Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.)
Market class, cooking time, quality, and milled grain yield are largely influenced by the seed size and shape of the lentil (Lens culinaris Medik.); thus, they are considered to be important quality traits. To unfold the pathways regulating seed size in lentils, a transcriptomic approach was perform...
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Frontiers Media S.A.
2022-08-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.942079/full |
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| author | Haragopal Dutta Gyan P. Mishra Muraleedhar S. Aski Tejas C. Bosamia Dwijesh C. Mishra Jyotika Bhati Subodh Kumar Sinha Dunna Vijay Manjunath Prasad C. T. Shouvik Das Prashant Anupama-Mohan Pawar Atul Kumar Kuldeep Tripathi Ranjeet Ranjan Kumar Devendra Kumar Yadava Shiv Kumar Harsh Kumar Dikshit |
| author_facet | Haragopal Dutta Gyan P. Mishra Muraleedhar S. Aski Tejas C. Bosamia Dwijesh C. Mishra Jyotika Bhati Subodh Kumar Sinha Dunna Vijay Manjunath Prasad C. T. Shouvik Das Prashant Anupama-Mohan Pawar Atul Kumar Kuldeep Tripathi Ranjeet Ranjan Kumar Devendra Kumar Yadava Shiv Kumar Harsh Kumar Dikshit |
| author_sort | Haragopal Dutta |
| collection | DOAJ |
| description | Market class, cooking time, quality, and milled grain yield are largely influenced by the seed size and shape of the lentil (Lens culinaris Medik.); thus, they are considered to be important quality traits. To unfold the pathways regulating seed size in lentils, a transcriptomic approach was performed using large-seeded (L4602) and small-seeded (L830) genotypes. The study has generated nearly 375 million high-quality reads, of which 98.70% were properly aligned to the reference genome. Among biological replicates, very high similarity in fragments per kilobase of exon per million mapped fragments values (R > 0.9) showed the consistency of RNA-seq results. Various differentially expressed genes associated mainly with the hormone signaling and cell division pathways, transcription factors, kinases, etc. were identified as having a role in cell expansion and seed growth. A total of 106,996 unigenes were used for differential expression (DE) analysis. String analysis identified various modules having certain key proteins like Ser/Thr protein kinase, seed storage protein, DNA-binding protein, microtubule-associated protein, etc. In addition, some growth and cell division–related micro-RNAs like miR3457 (cell wall formation), miR1440 (cell proliferation and cell cycles), and miR1533 (biosynthesis of plant hormones) were identified as having a role in seed size determination. Using RNA-seq data, 5254 EST-SSR primers were generated as a source for future studies aiming for the identification of linked markers. In silico validation using Genevestigator® was done for the Ser/Thr protein kinase, ethylene response factor, and Myb transcription factor genes. It is of interest that the xyloglucan endotransglucosylase gene was found differentially regulated, suggesting their role during seed development; however, at maturity, no significant differences were recorded for various cell wall parameters including cellulose, lignin, and xylose content. This is the first report on lentils that has unfolded the key seed size regulating pathways and unveiled a theoretical way for the development of lentil genotypes having customized seed sizes. |
| first_indexed | 2024-04-11T21:30:55Z |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-11T21:30:55Z |
| publishDate | 2022-08-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-0cdf9ca2ad1540f3a46bee42613178932022-12-22T04:01:57ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-08-011310.3389/fgene.2022.942079942079Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.)Haragopal Dutta0Gyan P. Mishra1Muraleedhar S. Aski2Tejas C. Bosamia3Dwijesh C. Mishra4Jyotika Bhati5Subodh Kumar Sinha6Dunna Vijay7Manjunath Prasad C. T.8Shouvik Das9Prashant Anupama-Mohan Pawar10Atul Kumar11Kuldeep Tripathi12Ranjeet Ranjan Kumar13Devendra Kumar Yadava14Shiv Kumar15Harsh Kumar Dikshit16Division of Genetics, Indian Agricultural Research Institute, New Delhi, IndiaDivision of Genetics, Indian Agricultural Research Institute, New Delhi, IndiaDivision of Genetics, Indian Agricultural Research Institute, New Delhi, IndiaPlant Omics Division, Central Salt and Marine Chemicals Research Institute, Bhavnagar, IndiaAgricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, IndiaAgricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, IndiaICAR-National Institute for Plant Biotechnology, New Delhi, IndiaDivision of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, IndiaDivision of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, IndiaLaboratory of Plant Cell Wall Biology, Regional Centre for Biotechnology, Faridabad, IndiaLaboratory of Plant Cell Wall Biology, Regional Centre for Biotechnology, Faridabad, IndiaDivision of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, IndiaGermplasm Evaluation Division, National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Biochemistry, Indian Agricultural Research Institute, New Delhi, IndiaDivision of Crop Science, Indian Council of Agricultural Research, New Delhi, India0South Asia and China Program, International Center for Agricultural Research in the Dry Areas, NASC Complex, New Delhi, IndiaDivision of Genetics, Indian Agricultural Research Institute, New Delhi, IndiaMarket class, cooking time, quality, and milled grain yield are largely influenced by the seed size and shape of the lentil (Lens culinaris Medik.); thus, they are considered to be important quality traits. To unfold the pathways regulating seed size in lentils, a transcriptomic approach was performed using large-seeded (L4602) and small-seeded (L830) genotypes. The study has generated nearly 375 million high-quality reads, of which 98.70% were properly aligned to the reference genome. Among biological replicates, very high similarity in fragments per kilobase of exon per million mapped fragments values (R > 0.9) showed the consistency of RNA-seq results. Various differentially expressed genes associated mainly with the hormone signaling and cell division pathways, transcription factors, kinases, etc. were identified as having a role in cell expansion and seed growth. A total of 106,996 unigenes were used for differential expression (DE) analysis. String analysis identified various modules having certain key proteins like Ser/Thr protein kinase, seed storage protein, DNA-binding protein, microtubule-associated protein, etc. In addition, some growth and cell division–related micro-RNAs like miR3457 (cell wall formation), miR1440 (cell proliferation and cell cycles), and miR1533 (biosynthesis of plant hormones) were identified as having a role in seed size determination. Using RNA-seq data, 5254 EST-SSR primers were generated as a source for future studies aiming for the identification of linked markers. In silico validation using Genevestigator® was done for the Ser/Thr protein kinase, ethylene response factor, and Myb transcription factor genes. It is of interest that the xyloglucan endotransglucosylase gene was found differentially regulated, suggesting their role during seed development; however, at maturity, no significant differences were recorded for various cell wall parameters including cellulose, lignin, and xylose content. This is the first report on lentils that has unfolded the key seed size regulating pathways and unveiled a theoretical way for the development of lentil genotypes having customized seed sizes.https://www.frontiersin.org/articles/10.3389/fgene.2022.942079/fullRNA-seqtranscription factorssignal transduction pathwayLens culinarisseed parameters |
| spellingShingle | Haragopal Dutta Gyan P. Mishra Muraleedhar S. Aski Tejas C. Bosamia Dwijesh C. Mishra Jyotika Bhati Subodh Kumar Sinha Dunna Vijay Manjunath Prasad C. T. Shouvik Das Prashant Anupama-Mohan Pawar Atul Kumar Kuldeep Tripathi Ranjeet Ranjan Kumar Devendra Kumar Yadava Shiv Kumar Harsh Kumar Dikshit Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.) Frontiers in Genetics RNA-seq transcription factors signal transduction pathway Lens culinaris seed parameters |
| title | Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.) |
| title_full | Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.) |
| title_fullStr | Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.) |
| title_full_unstemmed | Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.) |
| title_short | Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.) |
| title_sort | comparative transcriptome analysis unfolding the pathways regulating the seed size trait in cultivated lentil lens culinaris medik |
| topic | RNA-seq transcription factors signal transduction pathway Lens culinaris seed parameters |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.942079/full |
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