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Feng F, Yang G, Ma X, Zhang J, Huang C, Ma X, La Y, Yan P, Zhandui P, Liang C. Polymorphisms within the PRKG1 Gene of Gannan Yaks and Their Association with Milk Quality Characteristics. Foods 2024; 13:1913. [PMID: 38928854 PMCID: PMC11203268 DOI: 10.3390/foods13121913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Yak milk, known as the "liquid gold", is a nutritious food with extensive consumption. Compared with cow milk, yak milk contains higher levels of nutrients such as dry matter, milk fat, and milk protein, which demonstrates great potential for exploitation and utilization. Protein kinase cGMP-dependent 1 (PRKG1) is an important functional molecule in the cGMP signaling pathway, and its significant influence on milk fatty acids has been discovered. The aim of this study is to explore the correlation between single nucleotide polymorphisms (SNPs) in the PRKG1 gene and the quality traits of Gannan yak milk in order to identify candidate molecular markers for Gannan yak breeding. In this study, genotyping was performed on 172 healthy, 4-5-year-old lactating Gannan yaks with similar body types, naturally grazed, and two to three parity. Three SNPs (g.404195C>T, g.404213C>T, and g.760138T>C) were detected in the PRKG1 gene of Gannan yaks, which were uniformly distributed in the yak population. Linkage disequilibrium analysis was conducted, revealing complete linkage disequilibrium between g.404195C>T and g.404213C>T. After conducting a correlation analysis between SNPs in the PRKG1 gene and milk quality in Gannan yaks, we found that PRKG1 SNPs significantly increased the content of casein, protein, and SNFs in yak milk. Among them, the TT homozygous genotype at the PRKG1 g.404195C>T loci exhibited higher casein and protein contents compared to the CC and CT genotypes (p < 0.05). The SNP g.760138T>C locus was associated with casein, protein, SNFs, and TS traits (p < 0.05). The CC genotype had higher casein and protein contents than the TT and TA genotypes (p < 0.05). However, there were no significant differences in milk fat, lactose, and acidity among the three genotypes (p > 0.05). In summary, PRKG1 gene polymorphism can serve as a candidate molecular marker for improving milk quality in Gannan yaks.
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Affiliation(s)
- Fen Feng
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Guowu Yang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoyong Ma
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Juanxiang Zhang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chun Huang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yongfu La
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pingcuo Zhandui
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lasa 850004, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Plateau Agricultural Science and Technology Innovation Center, Lasa 850004, China
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Lv X, Chen W, Wang S, Cao X, Yuan Z, Getachew T, Mwacharo JM, Haile A, Sun W. Whole-genome resequencing of Dorper and Hu sheep to reveal selection signatures associated with important traits. Anim Biotechnol 2023; 34:3016-3026. [PMID: 36200839 DOI: 10.1080/10495398.2022.2127409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Dorper and Hu sheep exhibit different characteristics in terms of reproduction, growth, and meat quality. Comparison of the genomes of two breeds help to reveal important genomic information. In this study, whole genome resequencing of 30 individuals (Dorper, DB and Hu sheep, HY) identified 15,108,125 single nucleotide polymorphisms (SNPs). Population differentiation (Fst) and cross population extended haplotype homozygosity (XP-EHH) were performed for selective signal analysis. In total, 106 and 515 overlapped genes were present in both the Fst results and XP-EHH results in HY vs DB and in DB vs HY, respectively. In HY vs DB, 106 genes were enriched in 12 GO terms and 83 KEGG pathways, such as ATP binding (GO:0005524) and PI3K-Akt signaling pathway (oas04151). In DB vs HY, 515 genes were enriched in 109 GO terms and 215 KEGG pathways, such as skeletal muscle cell differentiation (GO:0035914) and MAPK signaling pathway (oas04010). According to the annotation results, we identified a series of candidate genes associated with reproduction (UNC5C, BMPR1B, and GLIS1), meat quality (MECOM, MEF2C, and MYF6), and immunity (GMDS, GALK1, and ITGB4). Our investigation has uncovered genomic information for important traits in sheep and provided a basis for subsequent studies of related traits.
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Affiliation(s)
- Xiaoyang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
| | - Weihao Chen
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shanhe Wang
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
| | - Tesfaye Getachew
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Aynalem Haile
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Genome-Wide Genetic Structure of Henan Indigenous Chicken Breeds. Animals (Basel) 2023; 13:ani13040753. [PMID: 36830540 PMCID: PMC9952073 DOI: 10.3390/ani13040753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
There are five indigenous chicken breeds in Henan Province, China. These breeds have their own unique phenotypic characteristics in terms of morphology, behavior, skin and feather color, and productive performance, but their genetic basis is not well understood. Therefore, we analyzed the genetic structure, genomic diversity, and migration history of Henan indigenous chicken populations and the selection signals and genes responsible for Henan gamecock unique phenotypes using whole genome resequencing. The results indicate that Henan native chickens clustered most closely with the chicken populations in neighboring provinces. Compared to other breeds, Henan gamecock's inbreeding and selection intensity were more stringent. TreeMix analysis revealed the gene flow from southern chicken breeds into the Zhengyang sanhuang chicken and from the Xichuan black-bone chicken into the Gushi chicken. Selective sweep analysis identified several genes and biological processes/pathways that were related to body size, head control, muscle development, reproduction, and aggression control. Additionally, we confirmed the association between genotypes of SNPs in the strong selective gene LCORL and body size and muscle development in the Gushi-Anka F2 resource population. These findings made it easier to understand the traits of the germplasm and the potential for using the Henan indigenous chicken.
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Tuersuntuoheti M, Zhang J, Zhou W, Zhang CL, Liu C, Chang Q, Liu S. Exploring the growth trait molecular markers in two sheep breeds based on Genome-wide association analysis. PLoS One 2023; 18:e0283383. [PMID: 36952432 PMCID: PMC10035858 DOI: 10.1371/journal.pone.0283383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 03/08/2023] [Indexed: 03/25/2023] Open
Abstract
Growth traits are quantitative traits controlled by multiple micro-effect genes. we identified molecular markers related to sheep growth traits, which formed the basis of molecular breeding. In this study, we randomly selected 100 Qira Black sheep and 84 German Merino sheep for the blood collection the jugular vein to genotype by using the Illumina Ovine SNP 50K Bead Chip. quality control criteria for statistical analysis were: rejection detection rate < 90% and minimum allele frequency (MAF) < 5%. Then, we performed Genome-wide association studies (GWAS) on sheep body weight, body height, body length, and chest circumference using mixed linear models. After getting 55 SNPs with significant correlation, they were annotated by reference genome of Ovis aries genome (Oar_v4.0) and We obtained a total of 84 candidate genes associated with production traits (BMPR1B, HSD17B3, TMEM63C, etc.). We selected BMPR1B for population validation and found a correlation between the FecB locus and body weight traits. Therefore, this study not only supplements the existing knowledge of molecular markers of sheep growth traits, but also has important theoretical significance and reference value for the mining of functional genes of sheep growth traits.
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Affiliation(s)
- Mirenisa Tuersuntuoheti
- College of Animal Science and Technology, Tarim University, Alar, China
- Tarim Science and Technology Key Laboratory of Xinjiang Production and Construction Corps, Alar, China
| | - Jihu Zhang
- College of Animal Science and Technology, Tarim University, Alar, China
- Tarim Science and Technology Key Laboratory of Xinjiang Production and Construction Corps, Alar, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Alar, China
- Tarim Science and Technology Key Laboratory of Xinjiang Production and Construction Corps, Alar, China
| | - Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Alar, China
- Tarim Science and Technology Key Laboratory of Xinjiang Production and Construction Corps, Alar, China
| | - Chunjie Liu
- College of Animal Science and Technology, Tarim University, Alar, China
- Tarim Science and Technology Key Laboratory of Xinjiang Production and Construction Corps, Alar, China
| | - Qianqian Chang
- College of Animal Science and Technology, Tarim University, Alar, China
- Tarim Science and Technology Key Laboratory of Xinjiang Production and Construction Corps, Alar, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Alar, China
- Tarim Science and Technology Key Laboratory of Xinjiang Production and Construction Corps, Alar, China
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Wu X, Zhou R, Zhang W, Cao B, Xia J, Caiyun W, Zhang X, Chu M, Yin Z, Ding Y. Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs. Anim Biosci 2021; 34:1895-1902. [PMID: 33705632 PMCID: PMC8563231 DOI: 10.5713/ab.20.0679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/07/2021] [Indexed: 11/27/2022] Open
Abstract
Objective Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency. Methods In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies. Results In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (FROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits. Conclusion This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.
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Affiliation(s)
- Xudong Wu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Ren Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Wei Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, P.R. China
| | - Bangji Cao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Jing Xia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Wang Caiyun
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Xiaodong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Mingxing Chu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing,100193, P. R. China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Yueyun Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
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Genome-Wide Association Study of Weaning Traits in Lori-Bakhtiari Sheep. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2020-0014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Abstract
Weaning traits, including preweaning daily gain (PWDG) and weaning weight (WW) are important economic traits, especially for meat type mammals, with high impacts on growth performance and survival rate in higher ages. This study was conducted to perform a genome-wide association study (GWAS) on weaning traits in a meat type breed of sheep. Body weight records of 7557 Lori-Bakhtiari sheep with PWDG and WW records were used to estimate breeding values (EBVs) using an animal mixed model. A total of 132 animals were selected by two-tailed selection strategy, based on EBVs for body weight and then were genotyped using Illumina 50k Ovine SNP chip. After quality control, a total of 130 animals and 41323 SNPs were remained for further analyses. De-regressed estimates of breeding values were used as a pseudo-phenotype in GWAS analysis. Based on Bonferroni-adjusted p-values, five SNPs, located on chromosomes 2, 3, 4, 12 and 22 were significantly (p < 0.05) associated with weaning traits and accounted for 5.06% and 0.37% of total genetic variations of PWDG and WW, respectively. Two SNPs on chromosomes 2 and 3 were located near to previously reported QTLs for weaning traits. Three genes, including ANGPTL7, mTOR and WDR11, were found within 50 kbp distances from the significant SNPs and thus could be considered as candidate genes for weaning traits. The detected QTLs and candidate genes could be studied for construction of breeding programs for genetic improvement of growth performance in meat type sheep.
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Cao Y, Song X, Shan H, Jiang J, Xiong P, Wu J, Shi F, Jiang Y. Genome-Wide Association Study of Body Weights in Hu Sheep and Population Verification of Related Single-Nucleotide Polymorphisms. Front Genet 2020; 11:588. [PMID: 32719712 PMCID: PMC7350885 DOI: 10.3389/fgene.2020.00588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
Body weight (BW) is a critical economic trait for meat production in sheep. The current study aimed to perform a genome-wide association study (GWAS) to detect significant single-nucleotide polymorphisms (SNPs) that are associated with BW in Hu sheep. The comparison and analysis of the G1 and G2 generations of a nucleus meat Hu sheep breeding herd revealed four SNPs identified by GWAS. The subsequent verification of the significant SNP loci in the Hu sheep G3 generation nucleus herd also detected nine SNPs in significant SNP regions. Two SNPs were significantly associated with the BW of Hu sheep (p < 0.05). OARX_76354330.1 and s64890.1 could be identified as functional SNPs for the growth traits of Hu sheep. CAPN6, as a candidate gene, was significantly different in the biceps femoris and longissimus dorsi muscles of weaning (60-day) and 6-month sheep, which facilitated the discovery of causal variants for BW and contributed to the marker-assisted selection breeding of Hu sheep.
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Affiliation(s)
- Yuhao Cao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xuemei Song
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, China
| | - Huili Shan
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junfang Jiang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Pei Xiong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jianliang Wu
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fangxiong Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yongqing Jiang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds. Animals (Basel) 2019; 9:ani9110958. [PMID: 31726757 PMCID: PMC6912326 DOI: 10.3390/ani9110958] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 12/19/2022] Open
Abstract
Hu sheep and Small-tailed Han sheep are the most widely raised and most famous maternal sheep breeds in China, which are known for precocious puberty, perennial oestrus and high fecundity (1-6 lambs each parity). Therefore, it is crucial to increase litter size of these two breeds for intensive sheep industry. The objective of this study was to identify potential genetic markers linked with sheep litter size located at ten genes. This study collected blood sample of 537 Hu sheep and 420 Small-tailed Han sheep with litter size of first parity. The average litter sizes in Hu sheep and Small-tailed Han sheep were 2.21 and 1.93. DNA-pooling sequencing method was used for detecting the potential single nucleotide polymorphisms (SNPs) in ten genes related to follicle development and female reproduction. SNPscan® was used for individually genotyping. As a result, a total of 78 putative SNPs in nine out of ten candidate genes (except NOG) were identified. In total, 50 SNPs were successfully genotyped in Hu sheep and Small-tailed Han sheep. After quality control, a total of 42 SNPs in Hu sheep and 44 SNPs in Small-tailed Han sheep were finally used for further analysis. Association analysis revealed that nine SNPs within six genes (KIT: g.70199073A>G, KITLG: g.124520653G>C, ADAMTS1: g.127753565T>C, ADAMTS1: g.127754640G>T, NCOA1: g.31928165C>T, NCOA1: g.32140565G>A, LIFR: g.35862868C>T, LIFR: g.35862947G>T and NGF: g.91795933T>C) were significantly associated with litter size in Hu sheep or Small-tailed Han sheep. A combined haplotypes analysis of the two loci (LIFR: g.35862868C>T and LIFR: g.35862947G>T) revealed that H2H3 (CTTT) combined haplotypes had the largest litter size than the rest combined haplotypes and more than those with either mutation alone in Small-tailed Han sheep. Taken together, our study suggests that nine significant SNPs in six genes can be served as useful genetic markers for MAS in sheep.
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Zlobin A, Volkova N, Borodin P, Aksenovich T, Tsepilov Y. Recent advances in understanding genetic variants associated with growth, carcass and meat productivity traits in sheep ( Ovis aries): an update. Arch Anim Breed 2019; 62:579-583. [PMID: 31893215 PMCID: PMC6904904 DOI: 10.5194/aab-62-579-2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 09/17/2019] [Indexed: 12/17/2022] Open
Abstract
Identification of quantitative trait loci (QTLs) and candidate genes that affect growth intensity is a prerequisite for the marker-assisted selection of economically important traits. The number of QTL studies on sheep is relatively small in comparison to those on cattle and pigs. The current QTL sheep database - Sheep QTLdb - contains information on 1658 QTLs for 225 different traits. A few genes and markers associated with growth, carcass and meat productivity traits have been reported. The information about QTLs from the Sheep QTLdb cannot be directly used in marker-assisted selection due to the lack of essential information such as effective and reference alleles, the effect direction etc., and it requires manual curation and validation. In this study we performed a comprehensive search for QTLs focusing on single nucleotide polymorphisms (SNPs) associated with growth and meat traits in sheep. The database contains information about 156 SNP-trait associations (123 unique SNPs) and a list of 165 associated genes. The updated information is freely available at https://github.com/Defrag1236/Ovines_2018 (last access: 18 September 2019). This information can be useful for further association studies and preliminary estimation of genetic variability for economically important traits in different breeds.
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Affiliation(s)
- Alexander S. Zlobin
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
| | - Natalia A. Volkova
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
| | - Pavel M. Borodin
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Tatiana I. Aksenovich
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
| | - Yakov A. Tsepilov
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
- Novosibirsk State University, Novosibirsk, Russia
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Yu H, You X, Li J, Zhang X, Zhang S, Jiang S, Lin X, Lin HR, Meng Z, Shi Q. A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping. SCIENCE CHINA-LIFE SCIENCES 2018. [DOI: 10.1007/s11427-017-9161-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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