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Khan IM, Khan A, Liu H, Khan MZ. Editorial: Genetic markers identification for animal production and disease resistance. Front Genet 2023; 14:1243793. [PMID: 37501722 PMCID: PMC10369344 DOI: 10.3389/fgene.2023.1243793] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023] Open
Affiliation(s)
- Ibrar Muhammad Khan
- Anhui Province Key Laboratory of Embryo Development and Reproduction Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Adnan Khan
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongyu Liu
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Muhammad Zahoor Khan
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The University of Agriculture, Dera Ismail Khan, Pakistan
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Deng T, Wu J, Abdel-Shafy H, Wang X, Lv H, Shaukat A, Zhou X, Zhou Y, Sun H, Wei P, Sun N, Huang Q, Xu L, Liu M, Lin Y, Yang L, Hua G. Comparative Genomic Analysis of the Thiolase Family and Functional Characterization of the Acetyl-Coenzyme A Acyltransferase-1 Gene for Milk Biosynthesis and Production of Buffalo and Cattle. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3325-3337. [PMID: 36780201 DOI: 10.1021/acs.jafc.2c07763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Cattle and buffalo served as the first and second largest dairy animals, respectively, providing 96% milk products worldwide. Understanding the mechanisms underlying milk synthesis is critical to develop the technique to improve milk production. Thiolases, also known as acetyl-coenzyme A acetyltransferases (ACAT), are an enzyme family that plays vital roles in lipid metabolism, including ACAT1, ACAT2, ACAA1, ACAA2, and HADHB. Our present study showed that these five members were orthologous in six livestock species including buffalo and cattle. Transcriptomic data analyses derived from different lactations stages showed that ACAA1 displayed different expression patterns between buffalo and cattle. Immunohistochemistry staining revealed that ACAA1 were dominantly located in the mammary epithelial cells of these two dairy animals. Knockdown of ACAA1 inhibited mammary epithelial cell proliferation and triglyceride and β-casein secretion by regulating related gene expressions in cattle and buffalo. In contrast, ACAA1 overexpression promoted cell proliferation and triglyceride secretion. Finally, three novel SNPs (g.-681A>T, g.-23117C>T, and g.-24348G>T) were detected and showed significant association with milk production traits of Mediterranean buffaloes. In addition, g.-681A>T mutation located in the promoter region changed transcriptional activity significantly. Our findings suggested that ACAA1 play a key role in regulating buffalo and cattle milk synthesis and provided basic information to further understand the dairy animal lactation physiology.
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Affiliation(s)
- Tingxian Deng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Guangxi Key Laboratory of Buffalo Genetic, Breeding and Reproduction, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Jiyun Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518038, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hamdy Abdel-Shafy
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Xiaojie Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Haimiao Lv
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aftab Shaukat
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518038, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Pengfei Wei
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Nan Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianzhi Huang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Linghua Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Miaoyu Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuxin Lin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- National Center for International Research on Animal Genetics, Breeding and Reproduction, Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Guohua Hua
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518038, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Center for International Research on Animal Genetics, Breeding and Reproduction, Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan 430070, China
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Shi L, Han B, Liu L, Lv X, Ma Z, Li C, Xu L, Li Y, Zhao F, Yang Y, Sun D. Determination of Genetic Effects of LIPK and LIPJ Genes on Milk Fatty Acids in Dairy Cattle. Genes (Basel) 2019; 10:genes10020086. [PMID: 30696079 PMCID: PMC6409763 DOI: 10.3390/genes10020086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/13/2019] [Accepted: 01/14/2019] [Indexed: 12/30/2022] Open
Abstract
In our previous genome-wide association study (GWAS) on milk fatty acids (FAs) in Chinese Holstein, we discovered 83 genome-wide significant single nucleotide polymorphisms (SNPs) associated with milk FAs. Two of them were close to lipase family member K (LIPK) and lipase family member J (LIPJ), respectively. Hence, this study is a follow-up to verify whether the LIPK and LIPJ have significant genetic effects on milk FAs in dairy cattle. By re-sequencing the entire exons, and 3 kb of 5′ and 3′ flanking regions, two and seven SNPs were identified in LIPK and LIPJ, respectively, including a novel SNP, ss158213049726. With the Haploview 4.1 software, we found that five of the SNPs in LIPJ formed a haplotype block (D′ = 0.96 ~ 1.00). Single-locus association analyses revealed that each SNP in LIPK and LIPJ was significantly associated with at least one milk FA (p = < 1.00 × 10−4 ~ 4.88 × 10−2), and the haplotype-based association analyses showed significant genetic effects on nine milk FAs (p = < 1.00 × 10−4 ~ 3.98 × 10−2). Out of these SNPs, the missense mutation in LIPK gene, rs42774527, could change the protein secondary structure and function predicted by SOPMA, SIFT, and PROVEAN softwares. With the Genomatix software, we predicted that two SNPs, rs110322221 in LIPK and rs211373799 in LIPJ, altered the transcription factors binding sites (TFBSs), indicating their potential regulation on promoter activity of the genes. Furthermore, we found that both LIPK and LIPJ had relatively high expressions in the mammary gland. In conclusion, our research is the first to demonstrate that LIPK and LIPJ genes have significant associations with milk FAs, and the identified SNPs might be served as genetic markers to optimize breeding programs for milk FAs in dairy cattle. This research deserves in-depth verification.
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Affiliation(s)
- Lijun Shi
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China.
| | - Bo Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China.
| | - Lin Liu
- Beijing Dairy Cattle Center, Qinghe'nanzhen Deshengmenwai Street, Chaoyang District, Beijing 100192, China.
| | - Xiaoqing Lv
- Beijing Dairy Cattle Center, Qinghe'nanzhen Deshengmenwai Street, Chaoyang District, Beijing 100192, China.
| | - Zhu Ma
- Beijing Dairy Cattle Center, Qinghe'nanzhen Deshengmenwai Street, Chaoyang District, Beijing 100192, China.
| | - Cong Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China.
| | - Lingna Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China.
| | - Yanhua Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China.
- Beijing Dairy Cattle Center, Qinghe'nanzhen Deshengmenwai Street, Chaoyang District, Beijing 100192, China.
| | - Feng Zhao
- Beijing Dairy Cattle Center, Qinghe'nanzhen Deshengmenwai Street, Chaoyang District, Beijing 100192, China.
| | - Yuze Yang
- Beijing General Station of Animal Husbandry, N0.96 Huizhongsi, Yayun Village, Chaoyang District, Beijing, 100101, China.
| | - Dongxiao Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China.
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Han B, Liang W, Liu L, Li Y, Sun D. Genetic association of the ACACB gene with milk yield and composition traits in dairy cattle. Anim Genet 2018. [PMID: 29521460 DOI: 10.1111/age.12651] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previously, we re-sequenced the whole genomes of eight Holstein bulls with high or low milk protein and fat percentage, and we detected two indels in the ACACB (acetyl-CoA carboxylase beta) gene that were polymorphic between the two groups. Thus, we considered ACACB as a promising candidate gene potentially affecting milk composition traits. Herein, we verified the genetic effects of ACACB on five milk traits in a Chinese Holstein population. We identified six SNPs in the 5'-promoter region, five in the 5'- untranslated region (UTR), 11 in exons, four in the 3'-UTR and three in the 3'-flanking region by re-sequencing the entire coding and regulatory regions of ACACB. One of these SNPs (ss1987461005) is reported here for the first time, and three of the SNPs (rs109482081, rs110819816 and rs109281947) were predicted to result in amino acid replacements. Genotype-phenotype association analyses showed that all the identified SNPs, except for ss1987461005, rs208919019 and rs134447911, were significantly associated with milk yield, fat yield, fat percentage, protein yield or protein percentage (P < 0.0001 to 0.0484). Linkage disequilibrium analyses were conducted among the identified SNPs to confirm the genetic associations. Two SNPs-rs135874354 (g.66218726T>C) and rs210928430 (g.66218117G>A)-were predicted to alter transcription factor binding sites in the 5'-promoter region of ACACB. A luciferase activity assay showed that the promoter activity of haplotype TG was significantly higher than that of CG (P = 0.0002) and that the promoter activity of haplotype TA was remarkably higher than that of CA (P = 7.4285E-09), showing that the T allele of rs135874354 increased promoter activity. Thus, rs135874354 was considered to be a potentially functional mutation. Our findings have, for the first time, profiled the genetic effect of ACACB on milk production traits in dairy cattle and revealed a potentially causal mutation that requires further the in-depth validation.
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Affiliation(s)
- B Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - W Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - L Liu
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - Y Li
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - D Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
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