Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows
Despite collective efforts to understand the complex regulation of reproductive traits, no causative genes and/or mutations have been reported yet. By integrating genomics and transcriptomics data, potential regulatory mechanisms may be unveiled, providing opportunities to dissect the genetic factor...
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-01-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/14/2/150 |
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| author | Wellison J. S. Diniz Juliana Afonso Nicholas C. Kertz Paul W. Dyce Priyanka Banerjee |
| author_facet | Wellison J. S. Diniz Juliana Afonso Nicholas C. Kertz Paul W. Dyce Priyanka Banerjee |
| author_sort | Wellison J. S. Diniz |
| collection | DOAJ |
| description | Despite collective efforts to understand the complex regulation of reproductive traits, no causative genes and/or mutations have been reported yet. By integrating genomics and transcriptomics data, potential regulatory mechanisms may be unveiled, providing opportunities to dissect the genetic factors governing fertility. Herein, we identified regulatory variants from RNA-Seq data associated with gene expression regulation in the uterine luminal epithelial cells of beef cows. We identified 4676 cis and 7682 trans eQTLs (expression quantitative trait loci) affecting the expression of 1120 and 2503 genes, respectively (FDR < 0.05). These variants affected the expression of transcription factor coding genes (71 cis and 193 trans eQTLs) and genes previously reported as differentially expressed between pregnant and nonpregnant cows. Functional over-representation analysis highlighted pathways related to metabolism, immune response, and hormone signaling (estrogen and GnRH) affected by eQTL-regulated genes (<i>p</i>-value ≤ 0.01). Furthermore, eQTLs were enriched in QTL regions for 13 reproduction-related traits from the CattleQTLdb (FDR ≤ 0.05). Our study provides novel insights into the genetic basis of reproductive processes in cattle. The underlying causal mechanisms modulating the expression of uterine genes warrant further investigation. |
| first_indexed | 2024-03-07T22:40:21Z |
| format | Article |
| id | doaj.art-197b036d1d6a47b6b9a28f663af680aa |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-07T22:40:21Z |
| publishDate | 2024-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-197b036d1d6a47b6b9a28f663af680aa2024-02-23T15:09:13ZengMDPI AGBiomolecules2218-273X2024-01-0114215010.3390/biom14020150Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef CowsWellison J. S. Diniz0Juliana Afonso1Nicholas C. Kertz2Paul W. Dyce3Priyanka Banerjee4Department of Animal Sciences, Auburn University, Auburn, AL 36849, USAEmbrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234, s/n, Fazenda Canchim, São Carlos 13560-970, SP, BrazilDepartment of Animal Sciences, Auburn University, Auburn, AL 36849, USADepartment of Animal Sciences, Auburn University, Auburn, AL 36849, USADepartment of Animal Sciences, Auburn University, Auburn, AL 36849, USADespite collective efforts to understand the complex regulation of reproductive traits, no causative genes and/or mutations have been reported yet. By integrating genomics and transcriptomics data, potential regulatory mechanisms may be unveiled, providing opportunities to dissect the genetic factors governing fertility. Herein, we identified regulatory variants from RNA-Seq data associated with gene expression regulation in the uterine luminal epithelial cells of beef cows. We identified 4676 cis and 7682 trans eQTLs (expression quantitative trait loci) affecting the expression of 1120 and 2503 genes, respectively (FDR < 0.05). These variants affected the expression of transcription factor coding genes (71 cis and 193 trans eQTLs) and genes previously reported as differentially expressed between pregnant and nonpregnant cows. Functional over-representation analysis highlighted pathways related to metabolism, immune response, and hormone signaling (estrogen and GnRH) affected by eQTL-regulated genes (<i>p</i>-value ≤ 0.01). Furthermore, eQTLs were enriched in QTL regions for 13 reproduction-related traits from the CattleQTLdb (FDR ≤ 0.05). Our study provides novel insights into the genetic basis of reproductive processes in cattle. The underlying causal mechanisms modulating the expression of uterine genes warrant further investigation.https://www.mdpi.com/2218-273X/14/2/150cow fertilityeQTLgene expressionregulatory variantsreproduction |
| spellingShingle | Wellison J. S. Diniz Juliana Afonso Nicholas C. Kertz Paul W. Dyce Priyanka Banerjee Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows Biomolecules cow fertility eQTL gene expression regulatory variants reproduction |
| title | Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows |
| title_full | Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows |
| title_fullStr | Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows |
| title_full_unstemmed | Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows |
| title_short | Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows |
| title_sort | mapping expression quantitative trait loci targeting candidate genes for pregnancy in beef cows |
| topic | cow fertility eQTL gene expression regulatory variants reproduction |
| url | https://www.mdpi.com/2218-273X/14/2/150 |
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