Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study
Early flowering, maturity, and plant height are important traits for linseed to fit in rice fallows, for rainfed agriculture, and for economically viable cultivation. Here, Multi-Locus Genome-Wide Association Study (ML-GWAS) was undertaken in an association mapping panel of 131 accessions, genotyped...
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.811924/full |
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| author | Ankit Saroha Ankit Saroha Deepa Pal Sunil S. Gomashe Akash Vikender Kaur Shraddha Ujjainwal S. Rajkumar J. Aravind J. Radhamani Rajesh Kumar Dinesh Chand Abhishek Sengupta Dhammaprakash Pandhari Wankhede |
| author_facet | Ankit Saroha Ankit Saroha Deepa Pal Sunil S. Gomashe Akash Vikender Kaur Shraddha Ujjainwal S. Rajkumar J. Aravind J. Radhamani Rajesh Kumar Dinesh Chand Abhishek Sengupta Dhammaprakash Pandhari Wankhede |
| author_sort | Ankit Saroha |
| collection | DOAJ |
| description | Early flowering, maturity, and plant height are important traits for linseed to fit in rice fallows, for rainfed agriculture, and for economically viable cultivation. Here, Multi-Locus Genome-Wide Association Study (ML-GWAS) was undertaken in an association mapping panel of 131 accessions, genotyped using 68,925 SNPs identified by genotyping by sequencing approach. Phenotypic evaluation data of five environments comprising 3 years and two locations were used. GWAS was performed for three flowering time traits including days to 5%, 50%, and 95% flowering, days to maturity, and plant height by employing five ML-GWAS methods: FASTmrEMMA, FASTmrMLM, ISIS EM-BLASSO, mrMLM, and pLARmEB. A total of 335 unique QTNs have been identified for five traits across five environments. 109 QTNs were stable as observed in ≥2 methods and/or environments, explaining up to 36.6% phenotypic variance. For three flowering time traits, days to maturity, and plant height, 53, 30, and 27 stable QTNs, respectively, were identified. Candidate genes having roles in flower, pollen, embryo, seed and fruit development, and xylem/phloem histogenesis have been identified. Gene expression of candidate genes for flowering and plant height were studied using transcriptome of an early maturing variety Sharda (IC0523807). The present study unravels QTNs/candidate genes underlying complex flowering, days to maturity, and plant height traits in linseed. |
| first_indexed | 2024-12-12T07:58:54Z |
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| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-12T07:58:54Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-ee25ff0142344cf4b5aad492c36df6422022-12-22T00:32:12ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-06-011310.3389/fgene.2022.811924811924Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association StudyAnkit Saroha0Ankit Saroha1Deepa Pal2Sunil S. Gomashe3 Akash4Vikender Kaur5Shraddha Ujjainwal6S. Rajkumar7J. Aravind8J. Radhamani9Rajesh Kumar10Dinesh Chand11Abhishek Sengupta12Dhammaprakash Pandhari Wankhede13Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaAmity Institute of Biotechnology, Amity University, Noida, IndiaDivision of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaICAR-National Bureau of Plant Genetic Resources, Regional Station Akola, Maharashtra, IndiaDivision of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, IndiaDivision of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaICAR-National Bureau of Plant Genetic Resources, Regional Station Akola, Maharashtra, IndiaAmity Institute of Biotechnology, Amity University, Noida, IndiaDivision of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, IndiaEarly flowering, maturity, and plant height are important traits for linseed to fit in rice fallows, for rainfed agriculture, and for economically viable cultivation. Here, Multi-Locus Genome-Wide Association Study (ML-GWAS) was undertaken in an association mapping panel of 131 accessions, genotyped using 68,925 SNPs identified by genotyping by sequencing approach. Phenotypic evaluation data of five environments comprising 3 years and two locations were used. GWAS was performed for three flowering time traits including days to 5%, 50%, and 95% flowering, days to maturity, and plant height by employing five ML-GWAS methods: FASTmrEMMA, FASTmrMLM, ISIS EM-BLASSO, mrMLM, and pLARmEB. A total of 335 unique QTNs have been identified for five traits across five environments. 109 QTNs were stable as observed in ≥2 methods and/or environments, explaining up to 36.6% phenotypic variance. For three flowering time traits, days to maturity, and plant height, 53, 30, and 27 stable QTNs, respectively, were identified. Candidate genes having roles in flower, pollen, embryo, seed and fruit development, and xylem/phloem histogenesis have been identified. Gene expression of candidate genes for flowering and plant height were studied using transcriptome of an early maturing variety Sharda (IC0523807). The present study unravels QTNs/candidate genes underlying complex flowering, days to maturity, and plant height traits in linseed.https://www.frontiersin.org/articles/10.3389/fgene.2022.811924/fullflowering timematurityplant heightmulti-locus GWASquantitative trait nucleotideslinseed |
| spellingShingle | Ankit Saroha Ankit Saroha Deepa Pal Sunil S. Gomashe Akash Vikender Kaur Shraddha Ujjainwal S. Rajkumar J. Aravind J. Radhamani Rajesh Kumar Dinesh Chand Abhishek Sengupta Dhammaprakash Pandhari Wankhede Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study Frontiers in Genetics flowering time maturity plant height multi-locus GWAS quantitative trait nucleotides linseed |
| title | Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study |
| title_full | Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study |
| title_fullStr | Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study |
| title_full_unstemmed | Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study |
| title_short | Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study |
| title_sort | identification of qtns associated with flowering time maturity and plant height traits in linum usitatissimum l using genome wide association study |
| topic | flowering time maturity plant height multi-locus GWAS quantitative trait nucleotides linseed |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.811924/full |
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