Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana
Alternative splicing (AS) of pre-mRNAs contributes to transcriptome diversity and enables plants to generate different protein isoforms from a single gene and/or fine-tune gene expression during different development stages and environmental changes. Although AS is pervasive, the genetic basis for d...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2019.01160/full |
| _version_ | 1819079859893174272 |
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| author | Waqas Khokhar Musa A. Hassan Musa A. Hassan Anireddy S. N. Reddy Saurabh Chaudhary Ibtissam Jabre Lee J. Byrne Naeem H. Syed |
| author_facet | Waqas Khokhar Musa A. Hassan Musa A. Hassan Anireddy S. N. Reddy Saurabh Chaudhary Ibtissam Jabre Lee J. Byrne Naeem H. Syed |
| author_sort | Waqas Khokhar |
| collection | DOAJ |
| description | Alternative splicing (AS) of pre-mRNAs contributes to transcriptome diversity and enables plants to generate different protein isoforms from a single gene and/or fine-tune gene expression during different development stages and environmental changes. Although AS is pervasive, the genetic basis for differential isoform usage in plants is still emerging. In this study, we performed genome-wide analysis in 666 geographically distributed diverse ecotypes of Arabidopsis thaliana to identify genomic regions [splicing quantitative trait loci (sQTLs)] that may regulate differential AS. These ecotypes belong to different microclimatic conditions and are part of the relict and non-relict populations. Although sQTLs were spread across the genome, we observed enrichment for trans-sQTL (trans-sQTLs hotspots) on chromosome one. Furthermore, we identified several sQTL (911) that co-localized with trait-linked single nucleotide polymorphisms (SNP) identified in the Arabidopsis genome-wide association studies (AraGWAS). Many sQTLs were enriched among circadian clock, flowering, and stress-responsive genes, suggesting a role for differential isoform usage in regulating these important processes in diverse ecotypes of Arabidopsis. In conclusion, the current study provides a deep insight into SNPs affecting isoform ratios/genes and facilitates a better mechanistic understanding of trait-associated SNPs in GWAS studies. To the best of our knowledge, this is the first report of sQTL analysis in a large set of Arabidopsis ecotypes and can be used as a reference to perform sQTL analysis in the Brassicaceae family. Since whole genome and transcriptome datasets are available for these diverse ecotypes, it could serve as a powerful resource for the biological interpretation of trait-associated loci, splice isoform ratios, and their phenotypic consequences to help produce more resilient and high yield crop varieties. |
| first_indexed | 2024-12-21T19:35:41Z |
| format | Article |
| id | doaj.art-a8558e39100f42e3aa29680c4b13168f |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-21T19:35:41Z |
| publishDate | 2019-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-a8558e39100f42e3aa29680c4b13168f2022-12-21T18:52:37ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-10-011010.3389/fpls.2019.01160460256Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thalianaWaqas Khokhar0Musa A. Hassan1Musa A. Hassan2Anireddy S. N. Reddy3Saurabh Chaudhary4Ibtissam Jabre5Lee J. Byrne6Naeem H. Syed7School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United KingdomDivision of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United KingdomCentre for Tropical Livestock Genetics and Health, University of Edinburgh, Edinburgh, United KingdomDepartment of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United StatesSchool of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United KingdomSchool of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United KingdomSchool of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United KingdomSchool of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United KingdomAlternative splicing (AS) of pre-mRNAs contributes to transcriptome diversity and enables plants to generate different protein isoforms from a single gene and/or fine-tune gene expression during different development stages and environmental changes. Although AS is pervasive, the genetic basis for differential isoform usage in plants is still emerging. In this study, we performed genome-wide analysis in 666 geographically distributed diverse ecotypes of Arabidopsis thaliana to identify genomic regions [splicing quantitative trait loci (sQTLs)] that may regulate differential AS. These ecotypes belong to different microclimatic conditions and are part of the relict and non-relict populations. Although sQTLs were spread across the genome, we observed enrichment for trans-sQTL (trans-sQTLs hotspots) on chromosome one. Furthermore, we identified several sQTL (911) that co-localized with trait-linked single nucleotide polymorphisms (SNP) identified in the Arabidopsis genome-wide association studies (AraGWAS). Many sQTLs were enriched among circadian clock, flowering, and stress-responsive genes, suggesting a role for differential isoform usage in regulating these important processes in diverse ecotypes of Arabidopsis. In conclusion, the current study provides a deep insight into SNPs affecting isoform ratios/genes and facilitates a better mechanistic understanding of trait-associated SNPs in GWAS studies. To the best of our knowledge, this is the first report of sQTL analysis in a large set of Arabidopsis ecotypes and can be used as a reference to perform sQTL analysis in the Brassicaceae family. Since whole genome and transcriptome datasets are available for these diverse ecotypes, it could serve as a powerful resource for the biological interpretation of trait-associated loci, splice isoform ratios, and their phenotypic consequences to help produce more resilient and high yield crop varieties.https://www.frontiersin.org/article/10.3389/fpls.2019.01160/fullsplicing quantitative trait loci (sQTL)Arabidopsis thalianaalternative splicingisoform usageGWASadaptation |
| spellingShingle | Waqas Khokhar Musa A. Hassan Musa A. Hassan Anireddy S. N. Reddy Saurabh Chaudhary Ibtissam Jabre Lee J. Byrne Naeem H. Syed Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana Frontiers in Plant Science splicing quantitative trait loci (sQTL) Arabidopsis thaliana alternative splicing isoform usage GWAS adaptation |
| title | Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana |
| title_full | Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana |
| title_fullStr | Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana |
| title_full_unstemmed | Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana |
| title_short | Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana |
| title_sort | genome wide identification of splicing quantitative trait loci sqtls in diverse ecotypes of arabidopsis thaliana |
| topic | splicing quantitative trait loci (sQTL) Arabidopsis thaliana alternative splicing isoform usage GWAS adaptation |
| url | https://www.frontiersin.org/article/10.3389/fpls.2019.01160/full |
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