077416 (uncharacterized protein) shown up-regulated expression during 15 and 20 DPA for both Gossypium barbadense and Gossypium darwinii. It will also explore the possible role Gossypium barbadense DNA segment associated with development of fiber quality. Furthermore, this research will decipher the underlying process of fiber development and the possible role of genes for fiber formation in both Sea Island and wild cotton species. |
| format | Article |
| id | doaj-art-487af8bc38c84bacb642909681f66a95 |
| institution | OA Journals |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-487af8bc38c84bacb642909681f66a952025-08-20T01:52:22ZengBMCBMC Plant Biology1471-22292025-05-0125112010.1186/s12870-025-06697-2Transcriptome dynamics along with expression analysis of key genes involved in fiber development between Gossypium barbadense and Gossypium darwiniiAllah Ditta0Xiaoyan Cai1Muhammad Shehzad2Sajid Fiaz3Yanchao Xu4Yuqing Hou5Zunaira Anwar6Aqsa Ijaz7Najla B. S. Al-Saud8Fang Liu9Kunbo Wang10Baohua Wang11Baohong Zhang12Ahmed M. Ramadan13Muhammad Kashif Riaz Khan14Zhongli Zhou15State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural SciencesState Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural SciencesState Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural SciencesInstitute of Molecular Biology and Biotechnology, The University of LahoreState Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural SciencesState Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural SciencesPakistan Institute of Applied and Engineering Sciences (PIEAS), NIAB-CState Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural SciencesDepartment of Biological Sciences, Faculty of Sciences, King Abdulaziz UniversityState Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural SciencesState Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural SciencesSchool of Life Sciences, Nantong UniversityDepartment of Biology, East Carolina UniversityDepartment of Biological Sciences, Faculty of Sciences, King Abdulaziz UniversityNuclear Institute for Agriculture and Biology (NIAB)State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural SciencesAbstract The transcriptome profiling for underpinning the role of key genes controlling formation of fiber in cultivated Gossypium barbadense compared to wild allotetraploid cotton Gossypium darwinii which remained less investigated. Owing to excellent fiber quality of both Gossypium barbadense and Gossypium darwinii and information obtained via Simple Sequence Repeat (SSR) markers, two lines: Xh-18 and darwinii 5–7 were selected for transcriptome sequencing during developmental stages i.e., fiber initiation, elongation, and secondary cell wall (SCW) biosynthesis followed by 0 day after anthesis (DPA), 5DPA, 10DPA, 15DPA and 25DPA, respectively. Twelve libraries of RNA-seq were generated and sequenced individually generating approximately 818 million clean reads of Gossypium darwinii. However, for Gossypium barbadense more than 844 million clean reads were recorded. The Pearson Correlation Coefficient (PCC) analysis results indicated that gene expressions for both Gossypium barbadense and Gossypium darwinii indicated more than 90% of the commonalities at the same stage of fiber growth. However, genes found among Gossypium darwinii at 5, 6 and 7 DPA and XH-18 at 10 and 25 DPA were found disimilar. The expression quantity of RNA sequencing data, 31 genes were found common throughout all stages of DPAs in Gossypium darwinii 5–7 whereas, 377 genes were common in Gossypium barbadense XH-18 at 0, 5, 10, 15, 20, and 25 DPA stages of fiber development. Three genes XLOC_080616 (LTPG2_ARATH/ NLTL2_ARATH; GPI-anchored 2 non-specific lipid transfer protein, similar to At2 g13820), XLOC_065471 (LPAT2_ARATH/LPAT2_BRAOL 1-acyl-sn-glycerol-3-phosphate acyltransferase2), and XLOC_077416 (uncharacterized protein) shown up-regulated expression during 15 and 20 DPA for both Gossypium barbadense and Gossypium darwinii. It will also explore the possible role Gossypium barbadense DNA segment associated with development of fiber quality. Furthermore, this research will decipher the underlying process of fiber development and the possible role of genes for fiber formation in both Sea Island and wild cotton species.https://doi.org/10.1186/s12870-025-06697-2Single sequence repeatsFiber developmentTranscriptome profileGene FunctionsDPAs |
| spellingShingle | Allah Ditta Xiaoyan Cai Muhammad Shehzad Sajid Fiaz Yanchao Xu Yuqing Hou Zunaira Anwar Aqsa Ijaz Najla B. S. Al-Saud Fang Liu Kunbo Wang Baohua Wang Baohong Zhang Ahmed M. Ramadan Muhammad Kashif Riaz Khan Zhongli Zhou Transcriptome dynamics along with expression analysis of key genes involved in fiber development between Gossypium barbadense and Gossypium darwinii BMC Plant Biology Single sequence repeats Fiber development Transcriptome profile Gene Functions DPAs |
| title | Transcriptome dynamics along with expression analysis of key genes involved in fiber development between Gossypium barbadense and Gossypium darwinii |
| title_full | Transcriptome dynamics along with expression analysis of key genes involved in fiber development between Gossypium barbadense and Gossypium darwinii |
| title_fullStr | Transcriptome dynamics along with expression analysis of key genes involved in fiber development between Gossypium barbadense and Gossypium darwinii |
| title_full_unstemmed | Transcriptome dynamics along with expression analysis of key genes involved in fiber development between Gossypium barbadense and Gossypium darwinii |
| title_short | Transcriptome dynamics along with expression analysis of key genes involved in fiber development between Gossypium barbadense and Gossypium darwinii |
| title_sort | transcriptome dynamics along with expression analysis of key genes involved in fiber development between gossypium barbadense and gossypium darwinii |
| topic | Single sequence repeats Fiber development Transcriptome profile Gene Functions DPAs |
| url | https://doi.org/10.1186/s12870-025-06697-2 |
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