Academic Journal
Genome-Wide Gene–Environment Interaction Analysis Identifies Novel Candidate Variants for Growth Traits in Beef Cattle
| Title: | Genome-Wide Gene–Environment Interaction Analysis Identifies Novel Candidate Variants for Growth Traits in Beef Cattle |
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| Authors: | Tianyu Deng, Keanning Li, Lili Du, Mang Liang, Li Qian, Qingqing Xue, Shiyuan Qiu, Lingyang Xu, Lupei Zhang, Xue Gao, Xianyong Lan, Junya Li, Huijiang Gao |
| Source: | Animals, Vol 14, Iss 11, p 1695 (2024) |
| Publisher Information: | MDPI AG, 2024. |
| Publication Year: | 2024 |
| Collection: | LCC:Veterinary medicine LCC:Zoology |
| Subject Terms: | genotype-by-environment interaction, robust estimator, cattle, gene-based analysis, gene-set analysis, Veterinary medicine, SF600-1100, Zoology, QL1-991 |
| More Details: | Complex traits are widely considered to be the result of a compound regulation of genes, environmental factors, and genotype-by-environment interaction (G × E). The inclusion of G × E in genome-wide association analyses is essential to understand animal environmental adaptations and improve the efficiency of breeding decisions. Here, we systematically investigated the G × E of growth traits (including weaning weight, yearling weight, 18-month body weight, and 24-month body weight) with environmental factors (farm and temperature) using genome-wide genotype-by-environment interaction association studies (GWEIS) with a dataset of 1350 cattle. We validated the robust estimator’s effectiveness in GWEIS and detected 29 independent interacting SNPs with a significance threshold of 1.67 × 10−6, indicating that these SNPs, which do not show main effects in traditional genome-wide association studies (GWAS), may have non-additive effects across genotypes but are obliterated by environmental means. The gene-based analysis using MAGMA identified three genes that overlapped with the GEWIS results exhibiting G × E, namely SMAD2, PALMD, and MECOM. Further, the results of functional exploration in gene-set analysis revealed the bio-mechanisms of how cattle growth responds to environmental changes, such as mitotic or cytokinesis, fatty acid β-oxidation, neurotransmitter activity, gap junction, and keratan sulfate degradation. This study not only reveals novel genetic loci and underlying mechanisms influencing growth traits but also transforms our understanding of environmental adaptation in beef cattle, thereby paving the way for more targeted and efficient breeding strategies. |
| Document Type: | article |
| File Description: | electronic resource |
| Language: | English |
| ISSN: | 2076-2615 |
| Relation: | https://www.mdpi.com/2076-2615/14/11/1695; https://doaj.org/toc/2076-2615 |
| DOI: | 10.3390/ani14111695 |
| Access URL: | https://doaj.org/article/e1253c5ef77f45fdb9df57ff62c542a7 |
| Accession Number: | edsdoj.1253c5ef77f45fdb9df57ff62c542a7 |
| Database: | Directory of Open Access Journals |
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| ISSN: | 20762615 |
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| DOI: | 10.3390/ani14111695 |
| Published in: | Animals |
| Language: | English |