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Sölzer N, Brügemann K, Yin T, König S. Genetic evaluations and genome-wide association studies for specific digital dermatitis diagnoses in dairy cows considering genotype × housing system interactions. J Dairy Sci 2024; 107:3724-3737. [PMID: 38216046 DOI: 10.3168/jds.2023-24207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024]
Abstract
The present study aimed to use detailed phenotyping for the claw disorder digital dermatitis (DD) considering specific DD stages in 2 housing systems (conventional cubicle barns [CON] and compost-bedded pack barns [CBPB]) to infer possible genotype × housing system interactions. The DD stages included 2,980 observations for the 3 traits DD-sick, DD-acute, and DD-chronic from 1,311 Holstein-Friesian and 399 Fleckvieh-Simmental cows. Selection of the 5 CBPB and 5 CON herds was based on a specific protocol to achieve a high level of herd similarity with regard to climate, feeding, milking system, and location, but with pronounced housing-system differences. Five other farms had a "mixed system" with 2 subherds, one representing CBPB and the other one CON. The CBPB system was represented by 899 cows (1,530 observations), and 811 cows (1,450 observations) represented the CON system. The average disease prevalence was 20.47% for DD-sick, 13.88% for DD-acute, and 5.34% for DD-chronic, with a higher prevalence in CON than in CBPB. After quality control of 50K genotypes, 38,495 SNPs from 926 cows remained for the ongoing genomic analyses. Genetic parameters for DD-sick, DD-acute, and DD-chronic were estimated by applying single-step approaches for single-trait repeatability animal models considering the whole dataset, and separately for the CON and CBPB subsets. Genetic correlations between same DD traits from different housing systems, and between DD-sick, DD-chronic, and DD-acute, were estimated via bivariate animal models. Heritabilities based on the whole dataset were 0.16 for DD-sick, 0.14 for DD-acute, and 0.11 for DD-chronic. A slight increase of heritabilities and genetic variances was observed in CON compared with the "well-being" CBPB system, indicating a stronger genetic differentiation of diseases in a more challenging environment. Genetic correlations between same DD traits recorded in CON or CBPB were close to 0.80, disproving obvious genotype × housing system interactions. Genetic correlations among DD-sick, DD-acute and DD-chronic ranged from 0.58 to 0.81. SNP main effects and SNP × housing system interaction effects were estimated simultaneously via GWAS, considering only the phenotypes from genotyped cows. Ongoing annotations of potential candidate genes focused on chromosomal segments 100 kb upstream and downstream from the significantly associated candidate SNP. GWAS for main effects indicated heterogeneous Manhattan plots especially for DD-acute and DD-chronic, indicating particularities in disease pathogenesis. Nevertheless, a few shared annotated potential candidate genes, that is, METTL25, AFF3, PRKG1, and TENM4 for DD-sick and DD-acute, were identified. These genes have direct or indirect effects on disease resistance or immunology. For the SNP × housing system interaction, the annotated genes ASXL1 and NOL4L on BTA 13 were relevant for DD-sick and DD-acute. Overall, the very similar genetic parameters for the same traits in different environments and negligible genotype × housing system interactions indicate only minor effects on genetic evaluations for DD due to housing-system particularities.
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Affiliation(s)
- Niklas Sölzer
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany.
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Prakapenka D, Liang Z, Zaabza HB, VanRaden PM, Van Tassell CP, Da Y. Large-Sample Genome-Wide Association Study of Resistance to Retained Placenta in U.S. Holstein Cows. Int J Mol Sci 2024; 25:5551. [PMID: 38791589 PMCID: PMC11122073 DOI: 10.3390/ijms25105551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/18/2024] [Accepted: 05/18/2024] [Indexed: 05/26/2024] Open
Abstract
A genome-wide association study of resistance to retained placenta (RETP) using 632,212 Holstein cows and 74,747 SNPs identified 200 additive effects with p-values < 10-8 on thirteen chromosomes but no dominance effect was statistically significant. The regions of 87.61-88.74 Mb of Chr09 about 1.13 Mb in size had the most significant effect in LOC112448080 and other highly significant effects in CCDC170 and ESR1, and in or near RMND1 and AKAP12. Four non-ESR1 genes in this region were reported to be involved in ESR1 fusions in humans. Chr23 had the largest number of significant effects that peaked in SLC17A1, which was involved in urate metabolism and transport that could contribute to kidney disease. The PKHD1 gene contained seven significant effects and was downstream of another six significant effects. The ACOT13 gene also had a highly significant effect. Both PKHD1 and ACOT13 were associated with kidney disease. Another highly significant effect was upstream of BOLA-DQA2. The KITLG gene of Chr05 that acts in utero in germ cell and neural cell development, and hematopoiesis was upstream of a highly significant effect, contained a significant effect, and was between another two significant effects. The results of this study provided a new understanding of genetic factors underlying RETP in U.S. Holstein cows.
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Affiliation(s)
- Dzianis Prakapenka
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Zuoxiang Liang
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Hafedh B. Zaabza
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Paul M. VanRaden
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Yang Da
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
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3
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Sanchez L, Campos-Chillon F, Sargolzaei M, Peterson DG, Sprayberry KA, McArthur G, Anderson P, Golden B, Pokharel S, Abo-Ismail MK. Molecular Mechanisms Associated with the Development of the Metritis Complex in Dairy Cattle. Genes (Basel) 2024; 15:439. [PMID: 38674374 PMCID: PMC11049392 DOI: 10.3390/genes15040439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/21/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
The metritis complex (MC), a group of post-partum uterine diseases, is associated with increased treatment costs and reduced milk yield and fertility. The goal of this study was to identify genetic variants, genes, or genomic regions that modulate MC disease. A genome-wide association study was performed using a single-locus mixed linear model of 1967 genotypes (624,460 SNPs) and metritis complex records. Then, in-silico functional analyses were performed to detect biological mechanisms and pathways associated with the development of MC. The ATP8A2, COX16, AMN, and TRAF3 genes, located on chromosomes 12, 10, and 21, were associated with MC at p ≤ 0.0001. These genes are involved in the regulation of cholesterol metabolism in the stromal tissue of the uterus, which can be directly associated with the mode of transmission for pathogens causing the metritis complex. The modulation of cholesterol abundance alters the efficiency of virulence factors and may affect the susceptibility of the host to infection. The SIPA1L1, DEPDC5, and RNF122 genes were also significantly associated with MC at p ≤ 0.0001 and are involved in the PI3k-Akt pathway, responsible for activating the autophagic processes. Thus, the dysregulation of these genes allows for unhindered bacterial invasion, replication, and survival within the endometrium.
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Affiliation(s)
- Leanna Sanchez
- Department of Animal Science, California Polytechnic State University, 1 Grand Ave., San Luis Obispo, CA 93407, USA; (L.S.); (F.C.-C.); (D.G.P.); (K.A.S.); (S.P.)
| | - Fernando Campos-Chillon
- Department of Animal Science, California Polytechnic State University, 1 Grand Ave., San Luis Obispo, CA 93407, USA; (L.S.); (F.C.-C.); (D.G.P.); (K.A.S.); (S.P.)
| | - Mehdi Sargolzaei
- Select Sires Inc., 11740 US-42, Plain City, OH 43064, USA;
- Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Daniel G. Peterson
- Department of Animal Science, California Polytechnic State University, 1 Grand Ave., San Luis Obispo, CA 93407, USA; (L.S.); (F.C.-C.); (D.G.P.); (K.A.S.); (S.P.)
| | - Kim A. Sprayberry
- Department of Animal Science, California Polytechnic State University, 1 Grand Ave., San Luis Obispo, CA 93407, USA; (L.S.); (F.C.-C.); (D.G.P.); (K.A.S.); (S.P.)
| | - Garry McArthur
- Swinging Udders Veterinary Services, 8418 Liberty Rd, Galt, CA 95632, USA;
| | - Paul Anderson
- Department of Computer Science and Software Engineering, California Polytechnic State University, 1 Grand Ave., San Luis Obispo, CA 93407, USA;
| | | | - Siroj Pokharel
- Department of Animal Science, California Polytechnic State University, 1 Grand Ave., San Luis Obispo, CA 93407, USA; (L.S.); (F.C.-C.); (D.G.P.); (K.A.S.); (S.P.)
| | - Mohammed K. Abo-Ismail
- Department of Animal Science, California Polytechnic State University, 1 Grand Ave., San Luis Obispo, CA 93407, USA; (L.S.); (F.C.-C.); (D.G.P.); (K.A.S.); (S.P.)
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El-Sayed A, Refaai M, Ateya A. Doppler ultrasonographic scan, gene expression and serum profile of immune, APPs and antioxidant markers in Egyptian buffalo-cows with clinical endometritis. Sci Rep 2024; 14:5698. [PMID: 38459095 PMCID: PMC10923904 DOI: 10.1038/s41598-024-56258-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/04/2024] [Indexed: 03/10/2024] Open
Abstract
The objective of this study was to elaborate Doppler ultrasonographic scan, genetic resistance and serum profile of markers associated with endometritis susceptibility in Egyptian buffalo-cows. The enrolled animals were designed as; twenty five apparently healthy buffalo-cows considered as a control group and twenty five infected buffalo with endometritis. There were significant (p < 0.05) increased of cervical diameter, endometrium thickness, uterine horn diameter, TAMEAN, TAMAX and blood flow through middle uterine artery with significant decrease of PI and RI values in endometritis buffalo-cows. Gene expression levels were considerably higher in endometritis-affected buffaloes than in resistant ones for the genes A2M, ADAMTS20, KCNT2, MAP3K4, MAPK14, FKBP5, FCAMR, TLR2, IRAK3, CCl2, EPHA4, and iNOS. The RXFP1, NDUFS5, TGF-β, SOD3, CAT, and GPX genes were expressed at substantially lower levels in endometritis-affected buffaloes. The PCR-DNA sequence verdicts of healthy and affected buffaloes revealed differences in the SNPs in the amplified DNA bases related to endometritis for the investigated genes. However, MAP3K4 elicited a monomorphic pattern. There was a significant decrease of red blood cells (RBCs) count, Hb and packed cell volume (PCV) with neutrophilia, lymphocytosis and monocytosis in endometritis group compared with healthy ones. The serum levels of Hp, SAA, Cp, IL-6, IL-10, TNF-α, NO and MDA were significantly (P˂0.05) increased, along with reduction of CAT, GPx, SOD and TAC in buffalo-cows with endometritis compared to healthy ones. The variability of Doppler ultrasonographic scan and studied genes alongside alterations in the serum profile of investigated markers could be a reference guide for limiting buffalo endometritis through selective breeding of natural resistant animals.
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Affiliation(s)
- Ahmed El-Sayed
- Department of Animal Health and Poultry, Animal and Poultry Production Division, Desert Research Center (DRC), Cairo, Egypt
| | - Mohamed Refaai
- Diagnostic Imaging and Endoscopy Unit, Agriculture Research Centre, Animal Reproduction Research Institute, Giza, Egypt
| | - Ahmed Ateya
- Department of Development of Animal Wealth, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.
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Cesarani A, Corte Pause F, Hidalgo J, Garcia A, Degano L, Vicario D, Macciota NPP, Stradaioli G. Genetic background of semen parameters in Italian Simmental bulls. ITALIAN JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.1080/1828051x.2022.2160665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Francesca Corte Pause
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Jorge Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Andre Garcia
- Angus Genetics Inc. - American Angus Association, Saint Joseph, MO, USA
| | - Lorenzo Degano
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | - Daniele Vicario
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | | | - Giuseppe Stradaioli
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
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Dos Santos EC, Boyer A, St-Jean G, Jakuc N, Gévry N, Price CA, Zamberlam G. Is the Hippo Pathway Effector Yes-Associated Protein a Potential Key Player of Dairy Cattle Cystic Ovarian Disease Pathogenesis? Animals (Basel) 2023; 13:2851. [PMID: 37760251 PMCID: PMC10525513 DOI: 10.3390/ani13182851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Cystic ovarian disease (COD) in dairy cattle is characterized by preovulatory follicles that become cysts, fail to ovulate and persist in the ovary; consequently, interfering with normal ovarian cyclicity. The intraovarian key players that orchestrate the alterations occurring in the preovulatory follicle and that culminate with cyst formation and persistence, however, remain uncertain. Interestingly, the Hippo pathway effector yes-associated protein (YAP) has been described in humans and mice as a key player of anovulatory cystic disorders. To start elucidating if YAP deregulation in ovarian follicle cells can be also involved in the pathogenesis of COD, we have generated a series of novel results using spontaneously occurring cystic follicles in cattle. We found that mRNA and protein levels of YAP are significantly higher in granulosa (GCs) and theca cells (TCs) isolated from cystic follicles (follicular structures of at least 20 mm in diameter) in comparison to respective cell types isolated from non-cystic large follicles (≥12 mm). In addition, immunohistochemistry and Western blot analyses used to determine YAP phosphorylation pattern suggest that YAP transcriptional activity is augmented is cystic GCs. These results were confirmed by a significant increase in the mRNA levels encoding for the classic YAP-TEAD transcriptional target genes CTGF, BIRC5 and ANKRD1 in GCs from follicle cysts in comparison to non-cystic large follicles. Taken together, these results provide considerable insight of a completely novel signaling pathway that seems to play an important role in ovarian cystic disease pathogenesis in dairy cattle.
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Affiliation(s)
- Esdras Corrêa Dos Santos
- Centre de Recherche en Reproduction et Fertilité (CRRF), Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
- Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
| | - Alexandre Boyer
- Centre de Recherche en Reproduction et Fertilité (CRRF), Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
- Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
| | - Guillaume St-Jean
- Centre de Recherche en Reproduction et Fertilité (CRRF), Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
| | - Natalia Jakuc
- Centre de Recherche en Reproduction et Fertilité (CRRF), Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
- Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
| | - Nicolas Gévry
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC J1K 0A5, Canada
| | - Christopher A. Price
- Centre de Recherche en Reproduction et Fertilité (CRRF), Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
- Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
| | - Gustavo Zamberlam
- Centre de Recherche en Reproduction et Fertilité (CRRF), Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
- Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire (FMV), Université de Montréal (UdeM), Saint-Hyacinthe, QC J2S 7C6, Canada
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de Souza TC, Pinto LFB, da Cruz VAR, de Oliveira HR, Pedrosa VB, Oliveira GA, Miglior F, Schenkel FS, Brito LF. A comprehensive characterization of longevity and culling reasons in Canadian Holstein cattle based on various systematic factors. Transl Anim Sci 2023; 7:txad102. [PMID: 37841322 PMCID: PMC10576516 DOI: 10.1093/tas/txad102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/25/2023] [Indexed: 10/17/2023] Open
Abstract
The decision of premature culling cows directly impacts the profitability of dairy farms. A comprehensive characterization of the primary causes of culling reasons would greatly improve both management and selection objectives in dairy cattle breeding programs. Therefore, this study aimed to analyze the temporal frequencies of 34 culling reasons in Canadian Holstein cows. After data editing and quality control, records from 3,096,872 cows culled from 9,683 herds spread across Canada were used for the analyses covering the periods from 1996 to 2020. Reproductive issues were the main culling reason accounting for 23.02%, followed by milk production (20.82%), health (20.39%), conformation problems (13.69%), economic factors (13.10%), accidents (5.67%), age-related causes (1.67%), and workability (1.63%). Nearly fifty-eight percent of cows were culled after 47 months of age. The observed frequencies of culling due to economic factors were lower than expected from 1996 to 2014 and higher than expected between 2015 and 2020. Reproduction issues had the highest culling frequencies during fall (24.54%), winter (24.02%), and spring (22.51%), while health issues were the most frequent (22.51%) culling reason in the summer season. Health issues (25.50%) and milk production (27.71%) were the most frequent culling reasons in the provinces of Quebec and Ontario, respectively. Reproductive issues showed the highest frequency across climates based on the Köppen climate classification, except for Csb (Dry-summer subtropical or Mediterranean climate) and Bsk (Middle latitude steppe climate), which correspond to small regions in Canada, where production was the most frequent culling reason (29.42% and 21.56%, respectively). Reproductive and milk performance issues were the two main culling reasons in most ecozones, except in Boreal Shield and Atlantic Marine, where health issues had the highest frequencies (25.12 and 23.75%, respectively). These results will contribute to improving management practices and selective decisions to reduce involuntary culling of Holstein cows.
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Affiliation(s)
- Taiana Cortez de Souza
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Hinayah Rojas de Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | - Gerson A Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
- Lactanet Canada, Guelph, ON, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
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Sun T, Pei S, Liu Y, Hanif Q, Xu H, Chen N, Lei C, Yue X. Whole genome sequencing of simmental cattle for SNP and CNV discovery. BMC Genomics 2023; 24:179. [PMID: 37020271 PMCID: PMC10077681 DOI: 10.1186/s12864-023-09248-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUD The single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity. RESULTS In this study, we performed a comprehensive analysis to explore the genetic variations (SNPs and CNVs) of high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls using the high-coverage (25×) short-read next generation sequencing and single-molecule long reads sequencing data. A total of ~ 15 million SNPs and 2,944 CNV regions (CNVRs) were detected in Simmental bulls, and a set of positive selected genes (PSGs) and CNVRs were found to be overlapped with quantitative trait loci (QTLs) involving immunity, muscle development, reproduction, etc. In addition, we detected two new variants in LEPR, which may be related to the artificial breeding to improve important economic traits. Moreover, a set of genes and pathways functionally related to male fertility were identified. Remarkably, a CNV on SPAG16 (chr2:101,427,468 - 101,429,883) was completely deleted in all poor sperm motility (PSM) bulls and half of the bulls in high sperm motility (HSM), which may play a crucial role in the bull-fertility. CONCLUSIONS In conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.
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Affiliation(s)
- Ting Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Shengwei Pei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Yangkai Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Haiyue Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China.
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van Staaveren N, Hyland E, Houlahan K, Lynch C, Miglior F, Kelton DF, Schenkel FS, Baes CF. Recording of calf diseases for potential use in breeding programs: a case study on calf respiratory illness and diarrhea. CANADIAN JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.1139/cjas-2022-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Calf diseases remain a challenge for dairy producers from both an economic and welfare perspective. Genetically selecting for disease resistance in calves is a promising approach that could contribute to sustainable dairy farming. Genetic evaluations, however, require well-defined and consistently recorded phenotypes to be successful. Therefore, this study aimed to understand the current state of calf disease recording on Ontario farms. Calf disease records of respiratory illness and diarrhea were available from the national milk recording organization (Lactanet Canada, Guelph, Ontario, Canada) from 2009 to 2020. A case study was conducted to describe calf disease diagnoses and recording practices by surveying a subset of 13 Ontario dairy producers. The percentage of milk recorded farms that recorded calf respiratory illness and calf diarrhea increased from 2.6% in 2009 to 11.1% in 2020. Potential sources of data loss were identified along the information chain from farm to genetic evaluation database. Clear definitions and thresholds to diagnose calf disease, standard operating procedures for data recording, as well as a data transfer pipeline, which includes exchange formats, are needed to facilitate the inclusion of calf health traits in genetic evaluations.
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Falchi L, Cesarani A, Mastrangelo S, Senczuk G, Portolano B, Pilla F, Macciotta NPP. Analysis of runs of homozygosity of cattle living in different climate zones. J Anim Sci 2023; 101:skad061. [PMID: 36802370 PMCID: PMC10066727 DOI: 10.1093/jas/skad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.
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Affiliation(s)
- Laura Falchi
- Dipartimento di Agraria, University of Sassari, 07100 Sassari, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, 07100 Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, 30602 Athens, USA
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
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11
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Wang A, Brito LF, Zhang H, Shi R, Zhu L, Liu D, Guo G, Wang Y. Exploring milk loss and variability during environmental perturbations across lactation stages as resilience indicators in Holstein cattle. Front Genet 2022; 13:1031557. [PMID: 36531242 PMCID: PMC9757536 DOI: 10.3389/fgene.2022.1031557] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/14/2022] [Indexed: 09/12/2023] Open
Abstract
Genetic selection for resilience is essential to improve the long-term sustainability of the dairy cattle industry, especially the ability of cows to maintain their level of production when exposed to environmental disturbances. Recording of daily milk yield provides an opportunity to develop resilience indicators based on milk losses and fluctuations in daily milk yield caused by environmental disturbances. In this context, our study aimed to explore milk loss traits and measures of variability in daily milk yield, including log-transformed standard deviation of milk deviations (Lnsd), lag-1 autocorrelation (Ra), and skewness of the deviations (Ske), as indicators of general resilience in dairy cows. The unperturbed dynamics of milk yield as well as milk loss were predicted using an iterative procedure of lactation curve modeling. Milk fluctuations were defined as a period of at least 10 successive days of negative deviations in which milk yield dropped at least once below 90% of the expected values. Genetic parameters of these indicators and their genetic correlation with economically important traits were estimated using single-trait and bivariate animal models and 8,935 lactations (after quality control) from 6,816 Chinese Holstein cows. In general, cows experienced an average of 3.73 environmental disturbances with a milk loss of 267 kg of milk per lactation. Each fluctuation lasted for 19.80 ± 11.46 days. Milk loss traits are heritable with heritability estimates ranging from 0.004 to 0.061. The heritabilities differed between Lnsd (0.135-0.250), Ra (0.008-0.058), and Ske (0.001-0.075), with the highest heritability estimate of 0.250 ± 0.020 for Lnsd when removing the first and last 10 days in milk in a lactation (Lnsd2). Based on moderate to high genetic correlations, lower Lnsd2 is associated with less milk losses, better reproductive performance, and lower disease incidence. These findings indicate that among the variables evaluated, Lnsd2 is the most promising indicator for breeding for improved resilience in Holstein cattle.
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Affiliation(s)
- Ao Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Hailiang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Rui Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Zhu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dengke Liu
- Hebei Sunlon Modern Agricultural Technology Co., Ltd., Dingzhou, China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co., Ltd., Beijing, China
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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12
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Sanchez MP, Tribout T, Fritz S, Guatteo R, Fourichon C, Schibler L, Delafosse A, Boichard D. New insights into the genetic resistance to paratuberculosis in Holstein cattle via single-step genomic evaluation. Genet Sel Evol 2022; 54:67. [PMID: 36243688 PMCID: PMC9569073 DOI: 10.1186/s12711-022-00757-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background Bovine paratuberculosis, or Johne’s disease (JD), is a contagious and incurable disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has adverse effects on animal welfare and is very difficult to control, leading to serious economic consequences. An important line of defense to this disease is host genetic resistance to MAP, which, when it will be more fully understood, could be improved through selective breeding. Using a large dataset of Holstein cows (161,253 animals including 56,766 cows with ELISA serological phenotypes and 12,431 animals with genotypes), we applied a single-step single nucleotide polymorphism (SNP) best linear unbiased prediction approach to investigate the genetic determinism underlying resistance to this disease (heritability estimate and identification of relevant genomic regions) and estimated genetic trends, reliability, and relative risk factors associated with genomic predictions. Results Resistance to JD was moderately heritable (0.14) and 16 genomic regions were detected that accounted for at least 0.05% of the breeding values variance (GV) in resistance to JD, and were located on chromosomes 1, 3, 5, 6, 7, 19, 20, 21, 23, 25, and 27, with the highest percentage of variance explained by regions on chromosomes 23 (0.36% GV), 5 (0.22% GV), 1 (0.14% GV), and 3 (0.13% GV). When estimated for the whole chromosomes, the autosomes with the largest overall contributions were chromosomes 3 (5.3% GV), 10 (4.8%), 23 (4.7%), 1 (3.6%), 7 (3.4%), 5 (2.9%), 12 (2.5%), 11 (2.2%), and 13 (2%). We estimated a slightly favorable genetic trend in resistance to JD over the last two decades, which can be explained by a low positive genetic correlation between resistance to JD and total merit index (+ 0.06). Finally, in a validation population of 907 cows, relatively reliable genomic predictions (reliability = 0.55) were obtained, which allowed the identification of cows at high risk of infection. Conclusions This study provides new insights into the genetic determinism of resistance to JD and shows that this trait can be predicted from SNP genotypes. It has led to the implementation of a single-step genomic evaluation that should rapidly become an effective tool for controlling paratuberculosis on French Holstein farms.
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Affiliation(s)
- Marie-Pierre Sanchez
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| | - Thierry Tribout
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Sébastien Fritz
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,Eliance, 149 Rue de Bercy, 75012, Paris, France
| | | | | | | | | | - Didier Boichard
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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13
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Luo H, Hu L, Brito LF, Dou J, Sammad A, Chang Y, Ma L, Guo G, Liu L, Zhai L, Xu Q, Wang Y. Weighted single-step GWAS and RNA sequencing reveals key candidate genes associated with physiological indicators of heat stress in Holstein cattle. J Anim Sci Biotechnol 2022; 13:108. [PMID: 35986427 PMCID: PMC9392250 DOI: 10.1186/s40104-022-00748-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background The study of molecular processes regulating heat stress response in dairy cattle is paramount for developing mitigation strategies to improve heat tolerance and animal welfare. Therefore, we aimed to identify quantitative trait loci (QTL) regions associated with three physiological indicators of heat stress response in Holstein cattle, including rectal temperature (RT), respiration rate score (RS), and drooling score (DS). We estimated genetic parameters for all three traits. Subsequently, a weighted single-step genome-wide association study (WssGWAS) was performed based on 3200 genotypes, 151,486 phenotypic records, and 38,101 animals in the pedigree file. The candidate genes located within the identified QTL regions were further investigated through RNA sequencing (RNA-seq) analyses of blood samples for four cows collected in April (non-heat stress group) and four cows collected in July (heat stress group). Results The heritability estimates for RT, RS, and DS were 0.06, 0.04, and 0.03, respectively. Fourteen, 19, and 20 genomic regions explained 2.94%, 3.74%, and 4.01% of the total additive genetic variance of RT, RS, and DS, respectively. Most of these genomic regions are located in the Bos taurus autosome (BTA) BTA3, BTA6, BTA8, BTA12, BTA14, BTA21, and BTA24. No genomic regions overlapped between the three indicators of heat stress, indicating the polygenic nature of heat tolerance and the complementary mechanisms involved in heat stress response. For the RNA-seq analyses, 2627 genes were significantly upregulated and 369 downregulated in the heat stress group in comparison to the control group. When integrating the WssGWAS, RNA-seq results, and existing literature, the key candidate genes associated with physiological indicators of heat stress in Holstein cattle are: PMAIP1, SBK1, TMEM33, GATB, CHORDC1, RTN4IP1, and BTBD7. Conclusions Physiological indicators of heat stress are heritable and can be improved through direct selection. Fifty-three QTL regions associated with heat stress indicators confirm the polygenic nature and complex genetic determinism of heat tolerance in dairy cattle. The identified candidate genes will contribute for optimizing genomic evaluation models by assigning higher weights to genetic markers located in these regions as well as to the design of SNP panels containing polymorphisms located within these candidate genes. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00748-6.
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14
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Fathoni A, Boonkum W, Chankitisakul V, Duangjinda M. An Appropriate Genetic Approach for Improving Reproductive Traits in Crossbred Thai-Holstein Cattle under Heat Stress Conditions. Vet Sci 2022; 9:vetsci9040163. [PMID: 35448661 PMCID: PMC9031002 DOI: 10.3390/vetsci9040163] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/19/2022] [Accepted: 03/26/2022] [Indexed: 01/16/2023] Open
Abstract
Thailand is a tropical country affected by global climate change and has high temperatures and humidity that cause heat stress in livestock. A temperature−humidity index (THI) is required to assess and evaluate heat stress levels in livestock. One of the livestock types in Thailand experiencing heat stress due to extreme climate change is crossbred dairy cattle. Genetic evaluations of heat tolerance in dairy cattle have been carried out for reproductive traits. Heritability values for reproductive traits are generally low (<0.10) because environmental factors heavily influence them. Consequently, genetic improvement for these traits would be slow compared to production traits. Positive and negative genetic correlations were found between reproductive traits and reproductive traits and yield traits. Several selection methods for reproductive traits have been introduced, i.e., the traditional method, marker-assisted selection (MAS), and genomic selection (GS). GS is the most promising technique and provides accurate results with a high genetic gain. Single-step genomic BLUP (ssGBLUP) has higher accuracy than the multi-step equivalent for fertility traits or low-heritability traits.
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Affiliation(s)
- Akhmad Fathoni
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (A.F.); (W.B.); (V.C.)
- Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Wuttigrai Boonkum
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (A.F.); (W.B.); (V.C.)
- Network Center for Animal Breeding and OMICS Research, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Vibuntita Chankitisakul
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (A.F.); (W.B.); (V.C.)
- Network Center for Animal Breeding and OMICS Research, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (A.F.); (W.B.); (V.C.)
- Network Center for Animal Breeding and OMICS Research, Khon Kaen University, Khon Kaen 40002, Thailand
- Correspondence: ; Tel.: +66-81-872-4207
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15
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The Transition Period Updated: A Review of the New Insights into the Adaptation of Dairy Cows to the New Lactation. DAIRY 2021. [DOI: 10.3390/dairy2040048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recent research on the transition period (TP) of dairy cows has highlighted the pivotal role of immune function in affecting the severity of metabolic challenges the animals face when approaching calving. This suggests that the immune system may play a role in the etiology of metabolic diseases occurring in early lactation. Several studies have indicated that the roots of immune dysfunctions could sink way before the “classical” TP (e.g., 3 weeks before and 3 weeks after calving), extending the time frame deemed as “risky” for the development of early lactation disorders at the period around the dry-off. Several distressing events occurring during the TP (i.e., dietary changes, heat stress) can boost the severity of pre-existing immune dysfunctions and metabolic changes that physiologically affect this phase of the lactation cycle, further increasing the likelihood of developing diseases. Based on this background, several operational and nutritional strategies could be adopted to minimize the detrimental effects of immune dysfunctions on the adaptation of dairy cows to the new lactation. A suitable environment (i.e., optimal welfare) and a balanced diet (which guarantees optimal nutrient partitioning to improve immune functions in cow and calf) are key aspects to consider when aiming to minimize TP challenges at the herd level. Furthermore, several prognostic behavioral and physiological indicators could help in identifying subjects that are more likely to undergo a “bad transition”, allowing prompt intervention through specific modulatory treatments. Recent genomic advances in understanding the linkage between metabolic disorders and the genotype of dairy cows suggest that genetic breeding programs aimed at improving dairy cows’ adaptation to the new lactation challenges (i.e., through increasing immune system efficiency or resilience against metabolic disorders) could be expected in the future. Despite these encouraging steps forward in understanding the physiological mechanisms driving metabolic responses of dairy cows during their transition to calving, it is evident that these processes still require further investigation, and that the TP—likely extended from dry-off—continues to be “the final frontier” for research in dairy sciences.
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16
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Araujo AC, Carneiro PLS, Oliveira HR, Schenkel FS, Veroneze R, Lourenco DAL, Brito LF. A Comprehensive Comparison of Haplotype-Based Single-Step Genomic Predictions in Livestock Populations With Different Genetic Diversity Levels: A Simulation Study. Front Genet 2021; 12:729867. [PMID: 34721524 PMCID: PMC8551834 DOI: 10.3389/fgene.2021.729867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
The level of genetic diversity in a population is inversely proportional to the linkage disequilibrium (LD) between individual single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs), leading to lower predictive ability of genomic breeding values (GEBVs) in high genetically diverse populations. Haplotype-based predictions could outperform individual SNP predictions by better capturing the LD between SNP and QTL. Therefore, we aimed to evaluate the accuracy and bias of individual-SNP- and haplotype-based genomic predictions under the single-step-genomic best linear unbiased prediction (ssGBLUP) approach in genetically diverse populations. We simulated purebred and composite sheep populations using literature parameters for moderate and low heritability traits. The haplotypes were created based on LD thresholds of 0.1, 0.3, and 0.6. Pseudo-SNPs from unique haplotype alleles were used to create the genomic relationship matrix ( G ) in the ssGBLUP analyses. Alternative scenarios were compared in which the pseudo-SNPs were combined with non-LD clustered SNPs, only pseudo-SNPs, or haplotypes fitted in a second G (two relationship matrices). The GEBV accuracies for the moderate heritability-trait scenarios fitting individual SNPs ranged from 0.41 to 0.55 and with haplotypes from 0.17 to 0.54 in the most (Ne ≅ 450) and less (Ne < 200) genetically diverse populations, respectively, and the bias fitting individual SNPs or haplotypes ranged between -0.14 and -0.08 and from -0.62 to -0.08, respectively. For the low heritability-trait scenarios, the GEBV accuracies fitting individual SNPs ranged from 0.24 to 0.32, and for fitting haplotypes, it ranged from 0.11 to 0.32 in the more (Ne ≅ 250) and less (Ne ≅ 100) genetically diverse populations, respectively, and the bias ranged between -0.36 and -0.32 and from -0.78 to -0.33 fitting individual SNPs or haplotypes, respectively. The lowest accuracies and largest biases were observed fitting only pseudo-SNPs from blocks constructed with an LD threshold of 0.3 (p < 0.05), whereas the best results were obtained using only SNPs or the combination of independent SNPs and pseudo-SNPs in one or two G matrices, in both heritability levels and all populations regardless of the level of genetic diversity. In summary, haplotype-based models did not improve the performance of genomic predictions in genetically diverse populations.
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Affiliation(s)
- Andre C Araujo
- Postgraduate Program in Animal Sciences, State University of Southwestern Bahia, Itapetinga, Brazil.,Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Paulo L S Carneiro
- Department of Biology, State University of Southwestern Bahia, Jequié, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Renata Veroneze
- Department of Animal Sciences, Federal University of Viçosa, Viçosa, Brazil
| | - Daniela A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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17
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May K, Sames L, Scheper C, König S. Genomic loci and genetic parameters for uterine diseases in first-parity Holstein cows and associations with milk production and fertility. J Dairy Sci 2021; 105:509-524. [PMID: 34656355 DOI: 10.3168/jds.2021-20685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/27/2021] [Indexed: 12/19/2022]
Abstract
Based on the clinical stage (e.g., vaginal discharge) and bacterial species, several forms of uterine diseases (UD) exist and can be classified as different traits [i.e., different stages of endometritis (EM) and metritis (MET)], which may differ in their genetic background and causal physiological mechanisms. Consequently, the present study aimed to study (1) the effect of UD on 305-d lactation and fertility, (2) the estimation of heritabilities for UD traits using pedigree- and SNP-based relationships, and (3) genome-wide associations to detect significant SNP markers and to infer candidate genes for UD traits. The data set contained herd manager and veterinarian recorded UD traits of 14,810 first-lactating genotyped Holstein cows from 63 large-scale contract herds. Binary defined UD traits (healthy or diseased) according to the clinical stage were endometritis catarrhalis (EM I), endometritis mucopurulenta (EM II), endometritis purulenta (EM III), pyometra (EM IV), endometritis (EM_SOD; superordinate diagnosis = no specific clinical stage defined), and MET. The binary defined trait UDall included all EM and MET diagnoses. The prevalence of UDall was 26.7%. The effect of UD on 305-d lactation and fertility was estimated via linear and generalized linear mixed models. We applied linear single-trait animal models and threshold models to estimate pedigree- and SNP-based heritabilities for UD traits, and bivariate linear models for genetic correlation estimations between UDall with 305-d lactation and fertility traits. A diagnosis for UDall had significant unfavorable effects on the female fertility traits calving interval, interval from calving to first service, days open, and nonreturn rate after 90 d, but was unrelated to 305-d lactation records for production traits milk yield, protein yield, and fat yield. Heritabilities for UDall and EM stages were close to zero, displaying maximal values of 0.05 for pedigree and 0.07 for SNP-based relationship matrices. For MET, pedigree- and SNP-based heritabilities were <0.001 and 0.07, respectively. Genetic correlations ranged from 0.20 to 0.31 between UDall with 305-d milk, protein, and fat yield, and from 0.17 to 0.40 with fertility traits. The GWAS revealed 5 SNP on bovine chromosomes (BTA) 1, 8, 10, 23 for UDall, 5 SNP on BTA 26 for EM I, 1 SNP on BTA 19 for EM II, 4 SNP on BTA 2, 18, 20, 25 for EM III, and 4 SNP on BTA 4, 16, 20 for EM IV above the significance threshold. For EM_SOD, we identified 15 significantly associated SNP on 4 chromosomes, and 4 significant SNP on BTA 3, 20, 22, 28 for MET. Marker associations for UD traits were annotated to 24 potential candidate genes using the ENSEMBL database. Six of these genes were previously reported to be involved in uterine defense mechanisms or in endometritis. Further detected genes contribute to immune response mechanisms during bacterial infections. Different SNP significantly influenced different UD stages, explaining the inter-individual variations in clinical severity of uterine infections.
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Affiliation(s)
- Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany.
| | - Lena Sames
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany
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18
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Asselstine V, Lam S, Miglior F, Brito LF, Sweett H, Guan L, Waters SM, Plastow G, Cánovas A. The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies. J Anim Sci 2021; 99:6377879. [PMID: 34586400 PMCID: PMC8480417 DOI: 10.1093/jas/skab193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Ruminant supply chains contribute 5.7 gigatons of CO2-eq per annum, which represents approximately 80% of the livestock sector emissions. One of the largest sources of emission in the ruminant sector is methane (CH4), accounting for approximately 40% of the sectors total emissions. With climate change being a growing concern, emphasis is being put on reducing greenhouse gas emissions, including those from ruminant production. Various genetic and environmental factors influence cattle CH4 production, such as breed, genetic makeup, diet, management practices, and physiological status of the host. The influence of genetic variability on CH4 yield in ruminants indicates that genomic selection for reduced CH4 emissions is possible. Although the microbiology of CH4 production has been studied, further research is needed to identify key differences in the host and microbiome genomes and how they interact with one another. The advancement of “-omics” technologies, such as metabolomics and metagenomics, may provide valuable information in this regard. Improved understanding of genetic mechanisms associated with CH4 production and the interaction between the microbiome profile and host genetics will increase the rate of genetic progress for reduced CH4 emissions. Through a systems biology approach, various “-omics” technologies can be combined to unravel genomic regions and genetic markers associated with CH4 production, which can then be used in selective breeding programs. This comprehensive review discusses current challenges in applying genomic selection for reduced CH4 emissions, and the potential for “-omics” technologies, especially metabolomics and metagenomics, to minimize such challenges. The integration and evaluation of different levels of biological information using a systems biology approach is also discussed, which can assist in understanding the underlying genetic mechanisms and biology of CH4 production traits in ruminants and aid in reducing agriculture’s overall environmental footprint.
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Affiliation(s)
- Victoria Asselstine
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Stephanie Lam
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Hannah Sweett
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Leluo Guan
- Livestock Gentec, Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, T6G 2C8, Canada
| | - Sinead M Waters
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, T6G 2C8, Canada
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Genome-wide association study of trypanosome prevalence and morphometric traits in purebred and crossbred Baoulé cattle of Burkina Faso. PLoS One 2021; 16:e0255089. [PMID: 34351956 PMCID: PMC8341487 DOI: 10.1371/journal.pone.0255089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/09/2021] [Indexed: 11/27/2022] Open
Abstract
In this study, single-SNP GWAS analyses were conducted to find regions affecting tolerance against trypanosomosis and morphometrics traits in purebred and crossbred Baoulé cattle of Burkina Faso. The trypanosomosis status (positive and negative) and a wide set of morphological traits were recorded for purebred Baoulé and crossbred Zebu x Baoulé cattle, and genotyped with the Illumina Bovine SNP50 BeadChip. After quality control, 36,203 SNPs and 619 animals including 343 purebred Baoulé and 279 crossbreds were used for the GWAS analyses. Several important genes were found that can influence morphological parameters. Although there were no genes identified with a reported strong connection to size traits, many of them were previously identified in various growth-related studies. A re-occurring theme for the genes residing in the regions identified by the most significant SNPs was pleiotropic effect on growth of the body and the cardiovascular system. Regarding trypanosomosis tolerance, two potentially important regions were identified in purebred Baoulé on chromosomes 16 and 24, containing the CFH, CRBN, TRNT1 and, IL5RA genes, and one additional genomic region in Baoulé, x Zebu crossbreds on chromosome 5, containing MGAT4C and NTS. Almost all of these regions and genes were previously related to the trait of interest, while the CRBN gene was to our knowledge presented in the context of trypanosomiasis tolerance for the first time.
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Honerlagen H, Reyer H, Oster M, Ponsuksili S, Trakooljul N, Kuhla B, Reinsch N, Wimmers K. Identification of Genomic Regions Influencing N-Metabolism and N-Excretion in Lactating Holstein- Friesians. Front Genet 2021; 12:699550. [PMID: 34335696 PMCID: PMC8318802 DOI: 10.3389/fgene.2021.699550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/18/2021] [Indexed: 12/03/2022] Open
Abstract
Excreted nitrogen (N) of dairy cows contribute to environmental eutrophication. The main N-excretory metabolite of dairy cows is urea, which is synthesized as a result of N-metabolization in the liver and is excreted via milk and urine. Genetic variation in milk urea (MU) has been postulated but the complex physiology behind the trait as well as the tremendous diversity of processes regulating the N-metabolism impede the consistent determination of causal regions in the bovine genome. In order to map the genetic determinants affecting N-excretion, MU and eight other N-excretory metabolites in milk and urine were assessed in a genome-wide association study. Therefore phenotypes of 371 Holstein- Friesians were obtained in a trial on a dairy farm under near commercial conditions. Genotype data comprised SNP information of the Bovine 50K MD Genome chip (45,613 SNPs). Significantly associated genomic regions for MU concentration revealed GJA1 (BTA 9), RXFP1, and FRY1 (both BTA 12) as putative candidates. For milk urea yield (MUY) a promising QTL on BTA 17 including SH3D19 emerged, whereas RCAN2, CLIC5, ENPP4, and ENPP5 (BTA 23) are suggested to influence urinary urea concentration. Minor N-fractions in milk (MN) may be regulated by ELF2 and SLC7A11 (BTA 17), whilst ITPR2 and MYBPC1 (BTA 5), STIM2 (BTA 6), SGCD (BTA 7), SLC6A2 (BTA 18), TMCC2 and MFSD4A (BTA 16) are suggested to have an impact on various non-urea-N (NUN) fractions excreted via urine. Our results highlight genomic regions and candidate genes for N-excretory metabolites and provide a deeper insight into the predisposed component to regulate the N-metabolism in dairy cows.
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Affiliation(s)
- Hanne Honerlagen
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Henry Reyer
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Michael Oster
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Nares Trakooljul
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Björn Kuhla
- Metabolism Efficiency Unit, Institute of Nutritional Physiology "Oskar Kellner," Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Norbert Reinsch
- Livestock Genetics and Breeding Unit, Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
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21
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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: 6] [Impact Index Per Article: 2.0] [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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22
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Oliveira Junior GA, Schenkel FS, Alcantara L, Houlahan K, Lynch C, Baes CF. Estimated genetic parameters for all genetically evaluated traits in Canadian Holsteins. J Dairy Sci 2021; 104:9002-9015. [PMID: 33934872 DOI: 10.3168/jds.2021-20227] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022]
Abstract
Genetic improvement is a crucial tool to deal with the increasing demand for high quality, sustainably produced dairy. Breeding programs are based on genetic parameters, such as heritability and genetic correlations, for economically important traits in a population. In this study, we estimated population genetic parameters and genetic trends for 67 traits evaluated on heifers and first-lactation Canadian Holstein cows. The data consisted of approximately 500,000 records with pedigree information collected from 1980 to 2019. Genetic parameters were estimated using bivariate linear animal models under a Bayesian approach. Analyses for the 67 traits resulted in 2,211 bivariate combinations, from which the estimated genetic parameters are reported here. The most highly heritable traits were fat percent (0.66) and protein percent (0.69), followed by stature (0.47). Lowest heritabilities (0.01) were observed for disease-related traits, such as lameness and toe ulcer, and calf survival. The genetic correlations between gestation length, calf size, and calving ease measured on both heifer and cows were close to unity. On the other hand, traits such as body condition score and pin width, cystic ovaries and sole ulcer, rear teat placement, and toe ulcer were genetically unrelated. This study reports genetic parameters that have not been previously published for Canadian Holstein cows, and provides updates of those previously estimated. These estimates are useful for building new indexes, updating existing selection indexes, and for predicting correlated responses due to inclusion of novel traits in the breeding programs.
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Affiliation(s)
- G A Oliveira Junior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - L Alcantara
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - K Houlahan
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - C Lynch
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Institute of Genetics, Department of Clinical Research and Veterinary Public Health, University of Bern, Bern, 3001, Switzerland
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23
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Lázaro SF, Tonhati H, Oliveira HR, Silva AA, Nascimento AV, Santos DJA, Stefani G, Brito LF. Genomic studies of milk-related traits in water buffalo (Bubalus bubalis) based on single-step genomic best linear unbiased prediction and random regression models. J Dairy Sci 2021; 104:5768-5793. [PMID: 33685677 DOI: 10.3168/jds.2020-19534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/02/2021] [Indexed: 01/14/2023]
Abstract
Genomic selection has been widely implemented in many livestock breeding programs, but it remains incipient in buffalo. Therefore, this study aimed to (1) estimate variance components incorporating genomic information in Murrah buffalo; (2) evaluate the performance of genomic prediction for milk-related traits using single- and multitrait random regression models (RRM) and the single-step genomic best linear unbiased prediction approach; and (3) estimate longitudinal SNP effects and candidate genes potentially associated with time-dependent variation in milk, fat, and protein yields, as well as somatic cell score (SCS) in multiple parities. The data used to estimate the genetic parameters consisted of a total of 323,140 test-day records. The average daily heritability estimates were moderate (0.35 ± 0.02 for milk yield, 0.22 ± 0.03 for fat yield, 0.42 ± 0.03 for protein yield, and 0.16 ± 0.03 for SCS). The highest heritability estimates, considering all traits studied, were observed between 20 and 280 d in milk (DIM). The genetic correlation estimates at different DIM among the evaluated traits ranged from -0.10 (156 to 185 DIM for SCS) to 0.61 (36 to 65 DIM for fat yield). In general, direct selection for any of the traits evaluated is expected to result in indirect genetic gains for milk yield, fat yield, and protein yield but also increase SCS at certain lactation stages, which is undesirable. The predicted RRM coefficients were used to derive the genomic estimated breeding values (GEBV) for each time point (from 5 to 305 DIM). In general, the tuning parameters evaluated when constructing the hybrid genomic relationship matrices had a small effect on the GEBV accuracy and a greater effect on the bias estimates. The SNP solutions were back-solved from the GEBV predicted from the Legendre random regression coefficients, which were then used to estimate the longitudinal SNP effects (from 5 to 305 DIM). The daily SNP effect for 3 different lactation stages were performed considering 3 different lactation stages for each trait and parity: from 5 to 70, from 71 to 150, and from 151 to 305 DIM. Important genomic regions related to the analyzed traits and parities that explain more than 0.50% of the total additive genetic variance were selected for further analyses of candidate genes. In general, similar potential candidate genes were found between traits, but our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the traits across parities. These results contribute to a better understanding of the genetic architecture of milk production traits in dairy buffalo and reinforce the relevance of incorporating genomic information to genetically evaluate longitudinal traits in dairy buffalo. Furthermore, the candidate genes identified can be used as target genes in future functional genomics studies.
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Affiliation(s)
- Sirlene F Lázaro
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Humberto Tonhati
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, ON, Canada
| | - Alessandra A Silva
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - André V Nascimento
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Daniel J A Santos
- Department of Animal and Avian Science, University of Maryland, College Park 20742
| | - Gabriela Stefani
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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24
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Sun T, Huang GY, Wang ZH, Teng SH, Cao YH, Sun JL, Hanif Q, Chen NB, Lei CZ, Liao YY. Selection signatures of Fuzhong Buffalo based on whole-genome sequences. BMC Genomics 2020; 21:674. [PMID: 32993537 PMCID: PMC7526191 DOI: 10.1186/s12864-020-07095-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Fuzhong buffalo, a native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. In addition, the Fuzhong buffalo also prepared for the bullfighting festival organized by the locals. The detection of the selective signatures in its genome can help in elucidating the selection mechanisms in its stamina and muscle development of a draft animal. RESULTS In this study, we analyzed 27 whole genomes of buffalo (including 15 Fuzhong buffalo genomes and 12 published buffalo genomes from Upper Yangtze region). The ZHp, ZFst, π-Ratio, and XP-EHH statistics were used to identify the candidate signatures of positive selection in Fuzhong buffalo. Our results detected a set of candidate genes involving in the pathways and GO terms associated with the response to exercise (e.g., ALDOA, STAT3, AKT2, EIF4E2, CACNA2D2, TCF4, CDH2), immunity (e.g., PTPN22, NKX2-3, PIK3R1, ITK, TMEM173), nervous system (e.g., PTPN21, ROBO1, HOMER1, MAGI2, SLC1A3, NRG3, SNAP47, CTNNA2, ADGRL3). In addition, we also identified several genes related to production and growth traits (e.g., PHLPP1, PRKN, MACF1, UCN3, RALGAPA1, PHKB, PKD1L). Our results depicted several pathways, GO terms, and candidate genes to be associated with response to exercise, immunity, nervous system, and growth traits. CONCLUSIONS The selective sweep analysis of the Fuzhong buffalo demonstrated positive selection pressure on potential target genes involved in behavior, immunity, and growth traits, etc. Our findings provided a valuable resource for future research on buffalo breeding and an insight into the mechanisms of artificial selection.
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Affiliation(s)
- Ting Sun
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Guang-Yun Huang
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China
| | - Zi-Hao Wang
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China
| | - Shao-Hua Teng
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China
| | - Yan-Hong Cao
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China
| | - Jun-Li Sun
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Ning-Bo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yu-Ying Liao
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China.
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25
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Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle. Animals (Basel) 2020; 10:ani10081425. [PMID: 32824035 PMCID: PMC7460448 DOI: 10.3390/ani10081425] [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: 07/12/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with important traits in Chinese Wagyu beef cattle. We identified a total of 29,271 ROH segments from 462 animals. Within each animal, an average number of ROH was 63.36 while an average length was 62.19 Mb. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events across all individuals. Of these, nine regions containing 154 candidate genes, were significantly associated with six traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length; p < 0.01). Moreover, we found 26 consensus ROH regions with frequencies exceeding 10%, and several regions overlapped with QTLs, which are associated with body weight, calving ease, and stillbirth. Among them, we observed 41 candidate genes, including BCKDHB, MAB21L1, SLC2A13, FGFR3, FGFRL1, CPLX1, CTNNA1, CORT, CTNNBIP1, and NMNAT1, which have been previously reported to be related to body conformation, meat quality, susceptibility, and reproductive traits. In summary, we assessed genome-wide autozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. Our study identified many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in beef cattle.
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26
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Brito LF, Oliveira HR, McConn BR, Schinckel AP, Arrazola A, Marchant-Forde JN, Johnson JS. Large-Scale Phenotyping of Livestock Welfare in Commercial Production Systems: A New Frontier in Animal Breeding. Front Genet 2020; 11:793. [PMID: 32849798 PMCID: PMC7411239 DOI: 10.3389/fgene.2020.00793] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Genomic breeding programs have been paramount in improving the rates of genetic progress of productive efficiency traits in livestock. Such improvement has been accompanied by the intensification of production systems, use of a wider range of precision technologies in routine management practices, and high-throughput phenotyping. Simultaneously, a greater public awareness of animal welfare has influenced livestock producers to place more emphasis on welfare relative to production traits. Therefore, management practices and breeding technologies in livestock have been developed in recent years to enhance animal welfare. In particular, genomic selection can be used to improve livestock social behavior, resilience to disease and other stress factors, and ease habituation to production system changes. The main requirements for including novel behavioral and welfare traits in genomic breeding schemes are: (1) to identify traits that represent the biological mechanisms of the industry breeding goals; (2) the availability of individual phenotypic records measured on a large number of animals (ideally with genomic information); (3) the derived traits are heritable, biologically meaningful, repeatable, and (ideally) not highly correlated with other traits already included in the selection indexes; and (4) genomic information is available for a large number of individuals (or genetically close individuals) with phenotypic records. In this review, we (1) describe a potential route for development of novel welfare indicator traits (using ideal phenotypes) for both genetic and genomic selection schemes; (2) summarize key indicator variables of livestock behavior and welfare, including a detailed assessment of thermal stress in livestock; (3) describe the primary statistical and bioinformatic methods available for large-scale data analyses of animal welfare; and (4) identify major advancements, challenges, and opportunities to generate high-throughput and large-scale datasets to enable genetic and genomic selection for improved welfare in livestock. A wide variety of novel welfare indicator traits can be derived from information captured by modern technology such as sensors, automatic feeding systems, milking robots, activity monitors, video cameras, and indirect biomarkers at the cellular and physiological levels. The development of novel traits coupled with genomic selection schemes for improved welfare in livestock can be feasible and optimized based on recently developed (or developing) technologies. Efficient implementation of genetic and genomic selection for improved animal welfare also requires the integration of a multitude of scientific fields such as cell and molecular biology, neuroscience, immunology, stress physiology, computer science, engineering, quantitative genomics, and bioinformatics.
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Affiliation(s)
- Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Betty R. McConn
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| | - Allan P. Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Aitor Arrazola
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | | | - Jay S. Johnson
- USDA-ARS Livestock Behavior Research Unit, West Lafayette, IN, United States
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27
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Grigoletto L, Santana MHA, Bressan FF, Eler JP, Nogueira MFG, Kadarmideen HN, Baruselli PS, Ferraz JBS, Brito LF. Genetic Parameters and Genome-Wide Association Studies for Anti-Müllerian Hormone Levels and Antral Follicle Populations Measured After Estrus Synchronization in Nellore Cattle. Animals (Basel) 2020; 10:E1185. [PMID: 32668804 PMCID: PMC7401547 DOI: 10.3390/ani10071185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/21/2022] Open
Abstract
Reproductive efficiency plays a major role in the long-term sustainability of livestock industries and can be improved through genetic and genomic selection. This study aimed to estimate genetic parameters (heritability and genetic correlation) and identify genomic regions and candidate genes associated with anti-Müllerian hormone levels (AMH) and antral follicle populations measured after estrous synchronization (AFP) in Nellore cattle. The datasets included phenotypic records for 1099 and 289 Nellore females for AFP and AMH, respectively, high-density single nucleotide polymorphism (SNP) genotypes for 944 animals, and 4129 individuals in the pedigree. The heritability estimates for AMH and AFP were 0.28 ± 0.07 and 0.30 ± 0.09, and the traits were highly and positively genetically correlated (rG = 0.81 ± 0.02). These findings indicated that these traits can be improved through selective breeding, and substantial indirect genetic gains are expected by selecting for only one of the two traits. A total of 31 genomic regions were shown to be associated with AMH or AFP, and two genomic regions located on BTA1 (64.9-65.0 Mb and 109.1-109.2 Mb) overlapped between the traits. Various candidate genes were identified to be potentially linked to important biological processes such as ovulation, tissue remodeling, and the immune system. Our findings support the use of AMH and AFP as indicator traits to genetically improve fertility rates in Nellore cattle and identify better oocyte donors.
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Affiliation(s)
- Laís Grigoletto
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900 São Paulo, Brazil; (M.H.A.S.); (F.F.B.); (J.P.E.); (J.B.S.F.)
| | - Miguel Henrique Almeida Santana
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900 São Paulo, Brazil; (M.H.A.S.); (F.F.B.); (J.P.E.); (J.B.S.F.)
| | - Fabiana Fernandes Bressan
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900 São Paulo, Brazil; (M.H.A.S.); (F.F.B.); (J.P.E.); (J.B.S.F.)
| | - Joanir Pereira Eler
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900 São Paulo, Brazil; (M.H.A.S.); (F.F.B.); (J.P.E.); (J.B.S.F.)
| | - Marcelo Fábio Gouveia Nogueira
- Department of Biological Sciences, School of Sciences and Languages, São Paulo State University, Assis, 19806-900 São Paulo, Brazil;
| | - Haja N. Kadarmideen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 102500 Lyngby, Denmark;
| | - Pietro Sampaio Baruselli
- College of Veterinary Medicine and Animal Science, University of Sao Paulo, 05508-270 São Paulo, Brazil;
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900 São Paulo, Brazil; (M.H.A.S.); (F.F.B.); (J.P.E.); (J.B.S.F.)
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
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Moreira FF, Oliveira HR, Volenec JJ, Rainey KM, Brito LF. Integrating High-Throughput Phenotyping and Statistical Genomic Methods to Genetically Improve Longitudinal Traits in Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:681. [PMID: 32528513 PMCID: PMC7264266 DOI: 10.3389/fpls.2020.00681] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/30/2020] [Indexed: 05/28/2023]
Abstract
The rapid development of remote sensing in agronomic research allows the dynamic nature of longitudinal traits to be adequately described, which may enhance the genetic improvement of crop efficiency. For traits such as light interception, biomass accumulation, and responses to stressors, the data generated by the various high-throughput phenotyping (HTP) methods requires adequate statistical techniques to evaluate phenotypic records throughout time. As a consequence, information about plant functioning and activation of genes, as well as the interaction of gene networks at different stages of plant development and in response to environmental stimulus can be exploited. In this review, we outline the current analytical approaches in quantitative genetics that are applied to longitudinal traits in crops throughout development, describe the advantages and pitfalls of each approach, and indicate future research directions and opportunities.
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Affiliation(s)
- Fabiana F. Moreira
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Jeffrey J. Volenec
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Katy M. Rainey
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Alvarenga AB, Veroneze R, Oliveira HR, Marques DBD, Lopes PS, Silva FF, Brito LF. Comparing Alternative Single-Step GBLUP Approaches and Training Population Designs for Genomic Evaluation of Crossbred Animals. Front Genet 2020; 11:263. [PMID: 32328083 PMCID: PMC7162606 DOI: 10.3389/fgene.2020.00263] [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: 10/27/2019] [Accepted: 03/05/2020] [Indexed: 02/06/2023] Open
Abstract
As crossbreeding is extensively used in some livestock species, we aimed to evaluate the performance of single-step GBLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) methods to predict Genomic Estimated Breeding Values (GEBVs) of crossbred animals. Different training population scenarios were evaluated: (SC1) ssGBLUP based on a single-trait model considering purebred and crossbred animals in a joint training population; (SC2) ssGBLUP based on a multiple-trait model to enable considering phenotypes recorded in purebred and crossbred training animals as different traits; (SC3) WssGBLUP based on a single-trait model considering purebred and crossbred animals jointly in the training population (both populations were used for SNP weights' estimation); (SC4) WssGBLUP based on a single-trait model considering only purebred animals in the training population (crossbred population only used for SNP weights' estimation); (SC5) WssGBLUP based on a single-trait model and the training population characterized by purebred animals (purebred population used for SNP weights' estimation). A complex trait was simulated assuming alternative genetic architectures. Different scaling factors to blend the inverse of the genomic (G -1) and pedigree (A 22 - 1 ) relationship matrices were also tested. The predictive performance of each scenario was evaluated based on the validation accuracy and regression coefficient. The genetic correlations across simulated populations in the different scenarios ranged from moderate to high (0.71-0.99). The scenario mimicking a completely polygenic trait (h Q T L 2 = 0) yielded the lowest validation accuracy (0.12; for SC3 and SC4). The simulated scenarios assuming 4,500 QTLs affecting the trait andh Q T L 2 = h 2 resulted in the greatest GEBV accuracies (0.47; for SC1 and SC2). The regression coefficients ranged from 0.28 (for SC3 assuming polygenic effect) to 1.27 (for SC2 considering 4,500 QTLs). In general, SC3 and SC5 resulted in inflated GEBVs, whereas other scenarios yielded deflated GEBVs. The scaling factors used to combine G -1 andA 22 - 1 had a small influence on the validation accuracies, but a greater effect on the regression coefficients. Due to the complexity of multiple-trait models and WssGBLUP analyses, and a similar predictive performance across the methods evaluated, SC1 is recommended for genomic evaluation in crossbred populations with similar genetic structures [moderate-to-high (0.71-0.99) genetic correlations between purebred and crossbred populations].
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Affiliation(s)
- Amanda B. Alvarenga
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
| | - Renata Veroneze
- Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | | | - Paulo S. Lopes
- Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
| | - Fabyano F. Silva
- Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Sablik P, Klenowicz A, Szewczuk M, Olszewski A, Dybus A. The Effect of Polymorphism in PGLYRP1 Gene on the Productivity and Health Traits in Holstein-Friesian Cattle. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420030138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sickinger M, Erteld EM, Wehrend A. Fertility following uterine torsion in dairy cows: A cross-sectional study. Vet World 2020; 13:92-95. [PMID: 32158156 PMCID: PMC7020130 DOI: 10.14202/vetworld.2020.92-95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/05/2019] [Indexed: 11/26/2022] Open
Abstract
Background and Aim: Dairy cows with uterine torsion often are susceptible to reduced fertility resulting in more costs and effort to restore the economy of those cows. The aim of our study was to examine and evaluate the possible associations between uterine torsion and consequent uterine involution disturbances, on the one hand, and between the degree and duration of uterine torsion with fertility parameters, on the other hand. Materials and Methods: Within 1.5 years, 115 dairy cows (German Browns, German Holsteins, and German Fleckvieh) that were suffering from uterine torsion were examined to evaluate the incidence of involution disturbances of the uterus and to examine the fertility after calving. Statistical analysis included correlation analyses between the degree and duration of torsion and fertility parameters (days open, days to conception, conception rate and services per conception, and intercalving interval) as well as incidence of involution disturbances. Results: The study revealed no statistically significant correlation between uterine involution and degree of uterine torsion. However, involution processes were significantly correlated to the time of the expulsion of the fetal membranes. Days to conception and intercalving intervals were significantly influenced by the presence of uterine torsion. Conclusion: Concerning fertility after uterine torsion, it was shown that reduced fertility is associated with the duration of uterine torsion (p=0.02) and time to drop of fetal membranes (p=0.02) but not with the degree of torsion (p=0.27).
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Affiliation(s)
- Marlene Sickinger
- Clinic for Ruminants, Justus-Liebig-University of Giessen, Frankfurter Straße 104, 35392 Giessen, Germany
| | - Eva-Maria Erteld
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals with Veterinary Ambulance, Justus-Liebig-University of Giessen, Frankfurter Straße 106, 35392 Giessen, Germany
| | - Axel Wehrend
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals with Veterinary Ambulance, Justus-Liebig-University of Giessen, Frankfurter Straße 106, 35392 Giessen, Germany
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Huang H, Cao J, Guo G, Li X, Wang Y, Yu Y, Zhang S, Zhang Q, Zhang Y. Genome-wide association study identifies QTLs for displacement of abomasum in Chinese Holstein cattle1. J Anim Sci 2019; 97:1133-1142. [PMID: 30715382 DOI: 10.1093/jas/skz031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 01/17/2019] [Indexed: 12/28/2022] Open
Abstract
Displacement of abomasum (DA) is one of the most common and important disorders in dairy cattle. The objective of the present study was to detect the quantitative trait loci (QTL) for DA in Chinese Holstein using single-step genomic BLUP methodology. A total of 60,556 producer-recorded DA event records from 32,190 cows, together with 2,336 genotyped animals with 40,054 SNP markers, were used for the analysis. Genomic data were incorporated into a threshold model for variance component estimation, and the estimated heritability of DA was 0.108 (SE = 0.086). Results of genome-wide association studies were reported as the proportion of genetic variance explained 20-SNP windows. Eight QTLs covering 129 genes on Bos taurus autosomes 2, 4, 7, 10, 14, 17, 20 showed associations with DA. Ten genes, namely BMP4, SOCS4, GCH1, DDHD1, ATG14, ACBP/DBI, SMO, AHCYL2, CYP7A1, and CACNA1A, involved in insulin metabolism and lipid metabolism pathways may be considered as candidate genes of DA in dairy. The identified QTLs, biological pathways, and associated genes underlying DA identified from the present study will contribute to the understanding of the genetic architecture of this complex disease.
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Affiliation(s)
- Hetian Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jie Cao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd., Beijing, China
| | - Xizhi Li
- Beijing Sunlon Livestock Development Co. Ltd., Beijing, China
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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