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Ooi E, Xiang R, Chamberlain AJ, Goddard ME. Archetypal clustering reveals physiological mechanisms linking milk yield and fertility in dairy cattle. J Dairy Sci 2024; 107:4726-4742. [PMID: 38369117 DOI: 10.3168/jds.2023-23699] [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: 05/05/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Fertility in dairy cattle has declined as an unintended consequence of single-trait selection for high milk yield. The unfavorable genetic correlation between milk yield and fertility is now well documented; however, the underlying physiological mechanisms are still uncertain. To understand the relationship between these traits, we developed a method that clusters variants with similar patterns of effects and, after the integration of gene expression data, identifies the genes through which they are likely to act. Biological processes that are enriched in the genes of each cluster were then identified. We identified several clusters with unique patterns of effects. One of the clusters included variants associated with increased milk yield and decreased fertility, where the "archetypal" variant (i.e., the one with the largest effect) was associated with the GC gene, whereas others were associated with TRIM32, LRRK2, and U6-associated snRNA. These genes have been linked to transcription and alternative splicing, suggesting that these processes are likely contributors to the unfavorable relationship between the 2 traits. Another cluster, with archetypal variant near DGAT1 and including variants associated with CDH2, BTRC, SFRP2, ZFHX3, and SLITRK5, appeared to affect milk yield but have little effect on fertility. These genes have been linked to insulin, adipose tissue, and energy metabolism. A third cluster with archetypal variant near ZNF613 and including variants associated with ROBO1, EFNA5, PALLD, GPC6, and PTPRT were associated with fertility but not milk yield. These genes have been linked to GnRH neuronal migration, embryonic development, or ovarian function. The use of archetypal clustering to group variants with similar patterns of effects may assist in identifying the biological processes underlying correlated traits. The method is hypothesis generating and requires experimental confirmation. However, we have uncovered several novel mechanisms potentially affecting milk production and fertility such as GnRH neuronal migration. We anticipate our method to be a starting point for experimental research into novel pathways, which have been previously unexplored within the context of dairy production.
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Affiliation(s)
- E Ooi
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
| | - R Xiang
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
| | - A J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
| | - M E Goddard
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
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van den Berg I, Chamberlain AJ, MacLeod IM, Nguyen TV, Goddard ME, Xiang R, Mason B, Meier S, Phyn CVC, Burke CR, Pryce JE. Using expression data to fine map QTL associated with fertility in dairy cattle. Genet Sel Evol 2024; 56:42. [PMID: 38844868 PMCID: PMC11154999 DOI: 10.1186/s12711-024-00912-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Female fertility is an important trait in dairy cattle. Identifying putative causal variants associated with fertility may help to improve the accuracy of genomic prediction of fertility. Combining expression data (eQTL) of genes, exons, gene splicing and allele specific expression is a promising approach to fine map QTL to get closer to the causal mutations. Another approach is to identify genomic differences between cows selected for high and low fertility and a selection experiment in New Zealand has created exactly this resource. Our objective was to combine multiple types of expression data, fertility traits and allele frequency in high- (POS) and low-fertility (NEG) cows with a genome-wide association study (GWAS) on calving interval in Australian cows to fine-map QTL associated with fertility in both Australia and New Zealand dairy cattle populations. RESULTS Variants that were significantly associated with calving interval (CI) were strongly enriched for variants associated with gene, exon, gene splicing and allele-specific expression, indicating that there is substantial overlap between QTL associated with CI and eQTL. We identified 671 genes with significant differential expression between POS and NEG cows, with the largest fold change detected for the CCDC196 gene on chromosome 10. Our results provide numerous candidate genes associated with female fertility in dairy cattle, including GYS2 and TIGAR on chromosome 5 and SYT3 and HSD17B14 on chromosome 18. Multiple QTL regions were located in regions with large numbers of copy number variants (CNV). To identify the causal mutations for these variants, long read sequencing may be useful. CONCLUSIONS Variants that were significantly associated with CI were highly enriched for eQTL. We detected 671 genes that were differentially expressed between POS and NEG cows. Several QTL detected for CI overlapped with eQTL, providing candidate genes for fertility in dairy cattle.
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Affiliation(s)
- Irene van den Berg
- Agriculture Victoria, AgriBio, Centre of AgriBioscience, 5 Ring Road, Bundoora, VIC, 3082, Australia.
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre of AgriBioscience, 5 Ring Road, Bundoora, VIC, 3082, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre of AgriBioscience, 5 Ring Road, Bundoora, VIC, 3082, Australia
| | - Tuan V Nguyen
- Agriculture Victoria, AgriBio, Centre of AgriBioscience, 5 Ring Road, Bundoora, VIC, 3082, Australia
| | - Mike E Goddard
- Agriculture Victoria, AgriBio, Centre of AgriBioscience, 5 Ring Road, Bundoora, VIC, 3082, Australia
- Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ruidong Xiang
- Agriculture Victoria, AgriBio, Centre of AgriBioscience, 5 Ring Road, Bundoora, VIC, 3082, Australia
- Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Brett Mason
- Agriculture Victoria, AgriBio, Centre of AgriBioscience, 5 Ring Road, Bundoora, VIC, 3082, Australia
| | | | | | | | - Jennie E Pryce
- Agriculture Victoria, AgriBio, Centre of AgriBioscience, 5 Ring Road, Bundoora, VIC, 3082, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
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Müller-Langhans K, Oberberger L, Zablotski Y, Engelmann S, Hoedemaker M, Kühn C, Schuberth HJ, Zerbe H, Petzl W, Meyerholz-Wohllebe MM. Cows with diverging haplotypes show differences in differential milk cell count, milk parameters and vaginal temperature after S. aureus challenge but not after E. coli challenge. BMC Vet Res 2024; 20:200. [PMID: 38745199 PMCID: PMC11094921 DOI: 10.1186/s12917-024-03996-y] [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: 01/05/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND In dairy cattle, mastitis causes high financial losses and impairs animal well-being. Genetic selection is used to breed cows with reduced mastitis susceptibility. Techniques such as milk cell flow cytometry may improve early mastitis diagnosis. In a highly standardized in vivo infection model, 36 half-sib cows were selected for divergent paternal Bos taurus chromosome 18 haplotypes (Q vs. q) and challenged with Escherichia coli for 24 h or Staphylococcus aureus for 96 h, after which the samples were analyzed at 12 h intervals. Vaginal temperature (VT) was recorded every three minutes. The objective of this study was to compare the differential milk cell count (DMCC), milk parameters (fat %, protein %, lactose %, pH) and VT between favorable (Q) and unfavorable (q) haplotype cows using Bayesian models to evaluate their potential as improved early indicators of differential susceptibility to mastitis. RESULTS After S. aureus challenge, compared to the Q half-sibship cows, the milk of the q cows exhibited higher PMN levels according to the DMCC (24 h, p < 0.001), a higher SCC (24 h, p < 0.01 and 36 h, p < 0.05), large cells (24 h, p < 0.05) and more dead (36 h, p < 0.001) and live cells (24 h, p < 0.01). The protein % was greater in Q milk than in q milk at 0 h (p = 0.025). In the S. aureus group, Q cows had a greater protein % (60 h, p = 0.048) and fat % (84 h, p = 0.022) than q cows. Initially, the greater VT of S. aureus-challenged q cows (0 and 12-24 h, p < 0.05) reversed to a lower VT in q cows than in Q cows (48-60 h, p < 0.05). Additionally, the following findings emphasized the validity of the model: in the S. aureus group all DMCC subpopulations (24 h-96 h, p < 0.001) and in the E. coli group nearly all DMCC subpopulations (12 h-24 h, p < 0.001) were higher in challenged quarters than in unchallenged quarters. The lactose % was lower in the milk samples of E. coli-challenged quarters than in those of S. aureus-challenged quarters (24 h, p < 0.001). Between 12 and 18 h, the VT was greater in cows challenged with E. coli than in those challenged with S. aureus (3-h interval approach, p < 0.001). CONCLUSION This in vivo infection model confirmed specific differences between Q and q cows with respect to the DMCC, milk component analysis results and VT results after S. aureus inoculation but not after E. coli challenge. However, compared with conventional milk cell analysis monitoring, e.g., the global SCC, the DMCC analysis did not provide refined phenotyping of the pathogen response.
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Affiliation(s)
- Katharina Müller-Langhans
- Clinic for Ruminants With Ambulatory Clinic and Herd Health Services, Center for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, Oberschleissheim, 85764, Germany
| | - Lisa Oberberger
- Institute for Infectious Diseases and Zoonoses, Ludwig-Maximilians-University Munich, Sonnenstrasse 24, Oberschleissheim, 85764, Germany
| | - Yury Zablotski
- Clinic for Ruminants With Ambulatory Clinic and Herd Health Services, Center for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, Oberschleissheim, 85764, Germany
| | - Susanne Engelmann
- Technical University Braunschweig, Institute for Microbiology, Inhoffenstrasse 7, Brunswick, 38124, Germany
- Helmholtz Center for Infection Research, Microbial Proteomics, Inhoffenstrasse 7, Brunswick, 38124, Germany
| | - Martina Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine Hanover Foundation, Bischofsholer Damm 15, Hanover, 30173, Germany
| | - Christa Kühn
- Research Institute for Farm Animal Biology, Genome Biology, Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany
- Agricultural and Environmental Faculty, University Rostock, Justus-Von-Liebig-Weg 6, Rostock, 18059, Germany
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems, 17493, Germany
| | - Hans-Joachim Schuberth
- Institute for Immunology, University of Veterinary Medicine Hanover Foundation, Bünteweg 2, Hanover, 30559, Germany
| | - Holm Zerbe
- Clinic for Ruminants With Ambulatory Clinic and Herd Health Services, Center for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, Oberschleissheim, 85764, Germany
| | - Wolfram Petzl
- Clinic for Ruminants With Ambulatory Clinic and Herd Health Services, Center for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, Oberschleissheim, 85764, Germany
| | - Marie Margarete Meyerholz-Wohllebe
- Clinic for Ruminants With Ambulatory Clinic and Herd Health Services, Center for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, Oberschleissheim, 85764, Germany.
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Baba T, Morota G, Kawakami J, Gotoh Y, Oka T, Masuda Y, Brito LF, Cockrum RR, Kawahara T. Longitudinal genome-wide association analysis using a single-step random regression model for height in Japanese Holstein cattle. JDS COMMUNICATIONS 2023; 4:363-368. [PMID: 37727246 PMCID: PMC10505781 DOI: 10.3168/jdsc.2022-0347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/22/2023] [Indexed: 09/21/2023]
Abstract
Growth traits, such as body weight and height, are essential in the design of genetic improvement programs of dairy cattle due to their relationship with feeding efficiency, longevity, and health. We investigated genomic regions influencing height across growth stages in Japanese Holstein cattle using a single-step random regression model. We used 72,921 records from birth to 60 mo of age with 4,111 animals born between 2000 and 2016. The analysis included 1,410 genotyped animals with 35,319 single nucleotide polymorphisms, consisting of 883 females with records and 527 bulls, and 30,745 animals with pedigree information. A single genomic region at the 58.4 megabase pair on chromosome 18 was consistently identified across 6 age points of 10, 20, 30, 40, 50, and 60 mo after multiple testing corrections for the significance threshold. Twelve candidate genes, previously reported for longevity and gestation length, were found near the identified genomic region. Another location near the identified region was also previously associated with body conformation, fertility, and calving difficulty. Functional Gene Ontology enrichment analysis suggested that the candidate genes regulate dephosphorylation and phosphatase activity. Our findings show that further study of the identified candidate genes will contribute to a better understanding of the genetic basis of height in Japanese Holstein cattle.
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Affiliation(s)
- Toshimi Baba
- Holstein Cattle Association of Japan, Hokkaido Branch, Sapporo, Hokkaido, Japan 001-8555
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Gota Morota
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Junpei Kawakami
- Holstein Cattle Association of Japan, Hokkaido Branch, Sapporo, Hokkaido, Japan 001-8555
| | - Yusaku Gotoh
- Holstein Cattle Association of Japan, Hokkaido Branch, Sapporo, Hokkaido, Japan 001-8555
| | - Taro Oka
- Holstein Cattle Association of Japan, Tokyo, Japan 164-0012
| | - Yutaka Masuda
- Department of Sustainable Agriculture, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan 069-8501
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Rebbeca R. Cockrum
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Takayoshi Kawahara
- Holstein Cattle Association of Japan, Hokkaido Branch, Sapporo, Hokkaido, Japan 001-8555
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Id-Lahoucine S, Casellas J, Suárez-Vega A, Fonseca PAS, Schenkel FS, Sargolzaei M, Cánovas A. Unravelling transmission ratio distortion across the bovine genome: identification of candidate regions for reproduction defects. BMC Genomics 2023; 24:383. [PMID: 37422635 DOI: 10.1186/s12864-023-09455-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Biological mechanisms affecting gametogenesis, embryo development and postnatal viability have the potential to alter Mendelian inheritance expectations resulting in observable transmission ratio distortion (TRD). Although the discovery of TRD cases have been around for a long time, the current widespread and growing use of DNA technologies in the livestock industry provides a valuable resource of large genomic data with parent-offspring genotyped trios, enabling the implementation of TRD approach. In this research, the objective is to investigate TRD using SNP-by-SNP and sliding windows approaches on 441,802 genotyped Holstein cattle and 132,991 (or 47,910 phased) autosomal SNPs. RESULTS The TRD was characterized using allelic and genotypic parameterizations. Across the whole genome a total of 604 chromosomal regions showed strong significant TRD. Most (85%) of the regions presented an allelic TRD pattern with an under-representation (reduced viability) of carrier (heterozygous) offspring or with the complete or quasi-complete absence (lethality) for homozygous individuals. On the other hand, the remaining regions with genotypic TRD patterns exhibited the classical recessive inheritance or either an excess or deficiency of heterozygote offspring. Among them, the number of most relevant novel regions with strong allelic and recessive TRD patterns were 10 and 5, respectively. In addition, functional analyses revealed candidate genes regulating key biological processes associated with embryonic development and survival, DNA repair and meiotic processes, among others, providing additional biological evidence of TRD findings. CONCLUSIONS Our results revealed the importance of implementing different TRD parameterizations to capture all types of distortions and to determine the corresponding inheritance pattern. Novel candidate genomic regions containing lethal alleles and genes with functional and biological consequences on fertility and pre- and post-natal viability were also identified, providing opportunities for improving breeding success in cattle.
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Affiliation(s)
- Samir Id-Lahoucine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Joaquim Casellas
- Departament de Ciència Animal I Dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Aroa Suárez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Pablo A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Select Sires, Inc, Plain City, OH, 43064, USA
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Dachs N, Upadhyay M, Hannemann E, Hauser A, Krebs S, Seichter D, Russ I, Gehrke LJ, Thaller G, Medugorac I. Quantitative trait locus for calving traits on Bos taurus autosome 18 in Holstein cattle is embedded in a complex genomic region. J Dairy Sci 2023; 106:1925-1941. [PMID: 36710189 DOI: 10.3168/jds.2021-21625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 10/10/2022] [Indexed: 01/31/2023]
Abstract
Although the quantitative trait locus (QTL) on chromosome 18 (BTA18) associated with paternal calving ease and stillbirth in Holstein Friesian cattle and its cross has been known for over 20 years, to our knowledge, the exact causal genetic sequence has yet escaped identification. The aim of this study was to re-examine the region of the published QTL on BTA18 and to investigate the possible reasons behind this elusiveness. For this purpose, we carried out a combined linkage disequilibrium and linkage analysis using genotyping data of 2,697 German Holstein Friesian (HF) animals and subsequent whole-genome sequencing (WGS) data analyses and genome assembly of HF samples. We confirmed the known QTL in the 95% confidence interval of 1.089 Mbp between 58.34 and 59.43 Mbp on BTA18. Additionally, these 4 SNPs in the near-perfect linkage disequilibrium with the QTL haplotype were identified: rs381577268 (on 57,816,137 bp, C/T), rs381878735 (on 59,574,329 bp, A/T), rs464221818 (on 59,329,176 bp, C/T), and rs472502785 (on 59,345,689 bp, T/C). Search for the causal mutation using short and long-read sequences, and methylation data of the BTA18 QTL region did not reveal any candidates though. The assembly showed problems in the region, as well as an abundance of segmental duplications within and around the region. Taking the QTL of BTA18 in Holstein cattle as an example, the data presented in this study comprehensively characterize the genomic features that could also be relevant for other such elusive QTL in various other cattle breeds and livestock species as well.
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Affiliation(s)
- Nina Dachs
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152 Martinsried, Germany; Tierzuchtforschung e.V. München, Senator-Gerauer-Str, 23, 85586 Poing, Germany
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152 Martinsried, Germany
| | - Elisabeth Hannemann
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152 Martinsried, Germany
| | - Andreas Hauser
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Doris Seichter
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str, 23, 85586 Poing, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str, 23, 85586 Poing, Germany
| | - Lilian Johanna Gehrke
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Olshausenstraße 40, 24098 Kiel, Germany; Vereinigte Informationssysteme Tierhaltung w.V. (vit) Verden, Heinrich-Schröder-Weg 1, 27283 Verden (Aller), Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152 Martinsried, Germany.
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Massender E, Oliveira HR, Brito LF, Maignel L, Jafarikia M, Baes CF, Sullivan B, Schenkel FS. Genome-wide association study for milk production and conformation traits in Canadian Alpine and Saanen dairy goats. J Dairy Sci 2023; 106:1168-1189. [PMID: 36526463 DOI: 10.3168/jds.2022-22223] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk, protein, and fat yields, and protein and fat percentages in first and later lactations) and conformation traits (body capacity, dairy character, feet and legs, fore udder, general appearance, rear udder, suspensory ligament, and teats) in the Canadian Alpine and Saanen breeds; and (2) to identify positional and functional candidate genes related to these traits. The data available for analysis included 305-d milk production records for 6,409 Alpine and 3,434 Saanen does in first lactation and 5,827 Alpine and 2,632 Saanen does in later lactations; as well as linear type conformation records for 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Both single-breed and multiple-breed GWAS were performed using single-trait animal models. Positional and functional candidate genes were then identified in downstream analyses. The GWAS identified 189 unique SNP that were significant at the chromosomal level, corresponding to 271 unique positional candidate genes within 50 kb up- and downstream, across breeds and traits. This study provides evidence for the economic importance of several candidate genes (e.g., CSN1S1, CSN2, CSN1S2, CSN3, DGAT1, and ZNF16) in the Canadian Alpine and Saanen populations that have been previously reported in other dairy goat populations. Moreover, several novel positional and functional candidate genes (e.g., RPL8, DCK, and MOB1B) were also identified. Overall, the results of this study have provided greater insight into the genetic architecture of milk production and conformation traits in the Canadian Alpine and Saanen populations. Greater understanding of these traits will help to improve dairy goat breeding programs.
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Affiliation(s)
- Erin Massender
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Hinayah R Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Laurence Maignel
- Canadian Centre for Swine Improvement Inc., Ottawa, ON, K1A 0C6, Canada
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Canadian Centre for Swine Improvement Inc., Ottawa, ON, K1A 0C6, Canada
| | - Christine F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Brian Sullivan
- Canadian Centre for Swine Improvement Inc., Ottawa, ON, K1A 0C6, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Čítek J, Brzáková M, Bauer J, Tichý L, Sztankóová Z, Vostrý L, Steyn Y. Genome-Wide Association Study for Body Conformation Traits and Fitness in Czech Holsteins. Animals (Basel) 2022; 12:ani12243522. [PMID: 36552441 PMCID: PMC10375906 DOI: 10.3390/ani12243522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
The aim of this study was a genome-wide association study (GWAS) on conformation traits using 25,486 genotyped Czech Holsteins, with 35,227 common SNPs for each genotype. Linear trait records were collected between 1995 and 2020. The Interbull information from Multiple Across Country Evaluation (MACE) was included for bulls that mostly had daughter records in a foreign country. When using the Bonferroni correction, the number of SNPs that were either significant or approached the significance threshold was low-dairy capacity composite on BTA4, feet and legs composite BTA21, total score BTA10, stature BTA24, body depth BTA6, angularity BTA20, fore udder attachment BTA10. Without the Bonferroni correction, the total number of significant or near of significance SNPs was 32. The SNPs were localized on BTA1,2,4,5,6,7,8,18,22,25,26,28 for dairy capacity composite, BTA15,21 for feet and legs composite, BTA10 for total score, BTA24 stature, BTA6,23 body depth, BTA20 angularity, BTA2 rump angle, BTA9,10 rear legs rear view, BTA2,19 rear legs side view, BTA10 fore udder attachment, BTA2 udder depth, BTA10 rear udder height, BTA12 central alignment, BTA24 rear teat placement, BTA8,29 rear udder width. The results provide biological information for the improvement of body conformation and fitness in the Holstein population.
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Affiliation(s)
- Jindřich Čítek
- Department of Genetics and Agricultural Biotechnology, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic
- Veterinary Research Institute, Hudcova 296, 621 00 Brno, Czech Republic
| | - Michaela Brzáková
- Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic
| | - Jiří Bauer
- Czech Moravian Breeders' Corporation, Benešovská 123, 252 09 Hradištko, Czech Republic
| | - Ladislav Tichý
- Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czech Republic
| | - Zuzana Sztankóová
- Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic
| | - Luboš Vostrý
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czech Republic
| | - Yvette Steyn
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens, GA 30602, USA
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9
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Alvarenga AB, Oliveira HR, Miller SP, Silva FF, Brito LF. Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits. Front Genet 2022; 13:794625. [PMID: 35444687 PMCID: PMC9014094 DOI: 10.3389/fgene.2022.794625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cattle temperament has been considered by farmers as a key breeding goal due to its relevance for cattlemen's safety, animal welfare, resilience, and longevity and its association with many economically important traits (e.g., production and meat quality). The definition of proper statistical models, accurate variance component estimates, and knowledge on the genetic background of the indicator trait evaluated are of great importance for accurately predicting the genetic merit of breeding animals. Therefore, 266,029 American Angus cattle with yearling temperament records (1-6 score) were used to evaluate statistical models and estimate variance components; investigate the association of sex and farm management with temperament; assess the weighted correlation of estimated breeding values for temperament and productive, reproductive efficiency and resilience traits; and perform a weighted single-step genome-wide association analysis using 69,559 animals genotyped for 54,609 single-nucleotide polymorphisms. Sex and extrinsic factors were significantly associated with temperament, including conception type, age of dam, birth season, and additional animal-human interactions. Similar results were observed among models including only the direct additive genetic effect and when adding other maternal effects. Estimated heritability of temperament was equal to 0.39 on the liability scale. Favorable genetic correlations were observed between temperament and other relevant traits, including growth, feed efficiency, meat quality, and reproductive traits. The highest approximated genetic correlations were observed between temperament and growth traits (weaning weight, 0.28; yearling weight, 0.28). Altogether, we identified 11 genomic regions, located across nine chromosomes including BTAX, explaining 3.33% of the total additive genetic variance. The candidate genes identified were enriched in pathways related to vision, which could be associated with reception of stimulus and/or cognitive abilities. This study encompasses large and diverse phenotypic, genomic, and pedigree datasets of US Angus cattle. Yearling temperament is a highly heritable and polygenic trait that can be improved through genetic selection. Direct selection for temperament is not expected to result in unfavorable responses on other relevant traits due to the favorable or low genetic correlations observed. In summary, this study contributes to a better understanding of the impact of maternal effects, extrinsic factors, and various genomic regions associated with yearling temperament in North American Angus cattle.
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Affiliation(s)
- Amanda B Alvarenga
- 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.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Stephen P Miller
- American Angus Association, Angus Genetics Inc., St Joseph, MO, United States
| | - Fabyano F Silva
- Department of Animal Sciences, Federal University of Vicosa, Viçosa, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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10
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Bermann M, Cesarani A, Misztal I, Lourenco D. Past, present, and future developments in single-step genomic models. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2053366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Matias Bermann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Alberto Cesarani
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Ignacy Misztal
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
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11
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Challenging Sustainable and Innovative Technologies in Cheese Production: A Review. Processes (Basel) 2022. [DOI: 10.3390/pr10030529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
It is well known that cheese yield and quality are affected by animal genetics, milk quality (chemical, physical, and microbiological), production technology, and the type of rennet and dairy cultures used in production. Major differences in the same type of cheese (i.e., hard cheese) are caused by the rennet and dairy cultures, which affect the ripening process. This review aims to explore current technological advancements in animal genetics, methods for the isolation and production of rennet and dairy cultures, along with possible applications of microencapsulation in rennet and dairy culture production, as well as the challenge posed to current dairy technologies by the preservation of biodiversity. Based on the reviewed scientific literature, it can be concluded that innovative approaches and the described techniques can significantly improve cheese production.
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12
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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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13
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Kava R, Peripolli E, Berton MP, Lemos M, Lobo RB, Stafuzza NB, Pereira AS, Baldi F. Genome-wide structural variations in Brazilian Senepol cattle, a tropically adapted taurine breed. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Johnsson M, Jungnickel MK. Evidence for and localization of proposed causative variants in cattle and pig genomes. Genet Sel Evol 2021; 53:67. [PMID: 34461824 PMCID: PMC8404348 DOI: 10.1186/s12711-021-00662-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/20/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding. RESULTS For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PHGK1, PRKAG3, PLRL, RYR1, SYNGR2 and VRTN) in cattle and pigs, and localized them in contemporary reference genomes. We review the evidence for their causality, by aiming to separate the evidence for the locus, the proposed causative gene and the proposed causative variant, and report the bioinformatic searches and tactics needed to localize the sequence variants in the cattle or pig genome. CONCLUSIONS Taken together, there is usually good evidence for the association at the locus level, some evidence for a specific causative gene at eight of the loci, and some experimental evidence for a specific causative variant at six of the loci. We recommend that researchers who report new potential causative variants use referenced coordinate systems, show local sequence context, and submit variants to repositories.
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Affiliation(s)
- Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - Melissa K. Jungnickel
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland, UK
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15
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Britt JH, Cushman RA, Dechow CD, Dobson H, Humblot P, Hutjens MF, Jones GA, Mitloehner FM, Ruegg PL, Sheldon IM, Stevenson JS. Review: Perspective on high-performing dairy cows and herds. Animal 2021; 15 Suppl 1:100298. [PMID: 34266782 DOI: 10.1016/j.animal.2021.100298] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 01/18/2023] Open
Abstract
Milk and dairy products provide highly sustainable concentrations of essential amino acids and other required nutrients for humans; however, amount of milk currently produced per dairy cow globally is inadequate to meet future needs. Higher performing dairy cows and herds produce more milk with less environmental impact per kg than lower performing cows and herds. In 2018, 15.4% of the world's dairy cows produced 45.4% of the world's dairy cow milk, reflecting the global contribution of high-performing cows and herds. In high-performing herds, genomic evaluations are utilized for multiple trait selection, welfare is monitored by remote sensing, rations are formulated at micronutrient levels, health care is focused on prevention and reproduction is managed with precision. Higher performing herds require more inputs and generate more waste products per cow, thus innovations in environmental management on such farms are essential for lowering environmental impacts. Our focus is to provide perspectives on technologies and practices that contribute most to sustainable production of milk from high-performing dairy cows and herds.
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Affiliation(s)
- J H Britt
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695-7621, USA.
| | - R A Cushman
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - C D Dechow
- Department of Animal Science, Pennsylvania State University, University Park, PA 16802, USA
| | - H Dobson
- Institute of Veterinary Science, University of Liverpool, Neston, CH64 7TE, UK
| | - P Humblot
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - M F Hutjens
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - G A Jones
- Central Sands Dairy, De Pere, WI 54115-9603, USA
| | - F M Mitloehner
- Department of Animal Science, University of California-Davis, Davis, CA 95616-5270, USA
| | - P L Ruegg
- Department of Large Animal Clinical Science, Michigan State University, East Lansing, MI 48824 USA
| | - I M Sheldon
- Swansea University Medical School, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - J S Stevenson
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS 66506-0201, USA
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16
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Schmidtmann C, Schönherz A, Guldbrandtsen B, Marjanovic J, Calus M, Hinrichs D, Thaller G. Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe. Genet Sel Evol 2021; 53:23. [PMID: 33676402 PMCID: PMC7936461 DOI: 10.1186/s12711-021-00613-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful. Results Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility. Conclusions This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible.
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Affiliation(s)
- Christin Schmidtmann
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany.
| | - Anna Schönherz
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.,Department of Animal Science, Aarhus University, 8830, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.,Department of Animal Sciences, Department of Animal Breeding and Husbandry, University of Bonn, 53115, Bonn, Germany
| | - Jovana Marjanovic
- Animal Breeding and Genomics, Wageningen University and Research, 6700AH, Wageningen, The Netherlands
| | - Mario Calus
- Animal Breeding and Genomics, Wageningen University and Research, 6700AH, Wageningen, The Netherlands
| | - Dirk Hinrichs
- Department of Animal Breeding, University of Kassel, 37213, Witzenhausen, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
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17
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Li B, VanRaden PM, Null DJ, O'Connell JR, Cole JB. Major quantitative trait loci influencing milk production and conformation traits in Guernsey dairy cattle detected on Bos taurus autosome 19. J Dairy Sci 2020; 104:550-560. [PMID: 33189290 DOI: 10.3168/jds.2020-18766] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/07/2020] [Indexed: 01/30/2023]
Abstract
The goal of this study was to identify potential quantitative trait loci (QTL) for 27 production, fitness, and conformation traits of Guernsey cattle through genome-wide association (GWA) analyses, with extra emphasis on BTA19, where major QTL were observed for several traits. Animals' de-regressed predicted transmitting abilities (PTA) from the December 2018 traditional US evaluation were used as phenotypes. All of the Guernsey cattle included in the QTL analyses were predictor animals in the reference population, ranging from 1,077 to 1,685 animals for different traits. Single-trait GWA analyses were carried out by a mixed-model approach for all 27 traits using imputed high-density genotypes. A major QTL was detected on BTA19, influencing several milk production traits, conformation traits, and livability of Guernsey cattle, and the most significant SNP lie in the region of 26.2 to 28.3 Mb. The myosin heavy chain 10 (MYH10) gene residing within this region was found to be highly associated with milk production and body conformation traits of dairy cattle. After the initial GWA analyses, which suggested that many significant SNP are in linkage with one another, conditional analyses were used for fine mapping. The top significant SNP on BTA19 were fixed as covariables in the model, one at a time, until no more significant SNP were detected on BTA19. After this fine-mapping approach was applied, only 1 significant SNP was detected on BTA19 for most traits, but multiple, independent significant SNP were found for protein yield, dairy form, and stature. In addition, the haplotype that hosts the major QTL on BTA19 was traced to a US Guernsey born in 1954. The haplotype is common in the breed, indicating a long-term influence of this QTL on the US Guernsey population.
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Affiliation(s)
- B Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD 20705-2350
| | - P M VanRaden
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD 20705-2350
| | - D J Null
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD 20705-2350
| | - J R O'Connell
- School of Medicine, University of Maryland, Baltimore 21201
| | - J B Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD 20705-2350.
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18
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Miles AM, Huson HJ. Graduate Student Literature Review: Understanding the genetic mechanisms underlying mastitis. J Dairy Sci 2020; 104:1183-1191. [PMID: 33162090 DOI: 10.3168/jds.2020-18297] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/16/2020] [Indexed: 01/24/2023]
Abstract
Mastitis is the costliest disease facing dairy producers today; consequently, it has been the subject of substantial research focus. Efforts have evolved from an initial focus on understanding the etiology of intramammary infections to the application of preventative measures, including attempts to breed cows that are resistant to infection. However, breeding for resistance to infection has proven difficult, given the complexity of the disease and the high expense associated with assembling high-quality genotypes and phenotypes. This review provides a brief background on mastitis; illustrates current understanding of the genetics influencing mastitis and the application of this knowledge; and discusses challenges and limitations in understanding these mechanisms and applying these findings to genetic improvement strategies.
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Affiliation(s)
- Asha M Miles
- Department of Animal Science, Cornell University, Ithaca, NY 14853.
| | - Heather J Huson
- Department of Animal Science, Cornell University, Ithaca, NY 14853.
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19
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Klápště J, Dungey HS, Telfer EJ, Suontama M, Graham NJ, Li Y, McKinley R. Marker Selection in Multivariate Genomic Prediction Improves Accuracy of Low Heritability Traits. Front Genet 2020; 11:499094. [PMID: 33193595 PMCID: PMC7662070 DOI: 10.3389/fgene.2020.499094] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 09/18/2020] [Indexed: 11/13/2022] Open
Abstract
Multivariate analysis using mixed models allows for the exploration of genetic correlations between traits. Additionally, the transition to a genomic based approach is simplified by substituting classic pedigrees with a marker-based relationship matrix. It also enables the investigation of correlated responses to selection, trait integration and modularity in different kinds of populations. This study investigated a strategy for the construction of a marker-based relationship matrix that prioritized markers using Partial Least Squares. The efficiency of this strategy was found to depend on the correlation structure between investigated traits. In terms of accuracy, we found no benefit of this strategy compared with the all-marker-based multivariate model for the primary trait of diameter at breast height (DBH) in a radiata pine (Pinus radiata) population, possibly due to the presence of strong and well-estimated correlation with other highly heritable traits. Conversely, we did see benefit in a shining gum (Eucalyptus nitens) population, where the primary trait had low or only moderate genetic correlation with other low/moderately heritable traits. Marker selection in multivariate analysis can therefore be an efficient strategy to improve prediction accuracy for low heritability traits due to improved precision in poorly estimated low/moderate genetic correlations. Additionally, our study identified the genetic diversity as a factor contributing to the efficiency of marker selection in multivariate approaches due to higher precision of genetic correlation estimates.
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Affiliation(s)
- Jaroslav Klápště
- Scion (New Zealand Forest Research Institute Ltd.), Rotorua, New Zealand
| | - Heidi S Dungey
- Scion (New Zealand Forest Research Institute Ltd.), Rotorua, New Zealand
| | - Emily J Telfer
- Scion (New Zealand Forest Research Institute Ltd.), Rotorua, New Zealand
| | - Mari Suontama
- Scion (New Zealand Forest Research Institute Ltd.), Rotorua, New Zealand.,Skogforsk, Umeå, Sweden
| | - Natalie J Graham
- Scion (New Zealand Forest Research Institute Ltd.), Rotorua, New Zealand
| | - Yongjun Li
- Scion (New Zealand Forest Research Institute Ltd.), Rotorua, New Zealand.,Agriculture Victoria, AgriBio Center, Bundoora, VIC, Australia
| | - Russell McKinley
- Scion (New Zealand Forest Research Institute Ltd.), Rotorua, New Zealand
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20
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Shabalina T, Yin T, König S. Survival analyses in Holstein cows considering direct disease diagnoses and specific SNP marker effects. J Dairy Sci 2020; 103:8257-8273. [DOI: 10.3168/jds.2020-18174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
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21
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Druet T, Legarra A. Theoretical and empirical comparisons of expected and realized relationships for the X-chromosome. Genet Sel Evol 2020; 52:50. [PMID: 32819272 PMCID: PMC7441635 DOI: 10.1186/s12711-020-00570-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/12/2020] [Indexed: 01/08/2023] Open
Abstract
Background X-chromosomal loci present different inheritance patterns compared to autosomal loci and must be modeled accordingly. Sexual chromosomes are not systematically considered in whole-genome relationship matrices although rules based on genealogical or marker information have been derived. Loci on the X-chromosome could have a significant contribution to the additive genetic variance, in particular for some traits such as those related to reproduction. Thus, accounting for the X-chromosome relationship matrix might be informative to better understand the architecture of complex traits (e.g., by estimating the variance associated to this chromosome) and to improve their genomic prediction. For such applications, previous studies have shown the benefits of combining information from genotyped and ungenotyped individuals. Results In this paper, we start by presenting rules to compute a genomic relationship matrix (GRM) for the X-chromosome (GX) without making any assumption on dosage compensation, and based on coding of gene content with 0/1 for males and 0/1/2 for females. This coding adjusts naturally to previously derived pedigree-based relationships (S) for the X-chromosome. When needed, we propose to accommodate and estimate dosage compensation and genetic heterogeneity across sexes via multiple trait models. Using a Holstein dairy cattle dataset, including males and females, we then empirically illustrate that realized relationships (GX) matches expectations (S). However, GX presents high deviations from S. GX has also a lower dimensionality compared to the autosomal GRM. In particular, individuals are frequently identical along the entire chromosome. Finally, we confirm that the heritability of gene content for markers on the X-chromosome that are estimated by using S is 1, further demonstrating that S and GX can be combined. For the pseudo-autosomal region, we demonstrate that the expected relationships vary according to position because of the sex-gradient. We end by presenting the rules to construct the 'H matrix’ by combining both relationship matrices. Conclusions This work shows theoretically and empirically that a pedigree-based relationship matrix built with rules specifically developed for the X-chromosome (S) matches the realized GRM for the X-chromosome. Therefore, applications that combine expected relationships and genotypes for markers on the X-chromosome should use S and GX.
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Affiliation(s)
- Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - Andres Legarra
- GenPhySE, INPT, INRAE, ENVT, 31326, Castanet Tolosan, France.
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22
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Stambuk CR, Staiger EA, Heins BJ, Huson HJ. Exploring physiological and genetic variation of digital cushion thickness in Holstein and Jersey cows and bulls. J Dairy Sci 2020; 103:9177-9194. [PMID: 32713698 DOI: 10.3168/jds.2020-18290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/15/2020] [Indexed: 11/19/2022]
Abstract
The objectives of our study were to expand phenotypic characterization of digital cushion thickness (DCT) to the Jersey breed and include mature bulls and to identify breed-specific quantitative trait loci (QTL) for DCT within the Jersey or Holstein breeds and common QTL across breeds and sexes to better understand biological regulation and guide future use of marker-assisted selection. In a cohort of 698 cows and 85 bulls (Holstein and Jersey) from 8 farms in New York State, data were collected on DCT, body condition score (BCS), withers height, and sacral height. All animals underwent sonographic examination of the digital cushion evaluated at the sole ulcer site for the right front and hind feet. Linear mixed models were conducted on DCT separately for cows and bulls with fixed effects of time point, breed, age, digit, and BCS group. The models included random effects to control for the random subset of animals per farm, repeated measures, and multiple measurements from each animal. The phenotypic results indicated that DCT varied by time point, breed, age, digit, and BCS group for cows and by breed, age, digit, and BCS group for bulls. For the genotypic study, 616 cow DNA samples were genotyped on the Illumina BovineHD 777K BeadChip (Illumina Inc., San Diego, CA), whereas 76 bull DNA samples were genotyped on different platforms ranging from 5K to 150K. Multiple genome-wide association studies were conducted to highlight pertinent phenotyping parameters and genetic markers for genomic selection. Data were separated into 8 data sets based on different combinations of breed and sex. Each data set was assessed for quality of markers and samples before conducting genome-wide association studies for DCT, testing the inheritance models and genetic variation of digit, foot, and average thickness. Ten markers passed the Bonferroni correction threshold and 9 passed false discovery rate from 10 genome-wide association studies using a combination of the covariates breed, sex, genotyping batch plate, age, BCS, withers height, and sacral height. Of the 43 candidate genes, 8 novel biologically plausible genes were identified on Bos taurus autosomes 3, 4, 7, and 9: SFRS18 and LRRFIP1 function in fat deposition, whereas AHR, BZW2, EFNA5, USP45, and VAV3 effect bone growth, and SOSTDC1 is related to epidermal keratinocyte function. The genetic markers associated with DCT in this study were explored for variation between cows and bulls within and across breeds for their potential use in marker-assisted selection.
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Affiliation(s)
- C R Stambuk
- Department of Animal Science, Cornell University, Ithaca, NY 14853
| | - E A Staiger
- Department of Animal Science, Cornell University, Ithaca, NY 14853
| | - B J Heins
- Department of Animal Science, University of Minnesota, St. Paul 55108
| | - H J Huson
- Department of Animal Science, Cornell University, Ithaca, NY 14853.
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Purfield DC, Evans RD, Berry DP. Breed- and trait-specific associations define the genetic architecture of calving performance traits in cattle. J Anim Sci 2020; 98:5829000. [PMID: 32365208 PMCID: PMC7247537 DOI: 10.1093/jas/skaa151] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/25/2020] [Indexed: 12/12/2022] Open
Abstract
Reducing the incidence of both the degree of assistance required at calving, as well as the extent of perinatal mortality (PM) has both economic and societal benefits. The existence of heritable genetic variability in both traits signifies the presence of underlying genomic variability. The objective of the present study was to locate regions of the genome, and by extension putative genes and mutations, that are likely to be underpinning the genetic variability in direct calving difficulty (DCD), maternal calving difficulty (MCD), and PM. Imputed whole-genome single-nucleotide polymorphism (SNP) data on up to 8,304 Angus (AA), 17,175 Charolais (CH), 16,794 Limousin (LM), and 18,474 Holstein-Friesian (HF) sires representing 5,866,712 calving events from descendants were used. Several putative quantitative trait loci (QTL) regions associated with calving performance both within and across dairy and beef breeds were identified, although the majority were both breed- and trait-specific. QTL surrounding and encompassing the myostatin (MSTN) gene were associated (P < 5 × 10−8) with DCD and PM in both the CH and LM populations. The well-known Q204X mutation was the fifth strongest association with DCD in the CH population and accounted for 5.09% of the genetic variance in DCD. In contrast, none of the 259 segregating variants in MSTN were associated (P > × 10−6) with DCD in the LM population but a genomic region 617 kb downstream of MSTN was associated (P < 5 × 10−8). The genetic architecture for DCD differed in the HF population relative to the CH and LM, where two QTL encompassing ZNF613 on Bos taurus autosome (BTA)18 and PLAG1 on BTA14 were identified in the former. Pleiotropic SNP associated with all three calving performance traits were also identified in the three beef breeds; 5 SNP were pleiotropic in AA, 116 in LM, and 882 in CH but no SNP was associated with more than one trait within the HF population. The majority of these pleiotropic SNP were on BTA2 surrounding MSTN and were associated with both DCD and PM. Multiple previously reported, but also novel QTL, associated with calving performance were detected in this large study. These also included QTL regions harboring SNP with the same direction of allele substitution effect for both DCD and MCD thus contributing to a more effective simultaneous selection for both traits.
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Affiliation(s)
- Deirdre C Purfield
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Co. Cork, Ireland.,Irish Cattle Breeding Federation, Bandon, Co. Cork, Ireland
| | - Ross D Evans
- Irish Cattle Breeding Federation, Bandon, Co. Cork, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
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24
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Novel approach to incorporate information about recessive lethal genes increases the accuracy of genomic prediction for mortality traits. Heredity (Edinb) 2020; 125:155-166. [PMID: 32533106 PMCID: PMC7426854 DOI: 10.1038/s41437-020-0329-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 01/30/2023] Open
Abstract
The genetic underpinnings of calf mortality can be partly polygenic and partly due to deleterious effects of recessive lethal alleles. Prediction of the genetic merits of selection candidates should thus take into account both genetic components contributing to calf mortality. However, simultaneously modeling polygenic risk and recessive lethal allele effects in genomic prediction is challenging due to effects that behave differently. In this study, we present a novel approach where mortality risk probabilities from polygenic and lethal allele components are predicted separately to compute the total risk probability of an individual for its future offspring as a basis for selection. We present methods for transforming genomic estimated breeding values of polygenic effect into risk probabilities using normal density and cumulative distribution functions and show computations of risk probability from recessive lethal alleles given sire genotypes and population recessive allele frequencies. Simulated data were used to test the novel approach as implemented in probit, logit, and linear models. In the simulation study, the accuracy of predicted risk probabilities was computed as the correlation between predicted mortality probabilities and observed calf mortality for validation sires. The results indicate that our novel approach can greatly increase the accuracy of selection for mortality traits compared with the accuracy of predictions obtained without distinguishing polygenic and lethal gene effects.
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25
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Fang L, Cai W, Liu S, Canela-Xandri O, Gao Y, Jiang J, Rawlik K, Li B, Schroeder SG, Rosen BD, Li CJ, Sonstegard TS, Alexander LJ, Van Tassell CP, VanRaden PM, Cole JB, Yu Y, Zhang S, Tenesa A, Ma L, Liu GE. Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle. Genome Res 2020; 30:790-801. [PMID: 32424068 PMCID: PMC7263193 DOI: 10.1101/gr.250704.119] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/01/2020] [Indexed: 12/13/2022]
Abstract
By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas and studied tissue specificity of genes in cattle. We demonstrated that tissue-specific genes significantly reflected the tissue-relevant biology, showing distinct promoter methylation and evolution patterns (e.g., brain-specific genes evolve slowest, whereas testis-specific genes evolve fastest). Through integrative analyses of those tissue-specific genes with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle, including blood/immune system (e.g., CCDC88C) for male fertility, brain (e.g., TRIM46 and RAB6A) for milk production, and multiple growth-related tissues (e.g., FGF6 and CCND2) for body conformation. We validated these findings by using epigenomic data across major somatic tissues and sperm. Collectively, our findings provided novel insights into the genetic and biological mechanisms underlying complex traits in cattle, and our transcriptome atlas can serve as a primary source for biological interpretation, functional validation, studies of adaptive evolution, and genomic improvement in livestock.
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Affiliation(s)
- Lingzhao Fang
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, United Kingdom
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Wentao Cai
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Oriol Canela-Xandri
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, United Kingdom
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Bingjie Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | | | - Leeson J Alexander
- Fort Keogh Livestock and Range Research Laboratory, Agricultural Research Service, USDA, Miles City, Montana 59301, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Paul M VanRaden
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Ying Yu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shengli Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, United Kingdom
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
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26
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Rio S, Mary-Huard T, Moreau L, Bauland C, Palaffre C, Madur D, Combes V, Charcosset A. Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering. PLoS Genet 2020; 16:e1008241. [PMID: 32130208 PMCID: PMC7075643 DOI: 10.1371/journal.pgen.1008241] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 03/16/2020] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
When handling a structured population in association mapping, group-specific allele effects may be observed at quantitative trait loci (QTLs) for several reasons: (i) a different linkage disequilibrium (LD) between SNPs and QTLs across groups, (ii) group-specific genetic mutations in QTL regions, and/or (iii) epistatic interactions between QTLs and other loci that have differentiated allele frequencies between groups. We present here a new genome-wide association (GWAS) approach to identify QTLs exhibiting such group-specific allele effects. We developed genetic materials including admixed progeny from different genetic groups with known genome-wide ancestries (local admixture). A dedicated statistical methodology was developed to analyze pure and admixed individuals jointly, allowing one to disentangle the factors causing the heterogeneity of allele effects across groups. This approach was applied to maize by developing an inbred "Flint-Dent" panel including admixed individuals that was evaluated for flowering time. Several associations were detected revealing a wide range of configurations of allele effects, both at known flowering QTLs (Vgt1, Vgt2 and Vgt3) and new loci. We found several QTLs whose effect depended on the group ancestry of alleles while others interacted with the genetic background. Our GWAS approach provides useful information on the stability of QTL effects across genetic groups and can be applied to a wide range of species.
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Affiliation(s)
- Simon Rio
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
- MIA, INRAE, AgroParisTech, Université Paris-Saclay, 75005, Paris, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Carine Palaffre
- UE 0394 SMH, INRAE, 2297 Route de l’INRA, 40390, Saint-Martin-de-Hinx, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
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27
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Pierce C, Speidel S, Coleman S, Enns R, Bailey D, Medrano J, Cánovas A, Meiman P, Howery L, Mandeville W, Thomas M. Genome-wide association studies of beef cow terrain-use traits using Bayesian multiple-SNP regression. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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28
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Freebern E, Santos DJA, Fang L, Jiang J, Parker Gaddis KL, Liu GE, VanRaden PM, Maltecca C, Cole JB, Ma L. GWAS and fine-mapping of livability and six disease traits in Holstein cattle. BMC Genomics 2020; 21:41. [PMID: 31931710 PMCID: PMC6958677 DOI: 10.1186/s12864-020-6461-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/07/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Health traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex traits and diseases. The objective of this study is to investigate the genetic basis of seven health traits in dairy cattle and to identify potential candidate genes associated with cattle health using GWAS, fine mapping, and analyses of multi-tissue transcriptome data. RESULTS We studied cow livability and six direct disease traits, mastitis, ketosis, hypocalcemia, displaced abomasum, metritis, and retained placenta, using de-regressed breeding values and more than three million imputed DNA sequence variants. After data edits and filtering on reliability, the number of bulls included in the analyses ranged from 11,880 (hypocalcemia) to 24,699 (livability). GWAS was performed using a mixed-model association test, and a Bayesian fine-mapping procedure was conducted to calculate a posterior probability of causality to each variant and gene in the candidate regions. The GWAS detected a total of eight genome-wide significant associations for three traits, cow livability, ketosis, and hypocalcemia, including the bovine Major Histocompatibility Complex (MHC) region associated with livability. Our fine-mapping of associated regions reported 20 candidate genes with the highest posterior probabilities of causality for cattle health. Combined with transcriptome data across multiple tissues in cattle, we further exploited these candidate genes to identify specific expression patterns in disease-related tissues and relevant biological explanations such as the expression of Group-specific Component (GC) in the liver and association with mastitis as well as the Coiled-Coil Domain Containing 88C (CCDC88C) expression in CD8 cells and association with cow livability. CONCLUSIONS Collectively, our analyses report six significant associations and 20 candidate genes of cattle health. With the integration of multi-tissue transcriptome data, our results provide useful information for future functional studies and better understanding of the biological relationship between genetics and disease susceptibility in cattle.
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Affiliation(s)
- Ellen Freebern
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Daniel J. A. Santos
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Lingzhao Fang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | | | - George E. Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Paul M. VanRaden
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, 27695 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
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29
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Vineeth MR, Surya T, Sivalingam J, Kumar A, Niranjan SK, Dixit SP, Singh K, Tantia MS, Gupta ID. Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle. Trop Anim Health Prod 2019; 52:1707-1715. [DOI: 10.1007/s11250-019-02180-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
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30
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Purfield DC, Evans RD, Carthy TR, Berry DP. Genomic Regions Associated With Gestation Length Detected Using Whole-Genome Sequence Data Differ Between Dairy and Beef Cattle. Front Genet 2019; 10:1068. [PMID: 31749838 PMCID: PMC6848454 DOI: 10.3389/fgene.2019.01068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/04/2019] [Indexed: 12/17/2022] Open
Abstract
While many association studies exist that have attempted to relate genomic markers to phenotypic performance in cattle, very few have considered gestation length as a phenotype, and of those that did, none used whole genome sequence data from multiple breeds. The objective of the present study was therefore to relate imputed whole genome sequence data to estimated breeding values for gestation length using 22,566 sires (representing 2,262,706 progeny) of multiple breeds [Angus (AA), Charolais (CH), Holstein-Friesian (HF), and Limousin (LM)]. The associations were undertaken within breed using linear mixed models that accounted for genomic relatedness among sires; a separate association analysis was undertaken with all breeds analysed together but with breed included as a fixed effect in the model. Furthermore, the genome was divided into 500 kb segments and whether or not segments harboured a single nucleotide polymorphism (SNP) with a P ≤ 1 × 10-4 common to different combinations of breeds was determined. Putative quantitative trait loci (QTL) regions associated with gestation length were detected in all breeds; significant associations with gestation length were only detected in the HF population and in the across-breed analysis of all 22,566 sires. Twenty-five SNPs were significantly associated (P ≤ 5 × 10-8) with gestation length in the HF population. Of the 25 significant SNPs, 18 were located within three QTLs on Bos taurus autosome number (BTA) 18, six were in two QTL on BTA19, and one was located within a QTL on BTA7. The strongest association was rs381577268, a downstream variant of ZNF613 located within a QTL spanning from 58.06 to 58.19 Mb on BTA18; it accounted for 1.37% of the genetic variance in gestation length. Overall there were 11 HF animals within the edited dataset that were homozygous for the T allele at rs381577268 and these had a 3.3 day longer (P < 0.0001) estimated breeding value (EBV) for gestation length than the heterozygous animals and a 4.7 day longer (P < 0.0001) EBV for gestation length than the homozygous CC animals. The majority of the 500 kb windows harboring a SNP with a P ≤ 1 × 10-4 were unique to a single breed and no window was shared among all four breeds for gestation length, suggesting any QTLs identified are breed-specific associations.
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Affiliation(s)
- Deirdre C Purfield
- Animal & Grassland Research and Innovation Centre, Teagasc, Cork, Ireland
| | | | - Tara R Carthy
- Animal & Grassland Research and Innovation Centre, Teagasc, Cork, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Cork, Ireland
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31
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Li B, Fang L, Null DJ, Hutchison JL, Connor EE, VanRaden PM, VandeHaar MJ, Tempelman RJ, Weigel KA, Cole JB. High-density genome-wide association study for residual feed intake in Holstein dairy cattle. J Dairy Sci 2019; 102:11067-11080. [PMID: 31563317 DOI: 10.3168/jds.2019-16645] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/19/2019] [Indexed: 01/27/2023]
Abstract
Improving feed efficiency (FE) of dairy cattle may boost farm profitability and reduce the environmental footprint of the dairy industry. Residual feed intake (RFI), a candidate FE trait in dairy cattle, can be defined to be genetically uncorrelated with major energy sink traits (e.g., milk production, body weight) by including genomic predicted transmitting ability of such traits in genetic analyses for RFI. We examined the genetic basis of RFI through genome-wide association (GWA) analyses and post-GWA enrichment analyses and identified candidate genes and biological pathways associated with RFI in dairy cattle. Data were collected from 4,823 lactations of 3,947 Holstein cows in 9 research herds in the United States. Of these cows, 3,555 were genotyped and were imputed to a high-density list of 312,614 SNP. We used a single-step GWA method to combine information from genotyped and nongenotyped animals with phenotypes as well as their ancestors' information. The estimated genomic breeding values from a single-step genomic BLUP were back-solved to obtain the individual SNP effects for RFI. The proportion of genetic variance explained by each 5-SNP sliding window was also calculated for RFI. Our GWA analyses suggested that RFI is a highly polygenic trait regulated by many genes with small effects. The closest genes to the top SNP and sliding windows were associated with dry matter intake (DMI), RFI, energy homeostasis and energy balance regulation, digestion and metabolism of carbohydrates and proteins, immune regulation, leptin signaling, mitochondrial ATP activities, rumen development, skeletal muscle development, and spermatogenesis. The region of 40.7 to 41.5 Mb on BTA25 (UMD3.1 reference genome) was the top associated region for RFI. The closest genes to this region, CARD11 and EIF3B, were previously shown to be related to RFI of dairy cattle and FE of broilers, respectively. Another candidate region, 57.7 to 58.2 Mb on BTA18, which is associated with DMI and leptin signaling, was also associated with RFI in this study. Post-GWA enrichment analyses used a sum-based marker-set test based on 4 public annotation databases: Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, Reactome pathways, and medical subject heading (MeSH) terms. Results of these analyses were consistent with those from the top GWA signals. Across the 4 databases, GWA signals for RFI were highly enriched in the biosynthesis and metabolism of amino acids and proteins, digestion and metabolism of carbohydrates, skeletal development, mitochondrial electron transport, immunity, rumen bacteria activities, and sperm motility. Our findings offer novel insight into the genetic basis of RFI and identify candidate regions and biological pathways associated with RFI in dairy cattle.
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Affiliation(s)
- B Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - L Fang
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350; Department of Animal and Avian Sciences, University of Maryland, College Park 20742; Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - D J Null
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - J L Hutchison
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - E E Connor
- Department of Animal and Food Sciences, University of Delaware, Newark 19716
| | - P M VanRaden
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - M J VandeHaar
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - R J Tempelman
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - K A Weigel
- Department of Dairy Science, University of Wisconsin, Madison 53706
| | - J B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350.
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32
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Meyerholz MM, Rohmeier L, Eickhoff T, Hülsebusch A, Jander S, Linden M, Macias L, Koy M, Heimes A, Gorríz-Martín L, Segelke D, Engelmann S, Schmicke M, Hoedemaker M, Petzl W, Zerbe H, Schuberth HJ, Kühn C. Genetic selection for bovine chromosome 18 haplotypes associated with divergent somatic cell score affects postpartum reproductive and metabolic performance. J Dairy Sci 2019; 102:9983-9994. [PMID: 31521359 DOI: 10.3168/jds.2018-16171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 07/15/2019] [Indexed: 11/19/2022]
Abstract
The susceptibility of animals to periparturient diseases has a great effect on the economic efficiency of dairy industries, on the frequency of antibiotic treatment, and on animal welfare. The use of selection for breeding cows with reduced susceptibility to diseases offers a sustainable tool to improve dairy cattle farming. Several studies have focused on the association of distinct bovine chromosome 18 genotypes or haplotypes with performance traits. The aim of this study was to test whether selection of Holstein Friesian heifers via SNP genotyping for alternative paternal chromosome 18 haplotypes associated with favorable (Q) or unfavorable (q) somatic cell scores influences postpartum reproductive and metabolic diseases. Thirty-six heifers (18 Q and 18 q) were monitored from 3 wk before calving until necropsy on d 39 (± 4 d) after calving. Health status and rectal temperature were measured daily, and body condition score and body weight were assessed once per week. Blood samples were drawn twice weekly, and levels of insulin, nonesterified fatty acids, insulin-like growth factor-I, growth hormone, and β-hydroxybutyrate were measured. Comparisons between the groups were performed using Fisher's exact test, chi-squared test, and the GLIMMIX procedure in SAS. Results showed that Q-heifers had reduced incidence of metritis compared with q-heifers and were less likely to develop fever. Serum concentrations of β-hydroxybutyrate were lower and insulin-like growth factor-I plasma concentrations were higher in Q- compared with q-heifers. However, the body condition score and withers height were comparable between haplotypes, but weight loss tended to be lower in Q-heifers compared with q-heifers. No differences between the groups were detected concerning retained fetal membranes, uterine involution, or onset of cyclicity. In conclusion, selection of chromosome 18 haplotypes associated with a reduced somatic cell score resulted in a decreased incidence of postpartum reproductive and metabolic diseases in this study. The presented data add to the existing knowledge aimed at avoiding negative consequences of genetic selection strategies in dairy cattle farming. The underlying causal mechanisms modulated by haplotypes in the targeted genomic region and immune competence necessitate further investigation.
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Affiliation(s)
- M M Meyerholz
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany; Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany.
| | - L Rohmeier
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany; Clinic for Swine, Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine, 30173 Hannover, Germany
| | - T Eickhoff
- Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany
| | - A Hülsebusch
- Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany
| | - S Jander
- Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany
| | - M Linden
- Faculty of Mathematics and Physics, Leibniz University, 30167 Hannover, Germany
| | - L Macias
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany
| | - M Koy
- Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany; Clinic for Poultry, University of Veterinary Medicine, 30559 Hannover, Germany
| | - A Heimes
- Leibniz Institute for Farm Animal Biology, Genome Biology, 18196 Dummerstorf, Germany
| | - L Gorríz-Martín
- Clinic for Cattle, University of Veterinary Medicine, 30173 Hannover, Germany
| | - D Segelke
- Vereinigte Informationssysteme Tierhaltung w.V. (VIT) Verden, 27283 Verden (Aller), Germany
| | - S Engelmann
- Institute for Microbiology, Technical University, 38106 Braunschweig, Germany; Microbial Proteomics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - M Schmicke
- Clinic for Cattle, University of Veterinary Medicine, 30173 Hannover, Germany
| | - M Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine, 30173 Hannover, Germany
| | - W Petzl
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany
| | - H Zerbe
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany
| | - H-J Schuberth
- Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany
| | - Ch Kühn
- Leibniz Institute for Farm Animal Biology, Genome Biology, 18196 Dummerstorf, Germany; Agricultural and Environmental Faculty, University Rostock, 18059 Rostock, Germany
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Fragomeni BO, Lourenco DAL, Legarra A, VanRaden PM, Misztal I. Alternative SNP weighting for single-step genomic best linear unbiased predictor evaluation of stature in US Holsteins in the presence of selected sequence variants. J Dairy Sci 2019; 102:10012-10019. [PMID: 31495612 DOI: 10.3168/jds.2019-16262] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/16/2019] [Indexed: 11/19/2022]
Abstract
Causal variants inferred from sequence data analysis are expected to increase accuracy of genomic selection. In this work we evaluated the gain in reliability of genomic predictions, for stature in US Holsteins, when adding selected sequence variants to a pre-existent SNP chip. Two prediction methods were tested: de-regressed proofs assuming heterogeneous (genomic BLUP; GBLUP) residual variances and by single-step GBLUP (ssGBLUP) using actual phenotypes. Phenotypic data included 3,999,631 records for stature on 3,027,304 Holstein cows. Genotypes on 54,087 SNP markers (54k) were available for 26,877 bulls. Additionally, 16,648 selected sequence variants were combined with the 54k markers, for a total of 70,735 (70k) markers. In all methods, SNP in the genomic relationship matrix (G) were unweighted or weighted iteratively, with weights derived either by SNP effects squared or by a nonlinear method that resembles BayesA (nonlinear A). Reliability of genomic predictions were obtained by cross validation. With unweighted G derived from 54k markers, the reliabilities (× 100) were 72.4 for GBLUP and 75.3 for ssGBLUP. With unweighted G derived from 70k markers, the reliabilities were 73.4 and 76.0, respectively. Weighting by nonlinear A changed reliabilities to 73.3, and 75.9, respectively. Addition of selected sequence variants had a small effect on reliabilities. Weighting by quadratic functions reduced reliabilities. Weighting by nonlinear A increased reliabilities for GBLUP but had only a small effect in ssGBLUP. Reliabilities for direct genomic values extracted from ssGBLUP using unweighted G with 54k were higher than reliabilities by any GBLUP. Thus, ssGBLUP seems to capture more information than GBLUP and there is less room for extra reliability. Improvements in GBLUP may be because the weights in G change the covariance structure, which can explain a proportion of the variance that is accounted for when a heterogeneous residual variance is assumed by considering a different number of daughters per bull.
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Affiliation(s)
- B O Fragomeni
- Department of Animal Science, University of Connecticut, Storrs-Mansfield 06269.
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - A Legarra
- Institut National de la Recherche Agronomique, UMR1388 GenPhySE, Castanet Tolosan, France 31326
| | - P M VanRaden
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - I Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
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Heimes A, Brodhagen J, Weikard R, Hammon HM, Meyerholz MM, Petzl W, Zerbe H, Engelmann S, Schmicke M, Hoedemaker M, Schuberth HJ, Kühn C. Characterization of functional traits with focus on udder health in heifers with divergent paternally inherited haplotypes on BTA18. BMC Vet Res 2019; 15:241. [PMID: 31296208 PMCID: PMC6624885 DOI: 10.1186/s12917-019-1988-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/30/2019] [Indexed: 11/10/2022] Open
Abstract
Background A major challenge in modern medicine and animal husbandry is the issue of antimicrobial resistance. One approach to solving this potential medical hazard is the selection of farm animals with less susceptibility to infectious diseases. Recent advances in functional genome analysis and quantitative genetics have opened the horizon to apply genetic marker information for efficiently identifying animals with preferential predisposition regarding health traits. The current study characterizes functional traits with a focus on udder health in dairy heifers. The animals were selected for having inherited alternative paternal haplotypes for a genomic region on Bos taurus chromosome (BTA) 18 genetically associated with divergent susceptibility to longevity and animal health, particularly mastitis. Results In the first weeks of lactation, the q heifers which had inherited the unfavorable (q) paternal haplotype displayed a significantly higher number of udder quarters with very low somatic cell count (< 10,000 cells / ml) compared to their paternal half-sib sisters with the favorable (Q) paternal haplotype. This might result in impaired mammary gland sentinel function towards invading pathogens. Furthermore, across the course of the first lactation, there was indication that q half-sib heifers showed higher somatic cell counts, a surrogate trait for udder health, in whole milkings compared to their paternal half-sib sisters with the favorable (Q) paternal haplotype. Moreover, heifers with the haplotype Q had a higher feed intake and higher milk yield compared to those with the q haplotype. Results of this study indicate that differences in milk production and calculated energy balance per se are not the main drivers of the genetically determined differences between the BTA18 Q and q groups of heifers. Conclusions The paternally inherited haplotype from a targeted BTA18 genomic region affect somatic cell count in udder quarters during the early postpartum period and might also contribute to further aspects of animal’s health and performance traits due to indirect effects on feed intake and metabolism. Electronic supplementary material The online version of this article (10.1186/s12917-019-1988-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A Heimes
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - J Brodhagen
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - R Weikard
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - H M Hammon
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Nutritional Physiology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - M M Meyerholz
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstr. 16, 85764, Oberschleißheim, Germany
| | - W Petzl
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstr. 16, 85764, Oberschleißheim, Germany
| | - H Zerbe
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstr. 16, 85764, Oberschleißheim, Germany
| | - S Engelmann
- Institute for Microbiology, Technical University Braunschweig, Postfach 3329, 38023, Braunschweig, Germany.,Microbial Proteomics, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - M Schmicke
- Clinic for Cattle, University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173, Hanover, Germany
| | - M Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173, Hanover, Germany
| | - H-J Schuberth
- Immunology Unit, University of Veterinary Medicine Hanover, Bünteweg 2, Geb. 261, 30559, Hanover, Germany
| | - C Kühn
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany. .,Agricultural and Environmental Faculty, University Rostock, Justus-von-Liebig-Weg 6, 18059, Rostock, Germany.
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Puckowska P, Borowska A, Szwaczkowski T, Oleński K, Kamiński S. Effects of a novel missense polymorphism within the SIGLEC5 gene on fertility traits in Holstein-Friesian cattle. Reprod Domest Anim 2019; 54:1163-1168. [PMID: 31165528 DOI: 10.1111/rda.13484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/30/2019] [Indexed: 11/29/2022]
Abstract
The aim of the study was to find functional polymorphism within two exons of the SIGLEC5 (sialic acid-binding Ig-like lectin-5) gene and to examine its effects on the production and fertility traits of cows and bulls. Two hundred seventytwo Holstein-Friesian cows and 574 bulls were included in the study. Novel missense polymorphism (A > G) within exon 3 causing substitution of amino acid arginine by glutamate in position 260 of SIGLEC5 protein (R260Q) was identified by sequencing and digestion by restriction enzyme Msp I. Basic production and fertility traits of cows and estimated breeding values (EBV) of bulls were analysed. The study demonstrated a significant association of SIGLEC5 R260Q polymorphism with days open and calving interval in cows as well as with breeding value for calving interval in bulls. An opposite effect of SIGLEC5 alleles for production and fertility traits was observed: the allele G increased the breeding value for the protein yield, while the allele A increased the breeding value for the calving interval. The current study suggests the involvement of SIGLEC5 R260Q polymorphism in biological processes related to fertility traits. This finding can be applied as a biomarker for a genetic improvement programme in Holstein-Friesian cattle.
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Affiliation(s)
- Paulina Puckowska
- Department of Animal Genetics, University of Warmia and Mazury, Olsztyn, Poland
| | - Alicja Borowska
- Department of Genetics and Animal Breeding, Poznań University of Life Sciences, Poznań, Poland
| | - Tomasz Szwaczkowski
- Department of Genetics and Animal Breeding, Poznań University of Life Sciences, Poznań, Poland
| | - Kamil Oleński
- Department of Animal Genetics, University of Warmia and Mazury, Olsztyn, Poland
| | - Stanislaw Kamiński
- Department of Animal Genetics, University of Warmia and Mazury, Olsztyn, Poland
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Ma L, Cole J, Da Y, VanRaden P. Symposium review: Genetics, genome-wide association study, and genetic improvement of dairy fertility traits. J Dairy Sci 2019; 102:3735-3743. [DOI: 10.3168/jds.2018-15269] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 08/16/2018] [Indexed: 12/13/2022]
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Fang L, Jiang J, Li B, Zhou Y, Freebern E, Vanraden PM, Cole JB, Liu GE, Ma L. Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle. Commun Biol 2019; 2:100. [PMID: 30886909 PMCID: PMC6418173 DOI: 10.1038/s42003-019-0341-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 02/06/2019] [Indexed: 12/19/2022] Open
Abstract
The length of gestation can affect offspring health and performance. Both maternal and fetal effects contribute to gestation length; however, paternal contributions to gestation length remain elusive. Using genome-wide association study (GWAS) in 27,214 Holstein bulls with millions of gestation records, here we identify nine paternal genomic loci associated with cattle gestation length. We demonstrate that these GWAS signals are enriched in pathways relevant to embryonic development, and in differentially methylated regions between sperm samples with long and short gestation length. We reveal that gestation length shares genetic and epigenetic architecture in sperm with calving ability, body depth, and conception rate. While several candidate genes are detected in our fine-mapping analysis, we provide evidence indicating ZNF613 as a promising candidate for cattle gestation length. Collectively, our findings support that the paternal genome and epigenome can impact gestation length potentially through regulation of the embryonic development. Lingzhao Fang et al. studied the paternal genetic variants that affect gestational length in cattle. They found that paternal genes from pathways involved in embryonic development were associated with gestation length, and that these were often found in differentially methylated regions of the genome.
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Affiliation(s)
- Lingzhao Fang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.,Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Bingjie Li
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Ellen Freebern
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Paul M Vanraden
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
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Liu M, Fang L, Liu S, Pan MG, Seroussi E, Cole JB, Ma L, Chen H, Liu GE. Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins. BMC Genomics 2019; 20:181. [PMID: 30845913 PMCID: PMC6407259 DOI: 10.1186/s12864-019-5552-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variations (CNVs) are structural variants consisting of large-scale insertions and deletions of genomic fragments. Exploring CNVs and estimating their effects on phenotypes are useful for genome selection but remain challenging in the livestock. RESULTS We identified 1043 CNV regions (CNVRs) from array comparative genomic hybridization (CGH) data of 47 Holstein bulls. Using a probe-based CNV association approach, we detected 87 CNVRs significantly (Bonferroni-corrected P value < 0.05) associated with at least one out of 41 complex traits. Within them, 39 CNVRs were simultaneously associated with at least 2 complex traits. Notably, 24 CNVRs were markedly related to daughter pregnancy rate (DPR). For example, CNVR661 containing CYP4A11 and CNVR213 containing CTR9, respectively, were associated with DPR and other traits related to reproduction, production, and body conformation. CNVR758 was also significantly related to DPR, with a nearby gene CAPZA3, encoding one of F-actin-capping proteins which play a role in determining sperm architecture and male fertility. We corroborated these CNVRs by examining their overlapped quantitative trait loci and comparing with previously published CNV results. CONCLUSION To our knowledge, this is one of the first genome-wide association studies based on CNVs called by array CGH in Holstein cattle. Our results contribute substantial information about the potential CNV impacts on reproduction, health, production, and body conformation traits, which lay the foundation for incorporating CNV into the future dairy cattle breeding program.
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Affiliation(s)
- Mei Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, 712100 Shaanxi China
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Lingzhao Fang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD USA
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Michael G. Pan
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Eyal Seroussi
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, Department of Quantitative and Molecular Genetics, HaMaccabim Road, P.O.B 15159, 7528809 Rishon LeTsiyon, Israel
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD USA
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, 712100 Shaanxi China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
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Morenikeji OB, Akinyemi MO, Wheto M, Ogunshola OJ, Badejo AA, Chineke CA. Transcriptome profiling of four candidate milk genes in milk and tissue samples of temperate and tropical cattle. J Genet 2019. [DOI: 10.1007/s12041-019-1060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Dechow CD, Liu WS. DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield. BMC Genomics 2018; 19:744. [PMID: 30309336 PMCID: PMC6182825 DOI: 10.1186/s12864-018-5124-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/27/2018] [Indexed: 11/15/2022] Open
Abstract
Background Milk yield for Holstein cows has doubled over five decades due to genetic selection and changes to management, but the molecular mechanisms that facilitated this increase are mostly unknown. Epigenetic modifications to the cattle genome are a plausible molecular mechanism to cause variation in milk yield and our objective was to describe genome-wide DNA methylation patterns in peripheral blood mononuclear cells (PBMC) from mature Holstein dairy cows with variable milk yield. Results Whole genome MeDIP-seq was performed following DNA extraction from PBMC of 6 lactating dairy cows from 4 different herds that varied in milk yield from 13,556 kg to 23,105 kg per 305 day lactation. We describe methylation across the genome and for 13,677 protein coding genes. Repetitive element reads were primarily mapped to satellite (36.4%), SINE (29.1%), and LINE (23.7%) regions and the majority (78.4%) of CpG sites were sequenced at least once. DNA methylation was generally low upstream of genes with the nadir occurring 95 bp prior to the transcription start site (TSS). Methylation was lower in the first exon than in later exons, was highest for introns near the intron-exon junctions, and declined downstream as the distance from the gene increased. We identified 72 differentially methylated regions (DMR) between high milk yield cows and their control, and 252 DMR across herd environments. Conclusions This reference methylome for cattle with extreme variation in milk yield phenotype provides a resource to more fully evaluate relationships between DNA methylation and phenotype in populations subject to selection. The detection of DMR in cows of varying milk yield suggests potential to exploit epigenetic variation in cattle improvement programs. Electronic supplementary material The online version of this article (10.1186/s12864-018-5124-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chad D Dechow
- Department of Animal Science, College of Agricultural Sciences, The Pennsylvania State University, 324 Henning Building, University Park, State College, PA, 16802, USA.
| | - Wan-Sheng Liu
- Department of Animal Science, College of Agricultural Sciences, The Pennsylvania State University, 324 Henning Building, University Park, State College, PA, 16802, USA
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Hosseini-Vardanjani SM, Shariati MM, Moradi Shahrebabak H, Tahmoorespur M. Incorporating Prior Knowledge of Principal Components in Genomic Prediction. Front Genet 2018; 9:289. [PMID: 30116258 PMCID: PMC6082966 DOI: 10.3389/fgene.2018.00289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 07/11/2018] [Indexed: 12/05/2022] Open
Abstract
Genomic prediction using a large number of markers is challenging, due to the curse of dimensionality as well as multicollinearity arising from linkage disequilibrium between markers. Several methods have been proposed to solve these problems such as Principal Component Analysis (PCA) that is commonly used to reduce the dimension of predictor variables by generating orthogonal variables. Usually, the knowledge from PCA is incorporated in genomic prediction, assuming equal variance for the PCs or a variance proportional to the eigenvalues, both treat variances as fixed. Here, three prior distributions including normal, scaled-t and double exponential were assumed for PC effects in a Bayesian framework with a subset of PCs. These developed PCR models (dPCRm) were compared to routine genomic prediction models (RGPM) i.e., ridge and Bayesian ridge regression, BayesA, BayesB, and PC regression with a subset of PCs but PC variances predefined as proportional to the eigenvalues (PCR-Eigen). The performance of methods was compared by simulating a single trait with heritability of 0.25 on a genome consisted of 3,000 SNPs on three chromosomes and QTL numbers of 15, 60, and 105. After 500 generations of random mating as the historical population, a population was isolated and mated for another 15 generations. The generations 8 and 9 of recent population were used as the reference population and the next six generations as validation populations. The accuracy and bias of predictions were evaluated within the reference population, and each of validation populations. The accuracies of dPCRm were similar to RGPM (0.536 to 0.664 vs. 0.542 to 0.671), and higher than the accuracies of PCR-Eigen (0.504 to 0.641) within reference population over different QTL numbers. Decline in accuracies in validation populations were from 0.633 to 0.310, 0.639 to 0.313, and 0.617 to 0.298 using dPCRm, RGPM and PCR-Eigen, respectively. Prediction biases of dPCRm and RGPM were similar and always much less than biases of PCR-Eigen. In conclusion assuming PC variances as random variables via prior specification yielded higher accuracy than PCR-Eigen and same accuracy as RGPM, while fewer predictors were used.
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Affiliation(s)
| | - Mohammad M. Shariati
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran
- *Correspondence: Mohammad M. Shariati
| | - Hossein Moradi Shahrebabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Tehran, Iran
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Hillestad B, Woolliams JA, Boison SA, Grove H, Meuwissen T, Våge DI, Klemetsdal G. Detection of runs of homozygosity in Norwegian Red: Density, criteria and genotyping quality control. ACTA AGR SCAND A-AN 2018. [DOI: 10.1080/09064702.2018.1501088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
| | - J. A. Woolliams
- Department of Animal and Aquacultural Sciences (IHA), Norwegian University of Life Sciences (NMBU), Ås, Norway
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | | | - H. Grove
- Department of Research and Development, Mahidol University, Salaya, Thailand
| | - T. Meuwissen
- Department of Animal and Aquacultural Sciences (IHA), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - D. I. Våge
- Department of Animal and Aquacultural Sciences (IHA), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - G. Klemetsdal
- Department of Animal and Aquacultural Sciences (IHA), Norwegian University of Life Sciences (NMBU), Ås, Norway
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Weller JI, Bickhart DM, Wiggans GR, Tooker ME, O'Connell JR, Jiang J, Ron M, VanRaden PM. Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins. J Dairy Sci 2018; 101:9089-9107. [PMID: 30031583 DOI: 10.3168/jds.2018-14816] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 05/19/2018] [Indexed: 12/14/2022]
Abstract
Experimental designs that exploit family information can provide substantial predictive power in quantitative trait nucleotide discovery projects. Concordance between quantitative trait locus genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects segregating in the US Holstein population with probabilities of <10-20 to accept the null hypotheses of no segregating gene affecting the trait within the chromosomal segment. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome; 471 Holstein bulls had a complete genome sequence, including 64 of the grandsires. Complete concordance was obtained only for stature on chromosome 14 and daughter pregnancy rate on chromosome 18. For each quantitative trait locus, effects of the 30 polymorphisms with highest concordance scores for the analyzed trait were computed by stepwise regression for predicted transmitting abilities of 26,750 bulls with progeny test and imputed genotypes. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: complete or almost complete concordance, nominal significance of the polymorphism effect after correction for all other polymorphisms, and marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. An intronic variant marker on chromosome 5 at 93,945,738 bp explained 7% of variance for fat percentage and 74% of total multiple-marker regression variance but was concordant for only 24 of 30 families. The missense polymorphism Phe279Tyr in GHR at 31,909,478 bp on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage on chromosome 14, 12 additional missense polymorphisms were found that had almost complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The only polymorphism found likely to improve predictive power for genomic evaluation of dairy cattle was on chromosome 15; that polymorphism had a frequency of 0.45 for the allele with economically positive effects on all production traits.
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Affiliation(s)
- J I Weller
- Institute of Animal Sciences, ARO, The Volcani Center, Rishon LeZion 7505101, Israel; USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350.
| | - D M Bickhart
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350; USDA, Agricultural Research Service, Cell Wall Biology and Utilization Laboratory, Madison, WI 53706
| | - G R Wiggans
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - M E Tooker
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - J R O'Connell
- University of Maryland School of Medicine, Baltimore 21201
| | - J Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park 20742
| | - M Ron
- Institute of Animal Sciences, ARO, The Volcani Center, Rishon LeZion 7505101, Israel
| | - P M VanRaden
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
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Mokhber M, Moradi-Shahrbabak M, Sadeghi M, Moradi-Shahrbabak H, Stella A, Nicolzzi E, Rahmaninia J, Williams JL. A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds. BMC Genomics 2018; 19:449. [PMID: 29890939 PMCID: PMC5996463 DOI: 10.1186/s12864-018-4759-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 05/04/2018] [Indexed: 01/25/2023] Open
Abstract
Background Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes. The Azeri and Kuzestani buffalos are the most common indigenous Iranian breeds which have been subjected to divergent selection and are well adapted to completely different regions. Examining the genetic structure of these populations may identify genomic regions associated with adaptation to the different environments and production goals. Results A set of 385 water buffalo samples from Azeri (N = 262) and Khuzestani (N = 123) breeds were genotyped using the Axiom® Buffalo Genotyping 90 K Array. The unbiased fixation index method (FST) was used to detect signatures of selection. In total, 13 regions with outlier FST values (0.1%) were identified. Annotation of these regions using the UMD3.1 Bos taurus Genome Assembly was performed to find putative candidate genes and QTLs within the selected regions. Putative candidate genes identified include FBXO9, NDFIP1, ACTR3, ARHGAP26, SERPINF2, BOLA-DRB3, BOLA-DQB, CLN8, and MYOM2. Conclusions Candidate genes identified in regions potentially under selection were associated with physiological pathways including milk production, cytoskeleton organization, growth, metabolic function, apoptosis and domestication-related changes include immune and nervous system development. The QTL identified are involved in economically important traits in buffalo related to milk composition, udder structure, somatic cell count, meat quality, and carcass and body weight. Electronic supplementary material The online version of this article (10.1186/s12864-018-4759-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mahdi Mokhber
- Department of Animal Science, Faculty of Agriculture, Urmia University, 11Km Sero Road, P. O. Box: 165, Urmia, 5756151818, Iran.
| | - Mohammad Moradi-Shahrbabak
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, P. O. Box: 4111, Karaj, 1417614418, Iran
| | - Mostafa Sadeghi
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, P. O. Box: 4111, Karaj, 1417614418, Iran
| | - Hossein Moradi-Shahrbabak
- Department of Animal Science, Faculty of Agricultural Science and Engineering, University College of Agriculture and Natural Resources (UTCAN), University of Tehran, P. O. Box: 4111, Karaj, 1417614418, Iran
| | - Alessandra Stella
- Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, 26900, Lodi, Italy
| | - Ezequiel Nicolzzi
- Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, 26900, Lodi, Italy
| | - Javad Rahmaninia
- Department of Animal Breeding and Genetics, Animal Science Research Institute of Iran (ASRI), Karaj, 3146618361, Iran
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
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Siebert L, Staton ME, Headrick S, Lewis M, Gillespie B, Young C, Almeida RA, Oliver SP, Pighetti GM. Genome-wide association study identifies loci associated with milk leukocyte phenotypes following experimental challenge with Streptococcus uberis. Immunogenetics 2018; 70:553-562. [PMID: 29862454 DOI: 10.1007/s00251-018-1065-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 05/25/2018] [Indexed: 01/09/2023]
Abstract
Mastitis is a detrimental disease in the dairy industry that decreases milk quality and costs upwards of $2 billion annually. Often, mastitis results from bacteria entering the gland through the teat opening. Streptococcus uberis is responsible for a high percentage of subclinical and clinical mastitis. Following an intramammary experimental challenge with S. uberis on Holstein cows (n = 40), milk samples were collected and somatic cell counts (SCC) were determined by the Dairy Herd Improvement Association Laboratory. Traditional genome-wide association studies (GWAS) have utilized test day SCC or SCC lactation averages to identify loci of interest. Our approach utilizes SCC collected following a S. uberis experimental challenge to generate three novel phenotypes: (1) area under the curve (AUC) of SCC for 0-7 days and (2) 0-28 days post-challenge; and (3) when SCC returned to below 200,000 cells/mL post-challenge (< 21 days, 21-28 days, or > 28 days). Polymorphisms were identified using Illumina's BovineSNP50 v2 DNA BeadChip. Associations were tested using Plink software and identified 16 significant (p < 1.0 × 10-4) single-nucleotide polymorphisms (SNPs) across the phenotypes. Most significant SNPs were in genes linked to cell signaling, migration, and apoptosis. Several have been recognized in relation to infectious processes (ATF7, SGK1, and PACRG), but others less so (TRIO, GLRA1, CELSR2, TIAM2, CPE). Further investigation of these genes and their roles in inflammation (e.g., SCC) can provide potential targets that influence resolution of mammary gland infection. Likewise, further investigation of the identified SNP with mastitis and other disease phenotypes can provide greater insight to the potential of these SNP as genetic markers.
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Affiliation(s)
- Lydia Siebert
- Department of Animal Science, The University of Tennessee, 2506 River Drive, Knoxville, TN, 37996, USA
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, The University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN, 37996, USA
| | - Susan Headrick
- Department of Animal Science, The University of Tennessee, 2506 River Drive, Knoxville, TN, 37996, USA
| | - Mark Lewis
- Department of Animal Science, The University of Tennessee, 2506 River Drive, Knoxville, TN, 37996, USA
| | - Barbara Gillespie
- Department of Animal Science, The University of Tennessee, 2506 River Drive, Knoxville, TN, 37996, USA
| | - Charles Young
- Zoetis, 100 Campus Drive, Florham Park, NJ, 07932, USA
| | - Raul A Almeida
- Department of Animal Science, The University of Tennessee, 2506 River Drive, Knoxville, TN, 37996, USA
| | - Stephen P Oliver
- Department of Animal Science, The University of Tennessee, 2506 River Drive, Knoxville, TN, 37996, USA.,AgResearch, The University of Tennessee, 2621 Morgan Circle, Knoxville, TN, 37996, USA
| | - Gina M Pighetti
- Department of Animal Science, The University of Tennessee, 2506 River Drive, Knoxville, TN, 37996, USA.
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Zhang C, Kemp RA, Stothard P, Wang Z, Boddicker N, Krivushin K, Dekkers J, Plastow G. Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants. Genet Sel Evol 2018; 50:14. [PMID: 29625549 PMCID: PMC5889553 DOI: 10.1186/s12711-018-0387-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 03/27/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Increasing marker density was proposed to have potential to improve the accuracy of genomic prediction for quantitative traits; whole-sequence data is expected to give the best accuracy of prediction, since all causal mutations that underlie a trait are expected to be included. However, in cattle and chicken, this assumption is not supported by empirical studies. Our objective was to compare the accuracy of genomic prediction of feed efficiency component traits in Duroc pigs using single nucleotide polymorphism (SNP) panels of 80K, imputed 650K, and whole-genome sequence variants using GBLUP, BayesB and BayesRC methods, with the ultimate purpose to determine the optimal method to increase genetic gain for feed efficiency in pigs. RESULTS Phenotypes of average daily feed intake (ADFI), average daily gain (ADG), ultrasound backfat depth (FAT), and loin muscle depth (LMD) were available for 1363 Duroc boars from a commercial breeding program. Genotype imputation accuracies reached 92.1% from 80K to 650K and 85.6% from 650K to whole-genome sequence variants. Average accuracies across methods and marker densities of genomic prediction of ADFI, FAT, LMD and ADG were 0.40, 0.65, 0.30 and 0.15, respectively. For ADFI and FAT, BayesB outperformed GBLUP, but increasing marker density had little advantage for genomic prediction. For ADG and LMD, GBLUP outperformed BayesB, while BayesRC based on whole-genome sequence data gave the best accuracies and reached up to 0.35 for LMD and 0.25 for ADG. CONCLUSIONS Use of genomic information was beneficial for prediction of ADFI and FAT but not for that of ADG and LMD compared to pedigree-based estimates. BayesB based on 80K SNPs gave the best genomic prediction accuracy for ADFI and FAT, while BayesRC based on whole-genome sequence data performed best for ADG and LMD. We suggest that these differences between traits in the effect of marker density and method on accuracy of genomic prediction are mainly due to the underlying genetic architecture of the traits.
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Affiliation(s)
- Chunyan Zhang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | | | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Zhiquan Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | | | - Kirill Krivushin
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Jack Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada.
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Tiezzi F, Arceo ME, Cole JB, Maltecca C. Including gene networks to predict calving difficulty in Holstein, Brown Swiss and Jersey cattle. BMC Genet 2018; 19:20. [PMID: 29609562 PMCID: PMC5880070 DOI: 10.1186/s12863-018-0606-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/15/2018] [Indexed: 11/10/2022] Open
Abstract
Background Calving difficulty or dystocia has a great economic impact in the US dairy industry. Reported risk factors associated with calving difficulty are feto-pelvic disproportion, gestation length and conformation. Different dairy cattle breeds have different incidence of calving difficulty, with Holstein having the highest dystocia rates and Jersey the lowest. Genomic selection becomes important especially for complex traits with low heritability, where the accuracy of conventional selection is lower. However, for complex traits where a large number of genes influence the phenotype, genome-wide association studies showed limitations. Biological networks could overcome some of these limitations and better capture the genetic architecture of complex traits. In this paper, we characterize Holstein, Brown Swiss and Jersey breed-specific dystocia networks and employ them in genomic predictions. Results Marker association analysis identified single nucleotide polymorphisms explaining the largest average proportion of genetic variance on BTA18 in Holstein, BTA25 in Brown Swiss, and BTA15 in Jersey. Gene networks derived from the genome-wide association included 1272 genes in Holstein, 1454 genes in Brown Swiss, and 1455 genes in Jersey. Furthermore, 256 genes in Holstein network, 275 genes in the Brown Swiss network, and 253 genes in the Jersey network were within previously reported dystocia quantitative trait loci. The across-breed network included 80 genes, with 9 genes being within previously reported dystocia quantitative trait loci. The gene-gene interactions in this network differed in the different breeds. Gene ontology enrichment analysis of genes in the networks showed Regulation of ARF GTPase was very significant (FDR ≤ 0.0098) on Holstein. Neuron morphogenesis and differentiation was the term most enriched (FDR ≤ 0.0539) on the across-breed network. Genomic prediction models enriched with network-derived relationship matrices did not outperform regular GBLUP models. Conclusions Regions identified in the genome were in the proximity of previously described quantitative trait loci that would most likely affect calving difficulty by altering the feto-pelvic proportion. Inclusion of identified networks did not increase prediction accuracy. The approach used in this paper could be extended to any instance with asymmetric distribution of phenotypes, for example, resistance to disease data. Electronic supplementary material The online version of this article (10.1186/s12863-018-0606-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Maria E Arceo
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD, 27705, USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA.
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Cole J, VanRaden P. Symposium review: Possibilities in an age of genomics: The future of selection indices. J Dairy Sci 2018; 101:3686-3701. [DOI: 10.3168/jds.2017-13335] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/22/2017] [Indexed: 11/19/2022]
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Taylor JF, Schnabel RD, Sutovsky P. Identification of genomic variants causing sperm abnormalities and reduced male fertility. Anim Reprod Sci 2018; 194:57-62. [PMID: 29454799 PMCID: PMC6503949 DOI: 10.1016/j.anireprosci.2018.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/08/2018] [Accepted: 02/09/2018] [Indexed: 12/18/2022]
Abstract
Whole genome sequencing has identified millions of bovine genetic variants; however, there is currently little understanding about which variants affect male fertility. It is imperative that we begin to link detrimental genetic variants to sperm phenotypes via the analysis of semen samples and measurement of fertility for bulls with alternate genotypes. Artificial insemination (AI) bulls provide a useful model system because of extensive fertility records, measured as sire conception rates (SCR). Genetic variants with moderate to large effects on fertility can be identified by sequencing the genomes of fertile and subfertile or infertile sires identified with high or low SCR as adult AI bulls or yearling bulls that failed Breeding Soundness Evaluation. Variants enriched in frequency in the sequences of subfertile/infertile bulls, particularly those likely to result in the loss of protein function or predicted to be severely deleterious to genes involved in sperm protein structure and function, semen quality or sperm morphology can be designed onto genotyping assays for validation of their effects on fertility. High throughput conventional and image-based flow cytometry, proteomics and cell imaging can be used to establish the functional effects of variants on sperm phenotypes. Integrating the genetic, fertility and sperm phenotype data will accelerate biomarker discovery and validation, improve routine semen testing in bull studs and identify new targets for cost-efficient AI dose optimization approaches such as semen nanopurification. This will maximize semen output from genetically superior sires and will increase the fertility of cattle. Better understanding of the relationships between male genotype and sperm phenotype may also yield new diagnostic tools and treatments for human male and idiopathic infertility.
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Affiliation(s)
- Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Peter Sutovsky
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
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50
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Dominance effects estimation of TLR4 and CACNA2D1 genes for health and production traits using logistic regression. J Genet 2018; 96:1027-1031. [PMID: 29321363 DOI: 10.1007/s12041-017-0870-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Knowledge of nonadditive variance and genetic effects can be helpful in explaining the total genetic variation formost of the traits. The objective of this study was to estimate dominance effects of several single-nucleotide polymorphism (SNP) genotypes for the production traits and clinical mastitis residual (CMR), in Holstein dairy cattle in a case-control study. Records of 305 days lactation were obtained for production traits and CMR. Animals were selected based on extreme values for CMR from mixed model analyses. Samples were genotyped for four SNP-single genotypes and their associations with production traits (breeding values for protein and fat yield, and protein and fat percentage) were estimated by applying logistic regression analyses. Calculation of contrast between both homozygous and heterozygous genotypes permitted to estimate dominance effects, which ranged from -0.49 to 0.35 standard deviation units for the production traits and clinical mastitis (CM), respectively. Results showed that the dominance effects may be important in contribution of total genetic effects for production traits and CM. Therefore, evaluation of animals based on additive variance alone and disregarding nonadditive effects may lead to failure in selection programmes and exactly estimating the genetic variation. The method that we used would help breeders in accurately estimation of genotypic values in a new genomic selection scenario including dominance effects.
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