1
|
Yang H, Zhu M, Wang M, Zhou H, Zheng J, Qiu L, Fan W, Yang J, Yu Q, Yang Y, Zhang W. Genome-wide comparative analysis reveals selection signatures for reproduction traits in prolific Suffolk sheep. Front Genet 2024; 15:1404031. [PMID: 38911299 PMCID: PMC11193351 DOI: 10.3389/fgene.2024.1404031] [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: 03/20/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
The identification of genome-wide selection signatures can reveal the potential genetic mechanisms involved in the generation of new breeds through natural or artificial selection. In this study, we screened the genome-wide selection signatures of prolific Suffolk sheep, a new strain of multiparous mutton sheep, to identify candidate genes for reproduction traits and unravel the germplasm characteristics and population genetic evolution of this new strain of Suffolk sheep. Whole-genome resequencing was performed at an effective sequencing depth of 20× for genomic diversity and population structure analysis. Additionally, selection signatures were investigated in prolific Suffolk sheep, Suffolk sheep, and Hu sheep using fixation index (F ST) and heterozygosity H) analysis. A total of 5,236.338 Gb of high-quality genomic data and 28,767,952 SNPs were obtained for prolific Suffolk sheep. Moreover, 99 selection signals spanning candidate genes were identified. Twenty-three genes were significantly associated with KEGG pathway and Gene Ontology terms related to reproduction, growth, immunity, and metabolism. Through selective signal analysis, genes such as ARHGEF4, CATIP, and CCDC115 were found to be significantly correlated with reproductive traits in prolific Suffolk sheep and were highly associated with the mTOR signaling pathway, the melanogenic pathway, and the Hippo signaling pathways, among others. These results contribute to the understanding of the evolution of artificial selection in prolific Suffolk sheep and provide candidate reproduction-related genes that may be beneficial for the establishment of new sheep breeds.
Collapse
Affiliation(s)
- Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Mengting Zhu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Mingyuan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Huaqian Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Jingjing Zheng
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Lixia Qiu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Wenhua Fan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Jinghui Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Wenzhe Zhang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| |
Collapse
|
2
|
Zhang D, Yue Y, Yuan C, An X, Guo T, Chen B, Liu J, Lu Z. DIA-Based Proteomic Analysis Reveals MYOZ2 as a Key Protein Affecting Muscle Growth and Development in Hybrid Sheep. Int J Mol Sci 2024; 25:2975. [PMID: 38474221 DOI: 10.3390/ijms25052975] [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: 12/18/2023] [Revised: 02/12/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Hybridization of livestock can be used to improve varieties, and different hybrid combinations produce unique breeding effects. In this study, male Southdown and Suffolk sheep were selected to hybridize with female Hu sheep to explore the effects of male parentage on muscle growth and the development of offspring. Using data-independent acquisition technology, we identified 119, 187, and 26 differentially abundant proteins (DAPs) between Hu × Hu (HH) versus Southdown × Hu (NH), HH versus Suffolk × Hu (SH), and NH versus SH crosses. Two DAPs, MYOZ2 and MYOM3, were common to the three hybrid groups and were mainly enriched in muscle growth and development-related pathways. At the myoblast proliferation stage, MYOZ2 expression decreased cell viability and inhibited proliferation. At the myoblast differentiation stage, MYOZ2 expression promoted myoblast fusion and enhanced the level of cell fusion. These findings provide new insights into the key proteins and metabolic pathways involved in the effect of male parentage on muscle growth and the development of hybrid offspring in sheep.
Collapse
Affiliation(s)
- Dan Zhang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yaojing Yue
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chao Yuan
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xuejiao An
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Tingting Guo
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bowen Chen
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| |
Collapse
|
3
|
Stefanetti V, Mancinelli AC, Pascucci L, Menchetti L, Castellini C, Mugnai C, Fiorilla E, Miniscalco B, Chiattelli D, Franciosini MP, Proietti PC. Effect of rearing systems on immune status, stress parameters, intestinal morphology, and mortality in conventional and local chicken breeds. Poult Sci 2023; 102:103110. [PMID: 37852051 PMCID: PMC10591014 DOI: 10.1016/j.psj.2023.103110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 10/20/2023] Open
Abstract
The majority of poultry meat used to be sourced from intensively housed birds. However, consumer preference has since demanded poultry producers develop more sustainable farming systems. Although free-range farming is considered beneficial for animal welfare, it is not as easy to standardize as an intensive system, which makes the choice of bird genotype appear crucial for alternative systems. In this study, we aimed to evaluate the effect of conventional and free-range rearing systems on the immune status, stress parameters, intestinal morphology and mortality in commercial hybrids (Ross 308) and local poultry strains, Bionda Piemontese (BP), Robusta Maculata (RM), BP x Sasso (BPxS), and RM x Sasso (RMxS). RNA was extracted from the jejunum and spleen to assess the mRNA expression of IL-2, IL-6, IL-10, IL-18, IL-1β, inducible nitric oxide synthase (iNOS), toll-like receptor (TLR)-4, and interferon gamma (IFN-γ). The heterophil:lymphocyte (H/L) ratio and intestinal histomorphometric evaluation were also calculated. We found that compared to the conventional system, the rearing system significantly affected the jejunum expression of IL-10, iNOS, IL-2, and IL-6, where these genes were upregulated in free-range system. A significant interaction between the rearing system and the genotype was also shown. More specifically, local breeds showed a significantly higher expression (P < 0.001) of IL-6 in the free-range system compared to the same genotypes in the conventional system. Moreover, IL-6 is constantly upregulated in local breeds within the free-range system compared to Ross hybrids. We also found significantly increased H/L and mortality rates in the latter, compared to the local breeds in the free-range reared system. The jejunum morphology also demonstrated a significantly higher villus height in BP and BPxS compared to the Ross hybrids. Overall, the results of our study confirm that the intense selection for growth in broiler chickens may have reduced their ability to react to the environmental stimuli related to free-range systems, resulting in a lower adaptability to a free-range environment, thus making them inappropriate for any farming system other than the conventional one. On the contrary, local chicken breeds are able to adapt and survive in the free-range system of rearing, and represent a genetic resource especially when adaptability to free-range conditions is required.
Collapse
Affiliation(s)
| | - Alice Cartoni Mancinelli
- Department of Agricultural, Environment and Food Science, University of Perugia, 06124 Perugia, Italy
| | - Luisa Pascucci
- Department of Veterinary Medicine, University of Perugia, 06124 Perugia, Italy
| | - Laura Menchetti
- School of Biosciences and Veterinary Medicine, University of Camerino, 62024 Matelica, Italy
| | - Cesare Castellini
- Department of Agricultural, Environment and Food Science, University of Perugia, 06124 Perugia, Italy
| | - Cecilia Mugnai
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Torino, Italy.
| | - Edoardo Fiorilla
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Torino, Italy
| | - Barbara Miniscalco
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Torino, Italy
| | - Diletta Chiattelli
- Department of Agricultural, Environment and Food Science, University of Perugia, 06124 Perugia, Italy
| | | | | |
Collapse
|
4
|
Liu X, Ma Z, Wang Y, Jia H, Wang Z, Zhang L. Heat stress exposure cause alterations in intestinal microbiota, transcriptome, and metabolome of broilers. Front Microbiol 2023; 14:1244004. [PMID: 37795292 PMCID: PMC10547010 DOI: 10.3389/fmicb.2023.1244004] [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: 06/24/2023] [Accepted: 08/18/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction Heat stress can affect the production of poultry through complex interactions between genes, metabolites and microorganisms. At present, it is unclear how heat stress affects genetic, metabolic and microbial changes in poultry, as well as the complex interactions between them. Methods Thus, at 28 days of age a total of 200 Arbor Acres broilers with similar body weights were randomly divided into the control (CON) and heat stress treatment (HS). There were 5 replicates in CON and HS, respectively, 20 per replication. From the 28-42 days, the HS was kept at 31 ± 1°C (9:00-17:00, 8 h) and other time was maintained at 21 ± 1°C as in the CON. At the 42nd day experiment, we calculated the growth performance (n = 8) of broilers and collected 3 and 6 cecal tissues for transcriptomic and metabolomic investigation and 4 cecal contents for metagenomic investigation of each treatment. Results and discussion The results indicate that heat stress significantly reduced the average daily gain and body weight of broilers (value of p < 0.05). Transcriptome KEGG enrichment showed that the differential genes were mainly enriched in the NF-kB signaling pathway. Metabolomics results showed that KEGG enrichment showed that the differential metabolites were mainly enriched in the mTOR signaling pathway. 16S rDNA amplicon sequencing results indicated that heat stress increased the relative abundance of Proteobacteria decreased the relative abundance of Firmicutes. Multi-omics analysis showed that the co-participating pathway of differential genes, metabolites and microorganisms KEGG enrichment was purine metabolism. Pearson correlation analysis found that ornithine was positively correlated with SULT1C3, GSTT1L and g_Lactobacillus, and negatively correlated with CALB1. PE was negatively correlated with CALB1 and CHAC1, and positively with g_Alistipes. In conclusion, heat stress can generate large amounts of reactive oxygen and increase the types of harmful bacteria, reduce intestinal nutrient absorption and antioxidant capacity, and thereby damage intestinal health and immune function, and reduce growth performance indicators. This biological process is manifested in the complex regulation, providing a foundational theoretical basis for solving the problem of heat stress.
Collapse
Affiliation(s)
| | | | | | | | - Zheng Wang
- Shanxi Key Lab. for the Modernization of TCVM, College of Life and Science, Shanxi Agricultural University, Taigu, China
| | - Lihuan Zhang
- Shanxi Key Lab. for the Modernization of TCVM, College of Life and Science, Shanxi Agricultural University, Taigu, China
| |
Collapse
|
5
|
Luna-Ramirez RI, Limesand SW, Goyal R, Pendleton AL, Rincón G, Zeng X, Luna-Nevárez G, Reyna-Granados JR, Luna-Nevárez P. Blood Transcriptomic Analyses Reveal Functional Pathways Associated with Thermotolerance in Pregnant Ewes Exposed to Environmental Heat Stress. Genes (Basel) 2023; 14:1590. [PMID: 37628641 PMCID: PMC10454332 DOI: 10.3390/genes14081590] [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: 06/30/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Environmental heat stress triggers a series of compensatory mechanisms in sheep that are dependent on their genetic regulation of thermotolerance. Our objective was to identify genes and regulatory pathways associated with thermotolerance in ewes exposed to heat stress. We performed next-generation RNA sequencing on blood collected from 16 pregnant ewes, which were grouped as tolerant and non-tolerant to heat stress according to a physiological indicator. Additional samples were collected to measure complete blood count. A total of 358 differentially expressed genes were identified after applying selection criteria. Gene expression analysis detected 46 GO terms and 52 KEGG functional pathways. The top-three signaling pathways were p53, RIG-I-like receptor and FoxO, which suggested gene participation in biological processes such as apoptosis, cell signaling and immune response to external stressors. Network analysis revealed ATM, ISG15, IRF7, MDM4, DHX58 and TGFβR1 as over-expressed genes with high regulatory potential. A co-expression network involving the immune-related genes ISG15, IRF7 and DXH58 was detected in lymphocytes and monocytes, which was consistent with hematological findings. In conclusion, transcriptomic analysis revealed a non-viral immune mechanism involving apoptosis, which is induced by external stressors and appears to play an important role in the molecular regulation of heat stress tolerance in ewes.
Collapse
Affiliation(s)
- Rosa I. Luna-Ramirez
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Sean W. Limesand
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Ravi Goyal
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Alexander L. Pendleton
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | - Xi Zeng
- Zoetis Inc., VMRD Genetics R&D, Kalamazoo, MI 49007, USA
| | - Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Javier R. Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| |
Collapse
|
6
|
Zhu M, Yang Y, Yang H, Zhao Z, Zhang H, Blair HT, Zheng W, Wang M, Fang C, Yu Q, Zhou H, Qi H. Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits. BMC Genomics 2023; 24:392. [PMID: 37434152 DOI: 10.1186/s12864-023-09479-y] [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: 04/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Sheep genomes undergo numerous genes losses, gains and mutation that generates genome variability among breeds of the same species after long time natural and artificial selection. However, the microevolution of native sheep in northwest China remains elusive. Our aim was to compare the genomes and relevant reproductive traits of four sheep breeds from different climatic environments, to unveil the selection challenges that this species cope with, and the microevolutionary differences in sheep genomes. Here, we resequenced the genomes of 4 representative sheep breeds in northwest China, including Kazakh sheep and Duolang sheep of native breeds, and Hu sheep and Suffolk sheep of exotic breeds with different reproductive characteristics. RESULTS We found that these four breeds had a similar expansion experience from ~ 10,000 to 1,000,000 years ago. In the past 10,000 years, the selection intensity of the four breeds was inconsistent, resulting in differences in reproductive traits. We explored the sheep variome and selection signatures by FST and θπ. The genomic regions containing genes associated with different reproductive traits that may be potential targets for breeding and selection were detected. Furthermore, non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds with different reproductive characteristics were found. We identified PAK1, CYP19A1 and PER1 as a likely causal gene for seasonal reproduction in native sheep through qPCR, Western blot and ELISA analyses. Also, the haplotype frequencies of 3 tested gene regions related to reproduction were significantly different among four sheep breeds. CONCLUSIONS Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.
Collapse
Affiliation(s)
- Mengting Zhu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China.
| | - Zongsheng Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China.
| | - Hongmei Zhang
- First Affiliated Hospital, School of Medical College, Shihezi University, Shihezi, Xinjiang, China
| | - Hugh T Blair
- Institute Veterinary, Animal & Biomedical Sciences, Massey University, Auckland, Palmerston North, New Zealand
| | - Wei Zheng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Mingyuan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Chenhui Fang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Huaqian Zhou
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Hangdong Qi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| |
Collapse
|
7
|
Zhao X, Luo H, Lu H, Ma L, Li Y, Dou J, Zhang J, Ma Y, Li J, Wang Y. RNA-Seq Analysis of Peripheral Whole Blood from Dairy Bulls with High and Low Antibody-Mediated Immune Responses-A Preliminary Study. Animals (Basel) 2023; 13:2208. [PMID: 37444006 DOI: 10.3390/ani13132208] [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: 05/16/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Enhancing the immune response through breeding is regarded as an effective strategy for improving animal health, as dairy cattle identified as high immune responders are reported to have a decreased prevalence of economically significant diseases. The identification of differentially expressed genes (DEGs) associated with immune responses might be an effective tool for breeding healthy dairy cattle. In this study, antibody-mediated immune responses (AMIRs) were induced by the immunization of hen egg white lysozyme (HEWL) in six Chinese Holstein dairy bulls divided into high- and low-AMIR groups based on their HEWL antibody level. Then, RNA-seq was applied to explore the transcriptome of peripheral whole blood between the two comparison groups. As a result, several major upregulated and downregulated genes were identified and attributed to the regulation of locomotion, tissue development, immune response, and detoxification. In addition, the result of the KEGG pathway analysis revealed that most DEGs were enriched in pathways related to disease, inflammation, and immune response, including antigen processing and presentation, Staphylococcus aureus infection, intestinal immune network for IgA production, cytokine-cytokine receptor interaction, and complement and coagulation cascades. Moreover, six genes (BOLA-DQA5, C5, CXCL2, HBA, LTF, and COL1A1) were validated using RT-qPCR, which may provide information for genomic selection in breeding programs. These results broaden the knowledge of the immune response mechanism in dairy bulls, which has strong implications for breeding cattle with an enhanced AMIR.
Collapse
Affiliation(s)
- Xiuxin Zhao
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, No. 23788, Gongyebei Road, Jinan 250100, China
- Shandong Ox Livestock Breeding Co., Ltd., Jinan 250100, China
| | - Hanpeng Luo
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haibo Lu
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Beijing Consortium for Innovative Bio-Breeding, Beijing 101206, China
| | - Longgang Ma
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yanqin Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, No. 23788, Gongyebei Road, Jinan 250100, China
| | - Jinhuan Dou
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junxing Zhang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yun Ma
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jianbin Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, No. 23788, Gongyebei Road, Jinan 250100, China
| | - Yachun Wang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Marinho GTB, Pandorfi H, da Silva MV, Montenegro AADA, de Sousa LDB, Desenzi R, da Silva JLB, de Oliveira-Júnior JF, Mesquita M, de Almeida GLP, Guiselini C, da Rosa Ferraz Jardim AM, Silva TGFD. Bioclimatic Zoning for Sheep Farming through Geostatistical Modeling in the State of Pernambuco, Brazil. Animals (Basel) 2023; 13:ani13061124. [PMID: 36978664 PMCID: PMC10044458 DOI: 10.3390/ani13061124] [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: 02/10/2023] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The Intergovernmental Panel on Climate Change (IPCC) has pointed out the high vulnerability of developing countries to climate change, which is expected to impact food and income security. Sheep farming is one of the main animal productions among the families located in the most vulnerable regions of the semiarid region of Pernambuco state, a Brazilian territory known for its high temperatures, low relative humidity, and high net solar radiation. Therefore, the objective of this study was to identify different regions of Pernambuco that may be more suitable for different breeds of sheep, based on non-parametric statistics and kriging maps of the temperature and humidity index (THI). THI values were determined based on mean annual temperature and wind speed extracted from the TerraClimate remote sensing database. Pernambuco state presented THI values ranging from 66 to 79, with the hair breeds having a high potential for exploitation in almost all territories, including the main meat-producing breeds. The East Friesian breed, a high milk producer, would be well suited to the Agreste mesoregion, a territory that, like the Pajeú and Moxotó microregions, also proved favorable for the introduction of three wool breeds (Suffolk, Poll Dorset, and Texel) known as major meat producers. The kriging maps of the THI values successfully allowed the identification of strategic development regions of Pernambuco state with high potential for sheep breeding.
Collapse
Affiliation(s)
| | - Héliton Pandorfi
- Department of Agricultural Engineering, Federal Rural University of Pernambuco, Recife 52171-900, Brazil
| | - Marcos Vinícius da Silva
- Department of Agricultural Engineering, Federal Rural University of Pernambuco, Recife 52171-900, Brazil
| | | | | | - Raquel Desenzi
- Department of Veterinary Medicine, Federal Rural University of Pernambuco, Recife 52171-900, Brazil
| | - Jhon Lennon Bezerra da Silva
- National Institute of the Semiarid, Center for Information Management and Popularization of Science, Campina Grande 58434-700, Brazil
| | | | - Márcio Mesquita
- Department of Agronomy, Federal University of Goiás, Goiânia 74690-900, Brazil
| | | | - Cristiane Guiselini
- Department of Agricultural Engineering, Federal Rural University of Pernambuco, Recife 52171-900, Brazil
| | | | | |
Collapse
|