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Zhou W, Zhang CL, Han Z, Li X, Bai X, Wang J, Yang R, Liu S. Genome-wide selection reveals candidate genes associated with multiple teats in Hu sheep. Anim Biotechnol 2024; 35:2380766. [PMID: 39034460 DOI: 10.1080/10495398.2024.2380766] [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: 07/23/2024]
Abstract
Increasing the number of teats in sheep helps to improve the survival rate of sheep lambs after birth. In order to analyze the candidate genes related to the formation of multiple teats in Hu sheep, the present study was conducted to investigate the genetic pattern of multiple teats in Hu sheep. In this study, based on genome-wide data from 157 Hu sheep, Fst, xp-EHH, Pi and iHS signaling were performed, and the top 5% signal regions of each analyzed result were annotated based on the Oar_v4.0 for sheep. The results show that a total of 142 SNP loci were selected. We found that PTPRG, TMEM117 and LRP1B genes were closely associated with polypodium formation in Hu sheep, in addition, among the candidate genes related to polypodium we found genes such as TMEM117, SLC25A21 and NCKAP5 related to milk traits. The present study screened out candidate genes for the formation of multiple teats at the genomic level in Hu sheep.
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Affiliation(s)
- Wen Zhou
- College of Animal Science and Technology, Tarim University, Xinjiang, China
| | - Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Xinjiang, China
| | - Xinyu Bai
- College of Animal Science and Technology, Tarim University, Xinjiang, China
| | - Jieru Wang
- College of Animal Science and Technology, Tarim University, Xinjiang, China
| | - Ruizhi Yang
- College of Animal Science and Technology, Tarim University, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Xinjiang, China
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Zhang F, Liu Q, Gong P, Wang Y, Shi C, Zhu L, Zhao J, Yao W, Luo J. Genome-wide association study provided insights into the polled phenotype and polled intersex syndrome (PIS) in goats. BMC Genomics 2024; 25:661. [PMID: 38956513 PMCID: PMC11218382 DOI: 10.1186/s12864-024-10568-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Breeding polled goats is a welfare-friendly approach for horn removal in comparison to invasive methods. To gain a comprehensive understanding of the genetic basis underlying polledness in goats, we conducted whole-genome sequencing of 106 Xinong Saanen dairy goats, including 33 horned individuals, 70 polled individuals, and 3 polled intersexuality syndrome (PIS) individuals. METHODS The present study employed a genome-wide association study (GWAS) and linkage disequilibrium (LD) analysis to precisely map the genetic locus underlying the polled phenotype in goats. RESULTS The analysis conducted in our study revealed a total of 320 genome-wide significant single nucleotide polymorphisms (SNPs) associated with the horned/polled phenotype in goats. These SNPs exhibited two distinct peaks on chromosome 1, spanning from 128,817,052 to 133,005,441 bp and from 150,336,143 to 150,808,639 bp. The present study identified three genome-wide significant SNPs, namely Chr1:129789816, Chr1:129791507, and Chr1:129791577, as potential markers of PIS-affected goats. The results of our LD analysis suggested a potential association between MRPS22 and infertile intersex individuals, as well as a potential association between ERG and the polled trait in goats. CONCLUSION We have successfully identified three marker SNPs closely linked to PIS, as well as several candidate genes associated with the polled trait in goats. These results may contribute to the development of SNP chips for early prediction of PIS in goats, thereby facilitating breeding programs aimed at producing fertile herds with polled traits.
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Affiliation(s)
- Fuhong Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Qingqing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumchi, 830000, P. R. China
| | - Yaling Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Chenbo Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Lu Zhu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Jianqing Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Weiwei Yao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China
| | - Jun Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, P. R. China.
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Zhong Z, Li G, Xu Z, Zeng H, Teng J, Feng X, Diao S, Gao Y, Li J, Zhang Z. Evaluating three strategies of genome-wide association analysis for integrating data from multiple populations. Anim Genet 2024; 55:265-276. [PMID: 38185881 DOI: 10.1111/age.13394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/24/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
In livestock, genome-wide association studies (GWAS) are usually conducted in a single population (single-GWAS) with limited sample size and detection power. To enhance the detection power of GWAS, meta-analysis of GWAS (meta-GWAS) and mega-analysis of GWAS (mega-GWAS) have been proposed to integrate data from multiple populations at the level of summary statistics or individual data, respectively. However, there is a lack of comparison for these different strategies, which makes it difficult to guide the best practice of GWAS integrating data from multiple study populations. To maximize the comparison of different association analysis strategies across multiple populations, we conducted single-GWAS, meta-GWAS, and mega-GWAS for the backfat thickness of 100 kg (BFT_100) and days to 100 kg (DAYS_100) within each of the three commercial pig breeds (Duroc, Yorkshire, and Landrace). Based on controlling the genome inflation factor to one, we calculated corrected p-values (pC ). In Yorkshire, with the largest sample size, mega-GWAS, meta-GWAS and single-GWAS detected 149, 38 and 20 significant SNPs (pC < 1E-5) associated with BFT_100, as well as 26, four, and one QTL, respectively. Among them, pC of SNPs from mega-GWAS was the lowest, followed by meta-GWAS and single-GWAS. The correlation of pC among the three GWAS strategies ranged from 0.60 to 0.75 and the correlation of SNP effect values between meta-GWAS and mega-GWAS was 0.74, all showing good agreement. Collectively, even though there are differences in the integration of individual data or summary statistics, integrating data from multiple populations is an effective means of genetic argument for complex traits, especially mega-GWAS versus single-GWAS.
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Affiliation(s)
- Zhanming Zhong
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Guangzhen Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhiting Xu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Haonan Zeng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jinyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xueyan Feng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shuqi Diao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yahui Gao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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Zhao X, Qiu Y, Meng F, Zhuang Z, Ruan D, Wu J, Ma F, Zheng E, Cai G, Yang J, Yang M, Wu Z. Genome-wide association studies for loin muscle area, loin muscle depth and backfat thickness in DLY pigs. Anim Genet 2024; 55:134-139. [PMID: 38098441 DOI: 10.1111/age.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 01/04/2024]
Abstract
This study aimed at identifying genes associated with loin muscle area (LMA), loin muscle depth (LMD) and backfat thickness (BFT). We performed single-trait and multi-trait genome-wide association studies (GWASs) after genotyping 685 Duroc × (Landrace × Yorkshire) (DLY) pigs using the Geneseek Porcine 50K SNP chip. In the single-trait GWASs, we identified two, eight and two significant SNPs associated with LMA, LMD and BFT, respectively, and searched genes within the 1 Mb region near the significant SNPs with relevant functions as candidate genes. Consequently, we identified one (DOCK5), three (PID1, PITX2, ELOVL6) and three (CCR1, PARP14, CASR) promising candidate genes for LMA, LMD and BFT, respectively. Moreover, the multi-trait GWAS identified four significant SNPs associated with the three traits. In conclusion, the GWAS analysis of LMA, LMD and BFT in a DLY pig population identified several associated SNPs and candidate genes, further deepening our understanding of the genetic basis of these traits, and they may be useful for marker-assisted selection to improve the three traits in DLY pigs.
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Affiliation(s)
- Xiang Zhao
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fanming Meng
- State Key Laboratory of Livestock and Poultry Breeding/Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fucai Ma
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Ming Yang
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
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Liu J, Xu L, Ding X, Ma Y. Genome-Wide Association Analysis of Reproductive Traits in Chinese Holstein Cattle. Genes (Basel) 2023; 15:12. [PMID: 38275594 PMCID: PMC10815438 DOI: 10.3390/genes15010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/27/2024] Open
Abstract
This study was to explore potential SNP loci for reproductive traits in Chinese Holstein cattle and identify candidate genes. Genome-wide Association Study based on mixed linear model was performed on 643 Holstein cattle using GeneSeek Bovine 50 K SNP chip. Our results detected forty significant SNP loci after Bonferroni correction. We identified five genes (VWC2L, STAT1, PPP3CA, LDB3, and CTNNA3) as being associated with pregnancy ratio of young cows, five genes (PAEP, ACOXL, EPAS1, GLRB, and MARVELD1) as being associated with pregnancy ratio of adult cows, and nine genes (PDE1B, SLCO1A2, ARHGAP26, ADAM10, APBB1, MON1B, COQ9, CDC42BPB, MARVELD1, and HPSE2) as being associated with daughter pregnancy rate. Our study may provide valuable insights into identifying genes related to reproductive traits and help promote the application of molecular breeding in dairy cows.
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Affiliation(s)
- Jiashuang Liu
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China;
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China;
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Xiangbin Ding
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China;
| | - Yi Ma
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China;
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Zhang C, Li C, Zhao P, Shao Q, Ma Y, Bai D, Liao C, He L, Huang S, Wang X. Effects of dietary Glycyrrhiza polysaccharide supplementation on growth performance, intestinal antioxidants, immunity and microbiota in weaned piglets. Anim Biotechnol 2023; 34:2273-2284. [PMID: 35714985 DOI: 10.1080/10495398.2022.2086878] [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
The aim of this study was to evaluate the effects of dietary Glycyrrhiza polysaccharide (GCP) supplementation on growth performance, intestinal antioxidants, immunity and microbiota in weaned piglets. One hundred and twenty 28-day-old weaned piglets were randomly assigned into five groups (four replicates per group) and fed a basal diet with GCP at 0, 500, 1000, 2000 and 4000 mg/kg for four weeks, respectively. Results showed that 1000 mg/kg GCP improved piglets' ADG and ADFI and reduced FCR (p < .05). Thus, the 0 and 1000 mg/kg GCP dose were selected for subsequent experiments. We found that 1000 mg/GCP increased SOD and T-AOC and decreased MDA in the jejunal mucosa (p < .05). Dietary 1000 mg/kg GCP also resulted in high levels of sIgA, IL-10 and TGF-β, whereas IL-2 dropped dramatically (p < .05). The relative expression levels of ZO-1, CLDN, OCLDN, TLR-4, IL-10, TGF-β, Nrf-2, SOD1 and CAT increased in the jejunal mucosa, whereas INF-γ decreased (p < .05). 1000 mg/kg GCP treatment altered the diversity and community composition of cecal microbiota in pigs, with increasing relative abundance of Bacteroidota and Lactobacillus at phylum and genus levels (p < .05), respectively. The results suggested that dietary 1000 mg/kg GCP could improve growth performance and intestinal health of weaned piglets.
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Affiliation(s)
- Cai Zhang
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang, P. R. China
| | - Chenxu Li
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang, P. R. China
| | - Pengli Zhao
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang, P. R. China
| | - Qi Shao
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang, P. R. China
| | - Yanbo Ma
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang, P. R. China
| | - Dongying Bai
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang, P. R. China
| | - Chengshui Liao
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang, P. R. China
| | - Lei He
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang, P. R. China
| | - Shucheng Huang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, P. R. China
| | - Xueying Wang
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang, P. R. China
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Zegeye T, Belay G, Vallejo-Trujillo A, Han J, Hanotte O. Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia. Front Genet 2023; 14:1050365. [PMID: 37600659 PMCID: PMC10432725 DOI: 10.3389/fgene.2023.1050365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
The Tigray region, where we found around eight per cent of the indigenous cattle population of Ethiopia, is considered as the historic centre of the country, with the ancient pre-Aksumite and Aksumite civilisations in contact with the civilisations of the Fertile Crescent and the Indian subcontinent. Here, we used whole genome sequencing data to characterise the genomic diversity, relatedness, and admixture of five cattle populations (Abergelle, Arado, Begait, Erob, and Raya) indigenous to the Tigray region of Ethiopia. We detected 28 to 29 million SNPs and 2.7 to 2.9 million indels in each population, of which 7% of SNPs and 34% of indels were novel. Functional annotation of the variants showed around 0.01% SNPs and 0.22%-0.27% indels in coding regions. Enrichment analysis of genes overlapping missense private SNPs revealed 20 significant GO terms and KEGG pathways that were shared by or specific to breeds. They included important genes associated with morphology (SCN4A, TAS1R2 and KCNG4), milk yield (GABRG1), meat quality (MMRN2, VWC2), feed efficiency (PCDH8 and SLC26A3), immune response (LAMC1, PCDH18, CELSR1, TLR6 and ITGA5), heat resistance (NPFFR1 and HTR7) and genes belonging to the olfactory gene family, which may be related to adaptation to harsh environments. Tigray indigenous cattle are very diverse. Their genome-wide average nucleotide diversity ranged from 0.0035 to 0.0036. The number of heterozygous SNPs was about 0.6-0.7 times higher than homozygous ones. The within-breed average number of ROHs ranged from 777.82 to 1000.45, with the average sum of the length of ROHs ranging from 122.01 Mbp to 163.88 Mbp. The genomic inbreeding coefficients differed among animals and breeds, reaching up to 10% in some Begait and Raya animals. Tigray indigenous cattle shared a common ancestry with Asian indicine (85.6%-88.7%) and African taurine (11.3%-14.1%) cattle, with very small, if any, European taurine introgression. This study identified high within-breed genetic diversity representing an opportunity for breeding improvement programs and, also, significant novel variants that could increase the number of known cattle variants, an important contribution to the knowledge of domestic cattle genetic diversity.
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Affiliation(s)
- Tsadkan Zegeye
- Mekelle Agricultural Research Center, Tigray Agricultural Research Institute, Mekelle, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adriana Vallejo-Trujillo
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jianlin Han
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Olivier Hanotte
- Live Gene—CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Cells, Organism and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Miao Y, Zhao Y, Wan S, Mei Q, Wang H, Fu C, Li X, Zhao S, Xu X, Xiang T. Integrated analysis of genome-wide association studies and 3D epigenomic characteristics reveal the BMP2 gene regulating loin muscle depth in Yorkshire pigs. PLoS Genet 2023; 19:e1010820. [PMID: 37339141 DOI: 10.1371/journal.pgen.1010820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND The lack of integrated analysis of genome-wide association studies (GWAS) and 3D epigenomics restricts a deep understanding of the genetic mechanisms of meat-related traits. With the application of techniques as ChIP-seq and Hi-C, the annotations of cis-regulatory elements in the pig genome have been established, which offers a new opportunity to elucidate the genetic mechanisms and identify major genetic variants and candidate genes that are significantly associated with important economic traits. Among these traits, loin muscle depth (LMD) is an important one as it impacts the lean meat content. In this study, we integrated cis-regulatory elements and genome-wide association studies (GWAS) to identify candidate genes and genetic variants regulating LMD. RESULTS Five single nucleotide polymorphisms (SNPs) located on porcine chromosome 17 were significantly associated with LMD in Yorkshire pigs. A 10 kb quantitative trait locus (QTL) was identified as a candidate functional genomic region through the integration of linkage disequilibrium and linkage analysis (LDLA) and high-throughput chromosome conformation capture (Hi-C) analysis. The BMP2 gene was identified as a candidate gene for LMD based on the integrated results of GWAS, Hi-C meta-analysis, and cis-regulatory element data. The identified QTL region was further verified through target region sequencing. Furthermore, through using dual-luciferase assays and electrophoretic mobility shift assays (EMSA), two SNPs, including SNP rs321846600, located in the enhancer region, and SNP rs1111440035, located in the promoter region, were identified as candidate SNPs that may be functionally related to the LMD. CONCLUSIONS Based on the results of GWAS, Hi-C, and cis-regulatory elements, the BMP2 gene was identified as an important candidate gene regulating variation in LMD. The SNPs rs321846600 and rs1111440035 were identified as candidate SNPs that are functionally related to the LMD of Yorkshire pigs. Our results shed light on the advantages of integrating GWAS with 3D epigenomics in identifying candidate genes for quantitative traits. This study is a pioneering work for the identification of candidate genes and related genetic variants regulating one key production trait (LMD) in pigs by integrating genome-wide association studies and 3D epigenomics.
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Affiliation(s)
- Yuanxin Miao
- Research Institute of Agricultural Biotechnology, Jingchu University of Technology, Jingmen, China
| | - Yunxia Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Siqi Wan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Quanshun Mei
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Heng Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Chuanke Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan laboratory, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Tao Xiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
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Desire S, Johnsson M, Ros-Freixedes R, Chen CY, Holl JW, Herring WO, Gorjanc G, Mellanby RJ, Hickey JM, Jungnickel MK. A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines. Genet Sel Evol 2023; 55:42. [PMID: 37322449 DOI: 10.1186/s12711-023-00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) aim at identifying genomic regions involved in phenotype expression, but identifying causative variants is difficult. Pig Combined Annotation Dependent Depletion (pCADD) scores provide a measure of the predicted consequences of genetic variants. Incorporating pCADD into the GWAS pipeline may help their identification. Our objective was to identify genomic regions associated with loin depth and muscle pH, and identify regions of interest for fine-mapping and further experimental work. Genotypes for ~ 40,000 single nucleotide morphisms (SNPs) were used to perform GWAS for these two traits, using de-regressed breeding values (dEBV) for 329,964 pigs from four commercial lines. Imputed sequence data was used to identify SNPs in strong ([Formula: see text] 0.80) linkage disequilibrium with lead GWAS SNPs with the highest pCADD scores. RESULTS Fifteen distinct regions were associated with loin depth and one with loin pH at genome-wide significance. Regions on chromosomes 1, 2, 5, 7, and 16, explained between 0.06 and 3.55% of the additive genetic variance and were strongly associated with loin depth. Only a small part of the additive genetic variance in muscle pH was attributed to SNPs. The results of our pCADD analysis suggests that high-scoring pCADD variants are enriched for missense mutations. Two close but distinct regions on SSC1 were associated with loin depth, and pCADD identified the previously identified missense variant within the MC4R gene for one of the lines. For loin pH, pCADD identified a synonymous variant in the RNF25 gene (SSC15) as the most likely candidate for the muscle pH association. The missense mutation in the PRKAG3 gene known to affect glycogen content was not prioritised by pCADD for loin pH. CONCLUSIONS For loin depth, we identified several strong candidate regions for further statistical fine-mapping that are supported in the literature, and two novel regions. For loin muscle pH, we identified one previously identified associated region. We found mixed evidence for the utility of pCADD as an extension of heuristic fine-mapping. The next step is to perform more sophisticated fine-mapping and expression quantitative trait loci (eQTL) analysis, and then interrogate candidate variants in vitro by perturbation-CRISPR assays.
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Affiliation(s)
- Suzanne Desire
- The Roslin Institute, The University of Edinburgh, Midlothian, UK.
| | - Martin Johnsson
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roger Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Ching-Yi Chen
- The Pig Improvement Company, Genus Plc, Hendersonville, TN, USA
| | - Justin W Holl
- The Pig Improvement Company, Genus Plc, Hendersonville, TN, USA
| | | | - Gregor Gorjanc
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Richard J Mellanby
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - John M Hickey
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
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10
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Qiao R, Zhang M, Zhang B, Li X, Han X, Wang K, Li X, Yang F, Hu P. Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs. Front Genet 2022; 13:1039838. [PMID: 36437945 PMCID: PMC9681789 DOI: 10.3389/fgene.2022.1039838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Yunan is a crossed lean meat pig breed in China. Backfat thickness is the gold standard for carcass quality grading. However, over 14 years after breed registration, the backfat of Yunan thickened and the consistency of backfat thickness decreased. Meanwhile, no genetic study has been ever performed on Yunan population. So, in this study we collected all the 120 nucleus individuals of Yunan and recorded six backfat traits of them, carried out population genetic structure analysis, selection signals analysis and genome-wide association study of Yunan pigs with the help of their founder population Duroc and Chinese native Huainan pigs, to determine the genomic loci on backfat of Yunan. Genetic diversity indexes suggested Yunan pigs had no inbreeding risk while population genetic structure showed they had few molecular pedigrees and were stratified. A total of 71 common selection signals affecting growth and fat deposition were detected by FST and XP-CLR methods. 34 significant loci associated with six backfat traits were detected, among which a 1.40 Mb region on SSC4 (20.03–21.43 Mb) were outstanding as the strong region underlying backfat. This region was common with the results of selection signature analysis, former reported QTLs for backfat and was common for different kinds of backfat traits at different development stage. ENPP2, EXT1 and SLC30A8 genes around were fat deposition related genes and were of Huainan pig’s origin, among which Type 2 diabetes related gene SLC30A8 was the most reasonable for being in a 193.21 Kb haplotype block of the 1.40 Mb region. Our results had application value for conservation, mating and breeding improvement of backfat thickness of Yunan pigs and provided evidence for a human function gene might be reproduced in pigs.
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Affiliation(s)
- Ruimin Qiao
- *Correspondence: Ruimin Qiao, ; Panyang Hu, hpy9809.@163.com
| | | | | | | | | | | | | | | | - Panyang Hu
- *Correspondence: Ruimin Qiao, ; Panyang Hu, hpy9809.@163.com
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11
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Addo S, Jung L. An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs. Front Genet 2022; 13:909986. [DOI: 10.3389/fgene.2022.909986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16–26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs.
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12
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Guan X, Zhao S, Xiang W, Jin H, Chen N, Lei C, Jia Y, Xu L. Genetic Diversity and Selective Signature in Dabieshan Cattle Revealed by Whole-Genome Resequencing. BIOLOGY 2022; 11:biology11091327. [PMID: 36138806 PMCID: PMC9495734 DOI: 10.3390/biology11091327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/07/2022] [Accepted: 09/04/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary To protect the genetic resources of Chinese native cattle breeds, we investigated the genetic structure, genetic diversity and genetic signature from artificial or natural selection by sequencing 32 bovine genomes from the breeding farm of the Dabieshan population. We discovered that the ancestral contributions of Dabieshan originated from Chinese indicine and East Asian taurine on the autosomal genome, which had abundant genomic diversity. Some candidate genes associated with fertility, feed efficiency, fat deposition, immune response, heat resistance and the coat color were identified by a selective sweep. The SNPs data were based on genomics, which could establish a foundation for breed amelioration and support conservation for indigenous cattle breeds. Abstract Dabieshan cattle are a typical breed of southern Chinese cattle that have the characteristics of muscularity, excellent meat quality and tolerance to temperature and humidity. Based on 148 whole-genome data, our analysis disclosed the ancestry components of Dabieshan cattle with Chinese indicine (0.857) and East Asian taurine (0.139). The Dabieshan genome demonstrated a higher genomic diversity compared with the other eight populations, supported by the observed nucleotide diversity, linkage disequilibrium decay and runs of homozygosity. The candidate genes were detected by a selective sweep, which might relate to the fertility (GPX5, GPX6), feed efficiency (SLC2A5), immune response (IGLL1, BOLA-DQA2, BOLA-DQB), heat resistance (DnaJC1, DnaJC13, HSPA4), fat deposition (MLLT10) and the coat color (ASIP). We also identified the “East Asian taurine-like” segments in Dabieshan cattle, which might contribute to meat quality traits. The results revealed by the unique and valuable genomic data can build a foundation for the genetic improvement and conservation of genetic resources for indigenous cattle breeds.
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Affiliation(s)
- Xiwen Guan
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Shuanping Zhao
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Weixuan Xiang
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Hai Jin
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Yutang Jia
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Lei Xu
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Correspondence: ; Tel.: +86-153-7547-2704
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13
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Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs. Genes (Basel) 2022; 13:genes13081454. [PMID: 36011365 PMCID: PMC9407794 DOI: 10.3390/genes13081454] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 12/24/2022] Open
Abstract
Growth rate plays a critical role in the pig industry and is related to quantitative traits controlled by many genes. Here, we aimed to identify causative mutations and candidate genes responsible for pig growth traits. In this study, 2360 Duroc pigs were used to detect significant additive, dominance, and epistatic effects associated with growth traits. As a result, a total number of 32 significant SNPs for additive or dominance effects were found to be associated with various factors, including adjusted age at a specified weight (AGE), average daily gain (ADG), backfat thickness (BF), and loin muscle depth (LMD). In addition, the detected additive significant SNPs explained 2.49%, 3.02%, 3.18%, and 1.96% of the deregressed estimated breeding value (DEBV) variance for AGE, ADG, BF, and LMD, respectively, while significant dominance SNPs could explain 2.24%, 13.26%, and 4.08% of AGE, BF, and LMD, respectively. Meanwhile, a total of 805 significant epistatic effects SNPs were associated with one of ADG, AGE, and LMD, from which 11 sub-networks were constructed. In total, 46 potential genes involved in muscle development, fat deposition, and regulation of cell growth were considered as candidates for growth traits, including CD55 and NRIP1 for AGE and ADG, TRIP11 and MIS2 for BF, and VRTN and ZEB2 for LMD, respectively. Generally, in this study, we detected both new and reported variants and potential candidate genes for growth traits of Duroc pigs, which might to be taken into account in future molecular breeding programs to improve the growth performance of pigs.
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14
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Davoudi P, Do DN, Colombo SM, Rathgeber B, Miar Y. Application of Genetic, Genomic and Biological Pathways in Improvement of Swine Feed Efficiency. Front Genet 2022; 13:903733. [PMID: 35754793 PMCID: PMC9220306 DOI: 10.3389/fgene.2022.903733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/20/2022] [Indexed: 12/24/2022] Open
Abstract
Despite the significant improvement of feed efficiency (FE) in pigs over the past decades, feed costs remain a major challenge for producers profitability. Improving FE is a top priority for the global swine industry. A deeper understanding of the biology underlying FE is crucial for making progress in genetic improvement of FE traits. This review comprehensively discusses the topics related to the FE in pigs including: measurements, genetics, genomics, biological pathways and the advanced technologies and methods involved in FE improvement. We first provide an update of heritability for different FE indicators and then characterize the correlations of FE traits with other economically important traits. Moreover, we present the quantitative trait loci (QTL) and possible candidate genes associated with FE in pigs and outline the most important biological pathways related to the FE traits in pigs. Finally, we present possible ways to improve FE in swine including the implementation of genomic selection, new technologies for measuring the FE traits, and the potential use of genome editing and omics technologies.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
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15
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Wang K, Wang S, Ji X, Chen D, Shen Q, Yu Y, Xiao W, Wu P, Tang G. Genome-wide association studies identified loci associated with both feed conversion ratio and residual feed intake in Yorkshire pigs. Genome 2022; 65:405-412. [PMID: 35594567 DOI: 10.1139/gen-2021-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Feed occupies a significant proportion in the production cost of pigs, and the feed efficiency (FE) in pigs are of utmost economic importance. Hence, the objective of this study is to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with FE related traits, including feed conversion ratio (FCR) and residual feed intake (RFI). A genome-wide association study (GWAS) was conducted for FCR and RFI in 169 Yorkshire pigs using whole-genome sequencing data. A total of 23 and 33 suggestive significant SNPs (P<1×10^(-6)) were detected for FCR and RFI, respectively. However, none of the SNPs achieved the genome-wide significance threshold (P<5×10^(-8)). Importantly, three common SNPs (SSC7:7987268, SSC13:42350250, and SSC13:42551718) were associated with both FCR and RFI. Additionally, the NEDD9 gene related to FCR and RFI traits was overlapped. This study detected novel SNPs on SSC7 and SSC13 common for FCR and RFI. These results provide new insights into the genetic mechanisms and candidate genes of FE-related traits in pigs.
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Affiliation(s)
- Kai Wang
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Shujie Wang
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Xiang Ji
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Dong Chen
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Qi Shen
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Yang Yu
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Weihang Xiao
- Sichuan Agricultural University, 12529, Yaan, Sichuan, China, 625014;
| | - Pingxian Wu
- Chongqing Academy of Animal Science, Chongqing, China, 402460;
| | - Guoqing Tang
- Sichuan Agricultural University, 12529, Yaan, Sichuan, China, 625014;
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16
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Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species. Genes (Basel) 2022; 13:genes13020297. [PMID: 35205343 PMCID: PMC8872339 DOI: 10.3390/genes13020297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.
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17
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Halli K, Bohlouli M, Schulz L, Sundrum A, König S. Estimation of direct and maternal genetic effects and annotation of potential candidate genes for weight and meat quality traits in a genotyped outdoor dual-purpose cattle breed. Transl Anim Sci 2022; 6:txac022. [PMID: 35308836 PMCID: PMC8925308 DOI: 10.1093/tas/txac022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 12/03/2022] Open
Abstract
With regard to potential applications of genomic selection in small numbered breeds, we evaluated genomic models and focused on potential candidate gene annotations for weight and meat quality traits in the local Rotes Höhenvieh (RHV) breed. Traits included 6,003 birth weights (BWT), 5,719 200 d-weights (200dw), 4,594 365 d-weights (365dw), and 547 records for intramuscular fat content (IMF). A total of 581,304 SNP from 370 genotyped cattle with phenotypic records were included in genomic analyses. Model evaluations focused on single- and multiple-trait models with direct and with direct and maternal genetic effects. Genetic relationship matrices were based on pedigree (A-matrix), SNP markers (G-matrix), or both (H-matrix). Genome-wide association studies (GWASs) were carried out using linear mixed models to identify potential candidate genes for the traits of interest. De-regressed proofs (DRP) for direct and maternal genetic components were used as pseudo-phenotypes in the GWAS. Accuracies of direct breeding values were higher from models based on G or on H compared to A. Highest accuracies (> 0.89) were obtained for IMF with multiple-trait models using the G-matrix. Direct heritabilities with maternal genetic effects ranged from 0.62 to 0.66 for BWT, from 0.45 to 0.55 for 200dW, from 0.40 to 0.44 for 365dW, and from 0.48 to 0.75 for IMF. Maternal heritabilities for BWT, 200dW, and 365dW were in a narrow range from 0.21 to 0.24, 0.24 to 0.27, and 0.21 to 0.25, respectively, and from 0.25 to 0.65 for IMF. Direct genetic correlations among body weight traits were positive and favorable, and very similar from different models but showed a stronger variation with 0.31 (A), −0.13 (G), and 0.45 (H) between BWT and IMF. In gene annotations, we identified 6, 3, 1, and 6 potential candidate genes for direct genetic effect on BWT, 200dW, 365dW, and IMF traits, respectively. Regarding maternal genetic effects, four (SHROOM3, ZNF609, PECAM1, and TEX2) and two (TMEM182 and SEC11A) genes were detected as potential candidate genes for BWT and 365dW, respectively. Potential candidate genes for maternal effect on IMF were GRHL2, FGA, FGB, and CTNNA3. As the most important finding from a practical breeding perspective, a small number of genotyped RHV cattle enabled accurate breeding values for high heritability IMF.
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Affiliation(s)
- K Halli
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, Giessen, Germany
| | - M Bohlouli
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, Giessen, Germany
| | - L Schulz
- Department of Animal Nutrition and Animal Health, Kassel University, Witzenhausen, Germany
| | - A Sundrum
- Department of Animal Nutrition and Animal Health, Kassel University, Witzenhausen, Germany
| | - S König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, Giessen, Germany
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18
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Dauben CM, Pröll-Cornelissen MJ, Heuß EM, Appel AK, Henne H, Roth K, Schellander K, Tholen E, Große-Brinkhaus C. Genome-wide associations for immune traits in two maternal pig lines. BMC Genomics 2021; 22:717. [PMID: 34610786 PMCID: PMC8491387 DOI: 10.1186/s12864-021-07997-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Background In recent years, animal welfare and health has become more and more important in pig breeding. So far, numerous parameters have been considered as important biomarkers, especially in the immune reaction and inflammation. Previous studies have shown moderate to high heritabilities in most of these traits. However, the genetic background of health and robustness of pigs needs to be extensively clarified. The objective of this study was to identify genomic regions with a biological relevance for the immunocompetence of piglets. Genome-wide Association Studies (GWAS) in 535 Landrace (LR) and 461 Large White (LW) piglets were performed, investigating 20 immune relevant traits. Besides the health indicators of the complete and differential blood count, eight different cytokines and haptoglobin were recorded in all piglets and their biological dams to capture mediating processes and acute phase reactions. Additionally, all animals were genotyped using the Illumina PorcineSNP60v2 BeadChip. Results In summary, GWAS detected 25 genome-wide and 452 chromosome-wide significant SNPs associated with 17 immune relevant traits in the two maternal pig lines LR and LW. Only small differences were observed considering the maternal immune records as covariate within the statistical model. Furthermore, the study identified across- and within-breed differences as well as relevant candidate genes. In LR more significant associations and related candidate genes were detected, compared with LW. The results detected in LR and LW are partly in accordance with previously identified quantitative trait loci (QTL) regions. In addition, promising novel genomic regions were identified which might be of interest for further detailed analysis. Especially putative pleiotropic regions on SSC5, SSC12, SSC15, SSC16 and SSC17 are of major interest with regard to the interacting structure of the immune system. The comparison with already identified QTL gives indications on interactions with traits affecting piglet survival and also production traits. Conclusion In conclusion, results suggest a polygenic and breed-specific background of immune relevant traits. The current study provides knowledge about regions with biological relevance for health and immune traits. Identified markers and putative pleiotropic regions provide first indications in the context of balancing a breeding-based modification of the porcine immune system. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-07997-1).
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Affiliation(s)
- Christina M Dauben
- Institute of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
| | | | - Esther M Heuß
- Institute of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
| | - Anne K Appel
- BHZP GmbH, An der Wassermühle 8, Dahlenburg-Ellringen, 21368, Germany
| | - Hubert Henne
- BHZP GmbH, An der Wassermühle 8, Dahlenburg-Ellringen, 21368, Germany
| | - Katharina Roth
- Institute of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
| | - Karl Schellander
- Institute of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
| | - Ernst Tholen
- Institute of Animal Sciences, University of Bonn, Endenicher Allee 15, Bonn, 53115, Germany
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Wu P, Wang K, Zhou J, Chen D, Jiang A, Jiang Y, Zhu L, Qiu X, Li X, Tang G. A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs. Commun Biol 2021; 4:891. [PMID: 34285319 PMCID: PMC8292486 DOI: 10.1038/s42003-021-02416-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Socially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-based GWAS on imputed whole-genome sequences. Nineteen SNPs and 25 haplotype loci are identified for direct genetic effects on four traits: average daily feed intake, average daily gain, days to 100 kg and time in feeder per day. Nineteen SNPs and 11 haplotype loci are identified for social genetic effects on average daily feed intake, average daily gain, days to 100 kg and feeding speed. Two significant SNPs from single-locus GWAS (SSC6:18,635,874 and SSC6:18,635,895) are shared by a significant haplotype locus with haplotype alleles 'GGG' for both direct genetic effects and social genetic effects in average daily feed intake. A candidate gene, MT3, which is involved in growth, nervous, and immune processes, is identified. We demonstrate the genetic differences between direct genetic effects and social genetic effects and provide an anchor for investigating the genetic architecture underlying direct genetic effects and social genetic effects on socially affected traits in pigs.
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Affiliation(s)
- Pingxian Wu
- grid.80510.3c0000 0001 0185 3134Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Kai Wang
- grid.80510.3c0000 0001 0185 3134Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Jie Zhou
- grid.80510.3c0000 0001 0185 3134Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Dejuan Chen
- grid.80510.3c0000 0001 0185 3134Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Anan Jiang
- grid.80510.3c0000 0001 0185 3134Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Yanzhi Jiang
- grid.80510.3c0000 0001 0185 3134College of Life Science, Sichuan Agricultural University, Yaan, Sichuan China
| | - Li Zhu
- grid.80510.3c0000 0001 0185 3134Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Xiaotian Qiu
- grid.410634.4National Animal Husbandry Service, Beijing, Beijing, China
| | - Xuewei Li
- grid.80510.3c0000 0001 0185 3134Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Guoqing Tang
- grid.80510.3c0000 0001 0185 3134Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan China
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20
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Fu L, Jiang Y, Wang C, Mei M, Zhou Z, Jiang Y, Song H, Ding X. A Genome-Wide Association Study on Feed Efficiency Related Traits in Landrace Pigs. Front Genet 2020; 11:692. [PMID: 32719719 PMCID: PMC7350416 DOI: 10.3389/fgene.2020.00692] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/05/2020] [Indexed: 12/27/2022] Open
Abstract
Feed efficiency (FE) traits in pigs are of utmost economic importance. Genetic improvement of FE related traits in pigs might significantly reduce production cost and energy consumption. Hence, our study aimed at identifying SNPs and candidate genes associated with FE related traits, including feed conversion ratio (FCR), average daily gain (ADG), average daily feed intake (ADFI), and residual feed intake (RFI). A genome-wide association study (GWAS) was performed for the four FE related traits in 296 Landrace pigs genotyped with PorcineSNP50 BeadChip. Two different single-trait methods, single SNP linear model GWAS (LM-GWAS) and single-step GWAS (ssGWAS), were implemented. Our results showed that the two methods showed high consistency with respect to SNP identification. A total of 32 common significant SNPs associated with the four FE related traits were identified. Bioinformatics analysis revealed eight common QTL regions, of which three QTL regions related to ADFI and RFI traits were overlapped. Gene ontology analysis revealed six common candidate genes (PRELID2, GPER1, PDX1, TEX2, PLCL2, ICAM2) relevant for the four FE related traits. These genes are involved in the processes of fat synthesis and decomposition, lipid transport process, insulin metabolism, among others. Our results provide, new insights into the genetic mechanisms and candidate function genes of FE related traits in pigs. However, further investigations to validate these results are warranted.
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Affiliation(s)
- Lu Fu
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yao Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chonglong Wang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Mengran Mei
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ziwen Zhou
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yifan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hailiang Song
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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21
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Li Y, Li B, Yang M, Han H, Chen T, Wei Q, Miao Z, Yin L, Wang R, Shen J, Li X, Xu X, Fang M, Zhao S. Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs. Front Genet 2020; 11:183. [PMID: 32292414 PMCID: PMC7118202 DOI: 10.3389/fgene.2020.00183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/14/2020] [Indexed: 12/19/2022] Open
Abstract
Birth weight of pigs is an important economic factor in the livestock industry. The identification of the genes and variants that underlie birth weight is of great importance. In this study, we integrated two genotyping methods, single nucleotide polymorphism (SNP) chip analysis and restriction site associated DNA sequencing (RAD-seq) to genotype genome-wide SNPs. In total, 45,175 and 139,634 SNPs were detected with the SNP chip and RAD-seq, respectively. The genome-wide association study (GWAS) of the combined SNP panels identified two significant loci located at chr1: 97,745,041 and chr4: 112,031,589, that explained 6.36% and 4.25% of the phenotypic variance respectively. To reduce interval containing causal variants, we imputed sequence-level SNPs in the GWAS identified regions and fine-mapped the causative variants into two narrower genomic intervals: a ∼100 kb interval containing 71 SNPs and a broader ∼870 kb interval with 432 SNPs. This fine-mapping highlighted four promising candidate genes, SKOR2, SMAD2, VAV3, and NTNG1. Additionally, the functional genes, SLC25A24, PRMT6 and STXBP3, are also located near the fine-mapping region. These results suggest that these candidate genes may have contribute substantially to the birth weight of pigs.
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Affiliation(s)
- Yong Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Bin Li
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Manman Yang
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Hu Han
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Tao Chen
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Qiang Wei
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Zepu Miao
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Lilin Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Ran Wang
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Junran Shen
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Ming Fang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, China
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22
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Yang P, Zhang Z, Xu J, Qu K, Lyv S, Wang X, Cai C, Li Z, Wang E, Xie J, Ru B, Xu Z, Lei C, Chen H, Huang B, Huang Y. The Association of the Copy Number Variation of the MLLT10 Gene with Growth Traits of Chinese Cattle. Animals (Basel) 2020; 10:ani10020250. [PMID: 32033330 PMCID: PMC7070264 DOI: 10.3390/ani10020250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/10/2020] [Accepted: 02/01/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Copy number variation is a common genetic polymorphism, mainly represented by submicroscopic levels of deletion and duplication, caused by rearrangement of the genome. It is well-known that the copy number variation of a gene is associated with growth traits of livestock. In this study, we detected the correlation between the copy number variation of the the MLLT10 gene and the growth traits of Chinese yellow cattle. We found that the copy number variation of the MLLT10 gene has a significant influence on hip width, rump length, hucklebone width, and cannon bone circumference of some Chinese yellow cattle breeds. The results provide preliminary suggestions for Chinese yellow cattle breeding and new insights about the future of copy number variation (CNV) as a new promising molecular marker in animal breeding. Abstract Copy number variation is a part of genomic structural variation and has caused widespread concern. According to the results of high-throughput screening of the MLLT10 gene, we found that the copy number variation region of the MLLT10 gene was correlated with bovine growth traits. We aimed to detect the MLLT10 gene copy number variation and provide materials for the Chinese yellow cattle breed. In this study, the SPSS software was used to analyze the correlation among the copy number type of six different cattle breeds (i.e., Qinchuan, Xianan, Jiaxian, Yanbian, Sinan, Yunling) and the corresponding growth traits. The results showed the following: In Qinchuan cattle, the copy number duplication type was greater than the deletion and normal types; in Xianan cattle, the copy number duplication and normal types were less as compared with the deletion type; and in Yunling cattle, the frequency of the duplication type was dominant among the three types of copy number variants. The correlation analysis result showed that there is a significant correlation between the copy number variation (CNV) of the MLLT10 gene and the growth traits of three cattle breeds. Furthermore, correlation analysis showed that MLLT10 CNV had positive effects on growth traits such as hip width, rump length, hucklebone width, and cannon bone circumference (p < 0.05). This study provides a basis for the molecular-assisted marker breeding of cattle and contributes to the breeding of cattle.
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Affiliation(s)
- Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 45002, China; (Z.Z.); (S.L.); (E.W.)
| | - Jiawei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Kaixing Qu
- Yunnan Academy of Grassland Animal Science, Kunming 650212, China;
| | - Shijie Lyv
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 45002, China; (Z.Z.); (S.L.); (E.W.)
| | - Xianwei Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Cuicui Cai
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 756000, China; (C.C.); (J.X.)
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 45002, China; (Z.Z.); (S.L.); (E.W.)
| | - Jianliang Xie
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 756000, China; (C.C.); (J.X.)
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Zejun Xu
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Bizhi Huang
- Yunnan Academy of Grassland Animal Science, Kunming 650212, China;
- Correspondence: (B.H.); (Y.H.)
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
- Correspondence: (B.H.); (Y.H.)
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23
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Bergamaschi M, Maltecca C, Fix J, Schwab C, Tiezzi F. Genome-wide association study for carcass quality traits and growth in purebred and crossbred pigs1. J Anim Sci 2020; 98:skz360. [PMID: 31768540 PMCID: PMC6978898 DOI: 10.1093/jas/skz360] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/25/2019] [Indexed: 12/29/2022] Open
Abstract
Carcass quality traits such as back fat (BF), loin depth (LD), and ADG are of extreme economic importance for the swine industry. This study aimed to (i) estimate the genetic parameters for such traits and (ii) conduct a single-step genome-wide association study (ssGWAS) to identify genomic regions that affect carcass quality and growth traits in purebred (PB) and three-way crossbred (CB) pigs. A total of 28,497 PBs and 135,768 CBs pigs were phenotyped for BF, LD, and ADG. Of these, 4,857 and 3,532 were genotyped using the Illumina PorcineSNP60K Beadchip. After quality control, 36,328 SNPs were available and were used to perform an ssGWAS. A bootstrap analysis (n = 1,000) and a signal enrichment analysis were performed to declare SNP significance. Genome regions were based on the variance explained by significant 10-SNP sliding windows. Estimates of PB heritability (SE) were 0.42 (0.019) for BF, 0.39 (0.020) for LD, and 0.35 (0.021) for ADG. Estimates of CB heritability were 0.49 (0.042) for BF, 0.27 (0.029) for LD, and 0.12 (0.021) for ADG. Genetic correlations (SE) across the two populations were 0.81 (0.02), 0.79 (0.04), and 0.56 (0.05), for BF, LD, and ADG, respectively. The variance explained by significant regions for each trait in PBs ranged from 1.51% to 1.35% for BF, from 4.02% to 3.18% for LD, and from 2.26% to 1.45% for ADG. In CBs, the variance explained by significant regions ranged from 1.88% to 1.37% for BF, from 1.29% to 1.23% for LD, and from 1.54% to 1.32% for ADG. In this study, we have described regions of the genome that determine carcass quality and growth traits of PB and CB pigs. These results provide evidence that there are overlapping and nonoverlapping regions in the genome influencing carcass quality and growth traits in PBs and three-way CB pigs.
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Affiliation(s)
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC
| | | | | | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC
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24
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Yang Q, Wu P, Wang K, Chen D, Zhou J, Ma J, Li M, Xiao W, Jiang A, Jiang Y, Bai L, Zhu L, Li X, Tang G. SNPs associated with body weight and backfat thickness in two pig breeds identified by a genome-wide association study. Genomics 2019; 111:1583-1589. [DOI: 10.1016/j.ygeno.2018.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 12/30/2022]
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25
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Hong L, Gu T, He Y, Zhou C, Hu Q, Wang X, Zheng E, Huang S, Xu Z, Yang J, Yang H, Li Z, Liu D, Cai G, Wu Z. Genome-Wide Analysis of Circular RNAs Mediated ceRNA Regulation in Porcine Embryonic Muscle Development. Front Cell Dev Biol 2019; 7:289. [PMID: 31803743 PMCID: PMC6877547 DOI: 10.3389/fcell.2019.00289] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022] Open
Abstract
Many circular RNAs (circRNAs) have been discovered in various tissues and cell types in pig. However, the temporal expression pattern of circRNAs during porcine embryonic muscle development remains unclear. Here, we present a panorama view of circRNA expression in embryonic muscle development at 33-, 65-, and 90-days post-coitus (dpc) from Duroc pigs. An unbiased analysis reveals that more than 5,000 circRNAs specifically express in embryonic muscle development. The amount and complexity of circRNA expression is most pronounced in skeletal muscle at day 33 of gestation. Our circRNAs annotation analyses show that “hot-spot” genes produce multiple circRNA isoforms and RNA binding protein (RBPs) may regulate the biogenesis of circRNAs. Furthermore, we observed that host genes of differentially expressed circRNA across porcine muscle development are enriched in skeletal muscle function. A competing endogenous RNA (ceRNA) network analysis of circRNAs reveals that circRNAs regulate muscle gene expression by functioning as miRNA sponges. Finally, our experimental validation demonstrated that circTUT7 regulate the expression of HMG20B in a ceRNA mechanism. Our analyses show that circRNAs are dynamically expressed and interacting with muscle genes through ceRNA manner, suggesting their critical functions in embryonic skeletal muscle development.
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Affiliation(s)
- Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yanjuan He
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Chen Zhou
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qun Hu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xingwang Wang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Sixiu Huang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zheng Xu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jie Yang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Huaqiang Yang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Dewu Liu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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26
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Wang Y, Zhang T, Wang C. Detection and analysis of genome-wide copy number variation in the pig genome using an 80 K SNP Beadchip. J Anim Breed Genet 2019; 137:166-176. [PMID: 31506991 DOI: 10.1111/jbg.12435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/23/2022]
Abstract
Copy number variation (CNV) is an important source of genetic variability in human or animal genomes and play key roles in phenotypic diversity and disease susceptibility. In the present study, we performed a genome-wide analysis for CNV detection using SNP genotyping data of 857 Large White pigs. A total of 312 CNV regions (CNVRs) were detected with the PennCNV algorithm, which covered 57.76 Mb of the pig genome and correspond to 2.36% of the genome sequence. The length of the CNVRs on autosomes ranged from 1.77 Kb to 1.76 Mb with an average of 185.11 Kb. Of these, 220 completely or partially overlapped with 1,092 annotated genes, which enriched a wide variety of biological processes. Comparisons with previously reported pig CNVR revealed 92 (29.49%) novel CNVRs. Experimentally, 80% of CNVRs selected randomly were validated by quantitative PCR (qPCR). We also performed an association analysis between some of the CNVRs and reproductive traits, with results demonstrating the potential importance of CNVR61 and CNVR283 associated with litter sizes. Notably, the GPER1 gene located in CNVR61 plays a key role in reproduction. Our study is an important complement to the CNV map in the pig genome and provides valuable information for investigating the association between genomic variation and economic traits.
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Affiliation(s)
- Yuan Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.,Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Tingrong Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Chuduan Wang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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27
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Zhuang Z, Li S, Ding R, Yang M, Zheng E, Yang H, Gu T, Xu Z, Cai G, Wu Z, Yang J. Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations. PLoS One 2019; 14:e0218263. [PMID: 31188900 PMCID: PMC6561594 DOI: 10.1371/journal.pone.0218263] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/29/2019] [Indexed: 01/07/2023] Open
Abstract
Loin muscle area (LMA) and loin muscle depth (LMD) are important traits influencing the production performance of breeding pigs. However, the genetic architecture of these two traits is still poorly understood. To discern the genetic architecture of LMA and LMD, a material consisting of 6043 Duroc pigs belonging to two populations with different genetic backgrounds was collected and applied in genome-wide association studies (GWAS) with a genome-wide distributed panel of 50K single nucleotide polymorphisms (SNPs). To improve the power of detection for common SNPs, we conducted a meta-analysis in these two pig populations and uncovered additional significant SNPs. As a result, we identified 75 significant SNPs for LMA and LMD on SSC6, 7, 12, 16, and 18. Among them, 25 common SNPs were associated with LMA and LMD. One pleiotropic quantitative trait locus (QTL), which was located on SSC7 with a 283 kb interval, was identified to affect LMA and LMD. Marker ALGA0040260 is a key SNP for this QTL, explained 1.77% and 2.48% of the phenotypic variance for LMA and LMD, respectively. Another genetic region on SSC16 (709 kb) was detected and displayed prominent association with LMA and the peak SNP, WU_10.2_16_35829257, contributed 1.83% of the phenotypic variance for LMA. Further bioinformatics analysis determined eight promising candidate genes (GCLC, GPX8, DAXX, FGF21, TAF11, SPDEF, NUDT3, and PACSIN1) with functions in glutathione metabolism, adipose and muscle tissues development and lipid metabolism. This study provides the first GWAS for the LMA and LMD of Duroc breed to analyze the underlying genetic variants through a large sample size. The findings further advance our understanding and help elucidate the genetic architecture of LMA, LMD and growth-related traits in pigs.
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Affiliation(s)
- Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Shaoyun Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Ming Yang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd, Guangdong, P.R. China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Huaqiang Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Ting Gu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Zheng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd, Guangdong, P.R. China
- * E-mail: (JY); (ZW)
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
- * E-mail: (JY); (ZW)
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28
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Wu P, Wang K, Yang Q, Zhou J, Chen D, Ma J, Tang Q, Jin L, Xiao W, Jiang A, Jiang Y, Zhu L, Li M, Li X, Tang G. Identifying SNPs and candidate genes for three litter traits using single-step GWAS across six parities in Landrace and Large White pigs. Physiol Genomics 2018; 50:1026-1035. [PMID: 30289746 DOI: 10.1152/physiolgenomics.00071.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Total number born (TNB), number born alive (NBA), and litter weight born alive (LWB) are critically important traits in pig production. The sow's parity is one of the major factors influencing litter traits. Because of monogenic or polygenic contributions and the presence of temporal gene effects in different sows' parities, it is difficult to clarify the biological and genetic background. To systematically explore the genetic mechanism of litter traits, we conducted 18 GWASs using single-step GWAS (ssGWAS) based on two breeds (908 Landrace and 1,130 Large White sow litter records) for each litter trait in different parities. A total of 300 Landrace and 300 Large White sows were genotyped by sequencing (GBS). ssGWAS was performed separately for each breed and each parity due to population stratification and temporal gene effect. In summary, we identified 80 (15 for Landrace and 65 for Large White), 227 (52 for Landrace, 175 for Large White), and 187 (34 for Landrace, 153 for Large White) single nucleotide polymorphisms (SNPs) affecting TNB, NBA, and LWB, respectively. Of them, we suggest that a total of 22 loci (SSC1: 125098202, SSC1: 117560058, SSC14: 147794697, SSC8: 84823302, SSC9: 143554876, and SSC9: 138766097 for Landrace; SSC1: 4023577, SSC1: 3859573, SSC1: 4891063, SSC16: 5197665, SSC10: 32050819, SSC13: 13552924, SSC13: 92819, SSC17: 3579607, SSC13: 196698221, SSC7: 30918403, SSC16: 46221484, SSC16: 46169204, SSC2: 41988642, SSC2: 44475457, SSC2: 42521875, and SSC7: 58411951 for Large White) are shared by TNB, NBA, and LWB. These results indicate the existence of gene temporal effect in each parity. Furthermore, our findings suggest four interesting candidate genes (FBXL7, ALDH1A2, LEPR, and DDX1) associated with litter traits in different parities that have a major effect on embryonic development progression. In conclusion, 22 crucial SNPs and four interesting candidate genes were identified for three litter traits across six parities. These findings advance our understanding of the genetic architecture of litter traits and confirm the presence of temporal gene effects in different parities. Importantly, functional validation studies for findings of particular interest are recommended in litter traits.
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Affiliation(s)
- Pingxian Wu
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Kai Wang
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Qiang Yang
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Jie Zhou
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Dejuan Chen
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Jideng Ma
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Qianzi Tang
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Long Jin
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Weihang Xiao
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Anan Jiang
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Yaan, Sichuan , China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China
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29
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Jiang Y, Tang S, Wang C, Wang Y, Qin Y, Wang Y, Zhang J, Song H, Mi S, Yu F, Xiao W, Zhang Q, Ding X. A genome-wide association study of growth and fatness traits in two pig populations with different genetic backgrounds. J Anim Sci 2018. [PMID: 29528397 DOI: 10.1093/jas/skx038] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Improvement in growth and fatness traits are the main objectives in pig all breeding programs. Tenth rib backfat thickness (10RIBBFT) and days to 100 kg (D100), which are good predictors of carcass lean content and growth rate, respectively, are economically important traits and also main breeding target traits in pigs. To investigate the genetic mechanisms of 10RIBBFT and D100 of pigs, we sampled 1,137 and 888 pigs from 2 Yorkshire populations of American and British origin, respectively, and conducted genome-wide association study (GWAS) through combined analysis and meta-analysis, to identify SNPs associated with 10RIBBFT and D100. A total of 11 and 7 significant SNPs were identified by combined analysis for 10RIBBFT and D100, respectively. And in meta-analysis, 8 and 7 significant SNPs were identified for 10RIBBFT and D100, respectively. Among them, 6 and 5 common significant SNPs in two analysis results were, respectively, identified associated with 10RIBBFT and D100, and correspondingly explained 2.09% and 0.52% of the additive genetic variance of 10RIBBFT and D100. Further bioinformatics analysis revealed 10 genes harboring or close to these common significant SNPs, 5 for 10RIBBFT and 5 for D100. In particular, Gene Ontology analysis highlighted 6 genes, PCK1, ANGPTL3, EEF1A2, TNFAIP8L3, PITX2, and PLA2G12, as promising candidate genes relevant with backfat thickness and growth. PCK1, ANGPTL3, EEF1A2, and TNFAIP8L3 could influence backfat thickness through phospholipid transport, regulation of lipid metabolic process through the glycerophospholipid biosynthesis and metabolism pathway, the metabolism of lipids and lipoproteins pathway. PITX2 has a crucial role in skeletal muscle tissue development and animal organ morphogenesis, and PLA2G12A plays a role in the lipid catabolic and phospholipid catabolic processes, which both are involved in the body weight pathway. All these candidate genes could directly or indirectly influence fat production and growth in Yorkshire pigs. Our findings provide novel insights into the genetic basis of growth and fatness traits in pigs. The candidate genes for D100 and 10RIBBFT are worthy of further investigation.
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Affiliation(s)
- Y Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - S Tang
- Beijing Station of Animal Husbandry, Beijing, P.R. China
| | - C Wang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Y Wang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Y Qin
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Y Wang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - J Zhang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - H Song
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - S Mi
- Beijing LM Pig Breeding Technology Co., Ltd., Beijing, P.R. China
| | - F Yu
- Beijing Shunxin Agricultural Co., Ltd., Beijing, P.R. China
| | - W Xiao
- Beijing Station of Animal Husbandry, Beijing, P.R. China
| | - Q Zhang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - X Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
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30
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Ding R, Yang M, Wang X, Quan J, Zhuang Z, Zhou S, Li S, Xu Z, Zheng E, Cai G, Liu D, Huang W, Yang J, Wu Z. Genetic Architecture of Feeding Behavior and Feed Efficiency in a Duroc Pig Population. Front Genet 2018; 9:220. [PMID: 29971093 PMCID: PMC6018414 DOI: 10.3389/fgene.2018.00220] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/29/2018] [Indexed: 11/13/2022] Open
Abstract
Increasing feed efficiency is a major goal of breeders as it can reduce production cost and energy consumption. However, the genetic architecture of feeding behavior and feed efficiency traits remains elusive. To investigate the genetic architecture of feed efficiency in pigs, three feeding behavior traits (daily feed intake, number of daily visits to feeder, and duration of each visit) and two feed efficiency traits (feed conversion ratio and residual feed intake) were considered. We performed genome-wide association studies (GWASs) of the five traits using a population of 1,008 Duroc pigs genotyped with an Illumina Porcine SNP50K BeadChip. A total of 9 genome-wide (P < 1.54E-06) and 35 suggestive (P < 3.08E-05) single nucleotide polymorphisms (SNPs) were detected. Two pleiotropic quantitative trait loci (QTLs) on SSC 1 and SSC 7 were found to affect more than one trait. Markers WU_10.2_7_18377044 and DRGA0001676 are two key SNPs for these two pleiotropic QTLs. Marker WU_10.2_7_18377044 on SSC 7 contributed 2.16 and 2.37% of the observed phenotypic variance for DFI and RFI, respectively. The other SNP DRGA0001676 on SSC 1 explained 3.22 and 5.46% of the observed phenotypic variance for FCR and RFI, respectively. Finally, functions of candidate genes and gene set enrichment analysis indicate that most of the significant pathways are associated with hormonal and digestive gland secretion during feeding. This study advances our understanding of the genetic mechanisms of feeding behavior and feed efficiency traits and provide an opportunity for increasing feeding efficiency using marker-assisted selection or genomic selection in pigs.
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Affiliation(s)
- Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Ming Yang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group, Co., Ltd., Guangdong, China
| | - Xingwang Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Shaoyun Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Zheng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China.,National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group, Co., Ltd., Guangdong, China
| | - Dewu Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China.,National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group, Co., Ltd., Guangdong, China
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31
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Genome-wide association studies for seven production traits highlight genomic regions useful to dissect dry-cured ham quality and production traits in Duroc heavy pigs. Animal 2018; 12:1777-1784. [PMID: 29706143 DOI: 10.1017/s1751731118000757] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Protected designation of origin dry-cured hams are obtained from heavy pigs (slaughtered at about 160 kg of live weight). A specific breeding program designed to improve meat quality for this production has included as key traits the level of intermuscular fat between the leg muscles and ham weight loss during the seasoning period together with a balance between fat and lean cuts. In this study we carried out genome-wide association studies for seven traits used in the genetic merit of Italian Duroc heavy pigs, five related to meat and carcass quality traits (visible intermuscular fat, ham weight loss at first salting, backfat thickness, ham weight and lean cuts), and two related to performance and efficiency traits (average daily gain and feed : gain ratio). A total of 573 performance-tested pigs were genotyped with the Illumina PorcineSNP60 BeadChip and genome-wide association analyses were carried out using the Bayes B approach with the 1 Mb window option of GenSel and random residuals for each of the seven traits. Detected windows were supported by independent single nucleotide polymorphism analyses with a linear mixed model (LMM) approach on the same animals for the same traits. A total of 30 windows identifying different quantitative trait loci (QTL) were detected and among those, 27 were confirmed by LMM in one of these traits. Among the confirmed windows, three QTL were reported for visible intermuscular fat, seven for ham weight loss at first salting and five and four for backfat thickness and lean cut, respectively. A total of eight QTL were detected for the other production traits. No overlapping QTL were reported except for one window on porcine chromosome 10 between lean cuts and ham weight that contained the CACNB2 gene that has been already associated with loin marbling score in other Duroc pigs. Several regions contained genes that have been already associated with production traits in other pig breeds, including Duroc lines, related to fat deposition or muscle structure. This work reports, for the first time, genome-wide association study results for several traits in Italian Duroc heavy pigs. These results will be useful to dissect the genetic basis for dry-cured ham production traits that determine the total genetic merit index of Italian Duroc pigs.
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32
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Wang Y, Ding X, Tan Z, Ning C, Xing K, Yang T, Pan Y, Sun D, Wang C. Genome-Wide Association Study of Piglet Uniformity and Farrowing Interval. Front Genet 2017; 8:194. [PMID: 29234349 PMCID: PMC5712316 DOI: 10.3389/fgene.2017.00194] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 11/15/2017] [Indexed: 02/04/2023] Open
Abstract
Piglet uniformity (PU) and farrowing interval (FI) are important reproductive traits related to production and economic profits in the pig industry. However, the genetic architecture of the longitudinal trends of reproductive traits still remains elusive. Herein, we performed a genome-wide association study (GWAS) to detect potential genetic variation and candidate genes underlying the phenotypic records at different parities for PU and FI in a population of 884 Large White pigs. In total, 12 significant SNPs were detected on SSC1, 3, 4, 9, and 14, which collectively explained 1–1.79% of the phenotypic variance for PU from parity 1 to 4, and 2.58–4.11% for FI at different stages. Of these, seven SNPs were located within 16 QTL regions related to swine reproductive traits. One QTL region was associated with birth body weight (related to PU) and contained the peak SNP MARC0040730, and another was associated with plasma FSH concentration (related to FI) and contained the SNP MARC0031325. Finally, some positional candidate genes for PU and FI were identified because of their roles in prenatal skeletal muscle development, fetal energy substrate, pre-implantation, and the expression of mammary gland epithelium. Identification of novel variants and candidate genes will greatly advance our understanding of the genetic mechanisms of PU and FI, and suggest a specific opportunity for improving marker assisted selection or genomic selection in pigs.
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Affiliation(s)
- Yuan Wang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhen Tan
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chao Ning
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kai Xing
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ting Yang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yongjie Pan
- Beijing Shunxin Agriculture Co., Ltd., Beijing, China
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chuduan Wang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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33
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Yang L, Xu L, Zhu B, Niu H, Zhang W, Miao J, Shi X, Zhang M, Chen Y, Zhang L, Gao X, Gao H, Li L, Liu GE, Li J. Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle. Sci Rep 2017; 7:14299. [PMID: 29085051 PMCID: PMC5662686 DOI: 10.1038/s41598-017-14768-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022] Open
Abstract
Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, we performed a genome-wide CNV analysis using high density SNP array in Chinese native cattle. In this study, we detected a total of 13,225 CNV events and 3,356 CNV regions (CNVRs), overlapping with 1,522 annotated genes. Among them, approximately 71.43 Mb of novel CNVRs were detected in the Chinese cattle population for the first time, representing the unique genomic resources in cattle. A new V i statistic was proposed to estimate the region-specific divergence in CNVR for each group based on unbiased estimates of pairwise V ST . We obtained 12 and 62 candidate CNVRs at the top 1% and top 5% of genome-wide V i value thresholds for each of four groups (North, Northwest, Southwest and South). Moreover, we identified many lineage-differentiated CNV genes across four groups, which were associated with several important molecular functions and biological processes, including metabolic process, response to stimulus, immune system, and others. Our findings provide some insights into understanding lineage-differentiated CNVs under divergent selection in the Chinese native cattle.
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Affiliation(s)
- Liu Yang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hong Niu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wengang Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jian Miao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xinping Shi
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei, 071001, China
| | - Ming Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland, 20705, USA
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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34
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Quan J, Ding R, Wang X, Yang M, Yang Y, Zheng E, Gu T, Cai G, Wu Z, Liu D, Yang J. Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 31:480-488. [PMID: 29059722 PMCID: PMC5838319 DOI: 10.5713/ajas.17.0356] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/08/2017] [Accepted: 10/09/2017] [Indexed: 12/28/2022]
Abstract
Objective Average daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population. Methods We performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models. Results After quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly associated with the ADG of pigs. We identified six quantitative trait loci (QTL) regions for ADG. These QTLs included four previously reported QTLs on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, and SSC13, as well as two novel QTLs on SSC6 and SSC16. In addition, we selected six candidate genes (general transcription factor 3C polypeptide 5, high mobility group AT-hook 2, nicotinamide phosphoribosyltransferase, oligodendrocyte transcription factor 1, pleckstrin homology and RhoGEF domain containing G4B, and ENSSSCG00000031548) associated with ADG on the basis of their physiological roles and positional information. These candidate genes are involved in skeletal muscle cell differentiation, diet-induced obesity, and nervous system development. Conclusion This study contributes to the identification of the casual mutation that underlies QTLs associated with ADG and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in ADG regulation.
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Affiliation(s)
- Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Xingwang Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Ming Yang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Co., Ltd, Yunfu 527400, China
| | - Yang Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Ting Gu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Co., Ltd, Yunfu 527400, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.,National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Co., Ltd, Yunfu 527400, China
| | - Dewu Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
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35
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Guo Y, Qiu H, Xiao S, Wu Z, Yang M, Yang J, Ren J, Huang L. A genome-wide association study identifies genomic loci associated with backfat thickness, carcass weight, and body weight in two commercial pig populations. J Appl Genet 2017; 58:499-508. [DOI: 10.1007/s13353-017-0405-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/30/2022]
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36
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Genome-wide association analysis reveals genetic loci and candidate genes for feeding behavior and eating efficiency in Duroc boars. PLoS One 2017; 12:e0183244. [PMID: 28813538 PMCID: PMC5559094 DOI: 10.1371/journal.pone.0183244] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/01/2017] [Indexed: 01/17/2023] Open
Abstract
Efficient use of feed resources is a challenge in the pork industry because the largest variability in expenditure is attributed to the cost of fodder. Efficiency of feeding is directly related to feeding behavior. In order to identify genomic regions controlling feeding behavior and eating efficiency traits, 338 Duroc boars were used in this study. The Illumina Porcine SNP60K BeadChip was used for genotyping. Data pertaining to individual daily feed intake (DFI), total daily time spent in feeder (TPD), number of daily visits to feeder (NVD), average duration of each visit (TPV), mean feed intake per visit (FPV), mean feed intake rate (FR), and feed conversion ratio (FCR) were collected for these pigs. Despite the limited sample size, the genome-wide association study was acceptable to detect candidate regions association with feeding behavior and eating efficiency traits in pigs. We detected three genome-wide (P < 1.40E-06) and 11 suggestive (P < 2.79E-05) single nucleotide polymorphism (SNP)-trait associations. Six SNPs were located in genomic regions where quantitative trait loci (QTLs) have previously been reported for feeding behavior and eating efficiency traits in pigs. Five candidate genes (SERPINA3, MYC, LEF1, PITX2, and MAP3K14) with biochemical and physiological roles that were relevant to feeding behavior and eating efficiency were discovered proximal to significant or suggestive markers. Gene ontology analysis indicated that most of the candidate genes were involved in the development of the hypothalamus (GO:0021854, P < 0.0398). Our results provide new insights into the genetic basis of feeding behavior and eating efficiency in pigs. Furthermore, some significant SNPs identified in this study could be incorporated into artificial selection programs for Duroc-related pigs to select for increased feeding efficiency.
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Hao X, Plastow G, Zhang C, Xu S, Hu Z, Yang T, Wang K, Yang H, Yin X, Liu S, Wang Z, Wang Z, Zhang S. Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations. BMC Genet 2017; 18:64. [PMID: 28679362 PMCID: PMC5499021 DOI: 10.1186/s12863-017-0532-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/28/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Piglet splay leg syndrome (PSL) is one of the most frequent genetic defects, and can cause considerable economic loss in pig production. The present understanding of etiology and pathogenesis of PSL is poor. The current study focused on identifying loci associated with PSL through a genome-wide association study (GWAS) performed with the Illumina Porcine60 SNP Beadchip v2.0. The study was a case/control design with four pig populations (Duroc, Landrace, Yorkshire and one crossbred of Landrace × Yorkshire). RESULT After quality control of the genotyping data, 185 animals (73 cases, 112 controls) and 43,495 SNPs were retained for further analysis. Principal components (PCs) identified from the genomic kinship matrix were included in the statistical model for correcting the effect of population structure. Seven chromosome-wide significant SNPs were identified on Sus scrofa chromosome 1 (SSC1), SSC2 (2 SNPs), SSC7, SSC15 (2 SNPs) and SSC16 after strict Bonferroni correction. Four genes (HOMER1 and JMY on SSC2, ITGA1 on SSC16, and RAB32 on SSC1) related to muscle development, glycogen metabolism and mitochondrial dynamics were identified as potential candidate genes for PSL. CONCLUSIONS We identified seven chromosome-wide significant SNPs associated with PSL and four potential candidate genes for PSL. To our knowledge, this is the first pilot study aiming to identify the loci associated with PSL using GWAS. Further investigations and validations for those findings are encouraged.
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Affiliation(s)
- Xingjie Hao
- Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070 China
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Graham Plastow
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Chunyan Zhang
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Sutong Xu
- Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Zhiqiu Hu
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Tianfu Yang
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Kai Wang
- Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Huawei Yang
- Hubei Tianzhong Stock Corporation, Wuhan, Hubei China
| | - Xiaoxue Yin
- Hubei Tianzhong Stock Corporation, Wuhan, Hubei China
| | - Shili Liu
- Hubei Tianzhong Stock Corporation, Wuhan, Hubei China
| | - Zhenghua Wang
- Hubei Tianzhong Stock Corporation, Wuhan, Hubei China
| | - Zhiquan Wang
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Shujun Zhang
- Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070 China
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Wang K, Liu Y, Xu Q, Liu C, Wang J, Ding C, Fang M. A post-GWAS confirming GPAT3
gene associated with pig growth and a significant SNP influencing its promoter activity. Anim Genet 2017; 48:478-482. [DOI: 10.1111/age.12567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Kejun Wang
- Department of Animal Genetics and Breeding; National Engineering Laboratory for Animal Breeding; MOA Laboratory of Animal Genetics and Breeding; College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
| | - Yufang Liu
- Department of Animal Genetics and Breeding; National Engineering Laboratory for Animal Breeding; MOA Laboratory of Animal Genetics and Breeding; College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
| | - Qiao Xu
- Department of Animal Genetics and Breeding; National Engineering Laboratory for Animal Breeding; MOA Laboratory of Animal Genetics and Breeding; College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
| | - Chengkun Liu
- Department of Animal Genetics and Breeding; National Engineering Laboratory for Animal Breeding; MOA Laboratory of Animal Genetics and Breeding; College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
| | - Jve Wang
- Department of Animal Genetics and Breeding; National Engineering Laboratory for Animal Breeding; MOA Laboratory of Animal Genetics and Breeding; College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
| | - Cui Ding
- Department of Animal Genetics and Breeding; National Engineering Laboratory for Animal Breeding; MOA Laboratory of Animal Genetics and Breeding; College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
| | - Meiying Fang
- Department of Animal Genetics and Breeding; National Engineering Laboratory for Animal Breeding; MOA Laboratory of Animal Genetics and Breeding; College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
- Beijing Key Laboratory for Animal Genetic Improvement; Beijing 100193 China
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Edea Z, Hong JK, Jung JH, Kim DW, Kim YM, Kim ES, Shin SS, Jung YC, Kim KS. Detecting selection signatures between Duroc and Duroc synthetic pig populations using high-density SNP chip. Anim Genet 2017; 48:473-477. [PMID: 28508507 DOI: 10.1111/age.12559] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2017] [Indexed: 01/02/2023]
Abstract
The development of high throughput genotyping techniques has facilitated the identification of selection signatures of pigs. The detection of genomic selection signals in a population subjected to differential selection pressures may provide insights into the genes associated with economically and biologically important traits. To identify genomic regions under selection, we genotyped 488 Duroc (D) pigs and 155 D × Korean native pigs (DKNPs) using the Porcine SNP70K BeadChip. By applying the FST and extended haplotype homozygosity (EHH-Rsb) methods, we detected genes under directional selection associated with growth/stature (DOCK7, PLCB4, HS2ST1, FBP2 and TG), carcass and meat quality (TG, COL14A1, FBXO5, NR3C1, SNX7, ARHGAP26 and DPYD), number of teats (LOC100153159 and LRRC1), pigmentation (MME) and ear morphology (SOX5), which are all mostly near or at fixation. These results could be a basis for investigating the underlying mutations associated with observed phenotypic variation. Validation using genome-wide association analysis would also facilitate the inclusion of some of these markers in genetic evaluation programs.
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Affiliation(s)
- Z Edea
- Department of Animal Science, Chungbuk National University, 28644, Cheongju, Korea
| | - J-K Hong
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Chunan, 31000, Korea
| | - J-H Jung
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 54896, Korea
| | - D-W Kim
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Chunan, 31000, Korea
| | - Y-M Kim
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Chunan, 31000, Korea
| | - E-S Kim
- Recombinetics, St. Paul MN, 55104, MN, USA
| | - S S Shin
- Department of Animal Science, Chungbuk National University, 28644, Cheongju, Korea
| | - Y C Jung
- Jung Pig and Customer Institute, Young-In, 16950, Korea
| | - K-S Kim
- Department of Animal Science, Chungbuk National University, 28644, Cheongju, Korea
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Reyer H, Shirali M, Ponsuksili S, Murani E, Varley PF, Jensen J, Wimmers K. Exploring the genetics of feed efficiency and feeding behaviour traits in a pig line highly selected for performance characteristics. Mol Genet Genomics 2017; 292:1001-1011. [PMID: 28500374 PMCID: PMC5594041 DOI: 10.1007/s00438-017-1325-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/04/2017] [Indexed: 12/21/2022]
Abstract
The consideration of feed efficiency traits is highly relevant in animal breeding due to economic and ecologic impacts of the efficient usage and utilization of feed resources. In pigs, corresponding observations are recorded using automatic feeding stations and serve as one of the main criteria in most pig selection programmes. Simultaneously, feeding stations also generate feeding behaviour data which represent a nearly unused resource and provide a valuable proxy measure of health status, animal welfare, and management practices. In the current study, an integrated approach was applied to a feed efficiency tested and genome-wide genotyped terminal sire line population. Therefore, genetic analyses were performed combining a single-marker based approach and a Bayesian multi-marker algorithm. Major quantitative trait loci (QTL) for feeding behaviour traits comprising daily occupation time, daily feeder visit, and daily feeding rate were identified on chromosomes 1, 4, 6, 7, 8, and 14. Feed efficiency was represented by feed conversion ratio and daily feed intake revealing prominent genomic regions on chromosomes 1, 6, 9, and 11. The positional and functional candidate genes identified are involved in transport processes like AQP4, SLC22A23, and SLC6A14 as well as energy sensing, generation, and utilization as exemplified by PPP3CA, IQGAP3, ECI2, and DnaJC15. These molecular features provide the first step towards the dissection of the genetic connection between distinct feeding behaviour patterns, feed efficiency and performance, health, and welfare traits driving the implementation of these traits in breeding programmes and pig husbandry.
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Affiliation(s)
- Henry Reyer
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Mahmoud Shirali
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
| | - Siriluck Ponsuksili
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Eduard Murani
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | | | - Just Jensen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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Brito LF, Kijas JW, Ventura RV, Sargolzaei M, Porto-Neto LR, Cánovas A, Feng Z, Jafarikia M, Schenkel FS. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers. BMC Genomics 2017; 18:229. [PMID: 28288562 PMCID: PMC5348779 DOI: 10.1186/s12864-017-3610-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/07/2017] [Indexed: 01/08/2023] Open
Abstract
Background The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. Results The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HO and HE was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROH and FPED was 0.129, −0.012, −0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. Conclusions In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds’ development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3610-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luiz F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.
| | - James W Kijas
- CSIRO Agriculture & Food, Brisbane, Queensland, Australia
| | - Ricardo V Ventura
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Beef Improvement Opportunities, Guelph, Ontario, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,The Semex Alliance, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Zeny Feng
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Canadian Centre for Swine Improvement Inc., Ottawa, Ontario, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
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Meng Q, Wang K, Liu X, Zhou H, Xu L, Wang Z, Fang M. Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:462-469. [PMID: 27809465 PMCID: PMC5394831 DOI: 10.5713/ajas.16.0548] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/12/2016] [Accepted: 10/24/2016] [Indexed: 01/16/2023]
Abstract
Objective The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.
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Affiliation(s)
- Qingli Meng
- Beijing Breeding Swine Center, Beijing 100194, China
| | - Kejun Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Haishen Zhou
- Beijing Breeding Swine Center, Beijing 100194, China
| | - Li Xu
- Beijing Breeding Swine Center, Beijing 100194, China
| | - Zhaojun Wang
- Beijing Breeding Swine Center, Beijing 100194, China
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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