La Trobe
258152_Khansefid,M_2018.pdf (1.33 MB)

Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Download (1.33 MB)
journal contribution
posted on 2023-03-23, 03:57 authored by Majid KhansefidMajid Khansefid, Jennie PryceJennie Pryce, S Bolormaa, Y Chen, CA Millen, Amanda ChamberlainAmanda Chamberlain, CJ Vander Jagt, ME Goddard
Background: The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association between genetic variants and gene expression in multiple individuals (eQTL mapping), or by comparing the expression of the alleles in a heterozygous individual (allele specific expression or ASE analysis). The aims of the study were to find and compare ASE and local eQTL in 4 bovine RNA-sequencing (RNA-Seq) datasets, validate them in an independent ASE study and investigate if they are associated with complex trait variation. Results: We present a novel method for distinguishing between ASE driven by polymorphisms in cis and parent of origin effects. We found that single nucleotide polymorphisms (SNPs) driving ASE are also often local eQTL and therefore presumably cis eQTL. These SNPs often, but not always, affect gene expression in multiple tissues and, when they do, the allele increasing expression is usually the same. However, there were systematic differences between ASE and local eQTL and between tissues and breeds. We also found that SNPs significantly associated with gene expression (p < 0.001) were likely to influence some complex traits (p < 0.001), which means that some mutations influence variation in complex traits by changing the expression level of genes. Conclusion: We conclude that ASE detects phenomenon that overlap with local eQTL, but there are also systematic differences between the SNPs discovered by the two methods. Some mutations influencing complex traits are actually eQTL and can be discovered using RNA-Seq including eQTL in the genes CAST, CAPN1, LCORL and LEPROTL1.

Funding

The authors would like to thank Dairy Futures Cooperative Research Centre (DF-CRC/DairyBio, Australia) for funding this research.

History

Publication Date

2018-11-03

Journal

BMC Genomics

Volume

19

Article Number

793

Pagination

18p.

Publisher

BioMed Central

ISSN

1471-2164

Rights Statement

© The Author(s) 2018 This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Usage metrics

    Journal Articles

    Categories

    No categories selected

    Licence

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC