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Yao H, Pan Z, Ma W, Zhao Z, Su Z, Yang J. Whole-Genome Resequencing Analysis of the Camelus bactrianus (Bactrian Camel) Genome Identifies Mutations and Genes Affecting Milk Production Traits. Int J Mol Sci 2024; 25:7836. [PMID: 39063078 PMCID: PMC11277051 DOI: 10.3390/ijms25147836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Milk production is an important trait that influences the economic value of camels. However, the genetic regulatory mechanisms underlying milk production in camels have not yet been elucidated. We aimed to identify candidate molecular markers that affect camel milk production. We classified Junggar Bactrian camels (9-10-year-old) as low-yield (<1.96 kg/d) or high-yield (>2.75 kg/d) based on milk production performance. Milk fat (5.16 ± 0.51 g/100 g) and milk protein (3.59 ± 0.22 g/100 g) concentrations were significantly lower in high-yielding camels than those in low-yielding camels (6.21 ± 0.59 g/100 g, and 3.93 ± 0.27 g/100 g, respectively) (p < 0.01). There were no apparent differences in gland tissue morphology between the low- and high-production groups. Whole-genome resequencing of 12 low- and 12 high-yield camels was performed. The results of selection mapping methods, performed using two methods (FST and θπ), showed that 264 single nucleotide polymorphism sites (SNPs) overlapped between the two methods, identifying 181 genes. These genes were mainly associated with the regulation of oxytocin, estrogen, ErbB, Wnt, mTOR, PI3K-Akt, growth hormone synthesis/secretion/action, and MAPK signaling pathways. A total of 123 SNPs were selected, based on significantly associated genomic regions and important pathways for SNP genotyping, for verification in 521 additional Bactrian camels. This analysis showed that 13 SNPs were significantly associated with camel milk production yield and 18 SNPs were significantly associated with camel milk composition percentages. Most of these SNPs were located in coding regions of the genome. However, five and two important mutation sites were found in the introns of CSN2 (β-casein) and CSN3 (κ-casein), respectively. Among the candidate genes, NR4A1, ADCY8, PPARG, CSN2, and CSN3 have previously been well studied in dairy livestock. These observations provide a basis for understanding the molecular mechanisms underlying milk production in camels as well as genetic markers for breeding programs aimed at improving milk production.
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Affiliation(s)
- Huaibing Yao
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (H.Y.); (Z.Z.)
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi 830017, China
| | - Zhangyuan Pan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Wanpeng Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; (W.M.); (Z.S.)
| | - Zhongkai Zhao
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (H.Y.); (Z.Z.)
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi 830017, China
| | - Zhanqiang Su
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; (W.M.); (Z.S.)
| | - Jie Yang
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (H.Y.); (Z.Z.)
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi 830017, China
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Kong S, Cai B, Li X, Zhou Z, Fang X, Yang X, Cai D, Luo X, Guo S, Nie Q. Assessment of selective breeding effects and selection signatures in Qingyuan partridge chicken and its strains. Poult Sci 2024; 103:103626. [PMID: 38513549 PMCID: PMC10966089 DOI: 10.1016/j.psj.2024.103626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/22/2024] [Accepted: 03/02/2024] [Indexed: 03/23/2024] Open
Abstract
Qingyuan partridge chicken (QYM) is a highly regarded native breed in China, highly esteemed for its exceptional breeding characteristics. However, the investigation into the selection signatures and its strains remains largely unexplored. In this study, blood sampling, DNA extracting, and high-depth resequencing were performed in 27 QYMs. Integrating the genomic data of 14 chicken (70 individuals) breeds from other researches, to analyze the genetic structure, selection signatures, and effects of selective breeding within QYM and its 3 strains (QYMA, QYMB, and QYMC). Population structure analysis revealed an independent QYM cluster, which exhibited distinct from other breeds, with each of its 3 strains displaying distinct clustering patterns. Linkage disequilibrium analysis highlighted QYMB's notably slower decay rate, potentially influenced by selection pressure from various production indicators. Examination of selection signatures uncovered genes and genetic mechanisms associated with genomic changes resulting from extensive selective breeding within the QYM and its strains. Intriguingly, diacylglycerol kinase beta (DGKB) and catenin alpha 2 (CTNNA2) were identified as commonly selected genes across the 3 QYM strains, linked to energy metabolism, muscle development, and fat metabolism. Our research validates the substantial impact of selective breeding on QYM and its strains, concurrently identifying genomic regions and signaling pathways associated with their distinctive characters. This research also establishes a fundamental framework for advancing yellow-feathered broiler breeding strategies.
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Affiliation(s)
- Shaofen Kong
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Bolin Cai
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiaojing Li
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhen Zhou
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiang Fang
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xin Yang
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Danfeng Cai
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xuehui Luo
- Qingyuan Chicken Research Institute, Qingcheng District, Qingyuan City, China
| | - Suyin Guo
- Animal Epidemic Prevention Center, Qingcheng District, Qingyuan City, China
| | - Qinghua Nie
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China.
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Hu M, Shi L, Yi W, Li F, Yan S. Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data. Anim Biosci 2024; 37:461-470. [PMID: 38271971 PMCID: PMC10915192 DOI: 10.5713/ab.23.0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/13/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. METHODS To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. RESULTS The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. CONCLUSION In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.
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Affiliation(s)
- Mingyue Hu
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Lulu Shi
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Wenfeng Yi
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Feng Li
- Shandong Binzhou Animal Science & Veterinary Medicine Academy, Binzhou, 256600,
China
| | - Shouqing Yan
- Department of Animal Science, Jilin University, Changchun 130062,
China
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Liu LL, Meng J, Ma HY, Cao H, Liu WJ. Candidate genes for litter size in Xinjiang sheep identified by Specific Locus Amplified Fragment (SLAF) sequencing. Anim Biotechnol 2023; 34:3053-3062. [PMID: 36244020 DOI: 10.1080/10495398.2022.2131561] [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: 11/01/2022]
Abstract
The aim of this study was to investigate the selection signatures at a genome-wide level in 'Pishan' sheep using Specific Locus Amplified Fragment (SLAF)-seq. Blood samples from 126 ewes were sequenced using SLAF tags, and the ovarian tissues from 8 ewes (Bashbay sheep, a single litter size group (SG group); 'Pishan' sheep, double litter size group (DG group)) were collected to detect expression levels by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Selection signature analysis was performed using global fixation index (Fst) and nucleotide diversity (π) ratio. A total of 1,192,168 high-quality SLAFs were identified. Notably, 2380 candidate regions under selection using two approaches were identified. A total of 2069 genes were identified, which were involved in dopaminergic synapses, thyroid hormone synthesis, ovarian steroidogenesis and thyroid hormone signalling pathways. Furthermore, Growth Differentiation Factor 9 (GDF9), Period Circadian Regulator 2 (PER2), Thyroid Stimulating Hormone Receptor (TSHR), and Nuclear Receptor Coactivator 1 (NCOA1) reside within these regions and pathways. The expression levels of GDF9 and PER2 genes in sheep tissue of the DG group were significantly higher than those in the SG group. These genes are interesting candidates for litter size and provide a starting point for further identification of conservation strategies for 'Pishan' sheep.
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Affiliation(s)
- Ling-Ling Liu
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jun Meng
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hai-Yu Ma
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hang Cao
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Wu-Jun Liu
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
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Paján-Jiménez V, Pazmiño-Rodríguez FD, Roldán-Santiago P, Dutro-Aceves A, de la Cruz-Cruz LA, Larrondo C. Effects of different load weights on the work performance and physiological and hematobiochemical responses in working water buffalo. Vet World 2023; 16:2349-2357. [PMID: 38152270 PMCID: PMC10750744 DOI: 10.14202/vetworld.2023.2349-2357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/23/2023] [Indexed: 12/29/2023] Open
Abstract
Background and Aim Working animals are important in agriculture because they play a role in various agricultural activities, including milk and meat production. Thus, they contribute to the development of rural communities. In this study, we aimed to evaluate the effects of different load weights on the work performance and the physiological and hematological responses of working water buffalo (Bubalus bubalis). Materials and Methods The work performances of 12 buffaloes (average weight 782.16 ± 21.62 kg) transporting 200, 350, and 500 kg of African palm fruits in metal baskets placed on their backs were evaluated. Work performance variables evaluated immediately after work were as follows: total number of trips (n), total weight (kg), distance traveled (km/day), working period (h), stopped time (h), and average speed (km/h). In addition, we evaluated physiological, biochemical, and hematological variables at three different times: before the start of work, immediately after work, and on the rest day. Results Among the load weights, 500 kg (total load carried = 4,138.88 kg) improved work efficiency compared to 200 kg loads (total load = 3,322.22 kg) (p = 0.0281). However, 500 kg loads resulted in slower average speed (2.4 km, p = 0.0164), shorter working period (2.39 h, p < 0.0001) and distance traveled (7.29 km, p < 0.0001), and less total number of trips (8.27 trips, p < 0.0001) compared to 350 and 200 kg load weights (3.45 and 3.52 km/h, 2.55 and 2.79 h, 8.71 and 9.75 km, 10.94 and 16.61 trips, respectively); and the heaviest loads resulted in significantly higher (p < 0.005) respiratory rate, pulse, heart rate, rectal temperature, glucose, lactate dehydrogenase, creatine kinase, total protein, white blood cell count, neutrophils, lymphocytes, monocytes, eosinophils, and basophils. In contrast, was associated with lower levels of red blood cells, hemoglobin, and hematocrit compared to lower loads. All differences were more pronounced in 500 kg (p < 0.005) compared to 200 kg loads. Conclusion Working buffaloes responded to work related to the transport of African palm fruits through various physiological, biochemical, and hematological changes. However, some variables remained close to the reference values reported in the literature for water buffaloes, and in general, all variables were reestablished during the rest day, indicating that these animals have adapted to working conditions.
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Affiliation(s)
- Visoky Paján-Jiménez
- 1. Maestría en Producción Animal, Universidad Tecnológica Equinoccial, Santo Domingo de los Tsachilas, Ecuador
| | - Fernando David Pazmiño-Rodríguez
- Universidad Técnica del Norte, Ecuador, Facultad de Ingeniería en Ciencias Agropecuarias y Ambientales, Carrera de Ingeniería Forestal
| | - Patricia Roldán-Santiago
- Departamento de Reproducción, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Av. Universidad, Colonia, C.U. C.P. 04510 Ciudad de México, México
| | - Anna Dutro-Aceves
- Escuela de Ciencias de la Salud, Medicina Veterinaria y Zootecnia, Universidad del Valle de México-Coyoacán, Calzada de Tlalpan 04910, Ciudad de México, México
| | - Luis Alberto de la Cruz-Cruz
- Escuela de Ciencias de la Salud, Medicina Veterinaria y Zootecnia, Universidad del Valle de México-Coyoacán, Calzada de Tlalpan 04910, Ciudad de México, México
- Preservación del Bienestar Animal/Manejo de la Fauna Silvestre, Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Ciudad de México, 04960, México
| | - Cristian Larrondo
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Viña del Mar, Chile
- AWEC Advisors S.L. Parc de Recerca Universitat Autònoma de Barcelona, Cerdanyola del Vallès, España
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Ben-Jemaa S, Adam G, Boussaha M, Bardou P, Klopp C, Mandonnet N, Naves M. Whole genome sequencing reveals signals of adaptive admixture in Creole cattle. Sci Rep 2023; 13:12155. [PMID: 37500674 PMCID: PMC10374910 DOI: 10.1038/s41598-023-38774-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and combined our data with sequenced genomes of 99 animals representative of European, African and indicine groups. We detect 17,228,983 single nucleotide polymorphisms (SNPs) in the GUA genome, providing the most detailed exploration, to date, of patterns of genetic variation in this breed. We confirm the higher level of African and indicine ancestries, compared to the European ancestry and we highlight the African origin of indicine ancestry in the GUA genome. We identify five strong candidate regions showing an excess of indicine ancestry and consistently supported across the different detection methods. These regions encompass genes with adaptive roles in relation to immunity, thermotolerance and physical activity. We confirmed a previously identified horn-related gene, RXFP2, as a gene under strong selective pressure in the GUA population likely owing to human-driven (socio-cultural) pressure. Findings from this study provide insight into the genetic mechanisms associated with resilience traits in livestock.
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Affiliation(s)
- Slim Ben-Jemaa
- INRAE, ASSET, 97170, Petit-Bourg, France.
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, 2049, Ariana, Tunisia.
| | | | - Mekki Boussaha
- AgroParisTech, GABI, INRAE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Philippe Bardou
- GenPhySE, Ecole Nationale Vétérinaire de Toulouse (ENVT), INRA, Université de Toulouse, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
- Sigenae, INRAE, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
| | - Christophe Klopp
- Genotoul Bioinfo, BioInfoMics, MIAT UR875, Sigenae, INRAE, Castanet-Tolosan, France
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Liu Y, Mu Y, Wang W, Ahmed Z, Wei X, Lei C, Ma Z. Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle. Front Vet Sci 2023; 10:1148070. [PMID: 37065216 PMCID: PMC10103646 DOI: 10.3389/fvets.2023.1148070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/01/2023] [Indexed: 04/03/2023] Open
Abstract
Qaidam cattle (CDM) are indigenous breed inhabiting Northwest China. In the present study, we newly sequenced 20 Qaidam cattle to investigate the copy number variants (CNVs) based on the ARS-UMD1.2 reference genome. We generated the CNV region (CNVR) datasets to explore the genomic CNV diversity and population stratification. The other four cattle breeds (Xizang cattle, XZ; Kazakh cattle, HSK; Mongolian cattle, MG; and Yanbian cattle, YB) from the regions of North China embracing 43 genomic sequences were collected and are distinguished from each of the other diverse populations by deletions and duplications. We also observed that the number of duplications was significantly more than deletions in the genome, which may be less harmful to gene formation and function. At the same time, only 1.15% of CNVRs overlapped with the exon region. Population differential CNVRs and functional annotations between the Qaidam cattle population and other cattle breeds revealed the functional genes related to immunity (MUC6), growth (ADAMTSL3), and adaptability (EBF2). Our analysis has provided numerous genomic characteristics of some Chinese cattle breeds, which are valuable as customized biological molecular markers in cattle breeding and production.
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Affiliation(s)
- Yangkai Liu
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Yanan Mu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Wenxiang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot, Pakistan
| | - Xudong Wei
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- Chuzhao Lei
| | - Zhijie Ma
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
- *Correspondence: Zhijie Ma
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Nazar M, Abdalla IM, Chen Z, Ullah N, Liang Y, Chu S, Xu T, Mao Y, Yang Z, Lu X. Genome-Wide Association Study for Udder Conformation Traits in Chinese Holstein Cattle. Animals (Basel) 2022; 12:2542. [PMID: 36230283 PMCID: PMC9559277 DOI: 10.3390/ani12192542] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Udder conformation traits are one of the most economic traits in dairy cows, greatly affecting animal health, milk production, and producer profitability in the dairy industry. Genetic analysis of udder structure and scores have been developed in Holstein cattle. In our research, we conducted a genome-wide association study for five udder traits, including anterior udder attachment (AUA), central suspensory ligament (CSL), posterior udder attachment height (PUAH), posterior udder attachment width (PUAW), and udder depth (UD), in which the fixed and random model circulating probability unification (FarmCPU) model was applied for the association analysis. The heritability and the standard errors of these five udder traits ranged from 0.04 ± 0.00 to 0.49 ± 0.03. Phenotype data were measured from 1000 Holstein cows, and the GeneSeek Genomic Profiler (GGP) Bovine 100 K SNP chip was used to analyze genotypic data in Holstein cattle. For GWAS analysis, 984 individual cows and 84,407 single-nucleotide polymorphisms (SNPs) remained after quality control; a total of 18 SNPs were found at the GW significant threshold (p < 5.90 × 10−7). Many candidate genes were identified within 200kb upstream or downstream of the significant SNPs, which include MGST1, MGST2, MTUS1, PRKN, STXBP6, GRID2, E2F8, CDH11, FOXP1, SLF1, TMEM117, SBF2, GC, ADGRB3, and GCLC. Pathway analysis revealed that 58 Gene Ontology (GO) terms and 18 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched with adjusted p values, and these GO terms and the KEGG pathway analysis were associated with biological information, metabolism, hormonal growth, and development processes. These results could give valuable biological information for the genetic architecture of udder conformation traits in dairy Holstein cattle.
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Affiliation(s)
- Mudasir Nazar
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | | | - Zhi Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Numan Ullah
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yan Liang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shuangfeng Chu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tianle Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Yongjiang Mao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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Zhang X, Chen N, Chen H, Lei C, Sun T. Comparative analyses of copy number variations between swamp and river buffalo. Gene X 2022; 830:146509. [PMID: 35460806 DOI: 10.1016/j.gene.2022.146509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Domestic buffalo is an important livestock in the tropical and sub-tropical region, including two types: swamp and river buffalo. The swamp buffalo is mainly used as draft animal, while the river buffalo is raised for milk production. In this study, based on the new high-quality buffalo reference genome UOA_WB_1, we firstly investigated the copy number variants in buffalo using whole-genome Illumina sequencing. A total of 3,734 CNV regions (CNVRs) were detected in 106 buffalo population with a total length of 23,429,066 bp, corresponding to ∼ 0.88% of the water buffalo genome (UOA_WB_1). Our results revealed a clear population differentiation in CNV between swamp and river buffalo. In addition, a total of 667 highly differentiated CNVRs (covering 886 genes) were detected between river and swamp buffalo population. We detected a set of CNVR-overlapping genes associated with exercise, immunity, nerve, and milk trait which exhibited different copy numbers between swamp and river buffalo population. This study provides valuable genome variation resources for buffalo and would contribute to understanding the genetic differences between swamp and river buffalo.
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Affiliation(s)
- Xianfu Zhang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, Zhejiang 311300, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
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10
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Luo X, Li J, Xiao C, Sun L, Xiang W, Chen N, Lei C, Lei H, Long Y, Long T, Suolang Q, Yi K. Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures. Front Genet 2022; 13:816379. [PMID: 35711927 PMCID: PMC9196905 DOI: 10.3389/fgene.2022.816379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/13/2022] [Indexed: 01/11/2023] Open
Abstract
Understanding the genetic diversity in Xiangxi cattle may facilitate our efforts toward further breeding programs. Here we compared 23 Xiangxi cattle with 78 published genomes of 6 worldwide representative breeds to characterize the genomic variations of Xiangxi cattle. Based on clustering models in population structure analysis, we displayed that Xiangxi cattle had a mutual genome ancestor with Chinese indicine, Indian indicine, and East Asian taurine. Population genetic diversity was analyzed by four methods (nucleotide diversity, inbreeding coefficient, linkage disequilibrium decay and runs of homozygosity), and we found that Xiangxi cattle had higher genomic diversity and weaker artificial selection than commercial breed cattle. Using four testing methods (θπ, CLR, FST, and XP-EHH), we explored positive selection regions harboring genes in Xiangxi cattle, which were related to reproduction, growth, meat quality, heat tolerance, and immune response. Our findings revealed the extent of sequence variation in Xiangxi cattle at the genome-wide level. All of our fruitful results can bring about a valuable genomic resource for genetic studies and breed protection in the future.
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Affiliation(s)
- Xiaoyu Luo
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Jianbo Li
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China
| | - Chentong Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Luyang Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Weixuan Xiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,School of Life Science, University of Bristol, Bristol, United Kingdom
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Hong Lei
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China
| | - Yun Long
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China.,Hunan De Nong Animal Husbandry Group Co. Ltd., Huayuan, China
| | - Ting Long
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China.,Hunan De Nong Animal Husbandry Group Co. Ltd., Huayuan, China
| | - Quji Suolang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
| | - Kangle Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China
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11
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Zhang X, Qu K, Jia P, Zhang J, Liu J, Lei C, Huang B. Assessing Genomic Diversity and Productivity Signatures in Dianzhong Cattle by Whole-Genome Scanning. Front Genet 2021; 12:719215. [PMID: 34675962 PMCID: PMC8523829 DOI: 10.3389/fgene.2021.719215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
Dianzhong cattle is a classic Chinese indigenous cattle breed with historical records dating back to 200 BC. But with its genomic differences having not been clearly elucidated, the quest for genomic characterization will be an essential step towards understanding the genomic basis of productivity and adaptation to survival under Chinese farming systems. Here we compared 10 Dianzhong cattle (four newly sequenced and six downloaded) with 29 published genomes of three underlying ancestral populations (Chinese zebu, Indian zebu, and Yanbian cattle) to characterize the genomic variations of Dianzhong cattle. Dianzhong cattle has a high nucleotide diversity (0.0034), second only to Chinese zebu. Together with analyses of linkage disequilibrium decay and runs of homozygosity, Dianzhong cattle displayed higher genomic diversity and weaker artificial selection compared with Yanbian cattle. From a selective sweep analysis by four methods (Fst, π-ratio, XP-CLR, and XP-EHH), the positive selective signals were mainly manifested in candidate genes and pathways related to heat resistance, growth and development, fat deposition, and male reproduction. Missense mutations were detected in candidate genes, SDS (c.944C > A and p.Ala315Glu), PDGFD (c.473A > G and p.Lys158Arg), and DDX4 (rs460251486, rs722912933, and rs517668236), which related to heat resistance, fat deposition, and spermatogenesis, respectively. Our findings unravel, at the genome-wide level, the unique diversity of Dianzhong cattle while emphasizing the opportunities for improvement of livestock productivity in further breeding programs.
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Affiliation(s)
- Xianfu Zhang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Peng Jia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
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