Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana
Abstract
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 sQTLmore »
- Authors:
-
- Canterbury Christ Church University, Canterbury, (United Kingdom). School of Human and Life Sciences
- The Roslin Institute, University of Edinburgh, Edinburgh, (United Kingdom). Division of Infection and Immunity; Univ. of Edinburgh, Edinburgh (United Kingdom). Centre for Tropical Livestock Genetics and Health
- Colorado State Univ., Fort Collins, CO (United States). Dept. of Biology and Program in Cell and Molecular Biology
- Canterbury Christ Church University, Canterbury, (United Kingdom). School of Human and Life Sciences
- Publication Date:
- Research Org.:
- Colorado State Univ., Fort Collins, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1628297
- Grant/Contract Number:
- SC0010733
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Plant Science
- Additional Journal Information:
- Journal Volume: 10; Journal ID: ISSN 1664-462X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- Plant Sciences; splicing quantitative trait loci (sQTL); Arabidopsis thaliana; alternative splicing; isoform usage; GWAS; adaptation
Citation Formats
Khokhar, Waqas, Hassan, Musa A., Reddy, Anireddy S. N., Chaudhary, Saurabh, Jabre, Ibtissam, Byrne, Lee J., and Syed, Naeem H. Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana. United States: N. p., 2019.
Web. doi:10.3389/fpls.2019.01160.
Khokhar, Waqas, Hassan, Musa A., Reddy, Anireddy S. N., Chaudhary, Saurabh, Jabre, Ibtissam, Byrne, Lee J., & Syed, Naeem H. Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana. United States. https://doi.org/10.3389/fpls.2019.01160
Khokhar, Waqas, Hassan, Musa A., Reddy, Anireddy S. N., Chaudhary, Saurabh, Jabre, Ibtissam, Byrne, Lee J., and Syed, Naeem H. Thu .
"Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana". United States. https://doi.org/10.3389/fpls.2019.01160. https://www.osti.gov/servlets/purl/1628297.
@article{osti_1628297,
title = {Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana},
author = {Khokhar, Waqas and Hassan, Musa A. and Reddy, Anireddy S. N. and Chaudhary, Saurabh and Jabre, Ibtissam and Byrne, Lee J. and Syed, Naeem H.},
abstractNote = {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.},
doi = {10.3389/fpls.2019.01160},
journal = {Frontiers in Plant Science},
number = ,
volume = 10,
place = {United States},
year = {Thu Oct 03 00:00:00 EDT 2019},
month = {Thu Oct 03 00:00:00 EDT 2019}
}
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