Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle
Meat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 CNVs and 10,102 CNV regions (CNVRs) based on the Bovine HD SNP...
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| Format: | Article |
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MDPI AG
2023-10-01
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| Series: | Foods |
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| Online Access: | https://www.mdpi.com/2304-8158/12/21/3986 |
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| author | Jiayuan Wu Tianyi Wu Xueyuan Xie Qunhao Niu Zhida Zhao Bo Zhu Yan Chen Lupei Zhang Xue Gao Xiaoyan Niu Huijiang Gao Junya Li Lingyang Xu |
| author_facet | Jiayuan Wu Tianyi Wu Xueyuan Xie Qunhao Niu Zhida Zhao Bo Zhu Yan Chen Lupei Zhang Xue Gao Xiaoyan Niu Huijiang Gao Junya Li Lingyang Xu |
| author_sort | Jiayuan Wu |
| collection | DOAJ |
| description | Meat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 CNVs and 10,102 CNV regions (CNVRs) based on the Bovine HD SNP array. Next, we performed a CNV-based genome-wide association analysis (GWAS) of six meat quality traits and identified 12 significant CNV segments corresponding to eight candidate genes, including <i>PCDH15</i>, <i>CSMD3</i>, etc. Using region-based association analysis, we further identified six CNV segments relevant to meat quality in beef cattle. Among these, <i>TRIM77</i> and <i>TRIM64</i> within CNVR4 on BTA29 were detected as candidate genes for backfat thickness (BFT). Notably, we identified a 34 kb duplication for meat color (MC) which was supported by read-depth signals, and this duplication was embedded within the keratin gene family including <i>KRT4</i>, <i>KRT78</i>, and <i>KRT79</i>. Our findings will help to dissect the genetic architecture of meat quality traits from the aspects of CNVs, and subsequently improve the selection process in breeding programs. |
| first_indexed | 2024-03-11T11:30:16Z |
| format | Article |
| id | doaj.art-fa5b62b74a03418b89c1a6a5637d5c24 |
| institution | Directory Open Access Journal |
| issn | 2304-8158 |
| language | English |
| last_indexed | 2024-03-11T11:30:16Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Foods |
| spelling | doaj.art-fa5b62b74a03418b89c1a6a5637d5c242023-11-10T15:02:58ZengMDPI AGFoods2304-81582023-10-011221398610.3390/foods12213986Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef CattleJiayuan Wu0Tianyi Wu1Xueyuan Xie2Qunhao Niu3Zhida Zhao4Bo Zhu5Yan Chen6Lupei Zhang7Xue Gao8Xiaoyan Niu9Huijiang Gao10Junya Li11Lingyang Xu12State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaCollege of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaMeat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 CNVs and 10,102 CNV regions (CNVRs) based on the Bovine HD SNP array. Next, we performed a CNV-based genome-wide association analysis (GWAS) of six meat quality traits and identified 12 significant CNV segments corresponding to eight candidate genes, including <i>PCDH15</i>, <i>CSMD3</i>, etc. Using region-based association analysis, we further identified six CNV segments relevant to meat quality in beef cattle. Among these, <i>TRIM77</i> and <i>TRIM64</i> within CNVR4 on BTA29 were detected as candidate genes for backfat thickness (BFT). Notably, we identified a 34 kb duplication for meat color (MC) which was supported by read-depth signals, and this duplication was embedded within the keratin gene family including <i>KRT4</i>, <i>KRT78</i>, and <i>KRT79</i>. Our findings will help to dissect the genetic architecture of meat quality traits from the aspects of CNVs, and subsequently improve the selection process in breeding programs.https://www.mdpi.com/2304-8158/12/21/3986copy number variationassociation analysismeat qualitybeef cattle |
| spellingShingle | Jiayuan Wu Tianyi Wu Xueyuan Xie Qunhao Niu Zhida Zhao Bo Zhu Yan Chen Lupei Zhang Xue Gao Xiaoyan Niu Huijiang Gao Junya Li Lingyang Xu Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle Foods copy number variation association analysis meat quality beef cattle |
| title | Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle |
| title_full | Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle |
| title_fullStr | Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle |
| title_full_unstemmed | Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle |
| title_short | Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle |
| title_sort | genetic association analysis of copy number variations for meat quality in beef cattle |
| topic | copy number variation association analysis meat quality beef cattle |
| url | https://www.mdpi.com/2304-8158/12/21/3986 |
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