Association of Variants in Innate Immune Genes <i>TLR4</i> and <i>TLR5</i> with Reproductive and Milk Production Traits in Czech Simmental Cattle
Bovine genes <i>TLR4</i> and <i>TLR5</i>, which encode antibacterial toll-like receptors, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle to identify variants associated with reproduction, udder health, and milk production traits. Variants were disc...
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| Format: | Article |
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MDPI AG
2023-12-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/15/1/24 |
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| author | Karel Novák Terezie Valčíková Kalifa Samaké Marek Bjelka |
| author_facet | Karel Novák Terezie Valčíková Kalifa Samaké Marek Bjelka |
| author_sort | Karel Novák |
| collection | DOAJ |
| description | Bovine genes <i>TLR4</i> and <i>TLR5</i>, which encode antibacterial toll-like receptors, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle to identify variants associated with reproduction, udder health, and milk production traits. Variants were discovered by hybrid resequencing of 164 bulls using HiSeq X-Ten and PacBio technologies and then individually genotyped. Nominal <i>p</i>-values < 0.05 for associations were detected in 18 combinations between 14 polymorphisms and 15 traits using one-way analysis of variance (ANOVA). The <i>TLR4</i> variants g.610C>T (rs43578094) and g.10310T>G (rs8193072) in reference AC000135.1 were strictly associated with the index of early reproductive disorders and maternal calving ease, respectively, at false discovery rate (FDR) < 0.05. A highly permissive false discovery rate cutoff of 0.6 separated seventeen combinations in both genes comprising eight positives. In the case of the <i>TLR4</i> variant g.9422T>C (rs8193060), indications were obtained for the association with as many as four reproductive traits: incidence of cystic ovaries, early reproductive disorders, calving ease, and production longevity. The permissive FDR interpretation for the <i>TLR5</i> data indicated associations with cyst incidence and early reproduction disorders with maternal calving ease. Moreover, three <i>TLR5</i> polymorphisms correlated with milk production traits. The discrepancy of the observed associations with the predicted impacts of the SNPs on protein function points to the role of haplotypes. Nevertheless, this question should be resolved on a larger scale. The observed associations are endorsed by independent evidence from the published functional roles in other species and by the published QTL mapping data. |
| first_indexed | 2024-03-08T10:54:43Z |
| format | Article |
| id | doaj.art-d57a85a779da441dac4c586d38bf27a3 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-08T10:54:43Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-d57a85a779da441dac4c586d38bf27a32024-01-26T16:41:26ZengMDPI AGGenes2073-44252023-12-011512410.3390/genes15010024Association of Variants in Innate Immune Genes <i>TLR4</i> and <i>TLR5</i> with Reproductive and Milk Production Traits in Czech Simmental CattleKarel Novák0Terezie Valčíková1Kalifa Samaké2Marek Bjelka3Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Prague-Uhříněves, Czech RepublicDepartment of Genetics, Czech University of Life Sciences, Kamýcká 129, 165 06 Prague, Czech RepublicDepartment of Genetics and Microbiology, Viničná 7, Charles University, 128 43 Prague, Czech RepublicBreeding Company CHD Impuls, 592 55 Bohdalec, Czech RepublicBovine genes <i>TLR4</i> and <i>TLR5</i>, which encode antibacterial toll-like receptors, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle to identify variants associated with reproduction, udder health, and milk production traits. Variants were discovered by hybrid resequencing of 164 bulls using HiSeq X-Ten and PacBio technologies and then individually genotyped. Nominal <i>p</i>-values < 0.05 for associations were detected in 18 combinations between 14 polymorphisms and 15 traits using one-way analysis of variance (ANOVA). The <i>TLR4</i> variants g.610C>T (rs43578094) and g.10310T>G (rs8193072) in reference AC000135.1 were strictly associated with the index of early reproductive disorders and maternal calving ease, respectively, at false discovery rate (FDR) < 0.05. A highly permissive false discovery rate cutoff of 0.6 separated seventeen combinations in both genes comprising eight positives. In the case of the <i>TLR4</i> variant g.9422T>C (rs8193060), indications were obtained for the association with as many as four reproductive traits: incidence of cystic ovaries, early reproductive disorders, calving ease, and production longevity. The permissive FDR interpretation for the <i>TLR5</i> data indicated associations with cyst incidence and early reproduction disorders with maternal calving ease. Moreover, three <i>TLR5</i> polymorphisms correlated with milk production traits. The discrepancy of the observed associations with the predicted impacts of the SNPs on protein function points to the role of haplotypes. Nevertheless, this question should be resolved on a larger scale. The observed associations are endorsed by independent evidence from the published functional roles in other species and by the published QTL mapping data.https://www.mdpi.com/2073-4425/15/1/24cattlegenotypingimmunityinflammationmammary glandparturition |
| spellingShingle | Karel Novák Terezie Valčíková Kalifa Samaké Marek Bjelka Association of Variants in Innate Immune Genes <i>TLR4</i> and <i>TLR5</i> with Reproductive and Milk Production Traits in Czech Simmental Cattle Genes cattle genotyping immunity inflammation mammary gland parturition |
| title | Association of Variants in Innate Immune Genes <i>TLR4</i> and <i>TLR5</i> with Reproductive and Milk Production Traits in Czech Simmental Cattle |
| title_full | Association of Variants in Innate Immune Genes <i>TLR4</i> and <i>TLR5</i> with Reproductive and Milk Production Traits in Czech Simmental Cattle |
| title_fullStr | Association of Variants in Innate Immune Genes <i>TLR4</i> and <i>TLR5</i> with Reproductive and Milk Production Traits in Czech Simmental Cattle |
| title_full_unstemmed | Association of Variants in Innate Immune Genes <i>TLR4</i> and <i>TLR5</i> with Reproductive and Milk Production Traits in Czech Simmental Cattle |
| title_short | Association of Variants in Innate Immune Genes <i>TLR4</i> and <i>TLR5</i> with Reproductive and Milk Production Traits in Czech Simmental Cattle |
| title_sort | association of variants in innate immune genes i tlr4 i and i tlr5 i with reproductive and milk production traits in czech simmental cattle |
| topic | cattle genotyping immunity inflammation mammary gland parturition |
| url | https://www.mdpi.com/2073-4425/15/1/24 |
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