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Zlobin AS, Volkova NA, Zinovieva NA, Iolchiev BS, Bagirov VA, Borodin PM, Axenovich TI, Tsepilov YA. Loci Associated with Negative Heterosis for Viability and Meat Productivity in Interspecific Sheep Hybrids. Animals (Basel) 2023; 13:ani13010184. [PMID: 36611792 PMCID: PMC9817718 DOI: 10.3390/ani13010184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023] Open
Abstract
Negative heterosis can occur on different economically important traits, but the exact biological mechanisms of this phenomenon are still unknown. The present study focuses on determining the genetic factors associated with negative heterosis in interspecific hybrids between domestic sheep (Ovis aries) and argali (Ovis ammon). One locus (rs417431015) associated with viability and two loci (rs413302370, rs402808951) associated with meat productivity were identified. One gene (ARAP2) was prioritized for viability and three for meat productivity (PDE2A, ARAP1, and PCDH15). The loci associated with meat productivity were demonstrated to fit the overdominant inheritance model and could potentially be involved int negative heterosis mechanisms.
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Affiliation(s)
- Alexander S. Zlobin
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences SB RAS, 630090 Novosibirsk, Russia
| | - Natalia A. Volkova
- L.K. Ernst Federal Science Center for Animal Husbandry, 101000 Moscow, Russia
| | | | - Baylar S. Iolchiev
- L.K. Ernst Federal Science Center for Animal Husbandry, 101000 Moscow, Russia
| | - Vugar A. Bagirov
- L.K. Ernst Federal Science Center for Animal Husbandry, 101000 Moscow, Russia
| | - Pavel M. Borodin
- Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | | | - Yakov A. Tsepilov
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences SB RAS, 630090 Novosibirsk, Russia
- Correspondence:
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Kim HJ, de Las Heras-Saldana S, Moghaddar N, Lee SH, Lim D, van der Werf JHJ. Genome-wide association study for carcass traits in Hanwoo cattle using additional relatives' information of non-genotyped animals. Anim Genet 2022; 53:863-866. [PMID: 35993261 DOI: 10.1111/age.13251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 11/27/2022]
Abstract
The aim of this study was to find significant genomic regions associated with carcass traits in Hanwoo cattle and to compare the benefit of using additional information from non-genotyped animals. Imputed whole-genome sequence data were used along with phenotypic data on 13 715 genotyped animals as well as phenotypes of 440 284 non-genotyped animals that were offspring of 454 genotyped sires. For carcass weight, 15 083 SNPs in 33 QTL regions and 313 candidate genes were identified. We found 410 SNPs in 17 QTL regions containing 122 candidate genes for back fat thickness. In total, 656 SNPs in 19 QTLs with 137 candidate genes for eye muscle area and 79 SNPs in 12 QTL regions with 77 candidate genes were identified for marbling score. The most important candidate genes included ZFAT, TG, PLAG1, CHCHD7, and TOX for carcass weight and eye muscle area, NOG for back fat thickness, and EVOVL5 for marbling score. This study showed that the use of phenotypic records on non-genotyped progeny along with imputed whole-genome sequence data increased the power of detecting new significant genomic regions.
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Affiliation(s)
- Hyoun Ju Kim
- School of Environmental & Rural Science, University of New England, Armidale, New South Wales, Australia.,Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, Korea
| | - Sara de Las Heras-Saldana
- School of Environmental & Rural Science, University of New England, Armidale, New South Wales, Australia.,Animal Genetics and Breeding Unit, University of New England, Armidale, New South Wales, Australia
| | - Nasir Moghaddar
- School of Environmental & Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Seung-Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Korea
| | - Julius H J van der Werf
- School of Environmental & Rural Science, University of New England, Armidale, New South Wales, Australia
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Vanvanhossou SFU, Yin T, Scheper C, Fries R, Dossa LH, König S. Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin. Front Genet 2021; 12:657282. [PMID: 34956303 PMCID: PMC8694269 DOI: 10.3389/fgene.2021.657282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.
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Affiliation(s)
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, Freising-Weihenstephan, Germany
| | - Luc Hippolyte Dossa
- School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
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Lu X, Abdalla IM, Nazar M, Fan Y, Zhang Z, Wu X, Xu T, Yang Z. Genome-Wide Association Study on Reproduction-Related Body-Shape Traits of Chinese Holstein Cows. Animals (Basel) 2021; 11:1927. [PMID: 34203505 PMCID: PMC8300307 DOI: 10.3390/ani11071927] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 12/24/2022] Open
Abstract
Reproduction is an important production activity for dairy cows, and their reproductive performance can directly affect the level of farmers' income. To better understand the genomic regions and biological pathways of reproduction-related traits of dairy cows, in the present study, three body shape traits-Loin Strength (LS), Rump Angle (RA), and Pin Width (PW)-were selected as indicators of the reproductive ability of cows, and we conducted genome-wide association analyses on them. The heritability of these three traits was medium, ranging from 0.20 to 0.38. A total of 11 significant single-nucleotide polymorphisms (SNPs) were detected associated with these three traits. Bioinformatics analysis was performed on genes close to the significant SNPs (within 200 Kb) of LS, RA, and PW, and we found that these genes were totally enriched in 20 gene ontology terms and six KEGG signaling pathways. Finally, the five genes CDH12, TARP, PCDH9, DTHD1, and ARAP2 were selected as candidate genes that might affect LS. The six genes LOC781835, FSTL4, ATG4C, SH3BP4, DMP1, and DSPP were selected as candidate genes that might affect RA. The five genes USP6NL, CNTN3, LOC101907665, UPF2, and ECHDC3 were selected as candidate genes that might affect the PW of Chinese Holstein cows. Our results could provide useful biological information for the improvement of body shape traits and contribute to the genomic selection of Chinese Holstein cows.
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Affiliation(s)
- Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Ismail Mohamed Abdalla
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Mudasir Nazar
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Yongliang Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Zhipeng Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Xinyue Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Tianle Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China;
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
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de las Heras-Saldana S, Chung KY, Kim H, Lim D, Gondro C, van der Werf JHJ. Differential Gene Expression in Longissimus Dorsi Muscle of Hanwoo Steers-New Insight in Genes Involved in Marbling Development at Younger Ages. Genes (Basel) 2020; 11:genes11111381. [PMID: 33233382 PMCID: PMC7700136 DOI: 10.3390/genes11111381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/06/2020] [Accepted: 11/19/2020] [Indexed: 12/25/2022] Open
Abstract
The Korean Hanwoo breed possesses a high capacity to accumulate intramuscular fat, which is measured as a marbling score in the beef industry. Unfortunately, the development of marbling is not completely understood and the identification of differentially expressed genes at an early age is required to better understand this trait. In this study, we took muscle samples from 12 Hanwoo steers at the age of 18 and 30 months. From the contrast between age and marbling score, we identified in total 1883 differentially expressed genes (FDR < 0.05 and logarithm fold change ≥ 1.5) with 782 genes up-regulated and 1101 down-regulated. Differences in gene expression were higher between the ages x marbling groups rather than between high and low marbling groups. At 18 months of age, the genes SLC38A4, ABCA10, APOL6, and two novel genes (ENSBTAG00000015330 and ENSBTAG00000046041) were up-regulated in the high marbling group. From the protein–protein interaction network analysis, we identified unique networks when comparing marbling scores between different ages. Nineteen genes (AGT, SERPINE1, ADORA1, FOS, LEP, FOXO1, FOXO3, ADIPOQ, ITGA1, SDC1, SDC4, ITGB3, ITGB4, CXCL10, ACTG2, MX1, EDN1, ACTA2, and ESPL1) were identified to have an important role in marbling development. Further analyses are needed to better understand the role of these genes.
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Affiliation(s)
- Sara de las Heras-Saldana
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia; (H.K.); (C.G.); (J.H.J.v.d.W.)
- Correspondence:
| | - Ki Yong Chung
- Department of Beef Science, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Hyounju Kim
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia; (H.K.); (C.G.); (J.H.J.v.d.W.)
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Korea
| | - Dajeong Lim
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Jeonbuk 55365, Korea;
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia; (H.K.); (C.G.); (J.H.J.v.d.W.)
- College of Agriculture & Resources, Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Julius H. J. van der Werf
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia; (H.K.); (C.G.); (J.H.J.v.d.W.)
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Naserkheil M, Bahrami A, Lee D, Mehrban H. Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle. Animals (Basel) 2020; 10:ani10101836. [PMID: 33050182 PMCID: PMC7601430 DOI: 10.3390/ani10101836] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Hanwoo is an indigenous cattle breed in Korea and popular for meat production owing to its rapid growth and high-quality meat. Its yearling weight and carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score) are economically important for the selection of young and proven bulls. In recent decades, the advent of high throughput genotyping technologies has made it possible to perform genome-wide association studies (GWAS) for the detection of genomic regions associated with traits of economic interest in different species. In this study, we conducted a weighted single-step genome-wide association study which combines all genotypes, phenotypes and pedigree data in one step (ssGBLUP). It allows for the use of all SNPs simultaneously along with all phenotypes from genotyped and ungenotyped animals. Our results revealed 33 relevant genomic regions related to the traits of interest. Gene set enrichment analysis indicated that the identified candidate genes were related to biological processes and functional terms that were involved in growth and lipid metabolism. In conclusion, these results suggest that the incorporation of GWAS results and network analysis can help us to better understand the genetic bases underlying growth and carcass traits. Abstract In recent years, studies on the biological mechanisms underlying complex traits have been facilitated by innovations in high-throughput genotyping technology. We conducted a weighted single-step genome-wide association study (WssGWAS) to evaluate backfat thickness, carcass weight, eye muscle area, marbling score, and yearling weight in a cohort of 1540 Hanwoo beef cattle using BovineSNP50 BeadChip. The WssGWAS uncovered thirty-three genomic regions that explained more than 1% of the additive genetic variance, mostly located on chromosomes 6 and 14. Among the identified window regions, seven quantitative trait loci (QTL) had pleiotropic effects and twenty-six QTL were trait-specific. Significant pathways implicated in the measured traits through Gene Ontology (GO) term enrichment analysis included the following: lipid biosynthetic process, regulation of lipid metabolic process, transport or localization of lipid, regulation of growth, developmental growth, and multicellular organism growth. Integration of GWAS results of the studied traits with pathway and network analyses facilitated the exploration of the respective candidate genes involved in several biological functions, particularly lipid and growth metabolism. This study provides novel insight into the genetic bases underlying complex traits and could be useful in developing breeding schemes aimed at improving growth and carcass traits in Hanwoo beef cattle.
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Affiliation(s)
- Masoumeh Naserkheil
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (M.N.); (A.B.)
| | - Abolfazl Bahrami
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (M.N.); (A.B.)
| | - Deukhwan Lee
- Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do 17579, Korea
- Correspondence: ; Tel.: +82-31-670-5091
| | - Hossein Mehrban
- Department of Animal Science, Shahrekord University, Shahrekord 88186-34141, Iran;
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de Las Heras-Saldana S, Lopez BI, Moghaddar N, Park W, Park JE, Chung KY, Lim D, Lee SH, Shin D, van der Werf JHJ. Use of gene expression and whole-genome sequence information to improve the accuracy of genomic prediction for carcass traits in Hanwoo cattle. Genet Sel Evol 2020; 52:54. [PMID: 32993481 PMCID: PMC7525992 DOI: 10.1186/s12711-020-00574-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022] Open
Abstract
Background In this study, we assessed the accuracy of genomic prediction for carcass weight (CWT), marbling score (MS), eye muscle area (EMA) and back fat thickness (BFT) in Hanwoo cattle when using genomic best linear unbiased prediction (GBLUP), weighted GBLUP (wGBLUP), and a BayesR model. For these models, we investigated the potential gain from using pre-selected single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) on imputed sequence data and from gene expression information. We used data on 13,717 animals with carcass phenotypes and imputed sequence genotypes that were split in an independent GWAS discovery set of varying size and a remaining set for validation of prediction. Expression data were used from a Hanwoo gene expression experiment based on 45 animals. Results Using a larger number of animals in the reference set increased the accuracy of genomic prediction whereas a larger independent GWAS discovery dataset improved identification of predictive SNPs. Using pre-selected SNPs from GWAS in GBLUP improved accuracy of prediction by 0.02 for EMA and up to 0.05 for BFT, CWT, and MS, compared to a 50 k standard SNP array that gave accuracies of 0.50, 0.47, 0.58, and 0.47, respectively. Accuracy of prediction of BFT and CWT increased when BayesR was applied with the 50 k SNP array (0.02 and 0.03, respectively) and was further improved by combining the 50 k array with the top-SNPs (0.06 and 0.04, respectively). By contrast, using BayesR resulted in limited improvement for EMA and MS. wGBLUP did not improve accuracy but increased prediction bias. Based on the RNA-seq experiment, we identified informative expression quantitative trait loci, which, when used in GBLUP, improved the accuracy of prediction slightly, i.e. between 0.01 and 0.02. SNPs that were located in genes, the expression of which was associated with differences in trait phenotype, did not contribute to a higher prediction accuracy. Conclusions Our results show that, in Hanwoo beef cattle, when SNPs are pre-selected from GWAS on imputed sequence data, the accuracy of prediction improves only slightly whereas the contribution of SNPs that are selected based on gene expression is not significant. The benefit of statistical models to prioritize selected SNPs for estimating genomic breeding values is trait-specific and depends on the genetic architecture of each trait.
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Affiliation(s)
| | - Bryan Irvine Lopez
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Nasir Moghaddar
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Ki Y Chung
- Department of Beef Science, Korea National College of Agriculture and Fisheries, Jeonju, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
| | - Seung H Lee
- Division of Animal and Dairy Science, Chungnam National University, Deajeon, 34148, Republic of Korea
| | - Donghyun Shin
- The Animal Molecular Genetics and Breeding Centre, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Julius H J van der Werf
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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Edea Z, Jung KS, Shin SS, Yoo SW, Choi JW, Kim KS. Signatures of positive selection underlying beef production traits in Korean cattle breeds. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:293-305. [PMID: 32568261 PMCID: PMC7288235 DOI: 10.5187/jast.2020.62.3.293] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/04/2020] [Accepted: 03/15/2020] [Indexed: 01/01/2023]
Abstract
The difference in the breeding programs and population history may have diversely
shaped the genomes of Korean native cattle breeds. In the absence of phenotypic
data, comparisons of breeds that have been subjected to different selective
pressures can aid to identify genomic regions and genes controlling qualitative
and complex traits. In this study to decipher genetic variation and identify
evidence of divergent selection, 3 Korean cattle breeds were genotyped using the
recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array.
The three Korean cattle breeds clustered according to their coat color
phenotypes and breeding programs. The Heugu breed reliably showed smaller
effective population size at all generations considered. Across the autosomal
chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and
Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the
two pairwise comparisons. The most important signals of selection were detected
on bovine chromosomes 14 (24.39–25.13 Mb) and 18 (13.34–15.07 Mb),
containing genes related to body size, and coat color (XKR4,
LYN, PLAG1, SDR16C5,
TMEM68, CDH15, MC1R, and
GALNS). Some of the candidate genes are also associated
with meat quality traits (ACSF3, EIF2B1,
BANP, APCDD1, and GALM)
and harbor quantitative trait locus (QTL) for beef production traits. Further
functional analysis revealed that the candidate genes (DBI,
ACSF3, HINT2, GBA2,
AGPAT5, SCAP, ELP6,
APOB, and RBL1) were involved in gene
ontology (GO) terms relevant to meat quality including fatty acid oxidation,
biosynthesis, and lipid storage. Candidate genes previously known to affect beef
production and quality traits could be used in the beef cattle selection
strategies.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Kyoung Sub Jung
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Sung-Sub Shin
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Song-Won Yoo
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Jae Won Choi
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
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Haplotype-Based Genome-Wide Association Study and Identification of Candidate Genes Associated with Carcass Traits in Hanwoo Cattle. Genes (Basel) 2020; 11:genes11050551. [PMID: 32423003 PMCID: PMC7290854 DOI: 10.3390/genes11050551] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/20/2022] Open
Abstract
Hanwoo, is the most popular native beef cattle in South Korea. Due to its extensive popularity, research is ongoing to enhance its carcass quality and marbling traits. In this study we conducted a haplotype-based genome-wide association study (GWAS) by constructing haplotype blocks by three methods: number of single nucleotide polymorphisms (SNPs) in a haplotype block (nsnp), length of genomic region in kb (Len) and linkage disequilibrium (LD). Significant haplotype blocks and genes associated with them were identified for carcass traits such as BFT (back fat thickness), EMA (eye Muscle area), CWT (carcass weight) and MS (marbling score). Gene-set enrichment analysis and functional annotation of genes in the significantly-associated loci revealed candidate genes, including PLCB1 and PLCB4 present on BTA13, coding for phospholipases, which might be important candidates for increasing fat deposition due to their role in lipid metabolism and adipogenesis. CEL (carboxyl ester lipase), a bile-salt activated lipase, responsible for lipid catabolic process was also identified within the significantly-associated haplotype block on BTA11. The results were validated in a different Hanwoo population. The genes and pathways identified in this study may serve as good candidates for improving carcass traits in Hanwoo cattle.
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Mastrangelo S, Ben Jemaa S, Ciani E, Sottile G, Moscarelli A, Boussaha M, Montedoro M, Pilla F, Cassandro M. Genome-wide detection of signatures of selection in three Valdostana cattle populations. J Anim Breed Genet 2020; 137:609-621. [PMID: 32219904 DOI: 10.1111/jbg.12476] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/28/2020] [Accepted: 03/08/2020] [Indexed: 12/15/2022]
Abstract
The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (FST ) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least two approaches in VPR, VPN and VCA, respectively. Most of these candidate regions were population-specific but we found one common genomic region spanning 2.38 Mb on BTA06 which either overlaps or is located close to runs of homozygosity islands detected in the three populations. This region included inter alia two well-known genes: KDR, a well-established coat colour gene, and CLOCK, which plays a central role in positive regulation of inflammatory response and in the regulation of the mammalian circadian rhythm. The other candidate regions identified harboured genes associated mainly with milk and meat traits as well as genes involved in immune response/inflammation or associated with behavioural traits. This last category of genes was mainly identified in VCA, which is selected for fighting ability. Overall, our results provide, for the first time, a glimpse into regions of the genome targeted by selection in Valdostana cattle. Finally, this study illustrates the relevance of using multiple complementary approaches to identify genomic regions putatively under selection in livestock.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, Bari, Italy
| | - Gianluca Sottile
- Dipartimento Scienze Economiche, Aziendali e Statistiche, University of Palermo, Palermo, Italy
| | - Angelo Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Mekki Boussaha
- INRAE, AgroParisTech, GABI, Université Paris Saclay, Jouy-en-Josas, France
| | - Marina Montedoro
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Rivolta d'Adda, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, Legnaro, Italy
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Srikanth K, Lee SH, Chung KY, Park JE, Jang GW, Park MR, Kim NY, Kim TH, Chai HH, Park WC, Lim D. A Gene-Set Enrichment and Protein-Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle. Genes (Basel) 2020; 11:E316. [PMID: 32188084 PMCID: PMC7140899 DOI: 10.3390/genes11030316] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10-7) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein-protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Seung-Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea;
| | - Ki-Yong Chung
- Department of Beef Science, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Gul-Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Mi-Rim Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Na Yeon Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Won Cheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
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Strillacci MG, Gorla E, Cozzi MC, Vevey M, Genova F, Scienski K, Longeri M, Bagnato A. A copy number variant scan in the autochthonous Valdostana Red Pied cattle breed and comparison with specialized dairy populations. PLoS One 2018; 13:e0204669. [PMID: 30261013 PMCID: PMC6160104 DOI: 10.1371/journal.pone.0204669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/12/2018] [Indexed: 11/24/2022] Open
Abstract
Copy number variants (CNVs) are an important source of genomic structural variation, recognized to influence phenotypic variation in many species. Many studies have focused on identifying CNVs within and between human and livestock populations alike, but only few have explored population-genetic properties in cattle based on CNVs derived from a high-density SNP array. We report a high-resolution CNV scan using Illumina’s 777k BovineHD Beadchip for Valdostana Red Pied (VRP), an autochthonous Italian dual-purpose cattle population reared in the Alps that did not undergo strong selection for production traits. After stringent quality control and filtering, CNVs were called across 108 bulls using the PennCNV software. A total of 6,784 CNVs were identified, summarized to 1,723 CNV regions (CNVRs) on 29 autosomes covering a total of ~59 Mb of the UMD3.1 assembly. Among the mapped CNVRs, there were 812 losses, 832 gains and 79 complexes. We subsequently performed a comparison of CNVs detected in the VRP and those available from published studies in the Italian Brown Swiss (IBS) and Mexican Holstein (HOL). A total of 171 CNVRs were common to all three breeds. Between VRP and IBS, 474 regions overlapped, while only 313 overlapped between VRP and HOL, indicating a more similar genetic background among populations with common origins, i.e. the Alps. The principal component, clustering and admixture analyses showed a clear separation of the three breeds into three distinct clusters. In order to describe the distribution of CNVs within and among breeds we used the pair VST statistic, considering only the CNVRs shared to more than 5 individuals (within breed). We identified unique and highly differentiated CNVs (n = 33), some of which could be due to specific breed selection and adaptation. Genes and QTL within these regions were characterized.
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Affiliation(s)
| | - Erica Gorla
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | | | - Mario Vevey
- Associazione Nazionale Allevatori Bovini Di Razza Valdostana, Gressan, Aosta, Italy
| | - Francesca Genova
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Kathy Scienski
- Department of Animal Science, Texas A&M University, College Station, Texas, United States of America
| | - Maria Longeri
- Department of Veterinary Medicine, University of Milan, Milan, Italy
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Edea Z, Jeoung YH, Shin SS, Ku J, Seo S, Kim IH, Kim SW, Kim KS. Genome-wide association study of carcass weight in commercial Hanwoo cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 31:327-334. [PMID: 29103288 PMCID: PMC5838337 DOI: 10.5713/ajas.17.0276] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/12/2017] [Accepted: 10/22/2017] [Indexed: 12/25/2022]
Abstract
Objective The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed. Methods Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler BeadChip. After applying the quality control of criteria of a call rate ≥90% and minor allele frequency (MAF) ≥0.01, a total of 15,235 autosomal SNPs were left for genome-wide association (GWA) analysis. The GWA tests were performed using single-locus mixed linear model. Age at slaughter was fitted as fixed effect and sire included as a covariate. The level of genome-wide significance was set at 3.28×10−6 (0.05/15,235), corresponding to Bonferroni correction for 15,235 multiple independent tests. Results By employing EMMAX approach which is based on a mixed linear model and accounts for population stratification and relatedness, we identified 17 and 16 loci significantly (p<0.001) associated with carcass weight for the additive and dominant models, respectively. The second most significant (p = 0.000049) SNP (ARS-BFGL-NGS-28234) on bovine chromosome 4 (BTA4) at 21 Mb had an allele substitution effect of 43.45 kg. Some of the identified regions on BTA2, 6, 14, 22, and 24 were previously reported to be associated with quantitative trait loci for carcass weight in several beef cattle breeds. Conclusion This is the first genome-wide association study using SNP chips on commercial Hanwoo steers, and some of the loci newly identified in this study may help to better DNA markers that determine increased beef production in commercial Hanwoo cattle. Further studies using a larger sample size will allow confirmation of the candidates identified in this study.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | | | - Sung-Sub Shin
- Korea Institute for Animal products Quality Evaluation, Sejong 30100, Korea
| | - Jaeul Ku
- Biomedical Research Center, Turbosoft Inc. Cheongju 28161, Korea
| | - Sungbo Seo
- Biomedical Research Center, Turbosoft Inc. Cheongju 28161, Korea
| | - Il-Hoi Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Sang-Wook Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
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Lee SH, Park BH, Sharma A, Dang CG, Lee SS, Choi TJ, Choy YH, Kim HC, Jeon KJ, Kim SD, Yeon SH, Park SB, Kang HS. Hanwoo cattle: origin, domestication, breeding strategies and genomic selection. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2014; 56:2. [PMID: 26290691 PMCID: PMC4534185 DOI: 10.1186/2055-0391-56-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 04/07/2014] [Indexed: 11/10/2022]
Abstract
Hanwoo (Korean cattle) is the native, taurine type of cattle breed of Korea and its history as a draft animal dates back to 5000 Years. In earlier times Hanwoo was used extensively for farming, transportation. Over the period of time, Hanwoo has changed to be meat type cattle. Full-scale production of Hanwoo as meat-type cattle has occurred since 1960s with the rapid growth of the Korean economy. Hanwoo is one of the most economically important species in Korea as it is a significant source of nutrition to the Korean people. Hanwoo beef is the most cherished food of Korea. One of the main goals of researchers is to increase the meat quality, quantity and taste of the beef. In this review we describe the origin, domestication of Hanwoo cattle and breeding program initiated from 1980's. Moreover the advent of technological advancement had provided us a platform to perform genome wide selection on economic traits and its implementation into traditional breeding programs.
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Affiliation(s)
- Seung-Hwan Lee
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeong-Chang, 232-950 Korea
| | - Byoung-Ho Park
- Animal Genetic and Breeding Division, National Institute of Animal Science, Cheon-An, Korea
| | - Aditi Sharma
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeong-Chang, 232-950 Korea
| | - Chang-Gwon Dang
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeong-Chang, 232-950 Korea
| | - Seung-Soo Lee
- Animal Genetic and Breeding Division, National Institute of Animal Science, Cheon-An, Korea
| | - Tae-Jeong Choi
- Animal Genetic and Breeding Division, National Institute of Animal Science, Cheon-An, Korea
| | - Yeon-Ho Choy
- Animal Genetic and Breeding Division, National Institute of Animal Science, Cheon-An, Korea
| | - Hyeong-Cheol Kim
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeong-Chang, 232-950 Korea
| | - Ki-Jun Jeon
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeong-Chang, 232-950 Korea
| | - Si-Dong Kim
- Animal Genetic and Breeding Division, National Institute of Animal Science, Cheon-An, Korea
| | - Seong-Heum Yeon
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeong-Chang, 232-950 Korea
| | - Soo-Bong Park
- Animal Genetic and Breeding Division, National Institute of Animal Science, Cheon-An, Korea
| | - Hee-Seol Kang
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeong-Chang, 232-950 Korea
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Lee SH, Lim D, Jang GW, Cho YM, Choi BH, Kim SD, Oh SJ, Lee JH, Yoon D, Park EW, Lee HK, Hong SK, Yang BS. Genome Wide Association Study to Identity QTL for Growth Taits in Hanwoo. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2012. [DOI: 10.5187/jast.2012.54.5.323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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