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Silva FG, Silva SR, Pereira AMF, Cerqueira JL, Conceição C. A Comprehensive Review of Bovine Colostrum Components and Selected Aspects Regarding Their Impact on Neonatal Calf Physiology. Animals (Basel) 2024; 14:1130. [PMID: 38612369 PMCID: PMC11010951 DOI: 10.3390/ani14071130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Colostrum contains macro- and micronutrients necessary to meet the nutritional and energy requirements of the neonatal calf, bioactive components that intervene in several physiological aspects, and cells and microorganisms that modulate the calf's immune system and gut microbiome. Colostrum is sometimes mistaken as transition milk, which, although more nutritive than whole milk, has a distinct biochemical composition. Furthermore, most research about colostrum quality and colostrum management focuses on the transfer of maternal IgG to the newborn calf. The remaining components of colostrum and transition milk have not received the same attention, despite their importance to the newborn animal. In this narrative review, a large body of literature on the components of bovine colostrum was reviewed. The variability of these components was summarized, emphasizing specific components that warrant deeper exploration. In addition, the effects of each component present in colostrum and transition milk on several key physiological aspects of the newborn calf are discussed.
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Affiliation(s)
- Flávio G. Silva
- Veterinary and Animal Research Centre (CECAV), Associate Laboratory of Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal (J.L.C.)
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Department of Zootechnics, School of Science and Technology, University of Évora, Pólo da Mitra Apartado 94, 7006-554 Évora, Portugal; (A.M.F.P.); (C.C.)
- Center for Research and Development in Agrifood Systems and Sustainability, Polytechnic Institute of Viana do Castelo, Agrarian School of Ponte de Lima, Rua D. Mendo Afonso, 147 Refóios do Lima, 4990-706 Ponte de Lima, Portugal
| | - Severiano R. Silva
- Veterinary and Animal Research Centre (CECAV), Associate Laboratory of Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal (J.L.C.)
| | - Alfredo M. F. Pereira
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Department of Zootechnics, School of Science and Technology, University of Évora, Pólo da Mitra Apartado 94, 7006-554 Évora, Portugal; (A.M.F.P.); (C.C.)
| | - Joaquim Lima Cerqueira
- Veterinary and Animal Research Centre (CECAV), Associate Laboratory of Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal (J.L.C.)
- Center for Research and Development in Agrifood Systems and Sustainability, Polytechnic Institute of Viana do Castelo, Agrarian School of Ponte de Lima, Rua D. Mendo Afonso, 147 Refóios do Lima, 4990-706 Ponte de Lima, Portugal
| | - Cristina Conceição
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Department of Zootechnics, School of Science and Technology, University of Évora, Pólo da Mitra Apartado 94, 7006-554 Évora, Portugal; (A.M.F.P.); (C.C.)
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Saif-Ur-Rehman M, Hassan FU, Reecy J, Deng T. Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan. Anim Biotechnol 2023; 34:1384-1396. [PMID: 35044288 DOI: 10.1080/10495398.2022.2026369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1-4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.
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Affiliation(s)
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
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Su M, Lin X, Xiao Z, She Y, Deng M, Liu G, Sun B, Guo Y, Liu D, Li Y. Genome-Wide Association Study of Lactation Traits in Chinese Holstein Cows in Southern China. Animals (Basel) 2023; 13:2545. [PMID: 37570353 PMCID: PMC10417049 DOI: 10.3390/ani13152545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/04/2023] [Accepted: 08/06/2023] [Indexed: 08/13/2023] Open
Abstract
Lactation traits are economically important for dairy cows. Southern China has a high-temperature and high-humidity climate, and environmental and genetic interactions greatly impact dairy cattle performance. The aim of this study was to identify novel single-nucleotide polymorphism sites and novel candidate genes associated with lactation traits in Chinese Holstein cows under high-temperature and humidity conditions in southern China. A genome-wide association study was performed for the lactation traits of 392 Chinese Holstein cows, using GGP Bovine 100 K SNP gene chips. Some 23 single nucleotide polymorphic loci significantly associated with lactation traits were screened. Among them, 16 were associated with milk fat rate, 7 with milk protein rate, and 3 with heat stress. A quantitative trait locus that significantly affects milk fat percentage in Chinese Holstein cows was identified within a window of approximately 0.5 Mb in the region of 0.4-0.9 Mb on Bos taurus autosome 14. According to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, ten genes (DGAT1, IDH2, CYP11B1, GFUS, CYC1, GPT, PYCR3, OPLAH, ALDH1A3, and NAPRT) associated with lactation fat percentage, milk yield, antioxidant activity, stress resistance, and inflammation and immune response were identified as key candidates for lactation traits. The results of this study will help in the development of an effective selection and breeding program for Chinese Holstein cows in high-temperature and humidity regions.
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Affiliation(s)
- Minqiang Su
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (M.S.); (X.L.); (Z.X.); (Y.S.); (M.D.); (G.L.); (B.S.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510640, China
| | - Xiaojue Lin
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (M.S.); (X.L.); (Z.X.); (Y.S.); (M.D.); (G.L.); (B.S.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510640, China
| | - Zupeng Xiao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (M.S.); (X.L.); (Z.X.); (Y.S.); (M.D.); (G.L.); (B.S.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510640, China
| | - Yuanhang She
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (M.S.); (X.L.); (Z.X.); (Y.S.); (M.D.); (G.L.); (B.S.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510640, China
| | - Ming Deng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (M.S.); (X.L.); (Z.X.); (Y.S.); (M.D.); (G.L.); (B.S.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510640, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (M.S.); (X.L.); (Z.X.); (Y.S.); (M.D.); (G.L.); (B.S.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510640, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (M.S.); (X.L.); (Z.X.); (Y.S.); (M.D.); (G.L.); (B.S.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510640, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (M.S.); (X.L.); (Z.X.); (Y.S.); (M.D.); (G.L.); (B.S.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510640, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (M.S.); (X.L.); (Z.X.); (Y.S.); (M.D.); (G.L.); (B.S.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510640, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (M.S.); (X.L.); (Z.X.); (Y.S.); (M.D.); (G.L.); (B.S.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510640, China
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Hu L, Zhang L, Li Q, Liu H, Xu T, Zhao N, Han X, Xu S, Zhao X, Zhang C. Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing. Front Genet 2022; 13:971464. [PMID: 36160022 PMCID: PMC9490000 DOI: 10.3389/fgene.2022.971464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 01/29/2023] Open
Abstract
Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.
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Affiliation(s)
- Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qi Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Hongjin Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tianwei Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Na Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xueping Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Technology Extension Service of Animal Husbandry of Qinghai, Xining, China
| | - Shixiao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xinquan Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- *Correspondence: Cunfang Zhang,
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Zhao Y, Zhang X, Li F, Zhang D, Zhang Y, Li X, Song Q, Zhou B, Zhao L, Wang J, Xu D, Cheng J, Li W, Lin C, Yang X, Zeng X, Wang W. Whole Genome Sequencing Analysis to Identify Candidate Genes Associated With the rib eye Muscle Area in Hu Sheep. Front Genet 2022; 13:824742. [PMID: 35368668 PMCID: PMC8964300 DOI: 10.3389/fgene.2022.824742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
In sheep meat production, the rib eye area is an important index to evaluate carcass traits. However, conventional breeding programs have led to slow genetic progression in rib eye muscle area. Operationalizing molecular marker assisted breeding is an optimized breeding method that might improve this situation. Therefore, the present study used whole genome sequencing data to excavate candidate genes associated with the rib eye muscle. Male Hu lambs (n = 776) with pedigrees and 274 lambs with no pedigree were included. The genetic parameters of the rib eye area were estimated using a mixed linear mixed model. The rib eye area showed medium heritability (0.32 ± 0.13). Whole-genome sequencing of 40 large rib eye sheep [17.97 ± 1.14, (cm2)] and 40 small rib eye sheep [7.89 ± 0.79, (cm2)] was performed. Case-control genome-wide association studies and the fixation index identified candidate rib eye-associated genes. Seven single nucleotide polymorphisms (SNPs) in six genes (ALS2, ST6GAL2, LOC105611989, PLXNA4, DPP6, and COL12A1) were identified as candidates. The study population was expanded to 1050 lambs to perform KASPar genotyping on five SNPs, which demonstrated that SNPs in LOC105611989, DPP6, and COL12A1 correlated significantly with the rib eye area, which could be used as genetic markers for molecular breeding of the rib eye area. The results provided genetic parameters estimated on the rib eye area and information for breeding based on carcass traits in Hu sheep.
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Affiliation(s)
- Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin, China
| | - Deyin Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qizhi Song
- Linze County Animal Disease Prevention and Control Center of Gansu Province, Linze, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Weimin Wang,
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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: 27] [Impact Index Per Article: 9.0] [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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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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