Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.)
Jute (Corchorus sp.), a commercially important and eco-friendly crop, is widely cultivated in Bangladesh, India, and China. Some varieties of this tropical plant such as the Corchorus. olitorius variety accession no. 2015 (acc. 2015) has been found to be low-temperature tolerant. The current study w...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-06-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1687157X24000799 |
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| author | Athoi Ganguly Shaheena Amin Al-Amin Farhana Tasnim Chowdhury Haseena Khan Mohammad Riazul Islam |
| author_facet | Athoi Ganguly Shaheena Amin Al-Amin Farhana Tasnim Chowdhury Haseena Khan Mohammad Riazul Islam |
| author_sort | Athoi Ganguly |
| collection | DOAJ |
| description | Jute (Corchorus sp.), a commercially important and eco-friendly crop, is widely cultivated in Bangladesh, India, and China. Some varieties of this tropical plant such as the Corchorus. olitorius variety accession no. 2015 (acc. 2015) has been found to be low-temperature tolerant. The current study was designed to explore the genome-wide variations present in the tolerant plant acc. 2015 in comparison to the sensitive farmer popular variety Corchorus. olitorius var. O9897 using the whole genome resequencing technique. Among different variations, intergenic Single Nucleotide Polymorphism (SNPs) and Insertion-Deletion (InDels) were found in the highest percentage whereas approximately 3% SNPs and 2% InDels were found in exonic regions in both plants. Gene enrichment analysis indicated the presence of acc. 2015 specific SNPs in the genes encoding peroxidase, ER lumen protein retaining receptor, and hexosyltransferase involved in stress response (GO:0006950) which were not present in sensitive variety O9897. Besides, distinctive copy number variation regions (CNVRs) comprising 120 gene loci were found in acc. 2015 with a gain of function from multiple copy numbers but absent in O9897. Gene ontology analysis revealed these gene loci to possess different receptors like kinases, helicases, phosphatases, transcription factors especially Myb transcription factors, regulatory proteins containing different binding domains, annexin, laccase, acyl carrier protein, potassium transporter, and vesicular transporter proteins that are responsible for low temperature induced adaptation pathways in plants. This work of identifying genomic variations linked to cold stress tolerance traits will help to develop successful markers that will pave the way to develop genetically modified cold-resistant jute lines for year-round cultivation to meet the demand for a sustainable fiber crop economy. |
| first_indexed | 2024-04-24T11:21:18Z |
| format | Article |
| id | doaj.art-48b12dedad60410186c4940c3c419a94 |
| institution | Directory Open Access Journal |
| issn | 1687-157X |
| language | English |
| last_indexed | 2024-04-24T11:21:18Z |
| publishDate | 2024-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-48b12dedad60410186c4940c3c419a942024-04-11T04:40:57ZengElsevierJournal of Genetic Engineering and Biotechnology1687-157X2024-06-01222100376Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.)Athoi Ganguly0Shaheena Amin1 Al-Amin2Farhana Tasnim Chowdhury3Haseena Khan4Mohammad Riazul Islam5Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, BangladeshMolecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh; Department of Biochemistry and Molecular Biology, National Institute of Science and Technology, Dhaka, BangladeshMolecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, BangladeshMolecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, BangladeshMolecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh; Corresponding authors.Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh; Corresponding authors.Jute (Corchorus sp.), a commercially important and eco-friendly crop, is widely cultivated in Bangladesh, India, and China. Some varieties of this tropical plant such as the Corchorus. olitorius variety accession no. 2015 (acc. 2015) has been found to be low-temperature tolerant. The current study was designed to explore the genome-wide variations present in the tolerant plant acc. 2015 in comparison to the sensitive farmer popular variety Corchorus. olitorius var. O9897 using the whole genome resequencing technique. Among different variations, intergenic Single Nucleotide Polymorphism (SNPs) and Insertion-Deletion (InDels) were found in the highest percentage whereas approximately 3% SNPs and 2% InDels were found in exonic regions in both plants. Gene enrichment analysis indicated the presence of acc. 2015 specific SNPs in the genes encoding peroxidase, ER lumen protein retaining receptor, and hexosyltransferase involved in stress response (GO:0006950) which were not present in sensitive variety O9897. Besides, distinctive copy number variation regions (CNVRs) comprising 120 gene loci were found in acc. 2015 with a gain of function from multiple copy numbers but absent in O9897. Gene ontology analysis revealed these gene loci to possess different receptors like kinases, helicases, phosphatases, transcription factors especially Myb transcription factors, regulatory proteins containing different binding domains, annexin, laccase, acyl carrier protein, potassium transporter, and vesicular transporter proteins that are responsible for low temperature induced adaptation pathways in plants. This work of identifying genomic variations linked to cold stress tolerance traits will help to develop successful markers that will pave the way to develop genetically modified cold-resistant jute lines for year-round cultivation to meet the demand for a sustainable fiber crop economy.http://www.sciencedirect.com/science/article/pii/S1687157X24000799Corchorus. olitorius accession no. 2015 (acc. 2015)Corchorus. olitorius var. O9897Single Nucleotide Polymorphisms (SNPs)Insertion Deletions (InDels)Copy Number Variations (CNVs)Gene Ontology (GO) |
| spellingShingle | Athoi Ganguly Shaheena Amin Al-Amin Farhana Tasnim Chowdhury Haseena Khan Mohammad Riazul Islam Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.) Journal of Genetic Engineering and Biotechnology Corchorus. olitorius accession no. 2015 (acc. 2015) Corchorus. olitorius var. O9897 Single Nucleotide Polymorphisms (SNPs) Insertion Deletions (InDels) Copy Number Variations (CNVs) Gene Ontology (GO) |
| title | Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.) |
| title_full | Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.) |
| title_fullStr | Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.) |
| title_full_unstemmed | Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.) |
| title_short | Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.) |
| title_sort | whole genome resequencing unveils low temperature stress tolerance specific genomic variations in jute corchorus sp |
| topic | Corchorus. olitorius accession no. 2015 (acc. 2015) Corchorus. olitorius var. O9897 Single Nucleotide Polymorphisms (SNPs) Insertion Deletions (InDels) Copy Number Variations (CNVs) Gene Ontology (GO) |
| url | http://www.sciencedirect.com/science/article/pii/S1687157X24000799 |
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