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Lee J, Kim J, Garrick DJ. Increasing the accuracy of genomic prediction in pure‐bred Limousin beef cattle by including cross‐bred Limousin data and accounting for an F94L variant in
MSTN. Anim Genet 2019; 50:621-633. [DOI: 10.1111/age.12846] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2019] [Indexed: 11/30/2022]
Affiliation(s)
- J. Lee
- Jung P&C Institute #1504 U‐TOWER, 120 Heungdeokjungang‐ro, Giheung‐gu Yongin‐si Gyeonggi‐do 16950 South Korea
| | - J.‐M. Kim
- Department of Animal Science and Technology Chung‐Ang University Anseong‐si Gyeonggi‐do 17546 Korea
| | - D. J. Garrick
- AL Rae Centre of Genetics and Breeding Massey University Private Bag 11 222 Palmerston North Hamilton 4442 New Zealand
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Moreira GCM, Salvian M, Boschiero C, Cesar ASM, Reecy JM, Godoy TF, Ledur MC, Garrick D, Mourão GB, Coutinho LL. Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens. BMC Genomics 2019; 20:669. [PMID: 31438838 PMCID: PMC6704653 DOI: 10.1186/s12864-019-6040-3] [Citation(s) in RCA: 12] [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: 06/13/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Poultry breeding programs have been focused on improvement of growth and carcass traits, however, this has resulted in correlated changes in internal organ weights and increased incidence of metabolic disorders. These disorders can affect feed efficiency or even cause death. We used a high density SNP array (600 K, Affymetrix) to estimate genomic heritability, perform genome-wide association analysis, and identify genomic regions and positional candidate genes (PCGs) associated with internal organ traits in an F2 chicken population. We integrated knowledge of haplotype blocks, selection signature regions and sequencing data to refine the list of PCGs. RESULTS Estimated genomic heritability for internal organ traits in chickens ranged from low (LUNGWT, 0.06) to high (GIZZWT, 0.45). A total of 20 unique 1 Mb windows identified on GGA1, 2, 4, 7, 12, 15, 18, 19, 21, 27 and 28 were significantly associated with intestine length, and weights or percentages of liver, gizzard or lungs. Within these windows, 14 PCGs were identified based on their biological functions: TNFSF11, GTF2F2, SPERT, KCTD4, HTR2A, RB1, PCDH7, LCORL, LDB2, NR4A2, GPD2, PTPN11, ITGB4 and SLC6A4. From those genes, two were located within haplotype blocks and three overlapped with selection signature regions. A total of 13,748 annotated sequence SNPs were in the 14 PCGs, including 156 SNPs in coding regions (124 synonymous, 26 non-synonymous, and 6 splice variants). Seven deleterious SNPs were identified in TNFSF11, NR4A2 or ITGB4 genes. CONCLUSIONS The results from this study provide novel insights to understand the genetic architecture of internal organ traits in chickens. The QTL detection performed using a high density SNP array covered the whole genome allowing the discovery of novel QTL associated with organ traits. We identified PCGs within the QTL involved in biological processes that may regulate internal organ growth and development. Potential functional genetic variations were identified generating crucial information that, after validation, might be used in poultry breeding programs to reduce the occurrence of metabolic disorders.
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Affiliation(s)
| | - Mayara Salvian
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Clarissa Boschiero
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Aline Silva Mello Cesar
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - James M. Reecy
- Department of Animal Science, Iowa State University (ISU), Ames, Iowa USA
| | - Thaís Fernanda Godoy
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | | | - Dorian Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Gerson Barreto Mourão
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Luiz L. Coutinho
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
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Lokapirnasari WP, Pribadi TB, Arif AA, Soeharsono S, Hidanah S, Harijani N, Najwan R, Huda K, Wardhani HCP, Rahman NFN, Yulianto AB. Potency of probiotics Bifidobacterium spp. and Lactobacillus casei to improve growth performance and business analysis in organic laying hens. Vet World 2019; 12:860-867. [PMID: 31440006 PMCID: PMC6661486 DOI: 10.14202/vetworld.2019.860-867] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 05/13/2019] [Indexed: 12/03/2022] Open
Abstract
Aim: This study aimed to determine the use of probiotics Bifidobacterium spp. and Lactobacillus casei as alternative antibiotic growth promoters (AGPs) to improve growth performance and business analysis. Materials and Methods: This study used a completely randomized factorial design. The first factor was the time of administration (1, 2, 3, and 4 weeks) and the second was the use of probiotics (control without probiotics; 0.1% AGP and 0.5% Bifidobacterium spp. + 0.25% L. casei). One hundred and eighty laying hens (Lohmann strain), of 30 weeks old, were divided into 12 treatment groups, composed of five replicates, each consisting of three laying hens. Results: The results showed that using 0.5% Bifidobacterium spp. + 0.25% L. casei in weeks 1 and 2 showed the lowest feed intake (FI) (112.11-112.19 g/day), the highest egg weight (60.28 g) in the 1st week, the lowest feed conversion ratio (FCR) (2.21-2.23), and highest feed efficiency (44.75-45.25%) for 3-4 weeks, and the highest hen-day production (86.66-86.90%) for 3-4 weeks and the most profitable business analysis (IDR. 30,353). Conclusions: Based on the results, it can be concluded that the addition of 0.5% Bifidobacterium spp. + 25% L. casei probiotics can be used as a substitute for AGP; it can reduce the FI and FCR, increasing egg weight, feed efficiency, and hen-day production, as well as illustrating the results of the most profitable business analysis.
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Affiliation(s)
- Widya Paramita Lokapirnasari
- Department of Animal Husbandry, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Mulyorejo, Kampus C, Universitas Airlangga, Surabaya, Indonesia.,Halal Research Center, Universitas Airlangga, Jl. Mulyorejo, Kampus C, Universitas Airlangga, Surabaya, Indonesia
| | - Teguh Bagus Pribadi
- Magister of Veterinary Agribusiness, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | - Anam Al Arif
- Department of Animal Husbandry, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Mulyorejo, Kampus C, Universitas Airlangga, Surabaya, Indonesia
| | - Soeharsono Soeharsono
- Department of Veterinary Anatomy, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | - Sri Hidanah
- Department of Animal Husbandry, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Mulyorejo, Kampus C, Universitas Airlangga, Surabaya, Indonesia
| | - Nenny Harijani
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | - Rifqy Najwan
- Magister of Veterinary Agribusiness, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | - Khoirul Huda
- Magister of Veterinary Agribusiness, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | | | - Nabil Fariz Noor Rahman
- Magister of Veterinary Agribusiness, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | - Andreas Berny Yulianto
- Sains Veteriner, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
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Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 2019; 20:294. [PMID: 32039702 PMCID: PMC7227232 DOI: 10.1186/s12864-019-5537-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Timur N Khamiruev
- Research Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences, Chita, Russia
| | - Marina I Selionova
- All-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian Center, Stavropol, 355017, Russia
| | - Sergey V Egorov
- Siberian Research Institute of Animal Husbandry, Krasnoobsk, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, UK.
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Zhang R, Miao J, Song Y, Zhang W, Xu L, Chen Y, Zhang L, Gao H, Zhu B, Li J, Gao X. Genome-wide association study identifies the PLAG1-OXR1 region on BTA14 for carcass meat yield in cattle. Physiol Genomics 2019; 51:137-144. [DOI: 10.1152/physiolgenomics.00112.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Carcass meat yield is an important carcass trait that contributes to the production efficiency and economic benefits in beef cattle. It is therefore critical to identify quantitative trait loci associated with carcass traits to enable selection. Our previous studies have identified several causal variants within the pleomorphic adenoma gene 1 ( PLAG1) and coiled-coil-helix-coiled-coil-helix domain-containing 7 ( CHCHD7) genes on BTA14 for carcass traits in Chinese Simmental. In the current study, we carried out a genome-wide association study for carcass meat yield in 472 Wagyu cattle with Bovine HD SNP array. Our results showed that 27 single nucleotide polymorphisms (SNPs) were identified for tenderloin weight (TDW), striploin weight (SPW), chuck roll weight (CRW), bicep weight (BPW), knuckle weight (KCW), and flank steak weight (FSW) in Wagyu cattle. Of these SNPs, 10 distinct SNPs were detected within the oxidation resistance 1 ( OXR1), fatty acid binding protein 5 ( FABP5), TNF receptor superfamily member 11b ( TNFRSF11B), and zinc finger CCCH-type containing 3 ( ZC3H3) genes on BTA14. Notably, three significant SNPs, BovineHD1400016738, BovineHD1400016743, and BovineHD1400016665 within OXR1, were shown strong linkage disequilibrium (r2 > 0.8) and significantly associated with CRW ( P = 1.37 × 10−8 ~ 1.94 × 10−8). Moreover, Ingenuity Pathway Analysis showed that OXR1, FABP5, and CAP1A genes were involved in a single network and FABP5 may regulate the expression of OXR1 gene via node gene, peroxisome proliferator-activated receptor gamma ( PPARG). Overall, this study suggests that OXR1 and FABP5 are candidate genes affecting carcass traits in Wagyu and the PLAG1-OXR1 region on BTA14 as a putative susceptibility locus for carcass meat yield for both Chinese Simmental and Wagyu.
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Affiliation(s)
- Rui Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Miao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuxin Song
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wengang Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Lippolis J, Powell E, Reinhardt T, Thacker T, Casas E. Symposium review: Omics in dairy and animal science—Promise, potential, and pitfalls. J Dairy Sci 2019; 102:4741-4754. [DOI: 10.3168/jds.2018-15267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/06/2018] [Indexed: 01/08/2023]
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Xu L, Zhu B, Wang Z, Xu L, Liu Y, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L, Li J. Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle. Animals (Basel) 2019; 9:ani9030083. [PMID: 30845681 PMCID: PMC6466336 DOI: 10.3390/ani9030083] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Evaluation of the population structure and linkage disequilibrium can offer important insights to fully understand the genetic diversity and population history of cattle, which can enable us to appropriately design and implement GWAS and GS in cattle. In this study, we characterized the extent of genome-wide LD and the haplotype block structure, and estimated the persistence of phase of Chinese indigenous cattle with Illumina BovineHD BeadChip. According to our study, 58K, 87K, 95K, 52K, and 52K markers would be necessary for SCHC, NCC, SWC, SIM, and WAG, respectively, in the implementation of GWAS and GS and combining a multipopulation with high persistence of phase is feasible for the implication of genomic selection for Chinese beef cattle. Abstract Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.
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Affiliation(s)
- Lei Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
| | - Bo Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Zezhao Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Ling Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Ying Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yan Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Lupei Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Xue Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Huijiang Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Lingyang Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Junya Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Xu L, Yang L, Wang L, Zhu B, Chen Y, Gao H, Gao X, Zhang L, Liu GE, Li J. Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle. BMC Genomics 2019; 20:31. [PMID: 30630414 PMCID: PMC6327516 DOI: 10.1186/s12864-018-5403-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Average daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef cattle industry. The molecular mechanisms of ADG have not yet been fully explored because most recent association studies for ADG are based on SNPs or haplotypes. We reported a systematic CNV discovery and association analysis for ADG in Chinese Simmental beef cattle. RESULTS Our study identified 4912 nonredundant CNVRs with a total length of ~ 248.7 Mb, corresponding to ~ 8.9% of the cattle genome. Using probe-based CNV association, we identified 24 and 12 significant SNP probes within five deletions and two duplications for ADG, respectively. Among them, we found one common deletion with 89 kb imbedded in LHFPL Tetraspan Subfamily Member 6 (LHFPL6) at 22.9 Mb on BTA12, which has high frequency (12.9%) dispersing across population. CNV selection test using VST statistic suggested this common deletion may be under positive selection in Chinese Simmental cattle. Moreover, this deletion was not overlapped with any candidate SNP for ADG compared with previous SNPs-based association studies, suggesting its important role for ADG. In addition, we identified one rare deletion near gene Growth Factor Receptor-bound Protein 10 (GRB10) at 5.1 Mb on BTA4 for ADG using both probe-based association and region-based approaches. CONCLUSIONS Our results provided some valuable insights to elucidate the genetic basis of ADG in beef cattle, and these findings offer an alternative perspective to understand the genetic mechanism of complex traits in terms of copy number variations in farm animals.
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Affiliation(s)
- Lingyang Xu
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Liu Yang
- Innovation Team of Cattle Genetic 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, 611130, China
| | - Lei Wang
- Beijing Genecast Biotechnology Co., Beijing, 100191, China
| | - Bo Zhu
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yan Chen
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huijiang Gao
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xue Gao
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lupei Zhang
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - George E Liu
- U.S. Department of Agriculture-Agricultural Research Services, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA.
| | - Junya Li
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Zanella R, Lago LV, da Silva AN, Pértille F, de Carvalho NS, do Carmo Panetto JC, Zanella GC, Facioli FL, da Silva MVGB. Genetic Characterization of Indubrasil Cattle Breed Population. Vet Sci 2018; 5:vetsci5040098. [PMID: 30513897 PMCID: PMC6313910 DOI: 10.3390/vetsci5040098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/19/2018] [Accepted: 11/29/2018] [Indexed: 11/27/2022] Open
Abstract
The Indubrasil breed was developed in the Brazilian region called Triângulo Mineiro as a result of a cross between zebu cattle. Initially, it was used as a terminal cross and currently it represents approximately 4.45% of all the Brazilian zebu cattle. Studies were conducted to estimate genetic parameters in the Indubrasil using pedigree information, however, until now, no study has been developed using large-scale genomic markers in this breed. Pedigree information are widely used to investigate population parameters; however, they can neglect some estimates when compared to the use of genomic markers. Therefore, the objective of this study was to investigate the population structure and the genetic diversity of Indubrasil cattle using a high-density Single Nucleotide Polymorphism (SNP) panel (Illumina BovineHD BeadChip 700k). Levels of genomic homozygosity were evaluated using three different approaches: Runs of homozygosity (FROH), % of homozygosis (FSNP), and inbreeding coefficient (Fx). Further, Runs of Homozygosity (ROH) segments conserved among the animals were investigated to identify possible regions associated with the breed characteristics. Our results indicate that even the Indubrasil breed having a small effective population size, the levels of homozygosity (FROH = 0.046) are still small. This was possibly caused by the cross conducted among different breeds for its development. It suggests no immediate risks associated with loss of genetic variation. This information might be used in breeding programs, for the breed conservation and for the expansion of the Indubrasil breed.
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Affiliation(s)
- Ricardo Zanella
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
- Docente do programa de Pós-Graduação em Bioexperimentação, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Luísa V Lago
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Arthur N da Silva
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Fábio Pértille
- Laboratório de Biotecnologia Animal, Departamento de Ciência Animal e Pastagens, Universidade de São Paulo/Escola Superior de Agricultura Luiz de Queiroz, Av. Pádua Dias, 11, 13418-900 Piracicaba, SP, Brazil.
| | - Nathã S de Carvalho
- Mestrando do Curso de Zootecnia, Universidade Federal do Rio Grande do Sul/Faculdade de Agronomia, Av. Bento Gonçalves, 7712, 91540-000 Porto Alegre, RS, Brazil.
| | | | - Giovana C Zanella
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Fernanda L Facioli
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
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Okada D, Endo S, Matsuda H, Ogawa S, Taniguchi Y, Katsuta T, Watanabe T, Iwaisaki H. An intersection network based on combining SNP coassociation and RNA coexpression networks for feed utilization traits in Japanese Black cattle. J Anim Sci 2018; 96:2553-2566. [PMID: 29762780 DOI: 10.1093/jas/sky170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 05/11/2018] [Indexed: 11/12/2022] Open
Abstract
Genome-wide association studies (GWAS) of quantitative traits have detected numerous genetic associations, but they encounter difficulties in pinpointing prominent candidate genes and inferring gene networks. The present study used a systems genetics approach integrating GWAS results with external RNA-expression data to detect candidate gene networks in feed utilization and growth traits of Japanese Black cattle, which are matters of concern. A SNP coassociation network was derived from significant correlations between SNPs with effects estimated by GWAS across 7 phenotypic traits. The resulting network genes contained significant numbers of annotations related to the traits. Using bovine transcriptome data from a public database, an RNA coexpression network was inferred based on the similarity of expression patterns across different tissues. An intersection network was then generated by superimposing the SNP and RNA networks and extracting shared interactions. This intersection network contained 4 tissue-specific modules: nervous system, reproductive system, muscular system, and glands. To characterize the structure (topographical properties) of the 3 networks, their scale-free properties were evaluated, which revealed that the intersection network was the most scale-free. In the subnetwork containing the most connected transcription factors (URI1, ROCK2, and ETV6), most genes were widely expressed across tissues, and genes previously shown to be involved in the traits were found. Results indicated that the current approach might be used to construct a gene network that better reflects biological information, providing encouragement for the genetic dissection of economically important quantitative traits.
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Affiliation(s)
- Daigo Okada
- Faculty of Agriculture, Kyoto University, Kyoto, Japan
| | - Satoko Endo
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | | | - Yukio Taniguchi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Toshio Watanabe
- National Livestock Breeding Center, Nishigo, Fukushima, Japan.,Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Nishigo, Fukushima, Japan
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61
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Khansefid M, Pryce JE, Bolormaa S, Chen Y, Millen CA, Chamberlain AJ, Vander Jagt CJ, Goddard ME. Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle. BMC Genomics 2018; 19:793. [PMID: 30390624 PMCID: PMC6215656 DOI: 10.1186/s12864-018-5181-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/17/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association between genetic variants and gene expression in multiple individuals (eQTL mapping), or by comparing the expression of the alleles in a heterozygous individual (allele specific expression or ASE analysis). The aims of the study were to find and compare ASE and local eQTL in 4 bovine RNA-sequencing (RNA-Seq) datasets, validate them in an independent ASE study and investigate if they are associated with complex trait variation. RESULTS We present a novel method for distinguishing between ASE driven by polymorphisms in cis and parent of origin effects. We found that single nucleotide polymorphisms (SNPs) driving ASE are also often local eQTL and therefore presumably cis eQTL. These SNPs often, but not always, affect gene expression in multiple tissues and, when they do, the allele increasing expression is usually the same. However, there were systematic differences between ASE and local eQTL and between tissues and breeds. We also found that SNPs significantly associated with gene expression (p < 0.001) were likely to influence some complex traits (p < 0.001), which means that some mutations influence variation in complex traits by changing the expression level of genes. CONCLUSION We conclude that ASE detects phenomenon that overlap with local eQTL, but there are also systematic differences between the SNPs discovered by the two methods. Some mutations influencing complex traits are actually eQTL and can be discovered using RNA-Seq including eQTL in the genes CAST, CAPN1, LCORL and LEPROTL1.
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Affiliation(s)
- Majid Khansefid
- Department of Agriculture and Food Systems, The University of Melbourne, Parkville, VIC, Australia. .,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.
| | - Jennie E Pryce
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,La Trobe University, Bundoora, Australia
| | - Sunduimijid Bolormaa
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Yizhou Chen
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Catriona A Millen
- Agricultural Business Research Institute, The University of New England, Armidale, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | | | - Michael E Goddard
- Department of Agriculture and Food Systems, The University of Melbourne, Parkville, VIC, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
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62
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Xu L, Zhang W, Shen H, Zhang Y, Zhao Y, Jia Y, Gao X, Zhu B, Xu L, Zhang L, Gao H, Li J, Chen Y. Genome-wide scanning reveals genetic diversity and signatures of selection in Chinese indigenous cattle breeds. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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63
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Ma M, Shen M, Qu L, Dou T, Guo J, Hu Y, Lu J, Li Y, Wang X, Wang K. Genome-wide association study for carcase traits in spent hens at 72 weeks old. ITALIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1080/1828051x.2018.1507626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Meng Ma
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China
| | - Manman Shen
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Liang Qu
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China
| | - Taocun Dou
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China
| | - Jun Guo
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China
| | - Yuping Hu
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China
| | - Jian Lu
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China
| | - Yongfeng Li
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China
| | - Xingguo Wang
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China
| | - Kehua Wang
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China
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64
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Maiorano AM, Lourenco DL, Tsuruta S, Ospina AMT, Stafuzza NB, Masuda Y, Filho AEV, Cyrillo JNDSG, Curi RA, Silva JAIIDV. Assessing genetic architecture and signatures of selection of dual purpose Gir cattle populations using genomic information. PLoS One 2018; 13:e0200694. [PMID: 30071036 PMCID: PMC6071998 DOI: 10.1371/journal.pone.0200694] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/02/2018] [Indexed: 12/31/2022] Open
Abstract
Gir is one of the main cattle breeds raised in tropical South American countries. Strong artificial selection through its domestication resulted in increased genetic differentiation among the countries in recent years. Over the years, genomic studies in Gir have become more common. However, studies of population structure and signatures of selection in divergent Gir populations are scarce and need more attention to better understand genetic differentiation, gene flow, and genetic distance. Genotypes of 173 animals selected for growth traits and 273 animals selected for milk production were used in this study. Clear genetic differentiation between beef and dairy populations was observed. Different criteria led to genetic divergence and genetic differences in allele frequencies between the two populations. Gene segregation in each population was forced by artificial selection, promoting isolation, and increasing genetic variation between them. Results showed evidence of selective forces in different regions of the genome. A total of 282 genes were detected under selection in the test population based on the fixation index (Fst), integrated haplotype score (iHS), and cross-population extend haplotype homozygosity (XP-EHH) approaches. The QTL mapping identified 35 genes associated with reproduction, milk composition, growth, meat and carcass, health, or body conformation traits. The investigation of genes and pathways showed that quantitative traits associated to fertility, milk production, beef quality, and growth were involved in the process of differentiation of these populations. These results would support further investigations of population structure and differentiation in the Gir breed.
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Affiliation(s)
- Amanda Marchi Maiorano
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
- * E-mail:
| | - Daniela Lino Lourenco
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Shogo Tsuruta
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Alejandra Maria Toro Ospina
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
| | - Nedenia Bonvino Stafuzza
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
| | - Yutaka Masuda
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | | | | | - Rogério Abdallah Curi
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, Sao Paulo, Brazil
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65
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Lyu S, Arends D, Nassar MK, Weigend A, Weigend S, Preisinger R, Brockmann GA. Reducing the interval of a growth QTL on chromosome 4 in laying hens. Anim Genet 2018; 49:467-471. [PMID: 30058133 DOI: 10.1111/age.12685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2018] [Indexed: 11/27/2022]
Abstract
In our previous research, we identified a QTL with an interval of 3.4 Mb for growth on chicken chromosome (GGA) 4 in an advanced intercross population of an initial cross between the New Hampshire inbred line (NHI) and the White Leghorn inbred line (WL77). In the current study, an association analysis was performed in a population of purebred white layers (WLA) with White Leghorn origin. Genotypic data of 130 SNPs within the previously identified 3.4-Mb region were obtained using a 60K SNP chip. In total, 24 significant SNPs (LOD ≥ 4.44) on GGA4 were detected for daily weigh gain from 8 to 14 weeks and two SNPs (LOD ≥ 4.80) for body weight at 14 weeks. The QTL interval was reduced by 1.9 Mb to an interval of 1.5 Mb (74.6-76.1 Mb) that harbors 15 genes. Furthermore, to identify additional loci for chicken growth, a genome-wide association study (GWAS) was carried out in a WLA population. The GWAS identified an additional QTL on GGA6 for body weight at six weeks (19.8-21.2 Mb). Our findings showed that by using a WLA population we were able to further reduce the QTL confidence interval previously detected using a NHI × WL77 advanced intercross population.
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Affiliation(s)
- S Lyu
- Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin, 10115, Germany
| | - D Arends
- Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin, 10115, Germany
| | - M K Nassar
- Department of Animal Production, Faculty of Agriculture, Cairo University, El-Gamma Str. 6, Giza, 12613, Egypt
| | - A Weigend
- Department of Breeding and Genetic Resources, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, 31535, Germany
| | - S Weigend
- Department of Breeding and Genetic Resources, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, 31535, Germany
| | - R Preisinger
- Lohmann Tierzucht GmbH, Am Seedeich 9-11, 27472, Cuxhaven, Germany
| | - G A Brockmann
- Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin, 10115, Germany
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66
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Li F, Han H, Lei Q, Gao J, Liu J, Liu W, Zhou Y, Li H, Cao D. Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology. J Appl Genet 2018; 59:305-312. [PMID: 29946990 DOI: 10.1007/s13353-018-0452-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022]
Abstract
Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models. Six SNP markers reached genome-wide significance. Of these, rs732048524, rs735522839, rs738991545, and rs15837818 were significantly associated with body weight at 28 days (BW28), while rs314086457 and rs315694878 were significantly associated with BW120. These SNPs are close to seven genes (PRSS23, ME3, FAM181B, NABP1, SDPR, TSSK6L2, and RBBP8). Moreover, 24 BW-associated SNPs reached "suggestive" genome-wide significance. Of these, 6, 13, 1, and 4 SNPs were associated with BW28, BW56, BW80, and BW120, respectively. These results would enrich the studies on BW and promote the use of Chinese chicken, especially the Wenshang Barred chicken.
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Affiliation(s)
- Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Jinbo Gao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Huimin Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China. .,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China.
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67
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Chang T, Xia J, Xu L, Wang X, Zhu B, Zhang L, Gao X, Chen Y, Li J, Gao H. A genome-wide association study suggests several novel candidate genes for carcass traits in Chinese Simmental beef cattle. Anim Genet 2018; 49:312-316. [DOI: 10.1111/age.12667] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2018] [Indexed: 02/05/2023]
Affiliation(s)
- T. Chang
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - J. Xia
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - L. Xu
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - X. Wang
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - B. Zhu
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - L. Zhang
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - X. Gao
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - Y. Chen
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - J. Li
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - H. Gao
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
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68
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Bhuiyan MSA, Lim D, Park M, Lee S, Kim Y, Gondro C, Park B, Lee S. Functional Partitioning of Genomic Variance and Genome-Wide Association Study for Carcass Traits in Korean Hanwoo Cattle Using Imputed Sequence Level SNP Data. Front Genet 2018; 9:217. [PMID: 29988410 PMCID: PMC6024024 DOI: 10.3389/fgene.2018.00217] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/28/2018] [Indexed: 11/25/2022] Open
Abstract
Quantitative traits are usually controlled by numerous genomic variants with small individual effects, and variances associated with those traits are explained in a continuous manner. However, the relative contributions of genomic regions to observed genetic variations have not been well explored using sequence level single nucleotide polymorphism (SNP) information. Here, imputed sequence level SNP data (11,278,153 SNPs) of 2109 Hanwoo steers (Korean native cattle) were partitioned according to functional annotation, chromosome, and minor allele frequency (MAF). Genomic relationship matrices (GRMs) were constructed for each classified region and fitted in the model both separately and together for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BFT), and marbling score (MS) traits. A genome-wide association study (GWAS) was performed to identify significantly associated variants in genic and exon regions using a linear mixed model, and the genetic contribution of each exonic SNP was determined using a Bayesian mixture model. Considering all SNPs together, the heritability estimates for CWT, EMA, BFT, and MS were 0.57 ± 0.05, 0.46 ± 0.05, 0.45 ± 0.05, and 0.49 ± 0.05, respectively, which reflected substantial genomic contributions. Joint analysis revealed that the variance explained by each chromosome was proportional to its physical length with weak linear relationships for all traits. Moreover, genomic variances explained by functional category and MAF class differed greatly among the traits studied in joint analysis. For example, exon regions had larger contributions for BFT (0.13 ± 0.08) and MS (0.22 ± 0.08), whereas intron and intergenic regions explained most of the total genomic variances for CWT and EMA (0.22 ± 0.09–0.32 ± 0.11). Considering different functional classes of exon regions and the per SNP contribution revealed the largest proportion of genetic variance was attributable to synonymous variants. GWAS detected 206 and 27 SNPs in genic and exon regions, respectively, on BTA4, BTA6, and BTA14 that were significantly associated with CWT and EMA. These SNPs were harbored by 31 candidate genes, among which TOX, FAM184B, PPARGC1A, PRKDC, LCORL, and COL1A2 were noteworthy. BayesR analysis found that most SNPs (>93%) had very small effects and the 4.02–6.92% that had larger effects (10-4 × σA2, 10-3 × σA2, and 10-2 × σA2) explained most of the total genetic variance, confirming polygenic components of the traits studied.
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Affiliation(s)
- Mohammad S A Bhuiyan
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, South Korea.,Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Dajeong Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju, South Korea
| | - Mina Park
- Animal Genetic Improvement Division, National Institute of Animal Science, Rural Development Administration, Seonghwan, South Korea
| | - Soohyun Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Yeongkuk Kim
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Cedric Gondro
- College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Byoungho Park
- Animal Genetic Improvement Division, National Institute of Animal Science, Rural Development Administration, Seonghwan, South Korea
| | - Seunghwan Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, South Korea
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69
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Wang X, Miao J, Xia J, Chang T, E G, Bao J, Jin S, Xu L, Zhang L, Zhu B, Gao X, Chen Y, Li J, Gao H. Identifying novel genes for carcass traits by testing G × E interaction through genome-wide meta-analysis in Chinese Simmental beef cattle. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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70
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Human-Mediated Introgression of Haplotypes in a Modern Dairy Cattle Breed. Genetics 2018; 209:1305-1317. [PMID: 29848486 PMCID: PMC6063242 DOI: 10.1534/genetics.118.301143] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Domestic animals can serve as model systems of adaptive introgression and their genomic signatures. In part, their usefulness as model systems is due to their well-known histories. Different breeding strategies such as introgression and artificial selection have generated numerous desirable phenotypes and superior performance in domestic animals. The modern Danish Red Dairy Cattle is studied as an example of an introgressed population. It originates from crossing the traditional Danish Red Dairy Cattle with the Holstein and Brown Swiss breeds, both known for high milk production. This crossing happened, among other things due to changes in the production system, to raise milk production and overall performance. The genomes of modern Danish Red Dairy Cattle are heavily influenced by regions introgressed from the Holstein and Brown Swiss breeds and under subsequent selection in the admixed population. The introgressed proportion of the genome was found to be highly variable across the genome. Haplotypes introgressed from Holstein and Brown Swiss contained or overlapped known genes affecting milk production, as well as protein and fat content (CD14, ZNF215, BCL2L12, and THRSP for Holstein origin and ITPR2, BCAT1, LAP3, and MED28 for Brown Swiss origin). Genomic regions with high introgression signals also contained genes and enriched QTL associated with calving traits, body confirmation, feed efficiency, carcass, and fertility traits. These introgressed signals with relative identity-by-descent scores larger than the median showing Holstein or Brown Swiss introgression are mostly significantly correlated with the corresponding test statistics from signatures of selection analyses in modern Danish Red Dairy Cattle. Meanwhile, the putative significant introgressed signals have a significant dependency with the putative significant signals from signatures of selection analyses. Artificial selection has played an important role in the genomic footprints of introgression in the genome of modern Danish Red Dairy Cattle. Our study on a modern cattle breed contributes to an understanding of genomic consequences of selective introgression by demonstrating the extent to which adaptive effects contribute to shape the specific genomic consequences of introgression.
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Santiago GG, Siqueira F, Cardoso FF, Regitano LCA, Ventura R, Sollero BP, Souza MD, Mokry FB, Ferreira ABR, Torres RAA. Genomewide association study for production and meat quality traits in Canchim beef cattle. J Anim Sci 2018; 95:3381-3390. [PMID: 28805909 DOI: 10.2527/jas.2017.1570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The commercial value of the bovine carcass is determined by a set of traits, such as weight, yield, back fat thickness, and marbling; therefore, the genetic improvement of growth, meat, and carcass quality traits is an important tool to add value to the supply chain. Genomewide association studies (GWAS) enable the identification of loci that control phenotypic expression of quantitative traits (QTL). Therefore, the objective of this work was to perform a GWAS to identify genomic regions and genes associated with growth, carcass traits, and meat quality in Canchim beef cattle. These traits were yearling weight (YW), rib eye area (REA), back fat thickness (BFT), and marbling (MARB). To increase sample size and marker density, genotype imputation was performed, and only markers imputed with greater than 95% accuracy were used. Genomewide association study was performed using a Bayesian approach, by the Bayes B statistical method, incorporating genotypes and phenotypes from 614 animals from both the Canchim breed and the MA genetic group (offspring of Charolais bulls and one-half Canchim + one-half Zebu cows). This investigation identified 1 and 4 genomic regions explaining 0.23 and 7.35% of the genetic variance for REA and YW, respectively. These regions harbor a total of 19 genes, 7 of which were classified for biological functions by functional analysis. Significant associations were not observed for BFT and MARB. The identification of QTL that had been previously described in the literature reinforces associations found in this study.
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72
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Zhang W, Xu L, Gao H, Wu Y, Gao X, Zhang L, Zhu B, Song Y, Bao J, Li J, Chen Y. Detection of candidate genes for growth and carcass traits using genome-wide association strategy in Chinese Simmental beef cattle. ANIMAL PRODUCTION SCIENCE 2018. [DOI: 10.1071/an16165] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In Chinese beef cattle industry, there are more than 60 million livestock, nearly half of which are Chinese Simmental beef cattle or Simmental crossbreds. Over the past decades, numerous quantitative trait loci for economic traits in cattle have been identified, while few studies for growth and carcass traits have been reported in Simmental beef cattle. In the present study, we conducted genome-wide association study based on BovineHD BeadChip and identified 41, 15, 3, 22 and 16 single-nucleotide polymorphisms significantly associated with average daily gain, liveweight before slaughter, carcass weight, dressing percentage and pure meat percentage respectively. In total, 18 candidate genes were found for growth and carcass traits, and four haplotype blocks for growth and carcass traits were discovered. These findings will facilitate detection of major genes and genetic variants involved in growth and carcass traits of beef cattle in further studies.
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73
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Tozaki T, Kikuchi M, Kakoi H, Hirota KI, Nagata SI. A genome-wide association study for body weight in Japanese Thoroughbred racehorses clarifies candidate regions on chromosomes 3, 9, 15, and 18. J Equine Sci 2017; 28:127-134. [PMID: 29270069 PMCID: PMC5735309 DOI: 10.1294/jes.28.127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/21/2017] [Indexed: 01/24/2023] Open
Abstract
Body weight is an important trait to confirm growth and development in humans and animals. In Thoroughbred racehorses, it is measured in the postnatal, training, and racing periods to evaluate growth and training
degrees. The body weight of mature Thoroughbred racehorses generally ranges from 400 to 600 kg, and this broad range is likely influenced by environmental and genetic factors. Therefore, a genome-wide association study
(GWAS) using the Equine SNP70 BeadChip was performed to identify the genomic regions associated with body weight in Japanese Thoroughbred racehorses using 851 individuals. The average body weight of these horses was
473.9 kg (standard deviation: 28.0) at the age of 3, and GWAS identified statistically significant SNPs on chromosomes 3 (BIEC2_808466, P=2.32E-14), 9 (BIEC2_1105503, P=1.03E-7), 15 (BIEC2_322669, P=9.50E-6), and 18
(BIEC2_417274, P=1.44E-14), which were associated with body weight as a quantitative trait. The genomic regions on chromosomes 3, 9, 15, and 18 included ligand-dependent nuclear receptor compressor-like protein (LCORL),
zinc finger and AT hook domain containing (ZFAT), tribbles pseudokinase 2 (TRIB2), and myostatin (MSTN), respectively, as candidate genes. LCORL and ZFAT are associated with withers height in horses, whereas MSTN affects
muscle mass. Thus, the genomic regions identified in this study seem to affect the body weight of Thoroughbred racehorses. Although this information is useful for breeding and growth management of the horses, the
production of genetically modified animals and gene doping (abuse/misuse of gene therapy) should be prohibited to maintain horse racing integrity.
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Affiliation(s)
- Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Mio Kikuchi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Hironaga Kakoi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Kei-Ichi Hirota
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Shun-Ichi Nagata
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
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Gutiérrez-Gil B, Esteban-Blanco C, Wiener P, Chitneedi PK, Suarez-Vega A, Arranz JJ. High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds. Genet Sel Evol 2017; 49:81. [PMID: 29115919 PMCID: PMC5674817 DOI: 10.1186/s12711-017-0354-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/19/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals. RESULTS Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included. CONCLUSIONS Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.
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Affiliation(s)
- Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
- Fundación Centro Supercomputación de Castilla y León, Campus de Vegazana, León, 24071 Spain
| | - Pamela Wiener
- Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - Praveen Krishna Chitneedi
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Aroa Suarez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Juan-Jose Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
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Lin YJ, Liao WL, Wang CH, Tsai LP, Tang CH, Chen CH, Wu JY, Liang WM, Hsieh AR, Cheng CF, Chen JH, Chien WK, Lin TH, Wu CM, Liao CC, Huang SM, Tsai FJ. Association of human height-related genetic variants with familial short stature in Han Chinese in Taiwan. Sci Rep 2017; 7:6372. [PMID: 28744006 PMCID: PMC5527114 DOI: 10.1038/s41598-017-06766-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 06/19/2017] [Indexed: 12/19/2022] Open
Abstract
Human height can be described as a classical and inherited trait model. Genome-wide association studies (GWAS) have revealed susceptible loci and provided insights into the polygenic nature of human height. Familial short stature (FSS) represents a suitable trait for investigating short stature genetics because disease associations with short stature have been ruled out in this case. In addition, FSS is caused only by genetically inherited factors. In this study, we explored the correlations of FSS risk with the genetic loci associated with human height in previous GWAS, alone and cumulatively. We systematically evaluated 34 known human height single nucleotide polymorphisms (SNPs) in relation to FSS in the additive model (p < 0.00005). A cumulative effect was observed: the odds ratios gradually increased with increasing genetic risk score quartiles (p < 0.001; Cochran-Armitage trend test). Six affected genes-ZBTB38, ZNF638, LCORL, CABLES1, CDK10, and TSEN15-are located in the nucleus and have been implicated in embryonic, organismal, and tissue development. In conclusion, our study suggests that 13 human height GWAS-identified SNPs are associated with FSS risk both alone and cumulatively.
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Affiliation(s)
- Ying-Ju Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.,Center for Personalized Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chung-Hsing Wang
- Children's Hospital of China Medical University, Taichung, Taiwan
| | - Li-Ping Tsai
- Department of Pediatrics, Buddhist Tzu Chi General Hospital, Taipei Branch, Taipei, Taiwan
| | - Chih-Hsin Tang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Chien-Hsiun Chen
- School of Chinese Medicine, China Medical University, Taichung, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jer-Yuarn Wu
- School of Chinese Medicine, China Medical University, Taichung, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wen-Miin Liang
- Graduate Institute of Biostatistics, School of Public Health, China Medical University, Taichung, Taiwan
| | - Ai-Ru Hsieh
- Graduate Institute of Biostatistics, School of Public Health, China Medical University, Taichung, Taiwan
| | - Chi-Fung Cheng
- Graduate Institute of Biostatistics, School of Public Health, China Medical University, Taichung, Taiwan
| | - Jin-Hua Chen
- Biostatistics Center and School of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Wen-Kuei Chien
- National Applied Research Laboratories, National Center for High-performance Computing, Hsinchu, Taiwan
| | - Ting-Hsu Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Chia-Ming Wu
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Chiu-Chu Liao
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Shao-Mei Huang
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan. .,School of Chinese Medicine, China Medical University, Taichung, Taiwan. .,Children's Hospital of China Medical University, Taichung, Taiwan. .,Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan.
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77
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Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle. BMC Genomics 2017; 18:386. [PMID: 28521758 PMCID: PMC5437562 DOI: 10.1186/s12864-017-3754-y] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 05/03/2017] [Indexed: 11/13/2022] Open
Abstract
Background Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations. Results Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE ≥ 1.0%) and a nominal P-value threshold (P ≤ 5e-05). Lead SNPs with PVE ≥ 2.0% were considered putative evidence of large-effect QTL (n = 52), whereas those with PVE ≥ 1.0% but < 2.0% were considered putative evidence for moderate-effect QTL (n = 35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained). Conclusions Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs ≤ 3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3754-y) contains supplementary material, which is available to authorized users.
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78
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Xia J, Fan H, Chang T, Xu L, Zhang W, Song Y, Zhu B, Zhang L, Gao X, Chen Y, Li J, Gao H. Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle. Sci Rep 2017; 7:42048. [PMID: 28169328 PMCID: PMC5294460 DOI: 10.1038/srep42048] [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: 07/19/2016] [Accepted: 01/06/2017] [Indexed: 12/26/2022] Open
Abstract
Single-marker genome-wide association study (GWAS) is a convenient strategy of genetic analysis that has been successful in detecting the association of a number of single-nucleotide polymorphisms (SNPs) with quantitative traits. However, analysis of individual SNPs can only account for a small proportion of genetic variation and offers only limited knowledge of complex traits. This inadequacy may be overcome by employing a gene-based GWAS analytic approach, which can be considered complementary to the single-SNP association analysis. Here we performed an initial single-SNP GWAS for bone weight (BW) and meat pH value with a total of 770,000 SNPs in 1141 Simmental cattle. Additionally, 21836 cattle genes collected from the Ensembl Genes 83 database were analyzed to find supplementary evidence to support the importance of gene-based association study. Results of the single SNP-based association study showed that there were 11 SNPs significantly associated with bone weight (BW) and two SNPs associated with meat pH value. Interestingly, all of these SNPs were located in genes detected by the gene-based association study.
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Affiliation(s)
- Jiangwei Xia
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Huizhong Fan
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Wengang Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Yuxin Song
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Bo Zhu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
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79
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HAN YJ, CHEN Y, LIU Y, LIU XL. Sequence variants of the LCORL gene and its association with growth and carcass traits in Qinchuan cattle in China. J Genet 2017; 96:9-17. [DOI: 10.1007/s12041-016-0732-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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80
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Song Y, Xu L, Chen Y, Zhang L, Gao H, Zhu B, Niu H, Zhang W, Xia J, Gao X, Li J. Genome-Wide Association Study Reveals the PLAG1 Gene for Knuckle, Biceps and Shank Weight in Simmental Beef Cattle. PLoS One 2016; 11:e0168316. [PMID: 27997562 PMCID: PMC5172584 DOI: 10.1371/journal.pone.0168316] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 11/30/2016] [Indexed: 12/04/2022] Open
Abstract
Carcass traits of beef cattle have been genetically improved to increase yield of high quality meat. Genome-wide association study (GWAS) is a powerful method to identify genetic variants associated with carcass traits. For the 770K genotyped SNPs from 1141 Chinese Simmental cattle, we used the compressed mixed linear model (CMLM) to perform a genome-wide association study for knuckle, biceps and shank of beef carcass traits. Seventeen significantly associated SNPs were found, which are located on BTA6, BTA14 and BTA15. Interestingly, one pleiotropic quantitative trait nucleotide (QTN), named BovineHD1400007259 (p < 10−8) within the well-known gene region PLAG1-CHCHD7 on BTA14, was found to govern variation of the knuckle, biceps and shank traits. The QTN accounted for 8.6% of phenotypic variance for biceps. In addition, 16 more SNPs distributed on BTA14 were detected as being associated with the carcass traits.
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Affiliation(s)
- Yuxin Song
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hong Niu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wengang Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiangwei Xia
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (JL); (XG)
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (JL); (XG)
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81
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Sevane N, Dunner S, Boado A, Cañon J. Polymorphisms in ten candidate genes are associated with conformational and locomotive traits in Spanish Purebred horses. J Appl Genet 2016; 58:355-361. [PMID: 27917442 DOI: 10.1007/s13353-016-0385-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/11/2016] [Accepted: 11/24/2016] [Indexed: 01/08/2023]
Abstract
The Spanish Purebred horses, also known as Andalusian horses, compete to the highest standards in international dressage events. Gait and conformation could be used as early selection criteria to detect young horses with promising dressage ability. Although the genetic background of equine size variation has been recently uncovered, the genetic basis of horse conformational and locomotive traits is not known, hampered by the complex genetic architecture underlying quantitative traits and the lack of phenotypic data. The aim of this study was to validate the loci associated with size in 144 Spanish Purebred horses, and to seek novel associations between loci previously associated with the development of osteochondrosis (OC) lesions and 20 conformational and locomotive traits. Ten loci were associated with different conformational and locomotive traits (LCORL/NCAPG, HMGA2, USP31, MECR, COL24A1, MGP, FAM184B, PTH1R, KLF3 and SGK1), and the LCORL/NCAPG association with size in the Spanish Purebred horse was validated. Except for HMGA2, all polymorphisms seem to influence both the prevalence of OC lesions and morphological characters, supporting the link between conformation and OC. Also, the implication of most genes in either immune and inflammatory responses and cellular growth, or ossification processes, reinforces the role that these mechanisms have in the aetiology of OC, as well as their reflection on the general conformation of the individual. These polymorphisms could be used in marker-assisted selection (MAS) programmes to improve desirable conformational traits, but taking into account their possible detrimental effect on OC prevalence.
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Affiliation(s)
- Natalia Sevane
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, 28040, Spain.
| | - Susana Dunner
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, 28040, Spain
| | - Ana Boado
- Traumatología Equina, El Boalo, Madrid, 28413, Spain
| | - Javier Cañon
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, 28040, Spain
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82
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Zhang W, Li J, Guo Y, Zhang L, Xu L, Gao X, Zhu B, Gao H, Ni H, Chen Y. Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle. Sci Rep 2016; 6:38073. [PMID: 27892541 PMCID: PMC5125095 DOI: 10.1038/srep38073] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/04/2016] [Indexed: 01/16/2023] Open
Abstract
Average daily gain (ADG) is the most economically important trait in beef cattle industry. Using genome-wide association study (GWAS) approaches, previous studies have identified several causal variants within the PLAG1, NCAPG and LCORL genes for ADG in cattle. Multi-strategy GWASs were implemented in this study to improve detection and to explore the causal genes and regions. In this study, we conducted GWASs based on the genotypes of 1,173 Simmental cattle. In the SNP-based GWAS, the most significant SNPs (rs109303784 and rs110058857, P = 1.78 × 10−7) were identified in the NCAPG intron on BTA6 and explained 4.01% of the phenotypic variance, and the independent and significant SNP (rs110406669, P = 5.18 × 10−6) explained 3.32% of the phenotypic variance. Similarly, in the haplotype-based GWAS, the most significant haplotype block, Hap-6-N1416 (P = 2.56 × 10−8), spanned 12.7 kb on BTA6 and explained 4.85% of the phenotypic variance. Also, in the gene-based GWAS, seven significant genes were obtained which included DCAF16 and NCAPG. Moreover, analysis of the transcript levels confirmed that transcripts abundance of NCAPG (P = 0.046) and DCAF16 (P = 0.046) were significantly correlated with the ADG trait. Overall, our results from the multi-strategy GWASs revealed the DCAF16-NCAPG region to be a susceptibility locus for ADG in cattle.
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Affiliation(s)
- Wengang Zhang
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Junya Li
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yong Guo
- Animal Science and Technology College, Beijing University of Agriculture (BUA), Beijing 102206, China
| | - Lupei Zhang
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lingyang Xu
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xue Gao
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Bo Zhu
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Huijiang Gao
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Hemin Ni
- Animal Science and Technology College, Beijing University of Agriculture (BUA), Beijing 102206, China
| | - Yan Chen
- Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
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83
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Tozaki T, Sato F, Ishimaru M, Kikuchi M, Kakoi H, Hirota KI, Nagata SI. Sequence variants of BIEC2-808543 near LCORL are associated with body composition in Thoroughbreds under training. J Equine Sci 2016; 27:107-114. [PMID: 27703405 PMCID: PMC5048357 DOI: 10.1294/jes.27.107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/20/2016] [Indexed: 12/18/2022] Open
Abstract
Ligand-dependent nuclear receptor compressor-like (LCORL) encodes a transcription factor, and its polymorphisms are associated with measures of skeletal frame
size and adult height in several species. Recently, the single nucleotide polymorphism (SNP) BIEC2-808543 located upstream of LCORL was identified as a genetic
diagnostic marker associated with withers height in Thoroughbreds. In this study, 322 Thoroughbreds-in-training were genotyped for BIEC2-808543 to evaluate the
association between genotype and body composition traits, including body weight, withers height, the ratio of body weight to withers height, chest
circumference, and cannon circumference. Of these, withers height and cannon circumference were significantly associated with LCORL genotypes throughout almost
the entire training period in males and females. Animals with a C/T genotype had higher withers height (maximum differences of 1.8 cm and 2.1 cm in males and
females, respectively) and cannon circumstance (maximum differences of 0.65 cm and 0.48 cm in males and females, respectively) compared with animals with a T/T
genotype. These results suggested that the regulation of LCORL expression influences the skeletal frame size in Thoroughbreds and thus, indirectly affects the
body weight. Although LCORL and BIEC2-808543 would be useful for selective breeding in Thoroughbreds, the production of genetically modified animals and gene
doping based on genetic information should be prohibited in order to maintain racing integrity.
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Affiliation(s)
- Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Fumio Sato
- Hidaka Training and Research Center, Japan Racing Association, Hokkaido 057-0171, Japan
| | - Mutsuki Ishimaru
- Hidaka Training and Research Center, Japan Racing Association, Hokkaido 057-0171, Japan
| | - Mio Kikuchi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Hironaga Kakoi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Kei-Ichi Hirota
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Shun-Ichi Nagata
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
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84
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Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK. Sci Rep 2016; 6:27296. [PMID: 27272025 PMCID: PMC4895181 DOI: 10.1038/srep27296] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 04/26/2016] [Indexed: 11/09/2022] Open
Abstract
The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150–154 Mb), Oar6 (4–49 Mb) and Oar13 (68–74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection.
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Wang W, Zhang T, Wang J, Zhang G, Wang Y, Zhang Y, Zhang J, Li G, Xue Q, Han K, Zhao X, Zheng H. Genome-wide association study of 8 carcass traits in Jinghai Yellow chickens using specific-locus amplified fragment sequencing technology. Poult Sci 2016; 95:500-6. [PMID: 26614681 PMCID: PMC4957485 DOI: 10.3382/ps/pev266] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Carcass traits are important to the commercial chicken industry, and understanding the genetics of these traits will be useful in the development of commercially viable varieties of chickens. We conducted a genome-wide association study based on 8 carcass trait phenotypes in a population of 400 43-week-old Jinghai Yellow chickens. Specific-locus amplified fragment sequencing technology was used to identify 90,961 single nucleotide polymorphisms (SNP) distributed among 29 chromosomes and the mitochondrial genome. SNP that were significantly associated with phenotypic traits were identified by a simple general linear model. Fifteen SNP attained genome-wide significance (P < 1.87E−6) and were associated with 5 of the 8 carcass traits; only one SNP was significantly associated with 2 traits (foot weight and wing weight). Twelve genes were associated with these 15 SNP. A region of chromosome 4 between 75.5 and 76.1 Mb was associated with carcass weight, foot weight, and wing weight. An 84-kb region on chromosome 3 (51.2 Mb) was associated with eviscerated weight and semi-eviscerated weight.
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Affiliation(s)
- Wenhao Wang
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
- Department of Life Science, Resources and Environment, Yichun University, Yichun 336000, China
- These authors contributed equally to this study
| | - Tao Zhang
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
- These authors contributed equally to this study
| | - Jinyu Wang
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
- Corresponding author:
| | - Genxi Zhang
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
| | - Yongjuan Wang
- JiangsuJinghai Poultry Industry Group CD, LTD, Nantong 226000, China
| | - Yinwen Zhang
- Biomarker Technologies Corporation, Beijing 100000, China
| | - Jianhui Zhang
- Biomarker Technologies Corporation, Beijing 100000, China
| | - Guohui Li
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
| | - Qian Xue
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
| | - Kunpeng Han
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
| | - Xiuhua Zhao
- Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 100000, China
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Randhawa IAS, Khatkar MS, Thomson PC, Raadsma HW. A Meta-Assembly of Selection Signatures in Cattle. PLoS One 2016; 11:e0153013. [PMID: 27045296 PMCID: PMC4821596 DOI: 10.1371/journal.pone.0153013] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/22/2016] [Indexed: 12/31/2022] Open
Abstract
Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species.
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Affiliation(s)
- Imtiaz A. S. Randhawa
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
- * E-mail:
| | - Mehar S. Khatkar
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
| | - Peter C. Thomson
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
| | - Herman W. Raadsma
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
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Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds. Genetics 2016; 203:433-50. [PMID: 27017625 DOI: 10.1534/genetics.115.181594] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 03/03/2016] [Indexed: 01/25/2023] Open
Abstract
Detecting the molecular basis of adaptation is one of the major questions in population genetics. With the advance in sequencing technologies, nearly complete interrogation of genome-wide polymorphisms in multiple populations is becoming feasible in some species, with the expectation that it will extend quickly to new ones. Here, we investigate the advantages of sequencing for the detection of adaptive loci in multiple populations, exploiting a recently published data set in cattle (Bos taurus). We used two different approaches to detect statistically significant signals of positive selection: a within-population approach aimed at identifying hard selective sweeps and a population-differentiation approach that can capture other selection events such as soft or incomplete sweeps. We show that the two methods are complementary in that they indeed capture different kinds of selection signatures. Our study confirmed some of the well-known adaptive loci in cattle (e.g., MC1R, KIT, GHR, PLAG1, NCAPG/LCORL) and detected some new ones (e.g., ARL15, PRLR, CYP19A1, PPM1L). Compared to genome scans based on medium- or high-density SNP data, we found that sequencing offered an increased detection power and a higher resolution in the localization of selection signatures. In several cases, we could even pinpoint the underlying causal adaptive mutation or at least a very small number of possible candidates (e.g., MC1R, PLAG1). Our results on these candidates suggest that a vast majority of adaptive mutations are likely to be regulatory rather than protein-coding variants.
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Wolc A, Arango J, Settar P, Fulton JE, O’Sullivan NP, Dekkers JCM, Fernando R, Garrick DJ. Mixture models detect large effect QTL better than GBLUP and result in more accurate and persistent predictions. J Anim Sci Biotechnol 2016; 7:7. [PMID: 26870325 PMCID: PMC4750167 DOI: 10.1186/s40104-016-0066-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/27/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Accurate evaluation of SNP effects is important for genome wide association studies and for genomic prediction. The genetic architecture of quantitative traits differs widely, with some traits exhibiting few if any quantitative trait loci (QTL) with large effects, while other traits have one or several easily detectable QTL with large effects. METHODS Body weight in broilers and egg weight in layers are two examples of traits that have QTL of large effect. A commonly used method for genome wide association studies is to fit a mixture model such as BayesB that assumes some known proportion of SNP effects are zero. In contrast, the most commonly used method for genomic prediction is known as GBLUP, which involves fitting an animal model to phenotypic data with the variance-covariance or genomic relationship matrix among the animals being determined by genome wide SNP genotypes. Genotypes at each SNP are typically weighted equally in determining the genomic relationship matrix for GBLUP. We used the equivalent marker effects model formulation of GBLUP for this study. We compare these two classes of models using egg weight data collected over 8 generations from 2,324 animals genotyped with a 42 K SNP panel. RESULTS Using data from the first 7 generations, both BayesB and GBLUP found the largest QTL in a similar well-recognized QTL region, but this QTL was estimated to account for 24 % of genetic variation with BayesB and less than 1 % with GBLUP. When predicting phenotypes in generation 8 BayesB accounted for 36 % of the phenotypic variation and GBLUP for 25 %. When using only data from any one generation, the same QTL was identified with BayesB in all but one generation but never with GBLUP. Predictions of phenotypes in generations 2 to 7 based on only 295 animals from generation 1 accounted for 10 % phenotypic variation with BayesB but only 6 % with GBLUP. Predicting phenotype using only the marker effects in the 1 Mb region that accounted for the largest effect on egg weight from generation 1 data alone accounted for almost 8 % variation using BayesB but had no predictive power with GBLUP. CONCLUSIONS In conclusion, In the presence of large effect QTL, BayesB did a better job of QTL detection and its genomic predictions were more accurate and persistent than those from GBLUP.
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Affiliation(s)
- Anna Wolc
- />Department of Animal Science, Iowa State University, 225D Kildee Hall, Ames, IA 50011 USA
- />Hy-Line International, Dallas Center, IA USA
| | | | | | | | | | - Jack C. M. Dekkers
- />Department of Animal Science, Iowa State University, 225D Kildee Hall, Ames, IA 50011 USA
| | - Rohan Fernando
- />Department of Animal Science, Iowa State University, 225D Kildee Hall, Ames, IA 50011 USA
| | - Dorian J. Garrick
- />Department of Animal Science, Iowa State University, 225D Kildee Hall, Ames, IA 50011 USA
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Matika O, Riggio V, Anselme-Moizan M, Law AS, Pong-Wong R, Archibald AL, Bishop SC. Genome-wide association reveals QTL for growth, bone and in vivo carcass traits as assessed by computed tomography in Scottish Blackface lambs. Genet Sel Evol 2016; 48:11. [PMID: 26856324 PMCID: PMC4745175 DOI: 10.1186/s12711-016-0191-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/28/2016] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Improving meat quality including taste and tenderness is critical to the protection and development of markets for sheep meat. Phenotypic selection for such measures of meat quality is constrained by the fact that these parameters can only be measured post-slaughter. Carcass composition has an impact on meat quality and can be measured on live animals using advanced imaging technologies such as X-ray computed tomography (CT). Since carcass composition traits are heritable, they are potentially amenable to improvement through marker-assisted and genomic selection. We conducted a genome-wide association study (GWAS) on about 600 Scottish Blackface lambs for which detailed carcass composition phenotypes, including bone, fat and muscle components, had been captured using CT and which were genotyped for ~40,000 single nucleotide polymorphisms (SNPs) using the Illumina OvineSNP50 chip. RESULTS We confirmed that the carcass composition traits were heritable with moderate to high (0.19-0.78) heritabilities. The GWAS analyses revealed multiple SNPs and quantitative trait loci (QTL) that were associated with effects on carcass composition traits and were significant at the genome-wide level. In particular, we identified a region on ovine chromosome 6 (OAR6) associated with bone weight and bone area that harboured SNPs with p values of 5.55 × 10(-8) and 2.63 × 10(-9), respectively. The same region had effects on fat area, fat density, fat weight and muscle density. We identified plausible positional candidate genes for these OAR6 QTL. We also detected a SNP that reached the genome-wide significance threshold with a p value of 7.28 × 10(-7) and was associated with muscle density on OAR1. Using a regional heritability mapping approach, we also detected regions on OAR3 and 24 that reached genome-wide significance for bone density. CONCLUSIONS We identified QTL on OAR1, 3, 24 and particularly on OAR6 that are associated with effects on muscle, fat and bone traits. Based on available evidence that indicates that these traits are genetically correlated with meat quality traits, these associated SNPs have potential applications in selective breeding for improved meat quality. Further research is required to determine whether the effects associated with the OAR6 QTL are caused by a single gene or several closely-linked genes.
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Affiliation(s)
- Oswald Matika
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.
| | - Valentina Riggio
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.
| | | | - Andrew S Law
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.
| | - Ricardo Pong-Wong
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.
| | - Alan L Archibald
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.
| | - Stephen C Bishop
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.
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90
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Biegelmeyer P, Gulias-Gomes CC, Caetano AR, Steibel JP, Cardoso FF. Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle. BMC Genet 2016; 17:32. [PMID: 26832943 PMCID: PMC4736111 DOI: 10.1186/s12863-016-0339-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/20/2016] [Indexed: 11/25/2022] Open
Abstract
Background The existence of moderate to high levels of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) affecting traits of interest is fundamental for the success of genome-wide association (GWAS) and genomic selection (GS) studies. Knowledge about the extent and the pattern of LD in livestock populations is essential to determine the density of single nucleotide polymorphisms (SNP) required for accurate GWAS and GS. Moreover, observed LD is related to historical effective population sizes (Ne), and can provide insights into the genetic diversity history of populations. Estimates of the consistency of linkage phase across breeds (RH,B) can be used to determine if there is sufficient relationship to use pooled reference populations in multi-breed GS programs. The objective of this study was to estimate LD levels, persistence of phase and effective population size in Hereford and Braford cattle populations sampled in Brazil. Results Mean LD estimates, measured using the squared correlation of alleles at two loci (r2), obtained between adjacent SNP across all chromosomes were 0.21 ± 0.27 for Herefords (391 samples with 41,241 SNP) and 0.16 ± 0.22 for Brafords (2044 samples and 41,207 SNP). Estimated r2 was > 0.2 and 0.3, respectively, for 34 and 25 % of adjacent markers in Herefords, and 26 and 17 % in Brafords. Estimated Ne for Brafords and Herefords at the current generation was 220 and 153 individuals, respectively. The two breeds demonstrated moderate to strong persistence of phase at all distances (RH,B = 0.53 to 0.97). The largest phase correlations were found in the 0 to 50 Kb bins (RH,B = 0.92 to 0.97). Estimated LD decreased rapidly with increasing distance between SNP, however, useful linkage for GWAS and GS (r2 > 0.2) was found spanning to ~50 Kb. Conclusions Panels containing about 50,000 and 150,000 SNP markers are necessary to detect minimal levels of LD between adjacent markers that would be useful for GWAS and GS studies to Hereford and Braford breeds, respectively. Markers are expected to be linked to the same QTL alleles in distances < 50 Kb in both populations due to observed high persistence of phase levels.
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Affiliation(s)
- Patrícia Biegelmeyer
- Programa de Pós-Graduação em Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil.
| | | | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. .,Programa de Pós-Graduação em Ciências Animais, Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Brasília, Distrito Federal, Brazil. .,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, Distrito Federal, Brazil.
| | | | - Fernando F Cardoso
- Programa de Pós-Graduação em Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil. .,Embrapa Pecuária Sul, Bagé, Rio Grande do Sul, Brazil. .,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, Distrito Federal, Brazil.
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91
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Yuan J, Wang K, Yi G, Ma M, Dou T, Sun C, Qu LJ, Shen M, Qu L, Yang N. Genome-wide association studies for feed intake and efficiency in two laying periods of chickens. Genet Sel Evol 2015; 47:82. [PMID: 26475174 PMCID: PMC4608132 DOI: 10.1186/s12711-015-0161-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 10/07/2015] [Indexed: 11/11/2022] Open
Abstract
Background Feed contributes to over 60 % of the total production costs in the poultry industry. Increasing feed costs prompt geneticists to include feed intake and efficiency as selection goals in breeding programs. In the present study, we used an F2 chicken population in a genome-wide association study (GWAS) to detect potential genetic variants and candidate genes associated with daily feed intake (FI) and feed efficiency, including residual feed intake (RFI) and feed conversion ratio (FCR). Methods A total of 1534 F2 hens from a White Leghorn and Dongxiang reciprocal cross were phenotyped for feed intake and efficiency between 37 and 40 weeks (FI1, RFI1, and FCR1) and between 57 and 60 weeks (FI2, RFI2, and FCR2), and genotyped using the chicken 600 K single nucleotide polymorphism (SNP) genotyping array. Univariate, bivariate, and conditional genome-wide association studies (GWAS) were performed with GEMMA, a genome-wide efficient mixed model association algorithm. The statistical significance threshold for association was inferred by the simpleM method. Results We identified eight genomic regions that each contained at least one genetic variant that showed a significant association with FI. Genomic regions on Gallus gallus (GGA) chromosome 4 coincided with known quantitative trait loci (QTL) that affect feed intake of layers. Of particular interest, eight SNPs on GGA1 in the region between 169.23 and 171.55 Mb were consistently associated with FI in both univariate and bivariate GWAS, which explained 3.72 and 2.57 % of the phenotypic variance of FI1 and FI2, respectively. The CAB39L gene can be considered as a promising candidate for FI1. For RFI, a haplotype block on GGA27 harbored a significant SNP associated with RFI2. The major allele of rs315135692 was favorable for a lower RFI, with a phenotypic difference of 3.35 g/day between opposite homozygous genotypes. Strong signals on GGA1 were detected in the bivariate GWAS for FCR. Conclusions The results demonstrated the polygenic nature of feed intake. GWAS identified novel variants and confirmed a QTL that was previously reported for feed intake in chickens. Genetic variants associated with feed efficiency may be used in genomic breeding programs to select more efficient layers. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0161-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingwei Yuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Kehua Wang
- Jiangsu Institute of Poultry Science, Yangzhou, 225125, People's Republic of China.
| | - Guoqiang Yi
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Meng Ma
- Jiangsu Institute of Poultry Science, Yangzhou, 225125, People's Republic of China.
| | - Taocun Dou
- Jiangsu Institute of Poultry Science, Yangzhou, 225125, People's Republic of China.
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Lu-Jiang Qu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Manman Shen
- Jiangsu Institute of Poultry Science, Yangzhou, 225125, People's Republic of China.
| | - Liang Qu
- Jiangsu Institute of Poultry Science, Yangzhou, 225125, People's Republic of China.
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Yi G, Shen M, Yuan J, Sun C, Duan Z, Qu L, Dou T, Ma M, Lu J, Guo J, Chen S, Qu L, Wang K, Yang N. Genome-wide association study dissects genetic architecture underlying longitudinal egg weights in chickens. BMC Genomics 2015; 16:746. [PMID: 26438435 PMCID: PMC4595193 DOI: 10.1186/s12864-015-1945-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 09/22/2015] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND As a major economic trait in chickens, egg weight (EW) receives widespread interests in breeding, production and consumption. However, limited information is available for underlying genetic architecture of longitudinal trend in EW. Herein, we measured EWs at nine time points from onset of laying to 60 week of age, and conducted comprehensive genome-wide association studies (GWAS) in 1,534 F2 hens derived from reciprocal crosses between White Leghorn and Dongxiang chickens. RESULTS Egg weights at all ages except the first egg weight (FEW) exhibited high SNP-based heritability estimates (0.47~0.60). Strong pair-wise genetic correlations (0.77~1.00) were found among all EWs. Nine separate univariate genome-wide screens suggested 73 signals showing significant associations with longitudinal EWs. After multivariate and conditional analyses, four variants on three chromosomes remained independent contributions. The minor alleles at two loci exerted consistent and positive substitution effects on EWs, and other two were negative. The four loci together accounted for 3.84 % of the phenotypic variance for FEW and 7.29~11.06 % for EWs from 32 to 60 week of age. We obtained five candidate genes, of which NCAPG harbors a non-synonymous SNP (rs14491030) causing a valine-to-alanine amino-acid substitution. Genome partitioning analysis indicated a strong linear correlation between the variance explained by each chromosome and its length, which provided evidence that EW follows a highly polygenic nature of inheritance. CONCLUSIONS Identification of significant genetic causes that together implicate EWs at different ages will greatly advance our understanding of the genetic basis behind longitudinal EWs, and would be helpful to illuminate the future breeding direction on how to select desired egg size.
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Affiliation(s)
- Guoqiang Yi
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Manman Shen
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Jingwei Yuan
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Congjiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Zhongyi Duan
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Liang Qu
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Taocun Dou
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Meng Ma
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Jian Lu
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Jun Guo
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Sirui Chen
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Kehua Wang
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Zhang GX, Fan QC, Wang JY, Zhang T, Xue Q, Shi HQ. Genome-wide association study on reproductive traits in Jinghai Yellow Chicken. Anim Reprod Sci 2015; 163:30-4. [PMID: 26498507 DOI: 10.1016/j.anireprosci.2015.09.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/23/2015] [Accepted: 09/25/2015] [Indexed: 01/27/2023]
Abstract
To identify molecular markers and candidate genes associated with reproductive traits, a genome-wide analysis was performed in Jinghai Yellow Chickens to analyze body weight at first oviposition (BWF), age at first oviposition (AFE), weight of the egg at first oviposition (FEW), egg weight at the age of 300 days (EW300), number of eggs produced by 300 days of age (EN300), egg hatchability (HA) and multiple selection index for egg production (MSI). The results showed that seven single nucleotide polymorphisms (SNPs) were associated with reproductive traits (P<1.80E-6, Bonferroni correction). The P-values of the seven SNPs were 5.62E-10, 3.45E-08, 9.76E-07, 8.90E-07, 1.12E-06, 1.42E-07 and 1.48E-07, respectively. These SNPs were located in close proximity to or within the sequence of the five candidate genes, including FAM184B, TTL, RGS1, FBLN5 and PCNX. An additional 46 SNPs that could be associated with reproductive traits were identified (P<3.59E-5, Bonferroni correction). Identification of the candidate genes as well as genome-wide SNPs that may be associated with reproductive traits will greatly advance the understanding of the genetic basis and molecular mechanisms underlying reproductive traits and may have practical significance in breeding programs for the improvements of reproductive traits in the Jinghai Yellow Chicken.
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Affiliation(s)
- G X Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Q C Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - J Y Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.
| | - T Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Q Xue
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - H Q Shi
- Jiangsu Jinghai Poultry Industry Group Co., Ltd., Nantong, Jiangsu, China
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Abstract
A recent progress on stature genetics has revealed simple genetic architecture in livestock animals in contrast to that in humans. PLAG1 and/or NCAPG‐LCORL, both of which are known as a locus for adult human height, have been detected for association with body weight/height in cattle and horses, and for selective sweep in dogs and pigs. The findings indicate a significant impact of these loci on mammalian growth or body size and usefulness of the natural variants for selective breeding. However, association with an unfavorable trait, such as late puberty or risk for a neuropathic disease, was also reported for the respective loci, indicating an importance to discriminate between causality and association. Here I review the recent findings on quantitative trait loci (QTL) for stature in livestock animals, mainly focusing on the PLAG1 and NCAPG‐LCORL loci. I also describe our recent efforts to identify the causative variation for the third major locus for carcass weight in Japanese Black cattle.
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95
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Sun C, Qu L, Yi G, Yuan J, Duan Z, Shen M, Qu L, Xu G, Wang K, Yang N. Genome-wide association study revealed a promising region and candidate genes for eggshell quality in an F2 resource population. BMC Genomics 2015; 16:565. [PMID: 26228268 PMCID: PMC4521446 DOI: 10.1186/s12864-015-1795-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 07/22/2015] [Indexed: 11/30/2022] Open
Abstract
Background Eggshell is subject to quality loss with aging process of laying hens, and damaged eggshells result in economic losses of eggs. However, the genetic architecture underlying the dynamic eggshell quality remains elusive. Here, we measured eggshell quality traits, including eggshell weight (ESW), eggshell thickness (EST) and eggshell strength (ESS) at 11 time points from onset of laying to 72 weeks of age and conducted comprehensive genome-wide association studies (GWAS) in 1534 F2 hens derived from reciprocal crosses between White Leghorn (WL) and Dongxiang chickens (DX). Results ESWs at all ages exhibited moderate SNP-based heritability estimates (0.30 ~ 0.46), while the estimates for EST (0.21 ~ 0.31) and ESS (0.20 ~ 0.27) were relatively low. Eleven independent univariate genome-wide screens for each trait totally identified 1059, 1026 and 1356 significant associations with ESW, EST and ESS, respectively. Most significant loci were in a region spanning from 57.3 to 71.4 Mb of chromosome 1 (GGA1), which together account for 8.4 ~ 16.5 % of the phenotypic variance for ESW from 32 to 72 weeks of age, 4.1 ~ 6.9 % and 2.95 ~ 16.1 % for EST and ESS from 40 to 72 weeks of age. According to linkage disequilibrium (LD) and conditional analysis, the significant SNPs in this region were in extremely strong linkage disequilibrium status. Ultimately, two missense SNPs in GGA1 and one in GGA4 were considered as promising loci on three independent genes including ITPR2, PIK3C2G, and NCAPG. The homozygotes of advantageously effective alleles on PIK3C2G and ITPR2 possessed the best eggshell quality and could partly counteract the negative effect of aging process. NCAPG had certain effect on eggshell quality for young hens. Conclusions Identification of the promising region as well as potential candidate genes will greatly advance our understanding of the genetic basis underlying dynamic eggshell quality and has the practical significance in breeding program for the improvement of eggshell quality, especially at the later part of laying cycle. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1795-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Congjiao Sun
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Liang Qu
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Guoqiang Yi
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Jingwei Yuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Zhongyi Duan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Manman Shen
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Guiyun Xu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Kehua Wang
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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96
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Identification of loci and genes for growth related traits from a genome-wide association study in a slow- × fast-growing broiler chicken cross. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0314-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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97
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Gutiérrez-Gil B, Arranz JJ, Wiener P. An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds. Front Genet 2015; 6:167. [PMID: 26029239 PMCID: PMC4429627 DOI: 10.3389/fgene.2015.00167] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 04/13/2015] [Indexed: 12/11/2022] Open
Abstract
This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity.
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Affiliation(s)
| | - Juan J Arranz
- Departamento de Producción Animal, Universidad de León León, Spain
| | - Pamela Wiener
- Division of Genetics and Genomics, Roslin Institute and R(D)SVS, University of Edinburgh Midlothian, UK
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98
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Sahana G, Höglund JK, Guldbrandtsen B, Lund MS. Loci associated with adult stature also affect calf birth survival in cattle. BMC Genet 2015; 16:47. [PMID: 25935543 PMCID: PMC4426170 DOI: 10.1186/s12863-015-0202-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/15/2015] [Indexed: 01/03/2023] Open
Abstract
Background Understanding the underlying pleiotropic relationships among quantitative traits is necessary in order to predict correlated responses to artificial selection. The availability of large-scale next-generation sequence data in cattle has provided an opportunity to examine whether pleiotropy is responsible for overlapping QTL in multiple economic traits. In the present study, we examined QTL affecting cattle stillbirth, calf size, and adult stature located in the same genomic region. Results A genome scan using imputed whole genome sequence variants revealed one QTL with large effects on the service sire calving index (SCI), and body conformation index (BCI) at the same location (~39 Mb) on chromosome 6 in Nordic Red cattle. The targeted region was analyzed for SCI and BCI component traits. The QTL peak included LCORL and NCAPG genes, which had been reported to influence fetal growth and adult stature in several species. The QTL exhibited large effects on calf size and stature in Nordic Red cattle. Two deviant haplotypes (HAP1 and HAP2) were resolved which increased calf size at birth, and affected adult body conformation. However, the haplotypes also resulted in increased calving difficulties and calf mortality due to increased calf size at birth. Haplotype locations overlapped, however linkage disequilibrium (LD) between the sites was low, suggesting that two independent mutations were responsible for similar effects. The difference in prevalence between the two haplotypes in Nordic Red subpopulations suggested independent origins in different populations. Conclusions Results of our study identified QTL with large effects on body conformation and service sire calving traits on chromosome 6 in cattle. We present robust evidence that variation at the LCORL and NCAPG locus affects calf size at birth and adult stature. We suggest the two deviant haplotypes within the QTL were due to two independent mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0202-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Goutam Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, P.O. Box 50, DK-8830, Tjele, Denmark.
| | - Johanna K Höglund
- Center for Quantitative Genetics and Genomics, Aarhus University, P.O. Box 50, DK-8830, Tjele, Denmark. .,Present address: Department of Animal Science, Aarhus University, P.O. Box 50, DK-8830, Tjele, Denmark.
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Aarhus University, P.O. Box 50, DK-8830, Tjele, Denmark.
| | - Mogens S Lund
- Center for Quantitative Genetics and Genomics, Aarhus University, P.O. Box 50, DK-8830, Tjele, Denmark.
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Composite Selection Signals for Complex Traits Exemplified Through Bovine Stature Using Multibreed Cohorts of European and African Bos taurus. G3-GENES GENOMES GENETICS 2015; 5:1391-401. [PMID: 25931611 PMCID: PMC4502373 DOI: 10.1534/g3.115.017772] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding the evolution and molecular architecture of complex traits is important in domestic animals. Due to phenotypic selection, genomic regions develop unique patterns of genetic diversity called signatures of selection, which are challenging to detect, especially for complex polygenic traits. In this study, we applied the composite selection signals (CSS) method to investigate evidence of positive selection in a complex polygenic trait by examining stature in phenotypically diverse cattle comprising 47 European and 8 African Bos taurus breeds, utilizing a panel of 38,033 SNPs genotyped on 1106 animals. CSS were computed for phenotypic contrasts between multibreed cohorts of cattle by classifying the breeds according to their documented wither height to detect the candidate regions under selection. Using the CSS method, clusters of signatures of selection were detected at 26 regions (9 in European and 17 in African cohorts) on 13 bovine autosomes. Using comparative mapping information on human height, 30 candidate genes mapped at 12 selection regions (on 8 autosomes) could be linked to bovine stature diversity. Of these 12 candidate gene regions, three contained known genes (i.e., NCAPG-LCORL, FBP2-PTCH1, and PLAG1-CHCHD7) related to bovine stature, and nine were not previously described in cattle (five in European and four in African cohorts). Overall, this study demonstrates the utility of CSS coupled with strategies of combining multibreed datasets in the identification and discovery of genomic regions underlying complex traits. Characterization of multiple signatures of selection and their underlying candidate genes will elucidate the polygenic nature of stature across cattle breeds.
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100
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Widmann P, Reverter A, Weikard R, Suhre K, Hammon HM, Albrecht E, Kuehn C. Systems biology analysis merging phenotype, metabolomic and genomic data identifies Non-SMC Condensin I Complex, Subunit G (NCAPG) and cellular maintenance processes as major contributors to genetic variability in bovine feed efficiency. PLoS One 2015; 10:e0124574. [PMID: 25875852 PMCID: PMC4398489 DOI: 10.1371/journal.pone.0124574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 03/11/2015] [Indexed: 12/24/2022] Open
Abstract
Feed efficiency is a paramount factor for livestock economy. Previous studies had indicated a substantial heritability of several feed efficiency traits. In our study, we investigated the genetic background of residual feed intake, a commonly used parameter of feed efficiency, in a cattle resource population generated from crossing dairy and beef cattle. Starting from a whole genome association analysis, we subsequently performed combined phenotype-metabolome-genome analysis taking a systems biology approach by inferring gene networks based on partial correlation and information theory approaches. Our data about biological processes enriched with genes from the feed efficiency network suggest that genetic variation in feed efficiency is driven by genetic modulation of basic processes relevant to general cellular functions. When looking at the predicted upstream regulators from the feed efficiency network, the Tumor Protein P53 (TP53) and Transforming Growth Factor beta 1 (TGFB1) genes stood out regarding significance of overlap and number of target molecules in the data set. These results further support the hypothesis that TP53 is a major upstream regulator for genetic variation of feed efficiency. Furthermore, our data revealed a significant effect of both, the Non-SMC Condensin I Complex, Subunit G (NCAPG) I442M (rs109570900) and the Growth /differentiation factor 8 (GDF8) Q204X (rs110344317) loci, on residual feed intake and feed conversion. For both loci, the growth promoting allele at the onset of puberty was associated with a negative, but favorable effect on residual feed intake. The elevated energy demand for increased growth triggered by the NCAPG 442M allele is obviously not fully compensated for by an increased efficiency in converting feed into body tissue. As a consequence, the individuals carrying the NCAPG 442M allele had an additional demand for energy uptake that is reflected by the association of the allele with increased daily energy intake as observed in our study.
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Affiliation(s)
- Philipp Widmann
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Genome Physiology Unit, Dummerstorf, Germany
| | | | - Rosemarie Weikard
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Genome Physiology Unit, Dummerstorf, Germany
| | - Karsten Suhre
- Weill Cornell Medical College in Qatar, Doha, State of Qatar
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Harald M. Hammon
- Leibniz Institute for Farm Animal Biology, Institute for Nutritional Physiology “Oskar Kellner”, Dummerstorf, Germany
| | - Elke Albrecht
- Leibniz Institute for Farm Animal Biology, Institute for Muscle Biology and Growth, Dummerstorf, Germany
| | - Christa Kuehn
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Genome Physiology Unit, Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
- * E-mail:
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