Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle
Abstract 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...
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| Format: | Article |
| Language: | English |
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BMC
2018-11-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5181-0 |
| _version_ | 1819263874954690560 |
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| author | Majid Khansefid Jennie E. Pryce Sunduimijid Bolormaa Yizhou Chen Catriona A. Millen Amanda J. Chamberlain Christy J. Vander Jagt Michael E. Goddard |
| author_facet | Majid Khansefid Jennie E. Pryce Sunduimijid Bolormaa Yizhou Chen Catriona A. Millen Amanda J. Chamberlain Christy J. Vander Jagt Michael E. Goddard |
| author_sort | Majid Khansefid |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-23T20:20:32Z |
| format | Article |
| id | doaj.art-6b8b83bec6ed40cd92197eb1d7449363 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-23T20:20:32Z |
| publishDate | 2018-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-6b8b83bec6ed40cd92197eb1d74493632022-12-21T17:32:33ZengBMCBMC Genomics1471-21642018-11-0119111810.1186/s12864-018-5181-0Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattleMajid Khansefid0Jennie E. Pryce1Sunduimijid Bolormaa2Yizhou Chen3Catriona A. Millen4Amanda J. Chamberlain5Christy J. Vander Jagt6Michael E. Goddard7Department of Agriculture and Food Systems, The University of MelbourneAgriculture Victoria, AgriBio, Centre for AgriBioscienceAgriculture Victoria, AgriBio, Centre for AgriBioscienceElizabeth Macarthur Agricultural Institute, NSW Department of Primary IndustriesAgricultural Business Research Institute, The University of New EnglandAgriculture Victoria, AgriBio, Centre for AgriBioscienceAgriculture Victoria, AgriBio, Centre for AgriBioscienceDepartment of Agriculture and Food Systems, The University of MelbourneAbstract 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.http://link.springer.com/article/10.1186/s12864-018-5181-0RNA-sequencingAllele specific expressionASE analysiseQTL mappingGenome-wide association studyGenetic variation of complex traits |
| spellingShingle | Majid Khansefid Jennie E. Pryce Sunduimijid Bolormaa Yizhou Chen Catriona A. Millen Amanda J. Chamberlain Christy J. Vander Jagt Michael E. Goddard Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle BMC Genomics RNA-sequencing Allele specific expression ASE analysis eQTL mapping Genome-wide association study Genetic variation of complex traits |
| title | Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle |
| title_full | Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle |
| title_fullStr | Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle |
| title_full_unstemmed | Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle |
| title_short | Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle |
| title_sort | comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle |
| topic | RNA-sequencing Allele specific expression ASE analysis eQTL mapping Genome-wide association study Genetic variation of complex traits |
| url | http://link.springer.com/article/10.1186/s12864-018-5181-0 |
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