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Schneider H, Haas V, Krizanac AM, Falker-Gieske C, Heise J, Tetens J, Thaller G, Bennewitz J. Mendelian randomization analysis of 34,497 German Holstein cows to infer causal associations between milk production and health traits. Genet Sel Evol 2024; 56:27. [PMID: 38589805 PMCID: PMC11000328 DOI: 10.1186/s12711-024-00896-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Claw diseases and mastitis represent the most important health issues in dairy cattle with a frequently mentioned connection to milk production. Although many studies have aimed at investigating this connection in more detail by estimating genetic correlations, they do not provide information about causality. An alternative is to carry out Mendelian randomization (MR) studies using genetic variants to investigate the effect of an exposure on an outcome trait mediated by genetic variants. No study has yet investigated the causal association of milk yield (MY) with health traits in dairy cattle. Hence, we performed a MR analysis of MY and seven health traits using imputed whole-genome sequence data from 34,497 German Holstein cows. We applied a method that uses summary statistics and removes horizontal pleiotropic variants (having an effect on both traits), which improves the power and unbiasedness of MR studies. In addition, genetic correlations between MY and each health trait were estimated to compare them with the estimates of causal effects that we expected. RESULTS All genetic correlations between MY and each health trait were negative, ranging from - 0.303 (mastitis) to - 0.019 (digital dermatitis), which indicates a reduced health status as MY increases. The only non-significant correlation was between MY and digital dermatitis. In addition, each causal association was negative, ranging from - 0.131 (mastitis) to - 0.034 (laminitis), but the number of significant associations was reduced to five nominal and two experiment-wide significant results. The latter were between MY and mastitis and between MY and digital phlegmon. Horizontal pleiotropic variants were identified for mastitis, digital dermatitis and digital phlegmon. They were located within or nearby variants that were previously reported to have a horizontal pleiotropic effect, e.g., on milk production and somatic cell count. CONCLUSIONS Our results confirm the known negative genetic connection between health traits and MY in dairy cattle. In addition, they provide new information about causality, which for example points to the negative energy balance mediating the connection between these traits. This knowledge helps to better understand whether the negative genetic correlation is based on pleiotropy, linkage between causal variants for both trait complexes, or indeed on a causal association.
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Affiliation(s)
- Helen Schneider
- Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany.
| | - Valentin Haas
- Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany
| | - Ana-Marija Krizanac
- Department of Animal Sciences, University of Göttingen, 37077, Göttingen, Germany
| | | | - Johannes Heise
- Vereinigte Informationssysteme Tierhaltung w.V. (VIT), 27283, Verden, Germany
| | - Jens Tetens
- Department of Animal Sciences, University of Göttingen, 37077, Göttingen, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts University of Kiel, 24098, Kiel, Germany
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany
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Kumar H, Panigrahi M, G Strillacci M, Sonejita Nayak S, Rajawat D, Ghildiyal K, Bhushan B, Dutt T. Detection of genome-wide copy number variation in Murrah buffaloes. Anim Biotechnol 2023; 34:3783-3795. [PMID: 37381739 DOI: 10.1080/10495398.2023.2227670] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Riverine Buffaloes, especially the Murrah breed because of their adaptability to harsh climatic conditions, is farmed in many countries to convert low-quality feed into valuable dairy products and meat. Here, we investigated the copy number variations (CNVs) in 296 Murrah buffalo using the Axiom® Buffalo Genotyping Array 90K (Affymetrix, Santa Clara, CA, USA). The CNVs were detected on the autosomes, using the Copy Number Analysis Module (CNAM) using the univariate analysis. 7937 CNVs were detected in 279 Buffaloes, the average length of the CNVs was 119,048.87 bp that ranged between 7800 and 4,561,030 bp. These CNVs were accounting for 10.33% of the buffalo genome, which was comparable to cattle, sheep, and goat CNV analyses. Further, CNVs were merged and 1541 CNVRs were detected using the Bedtools-mergeBed command. 485 genes were annotated within 196 CNVRs that were identified in at least 10 animals of Murrah population. Out of these, 40 CNVRs contained 59 different genes that were associated with 69 different traits. Overall, the study identified a significant number of CNVs and CNVRs in the Murrah breed of buffalo, with a wide range of lengths and frequencies across the autosomes. The identified CNVRs contained genes associated with important traits related to production and reproduction, making them potentially important targets for future breeding and genetic improvement efforts.
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Affiliation(s)
- Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Maria G Strillacci
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
| | | | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, India
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Nayak SS, Panigrahi M, Rajawat D, Ghildiyal K, Sharma A, Parida S, Bhushan B, Mishra BP, Dutt T. Comprehensive selection signature analyses in dairy cattle exploiting purebred and crossbred genomic data. Mamm Genome 2023; 34:615-631. [PMID: 37843569 DOI: 10.1007/s00335-023-10021-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/24/2023] [Indexed: 10/17/2023]
Abstract
The main objective of the current research was to locate, annotate, and highlight specific areas of the bovine genome that are undergoing intense positive selection. Here, we are analyzing selection signatures in crossbred (Bos taurus X Bos indicus), taurine (Bos taurus), and indicine (Bos indicus) cattle breeds. Indicine cattle breeds found throughout India are known for their higher heat tolerance and disease resilience. More breeds and more methods can provide a better understanding of the selection signature. So, we have worked on nine distinct cattle breeds utilizing seven different summary statistics, which is a fairly extensive approach. In this study, we carried out a thorough genome-wide investigation of selection signatures using bovine 50K SNP data. We have included the genotyped data of two taurine, two crossbreds, and five indicine cattle breeds, for a total of 320 animals. During the 1950s, these indicine (cebuine) cattle breeds were exported with the aim of enhancing the resilience of taurine breeds in Western countries. For this study, we employed seven summary statistics, including intra-population, i.e., Tajima's D, CLR, iHS, and ROH and inter-population statistics, i.e., FST, XP-EHH, and Rsb. The NCBI database, PANTHER 17.0, and CattleQTL database were used for annotation after finding the important areas under selection. Some genes, including EPHA6, CTNNA2, NPFFR2, HS6ST3, NPR3, KCNIP4, LIPK, SDCBP, CYP7A1, NSMAF, UBXN2B, UGDH, UBE2K, and DAB1, were shown to be shared by three or more different approaches. Therefore, it gives evidence of the most intense selection in these areas. These genes are mostly linked to milk production and adaptability traits. This study also reveals selection regions that contain genes which are crucial to numerous biological functions, including those associated with milk production, coat color, glucose metabolism, oxidative stress response, immunity and circadian rhythms.
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Affiliation(s)
- Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Anurodh Sharma
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - B P Mishra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
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Xu X, Guo Y, Li M, Duan Q, Li F, Wang J, Liu N, Huzheng J, Wang X, An X. Genome-wide association study for wattles trait in the dairy goat breed. Anim Biotechnol 2023; 34:3371-3377. [PMID: 36441629 DOI: 10.1080/10495398.2022.2149545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dairy goats are significant livestock that provide high-quality milk sources in the world. The wattles trait is an evident phenotypic character on the neck of a dairy goat, which is considered to be under genetic control. We collected samples of 189 dairy goats, including 94 with wattles and 95 without wattles, from four different farms and multiple dairy goat breeds. The samples were genotyped with the GeneSeek Genomic Profiler Goat 70 K SNP chip. Genome-wide association studies (GWAS) in wattles have identified associations with single nucleotide polymorphisms (SNPs) at chromosome 10. In this area, an extremely strong association locus was assigned to FMN1 (Formin 1) belongs to the formin homology family and is associated with limb deformity, other candidate genes of interest confirmed for wattles were ARHGAP11A (Rho GTPase Activating Protein 11 A) and GJD2 (Gap Junction Protein Delta 2). Meanwhile, we found the presence or absence of wattles had no significant effect on milk yield. This research will provide genetic resources useful to explore genetic factors affecting the trait.
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Affiliation(s)
- Xiaolong Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Yingwei Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Miaoyu Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Quyu Duan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Fu Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jintao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Nan Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jiamei Huzheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
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Bekele R, Taye M, Abebe G, Meseret S. Genomic Regions and Candidate Genes Associated with Milk Production Traits in Holstein and Its Crossbred Cattle: A Review. Int J Genomics 2023; 2023:8497453. [PMID: 37547753 PMCID: PMC10400298 DOI: 10.1155/2023/8497453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/09/2023] [Accepted: 07/19/2023] [Indexed: 08/08/2023] Open
Abstract
Genome-wide association studies (GWAS) are a powerful tool for identifying genomic regions and causative genes associated with economically important traits in dairy cattle, particularly complex traits, such as milk production. This is possible due to advances in next-generation sequencing technology. This review summarized information on identified candidate genes and genomic regions associated with milk production traits in Holstein and its crossbreds from various regions of the world. Milk production traits are important in dairy cattle breeding programs because of their direct economic impact on the industry and their close relationship with nutritional requirements. GWAS has been used in a large number of studies to identify genomic regions and candidate genes associated with milk production traits in dairy cattle. Many genomic regions and candidate genes have already been identified in Holstein and its crossbreds. Genes and single nucleotide polymorphisms (SNPs) that significantly affect milk yield (MY) were found in all autosomal chromosomes except chromosomes 27 and 29. Half of the reported SNPs associated with fat yield and fat percentage were found on chromosome 14. However, a large number of significant SNPs for protein yield (PY) and protein percentage were found on chromosomes 1, 5, and 20. Approximately 155 SNPs with significant influence on multiple milk production traits have been identified. Several promising candidate genes, including diacylglycerol O-acyltransferase 1, plectin, Rho GTPase activating protein 39, protein phosphatase 1 regulatory subunit 16A, and sphingomyelin phosphodiesterase 5 were found to have pleiotropic effects on all five milk production traits. Thus, to improve milk production traits it is of practical relevance to focus on significant SNPs and pleiotropic genes frequently found to affect multiple milk production traits.
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Affiliation(s)
- R. Bekele
- School of Animal and Range Sciences, College of Agriculture, Hawassa University, P.O. Box 5, Hawassa, Ethiopia
- Department of Animal Science, College of Agriculture and Natural Resource Sciences, Debre Berhan University, P.O. Box 445, Debre Berhan, Ethiopia
| | - M. Taye
- School of Animal and Range Sciences, College of Agriculture, Hawassa University, P.O. Box 5, Hawassa, Ethiopia
| | - G. Abebe
- School of Animal and Range Sciences, College of Agriculture, Hawassa University, P.O. Box 5, Hawassa, Ethiopia
| | - S. Meseret
- Livestock Genetics, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
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Sanchez MP, Escouflaire C, Baur A, Bottin F, Hozé C, Boussaha M, Fritz S, Capitan A, Boichard D. X-linked genes influence various complex traits in dairy cattle. BMC Genomics 2023; 24:338. [PMID: 37337145 DOI: 10.1186/s12864-023-09438-7] [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: 02/22/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The search for quantitative trait loci (QTL) affecting traits of interest in mammals is frequently limited to autosomes, with the X chromosome excluded because of its hemizygosity in males. This study aimed to assess the importance of the X chromosome in the genetic determinism of 11 complex traits related to milk production, milk composition, mastitis resistance, fertility, and stature in 236,496 cows from three major French dairy breeds (Holstein, Montbéliarde, and Normande) and three breeds of regional importance (Abondance, Tarentaise, and Vosgienne). RESULTS Estimates of the proportions of heritability due to autosomes and X chromosome (h²X) were consistent among breeds. On average over the 11 traits, h²X=0.008 and the X chromosome explained ~ 3.5% of total genetic variance. GWAS was performed within-breed at the sequence level (~ 200,000 genetic variants) and then combined in a meta-analysis. QTL were identified for most breeds and traits analyzed, with the exception of Tarentaise and Vosgienne and two fertility traits. Overall, 3, 74, 59, and 71 QTL were identified in Abondance, Montbéliarde, Normande, and Holstein, respectively, and most were associated with the most-heritable traits (milk traits and stature). The meta-analyses, which assessed a total of 157 QTL for the different traits, highlighted new QTL and refined the positions of some QTL found in the within-breed analyses. Altogether, our analyses identified a number of functional candidate genes, with the most notable being GPC3, MBNL3, HS6ST2, and DMD for dairy traits; TMEM164, ACSL4, ENOX2, HTR2C, AMOT, and IRAK1 for udder health; MAMLD1 and COL4A6 for fertility; and NRK, ESX1, GPR50, GPC3, and GPC4 for stature. CONCLUSIONS This study demonstrates the importance of the X chromosome in the genetic determinism of complex traits in dairy cattle and highlights new functional candidate genes and variants for these traits. These results could potentially be extended to other species as many X-linked genes are shared among mammals.
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Affiliation(s)
- Marie-Pierre Sanchez
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France.
| | | | | | - Fiona Bottin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | | | - Mekki Boussaha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | | | - Aurélien Capitan
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - Didier Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
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Masharing N, Sodhi M, Chanda D, Singh I, Vivek P, Tiwari M, Kumari P, Mukesh M. ddRAD sequencing based genotyping of six indigenous dairy cattle breeds of India to infer existing genetic diversity and population structure. Sci Rep 2023; 13:9379. [PMID: 37296129 PMCID: PMC10256769 DOI: 10.1038/s41598-023-32418-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/27/2023] [Indexed: 06/12/2023] Open
Abstract
The present investigation aimed to identify genome wide SNPs and to carry out diversity and population structure study using ddRAD-seq based genotyping of 58 individuals of six indigenous milch cattle breeds (Bos indicus) such as Sahiwal, Gir, Rathi, Tharparkar, Red Sindhi and Kankrej of India. A high percentage of reads (94.53%) were mapped to the Bos taurus (ARS-UCD1.2) reference genome assembly. Following filtration criteria, a total of 84,027 high quality SNPs were identified across the genome of 6 cattle breeds with the highest number of SNPs observed in Gir (34,743), followed by Red Sindhi (13,092), Kankrej (12,812), Sahiwal (8956), Tharparkar (7356) and Rathi (7068). Most of these SNPs were distributed in the intronic regions (53.87%) followed by intergenic regions (34.94%) while only 1.23% were located in the exonic regions. Together with analysis of nucleotide diversity (π = 0.373), Tajima's D (D value ranging from - 0.295 to 0.214), observed heterozygosity (HO ranging from 0.464 to 0.551), inbreeding coefficient (FIS ranging from - 0.253 to 0.0513) suggested for the presence of sufficient within breed diversity in the 6 major milch breeds of India. The phylogenetic based structuring, principal component and admixture analysis revealed genetic distinctness as well as purity of almost all of the 6 cattle breeds. Overall, our strategy has successfully identified thousands of high-quality genome wide SNPs that will further enrich the Bos indicus representation basic information about genetic diversity and structure of 6 major Indian milch cattle breeds which should have implications for better management and conservation of valuable indicine cattle diversity.
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Affiliation(s)
- Nampher Masharing
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Monika Sodhi
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Divya Chanda
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Inderpal Singh
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Prince Vivek
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manish Tiwari
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Parvesh Kumari
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manishi Mukesh
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India.
- ICAR-NBAGR, Karnal, Haryana, 132001, India.
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Schneider H, Segelke D, Tetens J, Thaller G, Bennewitz J. A genomic assessment of the correlation between milk production traits and claw and udder health traits in Holstein dairy cattle. J Dairy Sci 2023; 106:1190-1205. [PMID: 36460501 DOI: 10.3168/jds.2022-22312] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022]
Abstract
Claw diseases and mastitis represent the most important disease traits in dairy cattle with increasing incidences and a frequently mentioned connection to milk yield. Yet, many studies aimed to detect the genetic background of both trait complexes via fine-mapping of quantitative trait loci. However, little is known about genomic regions that simultaneously affect milk production and disease traits. For this purpose, several tools to detect local genetic correlations have been developed. In this study, we attempted a detailed analysis of milk production and disease traits as well as their interrelationship using a sample of 34,497 50K genotyped German Holstein cows with milk production and claw and udder disease traits records. We performed a pedigree-based quantitative genetic analysis to estimate heritabilities and genetic correlations. Additionally, we generated GWAS summary statistics, paying special attention to genomic inflation, and used these data to identify shared genomic regions, which affect various trait combinations. The heritability on the liability scale of the disease traits was low, between 0.02 for laminitis and 0.19 for interdigital hyperplasia. The heritabilities for milk production traits were higher (between 0.27 for milk energy yield and 0.48 for fat-protein ratio). Global genetic correlations indicate the shared genetic effect between milk production and disease traits on a whole genome level. Most of these estimates were not significantly different from zero, only mastitis showed a positive one to milk (0.18) and milk energy yield (0.13), as well as a negative one to fat-protein ratio (-0.07). The genomic analysis revealed significant SNPs for milk production traits that were enriched on Bos taurus autosome 5, 6, and 14. For digital dermatitis, we found significant hits, predominantly on Bos taurus autosome 5, 10, 22, and 23, whereas we did not find significantly trait-associated SNPs for the other disease traits. Our results confirm the known genetic background of disease and milk production traits. We further detected 13 regions that harbor strong concordant effects on a trait combination of milk production and disease traits. This detailed investigation of genetic correlations reveals additional knowledge about the localization of regions with shared genetic effects on these trait complexes, which in turn enables a better understanding of the underlying biological pathways and putatively the utilization for a more precise design of breeding schemes.
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Affiliation(s)
- Helen Schneider
- Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Dierck Segelke
- Vereinigte Informationssysteme Tierhaltung w.V. (VIT), 27283 Verden, Germany
| | - Jens Tetens
- Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts University of Kiel, 24098 Kiel, Germany
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany
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Modorov MV, Kleshcheva AA, Osintseva KR, Tkachenko IV, Sevost’yanov MY, Zezin NN. The Use of KASP Technology to Study Associations of Single Nucleotide Polymorphisms in the GPAD4, CCL3, DGKG, PPARGC1A, STAT1, and TLR4 Genes with Milk Production in Cattle. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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Liu D, Xu Z, Zhao W, Wang S, Li T, Zhu K, Liu G, Zhao X, Wang Q, Pan Y, Ma P. Genetic parameters and genome-wide association for milk production traits and somatic cell score in different lactation stages of Shanghai Holstein population. Front Genet 2022; 13:940650. [PMID: 36134029 PMCID: PMC9483179 DOI: 10.3389/fgene.2022.940650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to investigate the genetic parameters and genetic architectures of six milk production traits in the Shanghai Holstein population. The data used to estimate the genetic parameters consisted of 1,968,589 test-day records for 305,031 primiparous cows. Among the cows with phenotypes, 3,016 cows were genotyped with Illumina Bovine SNP50K BeadChip, GeneSeek Bovine 50K BeadChip, GeneSeek Bovine LD BeadChip v4, GeneSeek Bovine 150K BeadChip, or low-depth whole-genome sequencing. A genome-wide association study was performed to identify quantitative trait loci and genes associated with milk production traits in the Shanghai Holstein population using genotypes imputed to whole-genome sequences and both fixed and random model circulating probability unification and a mixed linear model with rMVP software. Estimated heritabilities (h2) varied from 0.04 to 0.14 for somatic cell score (SCS), 0.07 to 0.22 for fat percentage (FP), 0.09 to 0.27 for milk yield (MY), 0.06 to 0.23 for fat yield (FY), 0.09 to 0.26 for protein yield (PY), and 0.07 to 0.35 for protein percentage (PP), respectively. Within lactation, genetic correlations for SCS, FP, MY, FY, PY, and PP at different stages of lactation estimated in random regression model were ranged from -0.02 to 0.99, 0.18 to 0.99, 0.04 to 0.99, 0.04 to 0.99, 0.01 to 0.99, and 0.33 to 0.99, respectively. The genetic correlations were highest between adjacent DIM but decreased as DIM got further apart. Candidate genes included those related to production traits (DGAT1, MGST1, PTK2, and SCRIB), disease-related (LY6K, COL22A1, TECPR2, and PLCB1), heat stress–related (ITGA9, NDST4, TECPR2, and HSF1), and reproduction-related (7SK and DOCK2) genes. This study has shown that there are differences in the genetic mechanisms of milk production traits at different stages of lactation. Therefore, it is necessary to conduct research on milk production traits at different stages of lactation as different traits. Our results can also provide a theoretical basis for subsequent molecular breeding, especially for the novel genetic loci.
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Affiliation(s)
- Dengying Liu
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhong Xu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Wei Zhao
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shiyi Wang
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Tuowu Li
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Zhu
- Shanghai Dairy Cattle Breeding Centre Co, Ltd, Shanghai, China
| | - Guanglei Liu
- Shanghai Dairy Cattle Breeding Centre Co, Ltd, Shanghai, China
| | - Xiaoduo Zhao
- Shanghai Dairy Cattle Breeding Centre Co, Ltd, Shanghai, China
| | - Qishan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
- *Correspondence: Peipei Ma, ; Yuchun Pan,
| | - Peipei Ma
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Peipei Ma, ; Yuchun Pan,
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11
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Du A, Zhao F, Liu Y, Xu L, Chen K, Sun D, Han B. Genetic polymorphisms of PKLR gene and their associations with milk production traits in Chinese Holstein cows. Front Genet 2022; 13:1002706. [PMID: 36118870 PMCID: PMC9479125 DOI: 10.3389/fgene.2022.1002706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Our previous work had confirmed that pyruvate kinase L/R (PKLR) gene was expressed differently in different lactation periods of dairy cattle, and participated in lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, suggesting that PKLR is a candidate gene to affect milk production traits in dairy cattle. Here, we verified whether this gene has significant genetic association with milk yield and composition traits in a Chinese Holstein cow population. In total, we identified 21 single nucleotide polymorphisms (SNPs) by resequencing the entire coding region and partial flanking region of PKLR gene, in which, two SNPs were located in 5′ promoter region, two in 5′ untranslated region (UTR), three in introns, five in exons, six in 3′ UTR and three in 3′ flanking region. The single marker association analysis displayed that all SNPs were significantly associated with milk yield, fat and protein yields or protein percentage (p ≤ 0.0497). The haplotype block containing all the SNPs, predicted by Haploview, had a significant association with fat yield and protein percentage (p ≤ 0.0145). Further, four SNPs in 5′ regulatory region and eight SNPs in UTR and exon regions were predicted to change the transcription factor binding sites (TFBSs) and mRNA secondary structure, respectively, thus affecting the expression of PKLR, leading to changes in milk production phenotypes, suggesting that these SNPs might be the potential functional mutations for milk production traits in dairy cattle. In conclusion, we demonstrated that PKLR had significant genetic effects on milk production traits, and the SNPs with significant genetic effects could be used as candidate genetic markers for genomic selection (GS) in dairy cattle.
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Affiliation(s)
- Aixia Du
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Department of Animal Genetics and Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | | | - Yanan Liu
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Department of Animal Genetics and Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lingna Xu
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Department of Animal Genetics and Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kewei Chen
- Yantai Institute, China Agricultural University, Yantai, China
| | - Dongxiao Sun
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Department of Animal Genetics and Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Bo Han
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Department of Animal Genetics and Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Bo Han, /
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de Sousa Rego R, Jangarelli M, Soares MAM, Puerro de Melo AL, Rodrigues MT, de Oliveira HR, Garcia IS. Polymorphism in β-lactoglobulin gene and its association with dairy goats’ production traits. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Wang N, Gao J, Liu Y, Shi R, Chen S. Identification of crucial factors involved in Cynoglossus semilaevis sexual size dimorphism by GWAS and demonstration of zbed1 regulatory network by DAP-seq. Genomics 2022; 114:110376. [PMID: 35513290 DOI: 10.1016/j.ygeno.2022.110376] [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: 11/02/2021] [Revised: 04/07/2022] [Accepted: 04/27/2022] [Indexed: 01/14/2023]
Abstract
Sexual size dimorphism (SSD), whereby females and males exhibit different body sizes, are widely documented in animals. To explore crucial regulators implicated in female-biased SSD of Chinese tongue sole (Cynoglossus semilaevis), GWAS was conducted on 350 females and 59 males. Twenty SNPs and 25 genes including zbed1, nsd3, cdc45, klhl29, and smad4 with -log(p) > 7 were screened, mainly mapping to sex chromosome. The chromosome W-linked gene zbed1 attracted particular attention because it is a master key for cell proliferation. Thus, the regulatory network of zbed1 in C. semilaevis was explored by DAP-seq and 1352 peaks were discovered in the female brain. Moreover, zbed1 potentially regulated hippo signaling pathway, cell cycle, translation, and PI3k-Akt signaling pathway in C. semilaevis. These findings identify crucial SNPs and genes associated with female-biased SSD in C. semilaevis, also provide the first genome-wide survey for the zbed1 regulatory network in fish species.
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Affiliation(s)
- Na Wang
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China.
| | - Jin Gao
- Hainan Academy of Ocean and Fisheries Sciences, Haikou 570203, China
| | - Yang Liu
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Rui Shi
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Songlin Chen
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China.
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Lu X, Arbab AAI, Abdalla IM, Liu D, Zhang Z, Xu T, Su G, Yang Z. Genetic Parameter Estimation and Genome-Wide Association Study-Based Loci Identification of Milk-Related Traits in Chinese Holstein. Front Genet 2022; 12:799664. [PMID: 35154251 PMCID: PMC8836289 DOI: 10.3389/fgene.2021.799664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/07/2021] [Indexed: 11/22/2022] Open
Abstract
Accurately estimating the genetic parameters and revealing more genetic variants underlying milk production and quality are conducive to the genetic improvement of dairy cows. In this study, we estimate the genetic parameters of five milk-related traits of cows-namely, milk yield (MY), milk fat percentage (MFP), milk fat yield (MFY), milk protein percentage (MPP), and milk protein yield (MPY)-based on a random regression test-day model. A total of 95,375 test-day records of 9,834 cows in the lower reaches of the Yangtze River were used for the estimation. In addition, genome-wide association studies (GWASs) for these traits were conducted, based on adjusted phenotypes. The heritability, as well as the standard errors, of MY, MFP, MFY, MPP, and MPY during lactation ranged from 0.22 ± 0.02 to 0.31 ± 0.04, 0.06 ± 0.02 to 0.15 ± 0.03, 0.09 ± 0.02 to 0.28 ± 0.04, 0.07 ± 0.01 to 0.16 ± 0.03, and 0.14 ± 0.02 to 0.27 ± 0.03, respectively, and the genetic correlations between different days in milk (DIM) within lactations decreased as the time interval increased. Two, six, four, six, and three single nucleotide polymorphisms (SNPs) were detected, which explained 5.44, 12.39, 8.89, 10.65, and 7.09% of the phenotypic variation in MY, MFP, MFY, MPP, and MPY, respectively. Ten Kyoto Encyclopedia of Genes and Genomes pathways and 25 Gene Ontology terms were enriched by analyzing the nearest genes and genes within 200 kb of the detected SNPs. Moreover, 17 genes in the enrichment results that may play roles in milk production and quality were selected as candidates, including CAMK2G, WNT3A, WNT9A, PLCB4, SMAD9, PLA2G4A, ARF1, OPLAH, MGST1, CLIP1, DGAT1, PRMT6, VPS28, HSF1, MAF1, TMEM98, and F7. We hope that this study will provide useful information for in-depth understanding of the genetic architecture of milk production and quality traits, as well as contribute to the genomic selection work of dairy cows in the lower reaches of the Yangtze River.
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Affiliation(s)
- Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | | | | | - Dingding Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhipeng Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tianle Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Pedrosa VB, Schenkel FS, Chen SY, Oliveira HR, Casey TM, Melka MG, Brito LF. Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data. Genes (Basel) 2021; 12:genes12111830. [PMID: 34828436 PMCID: PMC8624223 DOI: 10.3390/genes12111830] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 12/22/2022] Open
Abstract
Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.
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Affiliation(s)
- Victor B. Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, Brazil
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Theresa M. Casey
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
| | - Melkaye G. Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI 54022, USA;
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Correspondence:
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16
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Jia R, Fu Y, Xu L, Li H, Li Y, Liu L, Ma Z, Sun D, Han B. Associations between polymorphisms of SLC22A7, NGFR, ARNTL and PPP2R2B genes and Milk production traits in Chinese Holstein. BMC Genom Data 2021; 22:47. [PMID: 34732138 PMCID: PMC8567656 DOI: 10.1186/s12863-021-01002-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/22/2021] [Indexed: 12/27/2022] Open
Abstract
Background Our preliminary work confirmed that, SLC22A7 (solute carrier family 22 member 7), NGFR (nerve growth factor receptor), ARNTL (aryl hydrocarbon receptor nuclear translocator like) and PPP2R2B (protein phosphatase 2 regulatory subunit Bβ) genes were differentially expressed in dairy cows during different stages of lactation, and involved in the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, so we considered these four genes as the candidates affecting milk production traits. In this study, we detected polymorphisms of the four genes and verified their genetic effects on milk yield and composition traits in a Chinese Holstein cow population. Results By resequencing the whole coding region and part of the flanking region of SLC22A7, NGFR, ARNTL and PPP2R2B, we totally found 20 SNPs, of which five were located in SLC22A7, eight in NGFR, three in ARNTL, and four in PPP2R2B. Using Haploview4.2, we found three haplotype blocks including five SNPs in SLC22A7, eight in NGFR and three in ARNTL. Single-SNP association analysis showed that 19 out of 20 SNPs were significantly associated with at least one of milk yield, fat yield, fat percentage, protein yield or protein percentage in the first and second lactations (P < 0.05). Haplotype-based association analysis showed that the three haplotypes were significantly associated with at least one of milk yield, fat yield, fat percentage, protein yield or protein percentage (P < 0.05). Further, we used SOPMA software to predict a SNP, 19:g.37095131C > T in NGFR, changed the structure of NGFR protein. In addition, we used Jaspar software to found that four SNPs, 19:g.37113872C > G,19:g.37113157C > T, and 19:g.37112276C > T in NGFR and 15:g.39320936A > G in ARNTL, could change the transcription factor binding sites and might affect the expression of the corresponding genes. These five SNPs might be the potential functional mutations for milk production traits in dairy cattle. Conclusions In summary, we proved that SLC22A7, NGFR, ARNTL and PPP2R2B have significant genetic effects on milk production traits. The valuable SNPs can be used as candidate genetic markers for genomic selection of dairy cattle, and the effects of these SNPs on other traits need to be further verified. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-01002-0.
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Affiliation(s)
- Ruike Jia
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yihan Fu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Lingna Xu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Houcheng Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yanhua Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.,Beijing Dairy Cattle Center, Beijing, 100192, China
| | - Lin Liu
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - Zhu Ma
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - Dongxiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Bo Han
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
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Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle. Animals (Basel) 2021; 11:ani11082259. [PMID: 34438715 PMCID: PMC8388412 DOI: 10.3390/ani11082259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/24/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Feet and leg problems are among the major reasons for dairy cows leaving the herd, as well as having direct association with production and reproduction efficiency, health (e.g., claw disorders and lameness) and welfare. Hence, understanding the genetic architecture underlying feet and conformation traits in dairy cattle offers new opportunities toward the genetic improvement and long-term selection. Through a genome-wide association study on Chinese Holstein cattle, we identified several candidate genes associated with feet and leg conformation traits. These results could provide useful information about the molecular breeding basis of feet and leg traits, thus improving the longevity and productivity of dairy cattle. Abstract Feet and leg conformation traits are considered one of the most important economical traits in dairy cattle and have a great impact on the profitability of milk production. Therefore, identifying the single nucleotide polymorphisms (SNPs), genes and pathways analysis associated with these traits might contribute to the genomic selection and long-term plan selection for dairy cattle. We conducted genome-wide association studies (GWASs) using the fixed and random model circulating probability unification (FarmCPU) method to identify SNPs associated with bone quality, heel depth, rear leg side view and rear leg rear view of Chinese Holstein cows. Phenotypic measurements were collected from 1000 individuals of Chinese Holstein cattle and the GeneSeek Genomic Profiler Bovine 100 K SNP chip was utilized for individual genotyping. After quality control, 984 individual cows and 84,906 SNPs remained for GWAS work; as a result, we identified 20 significant SNPs after Bonferroni correction. Several candidate genes were identified within distances of 200 kb upstream or downstream to the significant SNPs, including ADIPOR2, INPP4A, DNMT3A, ALDH1A2, PCDH7, XKR4 and CADPS. Further bioinformatics analyses showed 34 gene ontology terms and two signaling pathways were significantly enriched (p ≤ 0.05). Many terms and pathways are related to biological quality, metabolism and development processes; these identified SNPs and genes could provide useful information about the genetic architecture of feet and leg traits, thus improving the longevity and productivity of Chinese Holstein dairy cattle.
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Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle. Genes (Basel) 2021; 12:genes12081163. [PMID: 34440337 PMCID: PMC8391191 DOI: 10.3390/genes12081163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/16/2022] Open
Abstract
This genome-wide association study (GWAS) aimed to identify sequence variants (SVs) and candidate genes associated with fertility and health in endangered German Black Pied cattle (DSN) based on whole-genome sequence (WGS) data. We used 304 sequenced DSN cattle for the imputation of 1797 genotyped DSN to WGS. The final dataset included 11,413,456 SVs of 1886 cows. Cow traits were calving-to-first service interval (CTFS), non-return after 56 days (NR56), somatic cell score (SCS), fat-to-protein ratio (FPR), and three pre-corrected endoparasite infection traits. We identified 40 SVs above the genome-wide significance and suggestive threshold associated with CTFS and NR56, and three important potential candidate genes (ARHGAP21, MARCH11, and ZNF462). For SCS, most associations were observed on BTA 25. The GWAS revealed 61 SVs, a cluster of 10 candidate genes on BTA 13, and 7 pathways for FPR, including key mediators involved in milk fat synthesis. The strongest associations for gastrointestinal nematode and Dictyocaulus viviparus infections were detected on BTA 8 and 24, respectively. For Fasciola hepatica infections, the strongest associated SVs were located on BTA 4 and 7. We detected 200 genes for endoparasite infection traits, related to 16 pathways involved in host immune response during infection.
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Lu X, Abdalla IM, Nazar M, Fan Y, Zhang Z, Wu X, Xu T, Yang Z. Genome-Wide Association Study on Reproduction-Related Body-Shape Traits of Chinese Holstein Cows. Animals (Basel) 2021; 11:1927. [PMID: 34203505 PMCID: PMC8300307 DOI: 10.3390/ani11071927] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 12/24/2022] Open
Abstract
Reproduction is an important production activity for dairy cows, and their reproductive performance can directly affect the level of farmers' income. To better understand the genomic regions and biological pathways of reproduction-related traits of dairy cows, in the present study, three body shape traits-Loin Strength (LS), Rump Angle (RA), and Pin Width (PW)-were selected as indicators of the reproductive ability of cows, and we conducted genome-wide association analyses on them. The heritability of these three traits was medium, ranging from 0.20 to 0.38. A total of 11 significant single-nucleotide polymorphisms (SNPs) were detected associated with these three traits. Bioinformatics analysis was performed on genes close to the significant SNPs (within 200 Kb) of LS, RA, and PW, and we found that these genes were totally enriched in 20 gene ontology terms and six KEGG signaling pathways. Finally, the five genes CDH12, TARP, PCDH9, DTHD1, and ARAP2 were selected as candidate genes that might affect LS. The six genes LOC781835, FSTL4, ATG4C, SH3BP4, DMP1, and DSPP were selected as candidate genes that might affect RA. The five genes USP6NL, CNTN3, LOC101907665, UPF2, and ECHDC3 were selected as candidate genes that might affect the PW of Chinese Holstein cows. Our results could provide useful biological information for the improvement of body shape traits and contribute to the genomic selection of Chinese Holstein cows.
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Affiliation(s)
- Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Ismail Mohamed Abdalla
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Mudasir Nazar
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Yongliang Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Zhipeng Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Xinyue Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Tianle Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China;
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
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Kim S, Lim B, Cho J, Lee S, Dang CG, Jeon JH, Kim JM, Lee J. Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle. Animals (Basel) 2021; 11:ani11051392. [PMID: 34068321 PMCID: PMC8153329 DOI: 10.3390/ani11051392] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Milk production traits that are economically important in the dairy industry have been considered the main selection criteria for breeding. The present genome-wide association study was performed to identify chromosomal loci and candidate genes with potential effects on milk production phenotypes in a Korean Holstein population. A total of eight significant quantitative trait locus regions were identified for milk yield (Bos taurus autosome (BTA) 7 and 14), adjusted 305-d fat yield (BTA 3, 5, and 14), adjusted 305-d protein yield (BTA 8), and somatic cell score (BTA 8 and 23) of milk production traits. Furthermore, we discovered three main candidate genes (diacylglycerol O-acyltransferase 1 (DGAT1), phosphodiesterase 4B (PDE4B), and anoctamin 2 (ANO2)) through bioinformatics analysis. These genes may help to understand better the underlying genetic and molecular mechanisms for milk production phenotypes in the Korean Holstein population. Abstract We performed a genome-wide association study and fine mapping using two methods (single marker regression: frequentist approach and Bayesian C (BayesC): fitting selected single nucleotide polymorphisms (SNPs) in a Bayesian framework) through three high-density SNP chip platforms to analyze milk production phenotypes in Korean Holstein cattle (n = 2780). We identified four significant SNPs for each phenotype in the single marker regression model: AX-311625843 and AX-115099068 on Bos taurus autosome (BTA) 14 for milk yield (MY) and adjusted 305-d fat yield (FY), respectively, AX-428357234 on BTA 18 for adjusted 305-d protein yield (PY), and AX-185120896 on BTA 5 for somatic cell score (SCS). Using the BayesC model, we discovered significant 1-Mb window regions that harbored over 0.5% of the additive genetic variance effects for four milk production phenotypes. The concordant significant SNPs and 1-Mb window regions were characterized into quantitative trait loci (QTL). Among the QTL regions, we focused on a well-known gene (diacylglycerol O-acyltransferase 1 (DGAT1)) and newly identified genes (phosphodiesterase 4B (PDE4B), and anoctamin 2 (ANO2)) for MY and FY, and observed that DGAT1 is involved in glycerolipid metabolism, fat digestion and absorption, metabolic pathways, and retinol metabolism, and PDE4B is involved in cAMP signaling. Our findings suggest that the candidate genes in QTL are strongly related to physiological mechanisms related to the fat production and consequent total MY in Korean Holstein cattle.
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Affiliation(s)
- Sangwook Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea; (S.K.); (B.L.)
| | - Byeonghwi Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea; (S.K.); (B.L.)
| | - Joohyeon Cho
- Dairy Cattle Genetic Improvement Center, Nonghyup, Goyang 10292, Gyeonggi-do, Korea; (J.C.); (S.L.)
| | - Seokhyun Lee
- Dairy Cattle Genetic Improvement Center, Nonghyup, Goyang 10292, Gyeonggi-do, Korea; (J.C.); (S.L.)
| | - Chang-Gwon Dang
- Animal Genetics and Breeding Division, National Institute of Animal Science, RDA, Cheonan 31000, Chungcheongnam-do, Korea;
| | - Jung-Hwan Jeon
- Animal Welfare Research Team, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea;
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea; (S.K.); (B.L.)
- Correspondence: (J.-M.K.); (J.L.); Tel.: +82-31-670-3263 (J.-M.K. & J.L.); Fax: +82-31-675-3108 (J.-M.K. & J.L.)
| | - Jungjae Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea; (S.K.); (B.L.)
- Correspondence: (J.-M.K.); (J.L.); Tel.: +82-31-670-3263 (J.-M.K. & J.L.); Fax: +82-31-675-3108 (J.-M.K. & J.L.)
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Sutera AM, Di Gerlando R, Mastrangelo S, Sardina MT, D’Alessandro E, Portolano B, Tolone M. Genome-wide association study for milk production traits in an economically important local dairy sheep breed. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1963865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Anna Maria Sutera
- Dipartimento di Scienze Veterinarie, Università di Messina, Messina, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | | | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
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