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Khazaei-Koohpar H, Gholizadeh M, Hafezian SH, Esmaeili-Fard SM. Weighted single-step genome-wide association study for direct and maternal genetic effects associated with birth and weaning weights in sheep. Sci Rep 2024; 14:13120. [PMID: 38849438 PMCID: PMC11161479 DOI: 10.1038/s41598-024-63974-0] [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: 11/23/2023] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
Body weight is an important economic trait for sheep meat production, and its genetic improvement is considered one of the main goals in the sheep breeding program. Identifying genomic regions that are associated with growth-related traits accelerates the process of animal breeding through marker-assisted selection, which leads to increased response to selection. In this study, we conducted a weighted single-step genome-wide association study (WssGWAS) to identify potential candidate genes for direct and maternal genetic effects associated with birth weight (BW) and weaning weight (WW) in Baluchi sheep. The data used in this research included 13,408 birth and 13,170 weaning records collected at Abbas-Abad Baluchi Sheep Breeding Station, Mashhad-Iran. Genotypic data of 94 lambs genotyped by Illumina 50K SNP BeadChip for 54,241 markers were used. The proportion of variance explained by genomic windows was calculated by summing the variance of SNPs within 1 megabase (Mb). The top 10 window genomic regions explaining the highest percentages of additive and maternal genetic variances were selected as candidate window genomic regions associated with body weights. Our findings showed that for BW, the top-ranked genomic regions (1 Mb windows) explained 4.30 and 4.92% of the direct additive and maternal genetic variances, respectively. The direct additive genetic variance explained by the genomic window regions varied from 0.31 on chromosome 1 to 0.59 on chromosome 8. The highest (0.84%) and lowest (0.32%) maternal genetic variances were explained by genomic windows on chromosome 10 and 17, respectively. For WW, the top 10 genomic regions explained 6.38 and 5.76% of the direct additive and maternal genetic variances, respectively. The highest and lowest contribution of direct additive genetic variances were 1.37% and 0.42%, respectively, both explained by genomic regions on chromosome 2. For maternal effects on WW, the highest (1.38%) and lowest (0.41%) genetic variances were explained by genomic windows on chromosome 2. Further investigation of these regions identified several possible candidate genes associated with body weight. Gene ontology analysis using the DAVID database identified several functional terms, such as translation repressor activity, nucleic acid binding, dehydroascorbic acid transporter activity, growth factor activity and SH2 domain binding.
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Affiliation(s)
- Hava Khazaei-Koohpar
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.
| | - Seyed Hasan Hafezian
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Kern-Lunbery RJ, Rathert-Williams AR, Foote AP, Cunningham-Hollinger HC, Kuehn LA, Meyer AM, Lindholm-Perry AK. Genes involved in the cholecystokinin receptor signaling map were differentially expressed in the jejunum of steers with variation in residual feed intake. Vet Anim Sci 2024; 24:100357. [PMID: 38812584 PMCID: PMC11133974 DOI: 10.1016/j.vas.2024.100357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Abstract
The jejunum is a critical site for nutrient digestion and absorption, and variation in its ability to take up nutrients within the jejunum is likely to affect feed efficiency. The purpose of this study was to determine differences in gene expression in the jejunum of beef steers divergent for residual feed intake (RFI) in one cohort of steers (Year 1), and to validate those genes in animals from a second study (Year 2). Steers from Year 1 (n = 16) were selected for high and low RFI. Jejunum mucosal tissue was obtained for RNA-seq. Thirty-two genes were differentially expressed (PFDR≤0.15), and five were over-represented in pathways including inflammatory mediator, cholecystokinin receptor (CCKR) signaling, and p38 MAPK pathways. Several differentially expressed genes (ALOX12, ALPI, FABP6, FABP7, FLT1, GSTA2, MEF2B, PDK4, SPP1, and TTF2) have been previously associated with RFI in other studies. Real-time qPCR was used to validate nine differentially expressed genes in the Year 1 steers used for RNA-seq, and in the Year 2 validation cohort. Six genes were validated as differentially expressed (P < 0.1) using RT-qPCR in the Year 1 population. In the Year 2 population, five genes displayed the same direction of expression as the Year 1 population and 3 were differentially expressed (P < 0.1). The CCKR pathway is involved in digestion, appetite control, and regulation of body weight making it a compelling candidate for feed efficiency in cattle, and the validation of these genes in a second population of cattle is suggestive of a role in feed efficiency.
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Affiliation(s)
- Rebecca J. Kern-Lunbery
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
- Ward Laboratories, Inc., Kearney, NE 68848, USA
| | - Abigail R. Rathert-Williams
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
- University of Missouri, Division of Animal Sciences, Columbia, MO 65211, USA
| | - Andrew P. Foote
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
- Oklahoma State University, Department of Animal & Food Sciences, Stillwater, OK 74078, USA
| | | | - Larry A. Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Allison M. Meyer
- University of Missouri, Division of Animal Sciences, Columbia, MO 65211, USA
- University of Wyoming, Department of Animal Science, Laramie, WY 82071, USA
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Lu X, Suo L, Yan X, Li W, Su Y, Zhou B, Liu C, Yang L, Wang J, Ji D, Cuomu R, Cuoji A, Gui B, Wang Z, Jiang W, Wu Y, Su R. Genome-wide association analysis of fleece traits in Northwest Xizang white cashmere goat. Front Vet Sci 2024; 11:1409084. [PMID: 38872797 PMCID: PMC11171727 DOI: 10.3389/fvets.2024.1409084] [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: 03/29/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024] Open
Abstract
Northwest Xizang White Cashmere Goat (NXWCG) is the first new breed of cashmere goat in the Xizang Autonomous Region. It has significant characteristics of extremely high fineness, gloss, and softness. Genome-wide association analysis is an effective biological method used to measure the consistency and correlation of genotype changes between two molecular markers in the genome. In addition, it can screen out the key genes affecting the complex traits of biological individuals. The aim of this study was to analyze the genetic mechanism of cashmere trait variation in NXWCG and to discover SNP locus and key genes closely related to traits such as superfine cashmere. Additionally, the key genes near the obtained significant SNPs were analyzed by gene function annotation and biological function mining. In this study, the phenotype data of the four traits (cashmere length, fiber length, cashmere diameter, and cashmere production) were collected. GGP_Goat_70K SNP chip was used for genotyping the ear tissue DNA of the experimental group. Subsequently, the association of phenotype data and genotype data was performed using Gemma-0.98.1 software. A linear mixed model was used for the association study. The results showed that four fleece traits were associated with 18 significant SNPs at the genome level and 232 SNPs at the chromosome level, through gene annotated from Capra hircus genome using assembly ARS1. A total of 107 candidate genes related to fleece traits were obtained. Combined with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, we can find that CLNS1A, CCSER1, RPS6KC1, PRLR, KCNRG, KCNK9, and CLYBL can be used as important candidate genes for fleece traits of NXWCG. We used Sanger sequencing and suitability chi-square test to further verify the significant loci and candidate genes screened by GWAS, and the results show that the base mutations loci on the five candidate genes, CCSER1 (snp12579, 34,449,796, A → G), RPS6KC1 (snp41503, 69,173,527, A → G), KCNRG (snp41082, 67,134,820, G → A), KCNK9 (14:78472665, 78,472,665, G → A), and CLYBL (12: 9705753, 9,705,753, C → T), significantly affect the fleece traits of NXWCG. The results provide a valuable basis for future research and contribute to a better understanding of the genetic structure variation of the goat.
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Affiliation(s)
- Xiaotian Lu
- Institute of Animal Science, Xizang Academy of Agricultural and Animal Husbandry Science, Lhasa, China
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Langda Suo
- Institute of Animal Science, Xizang Academy of Agricultural and Animal Husbandry Science, Lhasa, China
- Sino-Arabian Joint Laboratory of Sheep and Goat Germplasm Innovation, Hohhot, China
| | - Xiaochun Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Wenze Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yixin Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Bohan Zhou
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Can Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Lepu Yang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Jiayin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - De Ji
- Institute of Animal Science, Xizang Academy of Agricultural and Animal Husbandry Science, Lhasa, China
- Key Laboratory of Animal Genetics and Breeding on Xizang Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, China
| | - Renqing Cuomu
- Institute of Animal Science, Xizang Academy of Agricultural and Animal Husbandry Science, Lhasa, China
- Key Laboratory of Animal Genetics and Breeding on Xizang Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, China
| | - Awang Cuoji
- Institute of Animal Science, Xizang Academy of Agricultural and Animal Husbandry Science, Lhasa, China
- Key Laboratory of Animal Genetics and Breeding on Xizang Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, China
| | - Ba Gui
- Institute of Animal Science, Xizang Academy of Agricultural and Animal Husbandry Science, Lhasa, China
- Key Laboratory of Animal Genetics and Breeding on Xizang Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Wei Jiang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yujiang Wu
- Institute of Animal Science, Xizang Academy of Agricultural and Animal Husbandry Science, Lhasa, China
- Key Laboratory of Animal Genetics and Breeding on Xizang Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
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Fonseca PAS, Suárez-Vega A, Arranz JJ, Gutiérrez-Gil B. Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits. Genet Sel Evol 2024; 56:40. [PMID: 38773423 PMCID: PMC11106937 DOI: 10.1186/s12711-024-00910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS). RESULTS In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits. CONCLUSIONS The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.
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Affiliation(s)
- Pablo A S Fonseca
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain.
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Reyer H, Abou-Soliman I, Schulze M, Henne H, Reinsch N, Schoen J, Wimmers K. Genome-Wide Association Analysis of Semen Characteristics in Piétrain Boars. Genes (Basel) 2024; 15:382. [PMID: 38540441 PMCID: PMC10969825 DOI: 10.3390/genes15030382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 06/14/2024] Open
Abstract
Since artificial insemination is common practice in pig breeding, the quality and persistence of the semen are decisive for the usability of individual boars. In the current study, genome-wide association analyses were performed to investigate the genetic variability underlying phenotypic variations in semen characteristics. These traits comprise sperm morphology and sperm motility under different temporal and thermal storage conditions, in addition to standard semen quality parameters. Two consecutive samples of the fourth and fifth ejaculates from the same boar were comprehensively analyzed in a genotyped Piétrain boar population. A total of 13 genomic regions on different chromosomes were identified that contain single-nucleotide polymorphisms significantly associated with these traits. Subsequent analysis of the genomic regions revealed candidate genes described to be involved in spermatogenesis, such as FOXL3, GPER1, PDGFA, PRKAR1B, SNRK, SUN1, and TSPO, and sperm motility, including ARRDC4, CEP78, DNAAF5, and GPER1. Some of these genes were also associated with male fertility or infertility in mammals (e.g., CEP78, GPER1). The analyses based on these laboriously determined and valuable phenotypes contribute to a better understanding of the genetic background of male fertility traits in pigs and could prospectively contribute to the improvement of sperm quality through breeding approaches.
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Affiliation(s)
- Henry Reyer
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
| | - Ibrahim Abou-Soliman
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
- Department of Animal and Poultry Breeding, Desert Research Center, Cairo 11753, Egypt
| | - Martin Schulze
- Institute for Reproduction of Farm Animals Schönow, 16321 Bernau, Germany;
| | | | - Norbert Reinsch
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
| | - Jennifer Schoen
- Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany;
- Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
- Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
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Silva DO, Fernandes Júnior GA, Fonseca LFS, Mota LFM, Bresolin T, Carvalheiro R, de Albuquerque LG. Genome-wide association study for stayability at different calvings in Nellore beef cattle. BMC Genomics 2024; 25:93. [PMID: 38254039 PMCID: PMC10804543 DOI: 10.1186/s12864-024-10020-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUNDING Stayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal's life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female's productive life. RESULTS The top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant. CONCLUSION Our results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.
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Affiliation(s)
- Diogo Osmar Silva
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil.
| | - Gerardo Alves Fernandes Júnior
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Larissa Fernanda Simielli Fonseca
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Lúcio Flávio Macedo Mota
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Tiago Bresolin
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Roberto Carvalheiro
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Lucia Galvão de Albuquerque
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, Brazil.
- National Council for Scientific and Technological Development (CNPq), Brasília, Brazil.
- Present address: Departamento de Zootecnia, Via de acesso Paulo Donato Castellane s/n., São Paulo, Jaboticabal, CEP: 14884-900, Brazil.
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Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Transcriptome Analysis Reveals Differentially Expressed circRNAs Associated with Fecundity in Small-Tail Han Sheep Thyroid with Different FecB Genotypes. Animals (Basel) 2023; 14:105. [PMID: 38200837 PMCID: PMC10777913 DOI: 10.3390/ani14010105] [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: 10/07/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Litter size is an economically important trait in sheep, and it is a complex trait controlled by multiple genes in multiple organs. Among them, the regulation of lamb number trait by the thyroid gland is a very important part. However, the molecular mechanisms of the thyroid gland in sheep reproduction remain unclear. Here, RNA-seq was used to detect transcriptome expression patterns in the thyroid gland between follicular phase (FP) and luteal phase (LP) in FecB BB (MM) and FecB ++ (ww) STH sheep, respectively, and to identify differentially expressed circRNAs (DECs) associated with reproduction. Bioinformatic analysis of the source genes of these DECs revealed that they can be enriched in multiple signaling pathways involved in the reproductive process of animals. We found that the source genes of these DECs, such as GNAQ, VEGFC, MAPK1, STAT1, and HSD17B7, may play important roles in the reproductive process of animals. To better understand the function of these DECs, we constructed circRNA-miRNA co-expression networks. Dual luciferase reporter assays suggested that a ceRNA regulatory mechanism between circ_0003259-oar-miR-133-TXLNA and circ_0012128-oar-miR-370-3p-FGFR1 may hold. All of these DEC expression profiles in the thyroid gland provide a novel resource for elucidating the regulatory mechanisms underlying STH sheep prolificacy.
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Affiliation(s)
- Cheng Chang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Ran Di
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Miaoceng Han
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
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Zhang CL, Zhang J, Tuersuntuoheti M, Zhou W, Han Z, Li X, Yang R, Zhang L, Zheng L, Liu S. Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166698. [PMID: 37683864 DOI: 10.1016/j.scitotenv.2023.166698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Sheep are important livestock animals that have evolved under various ecological pressures. Xinjiang is a region with diverse and harsh environments that have shaped many local sheep breeds with unique characteristics and environmental adaptability. However, these breeds are losing ecological flexibility due to the promotion of intensive farming practices. Here we sequenced 14 local sheep breeds from Xinjiang and analyzed their genetic structure and gene flow with other sheep breeds from neighboring regions. The Tibetan Plateau was the geographic origin of Xinjiang native sheep evolution. We performed genome-environment association analysis and identified Bio9: Mean Temperature of Driest Quarter and Bio15: Precipitation Seasonality as the key environmental factors affecting Xinjiang local sheep and the key genes involved in their survival and adaptation. We classified Xinjiang native sheep breeds into six groups based on their differential genes by pairwise selective sweep analysis and Community Network Analysis. We analyzed transcriptome expression data of 832 sheep tissues and detected tissue-specific enrichment of six group-specific genes in different biological systems. Our results revealed the genetic basis of year-round estrus, drought tolerance, hypoxia resistance, and cold tolerance traits of Xinjiang sheep breeds. Moreover, we proposed conservation strategies for Xinjiang local sheep breeds and provided theoretical guidance for breeding new sheep breeds under global extreme environments.
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Affiliation(s)
- Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Jihu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Mirenisa Tuersuntuoheti
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Ruizhi Yang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Lulu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Langman Zheng
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China.
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10
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Liu X, Chen J, Xu X, Liu J, Zhang J, Cheng H, Ahmed Z, Huang B, Lei C. A missense mutation of the WNK1 gene affects cold tolerance in Chinese domestic cattle. Anim Biotechnol 2023; 34:4803-4808. [PMID: 37079337 DOI: 10.1080/10495398.2023.2196316] [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: 04/21/2023]
Abstract
Inclement weather conditions, especially cold stress, have threatened the cattle industry. Cattle exposed to cold environments for a longer time suffer developmental delay, immunity decline, and eventually death. WNK1 is a member of With-no-lysine kinases (WNKs), widely expressed in animal organs and tissues. WNK1 and WNK4 are expressed in adipose tissue, and WNK4 promotes adipogenesis. WNK1 does not directly affect adipogenesis but has been shown to promote WNK4 expression in several tissues or organs. One missense mutation NC_037346.1:g.107692244, A > G, rs208265410 in the WNK1 gene was detected from the database of bovine genomic variation (BGVD). Here, we collected 328 individuals of 17 breeds representing four groups of Chinese cattle, northern group cattle, southern group cattle, central group cattle, and special group cattle (Tibetan cattle). We also collected the temperature and humidity data records from their relative locations. The frequencies of the G allele in Chinese breeds increased from northern China to southern China, and the frequencies of the A allele showed an opposite trend. Our results indicate that the WNK1 gene might be a candidate gene marker associated with cold tolerance.
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Affiliation(s)
- Xin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jialei Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xinlong Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Haijian Cheng
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot Azad Jammu and Kashmir Pakistan, Rawalakot, Pakistan
| | - Bizhi Huang
- 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, Yangling, China
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11
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Al Abri M, Alfoudari A, Mohammad Z, Almathen F, Al-Marzooqi W, Al-Hajri S, Al-Amri M, Bahbahani H. Assessing genetic diversity and defining signatures of positive selection on the genome of dromedary camels from the southeast of the Arabian Peninsula. Front Vet Sci 2023; 10:1296610. [PMID: 38098998 PMCID: PMC10720651 DOI: 10.3389/fvets.2023.1296610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Dromedary camels (Camelus dromedarius) are members of the Camelini tribe within the Camelidae family. They are distributed throughout North Africa, the Arabian Peninsula and Southeast Asia. This domestic species is characterized by its superior adaptability to the harsh desert environment. In this study, whole autosomal data of 29 dromedary samples from the Southeast Arabian Peninsula in Oman; 10 from Muscat, 14 from Al-Batinah, and 5 from Al-Sharqiya, were investigated to assess their genetic relationship and to define candidate signatures of positive selection. A minimal genetic distinction that separates Muscat dromedaries from the other two populations was observed, with a degree of genetic admixture between them. Using the de-correlated composite of multiple signals (DCMS) approach, a total of 47 candidate regions within the autosomes of these dromedary populations were defined with signatures of positive selection. These candidate regions harbor a total of 154 genes that are mainly associated with functional categories related to immune response, lipid metabolism and energy expenditure, optical and auditory functions, and long-term memory. Different functional genomic variants were called on the candidate regions and respective genes that warrant further investigation to find possible association with the different favorable phenotypes in dromedaries. The output of this study paves the way for further research efforts aimed at defining markers for use in genomic breeding programs, with the goal of conserving the genetic diversity of the species and enhancing its productivity.
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Affiliation(s)
- Mohammad Al Abri
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ahmad Alfoudari
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zainab Mohammad
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Waleed Al-Marzooqi
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Salim Al-Hajri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Mahmood Al-Amri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
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12
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Wang W, Du X, Chu M, He X. Photoperiod Induces the Epigenetic Change of the GNAQ Gene in OVX+E 2 Ewes. Int J Mol Sci 2023; 24:16442. [PMID: 38003630 PMCID: PMC10671395 DOI: 10.3390/ijms242216442] [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: 10/22/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
GNAQ, a member of the alpha subunit encoding the q-like G protein, is a critical gene in cell signaling, and multiple studies have shown that upregulation of GNAQ gene expression ultimately inhibits the proliferation of gonadotropin-releasing hormone (GnRH) neurons and GnRH secretion, and ultimately affects mammalian reproduction. Photoperiod is a key inducer which plays an important role in gene expression regulation by affecting epigenetic modification. However, fewer studies have confirmed how photoperiod induces epigenetic modifications of the GNAQ gene. In this study, we examined the expression and epigenetic changes of GNAQ in the hypothalamus in ovariectomized and estradiol-treated (OVX+E2) sheep under three photoperiod treatments (short photoperiod treatment for 42 days, SP42; long photoperiod treatment for 42 days, LP42; 42 days of short photoperiod followed by 42 days of long photoperiod, SP-LP42). The results showed that the expression of GNAQ was significantly higher in SP-LP42 than in SP42 and LP42 (p < 0.05). Whole genome methylation sequencing (WGBS) results showed that there are multiple differentially methylated regions (DMRs) and loci between different groups of GNAQ. Among them, the DNA methylation level of DMRs at the CpG1 locus in SP42 was significantly higher than that of SP-LP42 (p < 0.01). Subsequently, we confirmed that the core promoter region of the GNAQ gene was located with 1100 to 1500 bp upstream, and the DNA methylation level of all eight CpG sites in SP42 was significantly higher than those in LP42 (p < 0.01), and significantly higher than those in SP-LP42 (p < 0.01), except site 2 and site 4 in the first sequencing fragment (p < 0.05) in the core promoter region. The expression of acetylated GNAQ histone H3 was significantly higher than that of the control group under three different photoperiods (p < 0.01); the acetylation level of sheep hypothalamic GNAQ genomic protein H3 was significantly lower under SP42 than under SP-LP42 (p < 0.05). This suggests that acetylated histone H3 binds to the core promoter region of the GNAQ gene, implying that GNAQ is epigenetically regulated by photoperiod through histone acetylation. In summary, the results suggest that photoperiod can induce DNA methylation in the core promoter region and histone acetylation in the promoter region of the GNAQ gene, and hypothesize that the two may be key factors in regulating the differential expression of GNAQ under different photoperiods, thus regulating the hypothalamus-pituitary-gonadal axis (HPGA) through the seasonal estrus in sheep. The results of this study will provide some new information to understand the function of epigenetic modifications in reproduction in sheep.
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Affiliation(s)
| | | | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.W.); (X.D.)
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.W.); (X.D.)
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13
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Li C, Li J, Wang H, Zhang R, An X, Yuan C, Guo T, Yue Y. Genomic Selection for Live Weight in the 14th Month in Alpine Merino Sheep Combining GWAS Information. Animals (Basel) 2023; 13:3516. [PMID: 38003134 PMCID: PMC10668700 DOI: 10.3390/ani13223516] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Alpine Merino Sheep is a novel breed reared from Australian Merino Sheep as the father and Gansu Alpine Fine-Wool Sheep as the mother, living all year in cold and arid alpine areas with exceptional wool quality and meat performance. Body weight is an important economic trait of the Alpine Merino Sheep, but there is limited research on identifying the genes associated with live weight in the 14th month for improving the accuracy of the genomic prediction of this trait. Therefore, this study's sample comprised 1310 Alpine Merino Sheep ewes, and the Fine Wool Sheep 50K Panel was used for genome-wide association study (GWAS) analysis to identify candidate genes. Moreover, the trial population (1310 ewes) in this study was randomly divided into two groups. One group was used as the population for GWAS analysis and screened for the most significant top 5%, top 10%, top 15%, and top 20% SNPs to obtain prior marker information. The other group was used to estimate the genetic parameters based on the weight assigned by heritability combined with different prior marker information. The aim of this study was to compare the accuracy of genomic breeding value estimation when combined with prior marker information from GWAS analysis with the optimal linear unbiased prediction method for genome selection (GBLUP) for the breeding value of target traits. Finally, the accuracy was evaluated using the five-fold cross-validation method. This research provides theoretical and technical support to improve the accuracy of sheep genome selection and better guide breeding. The results demonstrated that eight candidate genes were associated with GWAS analysis, and the gene function query and literature search results suggested that FAM184B, NCAPG, MACF1, ANKRD44, DCAF16, FUK, LCORL, and SYN3 were candidate genes affecting live weight in the 14th month (WT), which regulated the growth of muscle and bone in sheep. In genome selection analysis, the heritability of GBLUP to calculate the WT was 0.335-0.374, the accuracy after five-fold cross-verification was 0.154-0.190, and after assigning different weights to the top 5%, top 10%, top 15%, and top 20% of the GWAS results in accordance with previous information to construct the G matrix, the accuracy of the WT in the GBLUP model was improved by 2.59-7.79%.
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Affiliation(s)
- Chenglan Li
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianye Li
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Haifeng Wang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Rui Zhang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- 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 Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- 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 Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- 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 Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- 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 Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (C.L.)
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
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14
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Ma X, Liu Y, Sun L, Hanif Q, Qu K, Liu J, Zhang J, Huang B, Lei C. A novel SNP of TECPR2 gene associated with heat tolerance in Chinese cattle. Anim Biotechnol 2023; 34:1050-1057. [PMID: 34877906 DOI: 10.1080/10495398.2021.2011305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Heat stress affects the animal production and causes serious economic losses to the husbandry. Tectonin beta-propeller repeat containing 2 (TECPR2) gene plays an important role in autophagy which may affect the temperature sensation in animals. A missense mutation (XM_024981840.1:c.3989 G > A p.Arg1330His) of the transcripts X4 in the bovine TECPR2 gene was identified. In this study, the c.3989 G > A variant in TECPR2 gene was genotyped in a total of 25 cattle breeds (520 individuals). Our results indicated that the frequency of A allele showed a decreasing pattern from southern cattle to northern cattle, while the frequency of G allele showed the opposite pattern, which was consistent with the climate distribution of China. Compared with the GG genotype, southern cattle carried more the AA and AG genotypes. Furthermore, the association results carried out that the frequencies of genotypes (GG, AG, AA) and the value of climate parameters (mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) were significantly correlated (p < 0.01). Hence, we speculated that the c.3989 G > A variant of TECPR2 gene was associated with the heat tolerance trait in Chinese cattle and the locus may be considered as a molecular marker for Chinese cattle breeding.
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Affiliation(s)
- Xiaohui Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yangkai Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Luyang Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, Yunnan, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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15
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Yudin NS, Larkin DM. Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds. Vavilovskii Zhurnal Genet Selektsii 2023; 27:463-470. [PMID: 37867610 PMCID: PMC10587008 DOI: 10.18699/vjgb-23-56] [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: 12/02/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 10/24/2023] Open
Abstract
It is known that different species of animals, when living in the same environmental conditions, can form similar phenotypes. The study of the convergent evolution of several species under the influence of the same environmental factor makes it possible to identify common mechanisms of genetic adaptation. Local cattle and sheep breeds have been formed over thousands of years under the influence of domestication, as well as selection aimed at adaptation to the local environment and meeting human needs. Previously, we identified a number of candidate genes in genome regions potentially selected during domestication and adaptation to the climatic conditions of Russia, in local breeds of cattle and sheep using whole genome genotyping data. However, these data are of low resolution and do not reveal most nucleotide substitutions. The aim of the work was to create, using the whole genome sequencing data, a list of genes associated with domestication, selection and adaptation in Russian cattle and sheep breeds, as well as to identify candidate genes and metabolic pathways for selection for cold adaptation. We used our original data on the search for signatures of selection in the genomes of Russian cattle (Yakut, Kholmogory, Buryat, Wagyu) and sheep (Baikal, Tuva) breeds. We used the HapFLK, DCMS, FST and PBS methods to identify DNA regions with signatures of selection. The number of candidate genes in potentially selective regions was 946 in cattle and 151 in sheep. We showed that the studied Russian cattle and sheep breeds have at least 10 genes in common, apparently involved in the processes of adaptation/selection, including adaptation to a cold climate, including the ASTN2, PM20D1, TMEM176A, and GLIS1 genes. Based on the intersection with the list of selected genes in at least two Arctic/Antarctic mammal species, 20 and 8 genes, have been identified in cattle and sheep, respectively, that are potentially involved in cold adaptation. Among them, the most promising for further research are the ASPH, NCKAP5L, SERPINF1, and SND1 genes. Gene ontology analysis indicated the existence of possible common biochemical pathways for adaptation to cold in domestic and wild mammals associated with cytoskeleton disassembly and apoptosis.
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Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
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16
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Discovering novel clues of natural selection on four worldwide goat breeds. Sci Rep 2023; 13:2110. [PMID: 36747064 PMCID: PMC9902602 DOI: 10.1038/s41598-023-27490-x] [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: 08/09/2022] [Accepted: 01/03/2023] [Indexed: 02/08/2023] Open
Abstract
In goat breeds, the domestication followed by artificial selection for economically important traits have shaped genetic variation within populations, leading to the fixation of specific alleles for specific traits. This led to the formation and evolution of many different breeds specialised and raised for a particular purpose. However, and despite the intensity of artificial selection, natural selection continues acting, possibly leaving a more diluted contribution over time, whose traces may be more difficult to capture. In order to explore selection footprints as response of environmental adaptation, we analysed a total of 993 goats from four transboundary goats breeds (Angora, Boer, Nubian and Saanen) genotyped with the SNP chip 50 K using outlier detection, runs of homozygosity and haplotype-based detection methods. Our results showed that all methods identified footprints on chromosome 6 (from 30 to 49 Mb) for two specific populations of Nubian goats sampled in Egypt. In Angora and Saanen breeds, we detected two selective sweeps using HapFLK, on chromosome 21 (from 52 to 55 Mb) and chromosome 25 (from 1 to 5 Mb) respectively. The analysis of runs of homozygosity showed some hotspots in all breeds. The overall investigation of the selected regions detected combining the different approaches and the gene ontology exploration revealed both novel and well-known loci related to adaptation, especially for heat stress. Our findings can help to better understand the balance between the two selective pressures in commercial goat breeds providing new insights on the molecular mechanisms of adaptation.
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Sánchez-Ramos R, Trujano-Chavez MZ, Gallegos-Sánchez J, Becerril-Pérez CM, Cadena-Villegas S, Cortez-Romero C. Detection of Candidate Genes Associated with Fecundity through Genome-Wide Selection Signatures of Katahdin Ewes. Animals (Basel) 2023; 13:ani13020272. [PMID: 36670812 PMCID: PMC9854690 DOI: 10.3390/ani13020272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
One of the strategies to genetically improve reproductive traits, despite their low inheritability, has been the identification of candidate genes. Therefore, the objective of this study was to detect candidate genes associated with fecundity through the fixation index (FST) and runs of homozygosity (ROH) of selection signatures in Katahdin ewes. Productive and reproductive records from three years were used and the genotypes (OvineSNP50K) of 48 Katahdin ewes. Two groups of ewes were identified to carry out the genetic comparison: with high fecundity (1.3 ± 0.03) and with low fecundity (1.1 ± 0.06). This study shows for the first time evidence of the influence of the CNOT11, GLUD1, GRID1, MAPK8, and CCL28 genes in the fecundity of Katahdin ewes; in addition, new candidate genes were detected for fecundity that were not reported previously in ewes but that were detected for other species: ANK2 (sow), ARHGAP22 (cow and buffalo cow), GHITM (cow), HERC6 (cow), DPF2 (cow), and TRNAC-GCA (buffalo cow, bull). These new candidate genes in ewes seem to have a high expression in reproduction. Therefore, future studies are needed focused on describing the physiological basis of changes in the reproductive behavior influenced by these genes.
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Affiliation(s)
- Reyna Sánchez-Ramos
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
| | | | - Jaime Gallegos-Sánchez
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
| | - Carlos Miguel Becerril-Pérez
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
- Agroecosistemas Tropicales, Colegio de Postgraduados, Campus Veracruz, Carretera Xalapa-Veracruz Km. 88.5, Manlio Favio Altamirano, Veracruz 91690, Mexico
| | - Said Cadena-Villegas
- Producción Agroalimentaria en Trópico, Colegio de Postgraduados, Campus Tabasco, Periférico Carlos A. Molina, Ranchería Rio Seco y Montaña, Heroica Cárdenas 86500, Mexico
| | - César Cortez-Romero
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
- Innovación en Manejo de Recursos Naturales, Colegio de Postgraduados, Campus San Luis Potosí, Agustín de Iturbide No. 73, Salinas de Hidalgo, San Luis Potosí 78622, Mexico
- Correspondence: ; Tel.: +52-5959-520-200 (ext. 4000)
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18
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Xiong J, Bao J, Hu W, Shang M, Zhang L. Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat. Front Genet 2023; 13:1044017. [PMID: 36685859 PMCID: PMC9852865 DOI: 10.3389/fgene.2022.1044017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.
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19
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Machová K, Marina H, Arranz JJ, Pelayo R, Rychtářová J, Milerski M, Vostrý L, Suárez-Vega A. Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms. Animal 2023; 17:100690. [PMID: 36566708 DOI: 10.1016/j.animal.2022.100690] [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: 08/31/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of FST were higher in Wallachian sheep (FST = 0.14) than in Sumava sheep (FST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the Ne estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (FHOM) among individuals, from -0.04 to 0.16 in Sumava and from -0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool.
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Affiliation(s)
- Karolína Machová
- Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic.
| | - Héctor Marina
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Juan Jose Arranz
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Rocío Pelayo
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Jana Rychtářová
- Institute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech Republic
| | - Michal Milerski
- Institute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech Republic
| | - Luboš Vostrý
- Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic
| | - Aroa Suárez-Vega
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
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20
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Chessari G, Criscione A, Tolone M, Bordonaro S, Rizzuto I, Riggio S, Macaluso V, Moscarelli A, Portolano B, Sardina MT, Mastrangelo S. High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context. Front Vet Sci 2023; 10:1127354. [PMID: 37205231 PMCID: PMC10185747 DOI: 10.3389/fvets.2023.1127354] [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: 12/19/2022] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise FST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and FST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.
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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Bordonaro
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Ilaria Rizzuto
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Silvia Riggio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Vito Macaluso
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Angelo Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
- *Correspondence: Salvatore Mastrangelo,
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21
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Assessing Genetic Diversity and Searching for Selection Signatures by Comparison between the Indigenous Livni and Duroc Breeds in Local Livestock of the Central Region of Russia. DIVERSITY 2022. [DOI: 10.3390/d14100859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Indigenous pig breeds are mainly associated with the adaptive capacity that is necessary to respond adequately to climate change, food security, and livelihood needs, and natural resources conservation. Livni pigs are an indigenous fat-type breed farmed in a single farm in the Orel region and located in the Central European part of the Russian Federation. To determine the genomic regions and genes that are affected by artificial selection, we conducted the comparative study of two pig breeds with different breeding histories and breeding objectives, i.e., the native fat-type Livni and meat-type Duroc breeds using the Porcine GGP HD BeadChip, which contains ~80,000 SNPs. To check the Livni pigs for possible admixture, the Landrace and the Large White breeds were included into the study of genetic diversity as these breeds participated in the formation of the Livni pigs. We observed the highest level of genetic diversity in Livni pigs compared to commercial breeds (UHE = 0.409 vs. 0.319–0.359, p < 0.001; AR = 1.995 vs. 1.894–1.964, p < 0.001). A slight excess of heterozygotes was found in all of the breeds. We identified 291 candidate genes, which were localized within the regions under putative selection, including 22 and 228 genes, which were specific for Livni and Duroc breeds, respectively, and 41 genes common for both breeds. A detailed analysis of the molecular functions identified the genes, which were related to the formation of meat and fat traits, and adaptation to environmental stress, including extreme temperatures, which were different between breeds. Our research results are useful for conservation and sustainable breeding of Livni breed, which shows a high level of genetic diversity. This makes Livni one of the valuable national pig genetic resources.
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22
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de Souza TC, de Souza TC, da Cruz VAR, Mourão GB, Pedrosa VB, Rovadoscki GA, Coutinho LL, de Camargo GMF, Costa RB, de Carvalho GGP, Pinto LFB. Estimates of heritability and candidate genes for primal cuts and dressing percentage in Santa Ines sheep. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Smith JL, Wilson ML, Nilson SM, Rowan TN, Schnabel RD, Decker JE, Seabury CM. Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle. BMC Genomics 2022; 23:517. [PMID: 35842584 PMCID: PMC9287884 DOI: 10.1186/s12864-022-08667-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Genotypic information produced from single nucleotide polymorphism (SNP) arrays has routinely been used to identify genomic regions associated with complex traits in beef and dairy cattle. Herein, we assembled a dataset consisting of 15,815 Red Angus beef cattle distributed across the continental U.S. and a union set of 836,118 imputed SNPs to conduct genome-wide association analyses (GWAA) for growth traits using univariate linear mixed models (LMM); including birth weight, weaning weight, and yearling weight. Genomic relationship matrix heritability estimates were produced for all growth traits, and genotype-by-environment (GxE) interactions were investigated. Results Moderate to high heritabilities with small standard errors were estimated for birth weight (0.51 ± 0.01), weaning weight (0.25 ± 0.01), and yearling weight (0.42 ± 0.01). GWAA revealed 12 pleiotropic QTL (BTA6, BTA14, BTA20) influencing Red Angus birth weight, weaning weight, and yearling weight which met a nominal significance threshold (P ≤ 1e-05) for polygenic traits using 836K imputed SNPs. Moreover, positional candidate genes associated with Red Angus growth traits in this study (i.e., LCORL, LOC782905, NCAPG, HERC6, FAM184B, SLIT2, MMRN1, KCNIP4, CCSER1, GRID2, ARRDC3, PLAG1, IMPAD1, NSMAF, PENK, LOC112449660, MOS, SH3PXD2B, STC2, CPEB4) were also previously associated with feed efficiency, growth, and carcass traits in beef cattle. Collectively, 14 significant GxE interactions were also detected, but were less consistent among the investigated traits at a nominal significance threshold (P ≤ 1e-05); with one pleiotropic GxE interaction detected on BTA28 (24 Mb) for Red Angus weaning weight and yearling weight. Conclusions Sixteen well-supported QTL regions detected from the GWAA and GxE GWAA for growth traits (birth weight, weaning weight, yearling weight) in U.S. Red Angus cattle were found to be pleiotropic. Twelve of these pleiotropic QTL were also identified in previous studies focusing on feed efficiency and growth traits in multiple beef breeds and/or their composites. In agreement with other beef cattle GxE studies our results implicate the role of vasodilation, metabolism, and the nervous system in the genetic sensitivity to environmental stress. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08667-6.
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Affiliation(s)
- Johanna L Smith
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA
| | - Miranda L Wilson
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA
| | - Sara M Nilson
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA
| | - Troy N Rowan
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.,Genetics Area Program, University of Missouri, Columbia, 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.,Genetics Area Program, University of Missouri, Columbia, 65211, USA.,Informatics Institute, University of Missouri, Columbia, 65211, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.,Genetics Area Program, University of Missouri, Columbia, 65211, USA.,Informatics Institute, University of Missouri, Columbia, 65211, USA
| | - Christopher M Seabury
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA.
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24
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Lakhanova K, Kedelbaev B, Yeleugaliyeva N, Korazbekova K. Study of melanin distribution in the hair cells of Karakul lambs of different colours. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Bao Q, Ma X, Jia C, Wu X, Wu Y, Meng G, Bao P, Chu M, Guo X, Liang C, Yan P. Resequencing and Signatures of Selective Scans Point to Candidate Genetic Variants for Hair Length Traits in Long-Haired and Normal-Haired Tianzhu White Yak. Front Genet 2022; 13:798076. [PMID: 35360871 PMCID: PMC8962741 DOI: 10.3389/fgene.2022.798076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/17/2022] [Indexed: 12/29/2022] Open
Abstract
Tianzhu white yak is a rare local yak breed with a pure white coat in China. In recent years, breeders have discovered long-haired individuals characterized by long hair on the forehead in the Tianzhu white yak, and the length and density of the hair on these two parts of the body are higher than that of the normal Tianzhu white yak. To elucidate the genetic mechanism of hair length in Tianzhu white yak, we re-sequence the whole genome of long-haired Tianzhu White yak (LTWY) (n = 10) and normal Tianzhu White yak (NTWY) (n = 10). Then, fixation index (F ST), θπ ratio, cross-population composite likelihood ratio (XP-CLR), integrated haplotype score (iHS), cross-population extended haplotype homozygosity (XP-EHH), and one composite method, the de-correlated composite of multiple signals (DCMS) were performed to discover the loci and genes related to long-haired traits. Based on five single methods, we found two hotspots of 0.2 and 1.1 MB in length on chromosome 6, annotating two (FGF5, CFAP299) and four genes (ATP8A1, SLC30A9, SHISA3, TMEM33), respectively. Function enrichment analysis of genes in two hotspots revealed Ras signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, and Rap1 signaling pathway were involved in the process of hair length differences. Besides, the DCMS method further found that four genes (ACOXL, PDPK1, MAGEL2, CDH1) were associated with hair follicle development. Henceforth, our work provides novel genetic insights into the mechanisms of hair growth in the LTWY.
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Affiliation(s)
- Qi Bao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Yak Breeding Engineering, Lanzhou, China
| | - Xiaoming Ma
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Yak Breeding Engineering, Lanzhou, China
| | - Congjun Jia
- Guangdong Meizhou Vocational and Technical College, Meizhou, China
| | - Xiaoyun Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Yak Breeding Engineering, Lanzhou, China
| | - Yi Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guangyao Meng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Yak Breeding Engineering, Lanzhou, China
| | - Pengjia Bao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Yak Breeding Engineering, Lanzhou, China
| | - Min Chu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Yak Breeding Engineering, Lanzhou, China
| | - Xian Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Yak Breeding Engineering, Lanzhou, China
| | - Chunnian Liang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Yak Breeding Engineering, Lanzhou, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Yak Breeding Engineering, Lanzhou, China
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26
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Zhu M, Zhang H, Yang H, Zhao Z, Blair HT, Liang H, Wu P, Yu Q. Targeting GNAQ in hypothalamic nerve cells to regulate seasonal estrus in sheep. Theriogenology 2022; 181:79-88. [DOI: 10.1016/j.theriogenology.2022.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/25/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022]
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27
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Igoshin AV, Deniskova TE, Yurchenko AA, Yudin NS, Dotsev AV, Selionova MI, Zinovieva NA, Larkin DM. Copy number variants in genomes of local sheep breeds from Russia. Anim Genet 2021; 53:119-132. [PMID: 34904242 DOI: 10.1111/age.13163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2021] [Indexed: 01/21/2023]
Abstract
Copy number variants (CNVs) are genomic structural variations that contribute to many adaptive and economically important traits in livestock. In this study, we detected CNVs in 354 animals from 16 Russian indigenous sheep breeds and analysed their possible functional roles. Our analysis of the entire sample set resulted in 4527 CNVs forming 1450 CNV regions (CNVRs). When constructing CNVRs for individual breeds, a total of 2715 regions ranging from 88 in Groznensk to 337 in Osetin breeds were identified. To make interbreed CNVR frequency comparison possible, we also identified core CNVRs using CNVs with overlapping chromosomal locations found in different breeds. This resulted in 137 interbreed CNVRs with frequency >15% in at least one breed. Functional enrichment analysis of genes affected by CNVRs in individual breeds revealed 12 breeds with significant enrichments in olfactory perception, PRAME family proteins, and immune response. Function of genes affected by interbreed and breed-specific CNVRs revealed candidates related to domestication, adaptation to high altitudes and cold climates, reproduction, parasite resistance, milk and meat qualities, wool traits, fat storage, and fat metabolism. Our work is the first attempt to uncover and characterise the CNV makeup of Russian indigenous sheep breeds. Further experimental and functional validation of CNVRs would help in developing new and improving existing sheep breeds.
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Affiliation(s)
- A V Igoshin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - T E Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - A A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - N S Yudin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - A V Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - M I Selionova
- Russian State Agrarian University, Moscow Timiryazev Agricultural Academy, Moscow, 127550, Russia
| | - N A Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - D M Larkin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Royal Veterinary College, University of London, London, NW1 0TU, UK
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28
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Luna-Nevárez G, Pendleton AL, Luna-Ramirez RI, Limesand SW, Reyna-Granados JR, Luna-Nevárez P. Genome-wide association study of a thermo-tolerance indicator in pregnant ewes exposed to an artificial heat-stressed environment. J Therm Biol 2021; 101:103095. [PMID: 34879913 DOI: 10.1016/j.jtherbio.2021.103095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022]
Abstract
Environmental heat stress negatively influences sheep production in warm semi-arid regions. An animal's ability to tolerate warm weather is difficult to measure naturally due to environmental variability and genetic variation between animals. In this study we developed a thermo-tolerance indicator (TTI) to define heat stress tolerance in pregnant sheep in a controlled environment. Next, we performed a genome-wide association study (GWAS) to identify genomic regions and target genes associated with thermo-tolerance in sheep. Pregnant Columbia-Rambouillet crossbred ewes (n = 127) were heat-stressed inside a climate-controlled chamber for 57 days by increasing the temperature-humidity index to ≥30. Rectal temperature (RT) and feed intake (FI) data were collected daily and used for the predictive TTI analysis. After the tenth day of heat stress, the regression analyses revealed that FI was stable; however, when the ewe's RT exceeded 39.8 °C their FI was less than thermo-tolerant ewes. This average predicted temperature was used to classify each ewe as heat stress tolerant (≤39.8 °C) and non-heat stress tolerant (>39.8 °C). A GWAS analysis was performed and genomic regions were compared between heat stress tolerant and non-tolerant ewes. The single-marker genomic analysis detected 16 single nucleotide polymorphisms (SNP) associated with heat stress tolerance (P < 0.0001), whereas the multi-marker Bayesian analysis identified 8 overlapped 1-Mb chromosomal regions accounting for 11.39% of the genetic variation associated with tolerance to heat stress. Four intragenic SNP showed a remarkable contribution to thermo-tolerance, and these markers were within the genes FBXO11 (rs407804467), PHC3 (rs414179061), TSHR (rs418575898) and STAT1 (rs417581105). In conclusion, genomic regions harboring four intragenic SNP were associated with heat stress tolerance, and these candidate genes are proposed to influence heat tolerance in pregnant ewes subjected to an artificially induced warm climate. Moreover, these genetic markers could be suitable for use in further genetic selection programs in sheep managed in semi-arid regions.
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Affiliation(s)
- Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Alexander L Pendleton
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Rosa I Luna-Ramirez
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Sean W Limesand
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Javier R Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México.
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29
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Tsartsianidou V, Sánchez-Molano E, Kapsona VV, Basdagianni Z, Chatziplis D, Arsenos G, Triantafyllidis A, Banos G. A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep. Genet Sel Evol 2021; 53:90. [PMID: 34856922 PMCID: PMC8641236 DOI: 10.1186/s12711-021-00682-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 02/07/2023] Open
Abstract
Background The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change. Results We detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h2 = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response. Conclusions Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00682-7.
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Affiliation(s)
- Valentina Tsartsianidou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
| | - Enrique Sánchez-Molano
- Division of Genetics and Genomics, School of Veterinary Studies, The Roslin Institute and Royal (Dick), University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Vanessa Varvara Kapsona
- Department of Animal and Veterinary Sciences, Scotland's Rural College, Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, UK
| | - Zoitsa Basdagianni
- Department of Animal Production, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dimitrios Chatziplis
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agriculture, International Hellenic University, Alexander Campus, 57400, Sindos, Greece
| | - Georgios Arsenos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Georgios Banos
- Department of Animal and Veterinary Sciences, Scotland's Rural College, Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, UK.,Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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30
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Chen ZH, Xu YX, Xie XL, Wang DF, Aguilar-Gómez D, Liu GJ, Li X, Esmailizadeh A, Rezaei V, Kantanen J, Ammosov I, Nosrati M, Periasamy K, Coltman DW, Lenstra JA, Nielsen R, Li MH. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep. Commun Biol 2021; 4:1307. [PMID: 34795381 PMCID: PMC8602413 DOI: 10.1038/s42003-021-02817-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.
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Affiliation(s)
- Ze-Hui Chen
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China ,grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Xi Xu
- grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Dong-Feng Wang
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Diana Aguilar-Gómez
- grid.47840.3f0000 0001 2181 7878Center for Computational Biology, University of California at Berkeley, Berkeley, CA 94720 USA
| | | | - Xin Li
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ali Esmailizadeh
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Vahideh Rezaei
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, The Sakha Republic (Yakutia), Yakutsk, Russia
| | - Maryam Nosrati
- grid.412462.70000 0000 8810 3346Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Kathiravan Periasamy
- grid.420221.70000 0004 0403 8399Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - David W. Coltman
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB T6G2E9 Canada
| | - Johannes A. Lenstra
- grid.5477.10000000120346234Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, Berkeley, CA, 94720, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, 94707, USA. .,Globe Institute, University of Copenhagen, 1350, København K, Denmark.
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China.
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Orlov YL, Anashkina AA. Life: Computational Genomics Applications in Life Sciences. Life (Basel) 2021; 11:life11111211. [PMID: 34833087 PMCID: PMC8622464 DOI: 10.3390/life11111211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 01/19/2023] Open
Affiliation(s)
- Yuriy L. Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia;
- Life Sciences Department, Novosibirsk State University, 630090 Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
- Correspondence:
| | - Anastasia A. Anashkina
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia;
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Detection of whole genome selection signatures of Pakistani Teddy goat. Mol Biol Rep 2021; 48:7273-7280. [PMID: 34609690 DOI: 10.1007/s11033-021-06726-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Natural and artificial selection tend to cause variability that contributes to shape the genome of livestock in a way that differentiates them among the animal kingdom. The particular aim here is to identify positive selection signatures with whole genome pooled-sequence data of Pakistani Teddy goat. METHODS AND RESULTS Paired-end alignment of 635,357,043 reads of Teddy goat with (ARS1) reference genome assembly was carried out. Pooled-Heterozygosity (Hp) and Tajima's D (TD) are applied for validation and getting better hits of selection signals, while pairwise FST statistics is conducted on Teddy vs. Bezoar (wild goat ancestor) for genomic differentiation, moreover annotation of regions under positive selection was also performed. Hp score with - ZHp > 5 detected six windows having highest hits on Chr. 29, 9, 25, 15 and 14 that harbor HRASLS5, LACE1 and AXIN1 genes which are candidate for embryonic development, lactation and body height. Secondly, - ZTD value of > 3.3 showed 4 windows with very strong hits on Chr.5 & 9 which harbor STIM1 and ADM genes related to body mass and weight. Lastly, - ZFST < - 5 generated four strong signals on Chr.5 & 12 harbor LOC102183233 gene. Other significant selection signatures encompass genes associated with wool production, prolificacy and coat colors traits in this breed. CONCLUSIONS In brief, this study identified the genes under selection in Pakistani Teddy goat that will be helpful to refining the marker-assisted breeding policies and converging required production traits within and across other goat breeds and to explore full genetic potential of this valued species of livestock.
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Abdelmanova AS, Dotsev AV, Romanov MN, Stanishevskaya OI, Gladyr EA, Rodionov AN, Vetokh AN, Volkova NA, Fedorova ES, Gusev IV, Griffin DK, Brem G, Zinovieva NA. Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens. BIOLOGY 2021; 10:biology10090876. [PMID: 34571753 PMCID: PMC8469556 DOI: 10.3390/biology10090876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 01/14/2023]
Abstract
Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.
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Affiliation(s)
- Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
- K.I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 23 Akademika Skryabina St., 109472 Moscow, Russia
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
| | - Olga I. Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Elena S. Fedorova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Igor V. Gusev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
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Abousoliman I, Reyer H, Oster M, Murani E, Mohamed I, Wimmers K. Genome-Wide Analysis for Early Growth-Related Traits of the Locally Adapted Egyptian Barki Sheep. Genes (Basel) 2021; 12:genes12081243. [PMID: 34440417 PMCID: PMC8394750 DOI: 10.3390/genes12081243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Sheep play a critical role in the agricultural and livestock sector in Egypt. For sheep meat production, growth traits such as birth and weaning weights are very important and determine the supply and income of local farmers. The Barki sheep originates from the northeastern coastal zone of Africa, and due to its good adaptation to the harsh environmental conditions, it contributes significantly to the meat production in these semi-arid regions. This study aimed to use a genome-wide SNP panel to identify genomic regions that are diversified between groups of individuals of Egyptian Barki sheep with high and low growth performance traits. In this context, from a phenotyped population of 140 lambs of Barki sheep, 69 lambs were considered for a genome-wide scan with the Illumina OvineSNP50 V2 BeadChip. The selected lambs were grouped into divergent subsets with significantly different performance for birth weight and weaning weight. After quality control, 63 animals and 40,383 SNPs were used for analysis. The fixation index (FST) for each SNP was calculated between the groups. The results verified genomic regions harboring some previously proposed candidate genes for traits related to body growth, i.e., EYA2, GDF2, GDF10, MEF2B, SLC16A7, TBX15, TFAP2B, and TNNC2. Moreover, novel candidate genes were proposed with known functional implications on growth processes such as CPXM2 and LRIG3. Subsequent association analysis showed significant effects of the considered SNPs on birth and weaning weights. Results highlight the genetic diversity associated with performance traits and thus the potential to improve growth traits in the Barki sheep breed.
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Affiliation(s)
- Ibrahim Abousoliman
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
- Desert Research Center, Department of Animal and Poultry Breeding, 1 Mathaf El-Matareya St., El-Matareya, Cairo 11753, Egypt;
| | - Henry Reyer
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
| | - Michael Oster
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
| | - Eduard Murani
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
| | - Ismail Mohamed
- Desert Research Center, Department of Animal and Poultry Breeding, 1 Mathaf El-Matareya St., El-Matareya, Cairo 11753, Egypt;
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 7, 18059 Rostock, Germany
- Correspondence: ; Tel.: +49-382-08-68-600
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Hou H, Wang X, Ding W, Xiao C, Cai X, Lv W, Tu Y, Zhao W, Yao J, Yang C. Whole‐genome sequencing reveals the artificial selection and local environmental adaptability of pigeons (
Columba livia
). Evol Appl 2021; 15:603-617. [PMID: 35505885 PMCID: PMC9046921 DOI: 10.1111/eva.13284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/17/2021] [Accepted: 07/12/2021] [Indexed: 12/16/2022] Open
Abstract
To meet human needs, domestic pigeons (Columba livia) with various phenotypes have been bred to provide genetic material for our research on artificial selection and local environmental adaptation. Seven pigeon breeds were resequenced and can be divided into commercial varieties (Euro‐pigeon, Shiqi, Shen King, Taishen, and Silver King), ornamental varieties (High Fliers), and local varieties (Tarim pigeon). Phylogenetic analysis based on population resequencing showed that one group contained local breeds and ornamental pigeons from China, whereas all commercial varieties were clustered together. It is revealed that the traditional Chinese ornamental pigeon is a branch of Tarim pigeon. Runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses revealed significant differences in the genetic diversity of the three types of pigeons. Genome sweep analysis revealed that the selected genes of commercial breeds were related to body size, reproduction, and plumage color. The genomic imprinting genes left by the ornamental pigeon breeds were mostly related to special human facial features and muscular dystrophy. The Tarim pigeon has evolved genes related to chemical ion transport, photoreceptors, oxidative stress, organ development, and olfaction in order to adapt to local environmental stress. This research provides a molecular basis for pigeon genetic resource evaluation and genetic improvement and suggests that the understanding of adaptive evolution should integrate the effects of various natural environmental characteristics.
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Affiliation(s)
- Haobin Hou
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Xiaoliang Wang
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Weixing Ding
- Shanghai Academy of Agricultural Sciences Shanghai China
| | - Changfeng Xiao
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Xia Cai
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Wenwei Lv
- National Poultry Engineer Research Center Shanghai China
| | - Yingying Tu
- National Poultry Engineer Research Center Shanghai China
| | - Weimin Zhao
- Shanghai Jinhuang Pigeon Company Shanghai China
| | - Junfeng Yao
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Changsuo Yang
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
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Bolormaa S, Swan AA, Stothard P, Khansefid M, Moghaddar N, Duijvesteijn N, van der Werf JHJ, Daetwyler HD, MacLeod IM. A conditional multi-trait sequence GWAS discovers pleiotropic candidate genes and variants for sheep wool, skin wrinkle and breech cover traits. Genet Sel Evol 2021; 53:58. [PMID: 34238208 PMCID: PMC8268212 DOI: 10.1186/s12711-021-00651-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/29/2021] [Indexed: 12/01/2022] Open
Abstract
Background Imputation to whole-genome sequence is now possible in large sheep populations. It is therefore of interest to use this data in genome-wide association studies (GWAS) to investigate putative causal variants and genes that underpin economically important traits. Merino wool is globally sought after for luxury fabrics, but some key wool quality attributes are unfavourably correlated with the characteristic skin wrinkle of Merinos. In turn, skin wrinkle is strongly linked to susceptibility to “fly strike” (Cutaneous myiasis), which is a major welfare issue. Here, we use whole-genome sequence data in a multi-trait GWAS to identify pleiotropic putative causal variants and genes associated with changes in key wool traits and skin wrinkle. Results A stepwise conditional multi-trait GWAS (CM-GWAS) identified putative causal variants and related genes from 178 independent quantitative trait loci (QTL) of 16 wool and skin wrinkle traits, measured on up to 7218 Merino sheep with 31 million imputed whole-genome sequence (WGS) genotypes. Novel candidate gene findings included the MAT1A gene that encodes an enzyme involved in the sulphur metabolism pathway critical to production of wool proteins, and the ESRP1 gene. We also discovered a significant wrinkle variant upstream of the HAS2 gene, which in dogs is associated with the exaggerated skin folds in the Shar-Pei breed. Conclusions The wool and skin wrinkle traits studied here appear to be highly polygenic with many putative candidate variants showing considerable pleiotropy. Our CM-GWAS identified many highly plausible candidate genes for wool traits as well as breech wrinkle and breech area wool cover. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00651-0.
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Affiliation(s)
- Sunduimijid Bolormaa
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia. .,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.
| | - Andrew A Swan
- Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.,Animal Genetics and Breeding Unit, University of New England, Armidale, NSW, 2351, Australia
| | - Paul Stothard
- Faculty of Agricultural, Life & Environmental Sciences, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Majid Khansefid
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia
| | - Nasir Moghaddar
- Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.,School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Naomi Duijvesteijn
- Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.,Hendrix Genetics, Boxmeer, The Netherlands
| | - Julius H J van der Werf
- Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.,School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia
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Sweet-Jones J, Lenis VP, Yurchenko AA, Yudin NS, Swain M, Larkin DM. Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits. Front Genet 2021; 12:612492. [PMID: 34220925 PMCID: PMC8253514 DOI: 10.3389/fgene.2021.612492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/10/2021] [Indexed: 12/25/2022] Open
Abstract
Background Advances in genetic tools applied to livestock breeding has prompted research into the previously neglected breeds adapted to harsh local environments. One such group is the Welsh mountain sheep breeds, which can be farmed at altitudes of 300 m above sea level but are considered to have a low productive value because of their poor wool quality and small carcass size. This is contrary to the lowland breeds which are more suited to wool and meat production qualities, but do not fare well on upland pasture. Herein, medium-density genotyping data from 317 individuals representing 15 Welsh sheep breeds were used alongside the whole-genome resequencing data of 14 breeds from the same set to scan for the signatures of selection and candidate genetic variants using haplotype- and SNP-based approaches. Results Haplotype-based selection scan performed on the genotyping data pointed to a strong selection in the regions of GBA3, PPARGC1A, APOB, and PPP1R16B genes in the upland breeds, and RNF24, PANK2, and MUC15 in the lowland breeds. SNP-based selection scan performed on the resequencing data pointed to the missense mutations under putative selection relating to a local adaptation in the upland breeds with functions such as angiogenesis (VASH1), anti-oxidation (RWDD1), cell stress (HSPA5), membrane transport (ABCA13 and SLC22A7), and insulin signaling (PTPN1 and GIGFY1). By contrast, genes containing candidate missense mutations in the lowland breeds are related to cell cycle (CDK5RAP2), cell adhesion (CDHR3), and coat color (MC1R). Conclusion We found new variants in genes with potentially functional consequences to the adaptation of local sheep to their environments in Wales. Knowledge of these variations is important for improving the adaptative qualities of UK and world sheep breeds through a marker-assisted selection.
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Affiliation(s)
- James Sweet-Jones
- Royal Veterinary College, University of London, London, United Kingdom
| | - Vasileios Panagiotis Lenis
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom.,School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
| | - Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Martin Swain
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, United Kingdom.,The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
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Tao L, He XY, Wang FY, Pan LX, Wang XY, Gan SQ, Di R, Chu MX. Identification of genes associated with litter size combining genomic approaches in Luzhong mutton sheep. Anim Genet 2021; 52:545-549. [PMID: 34002409 DOI: 10.1111/age.13078] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
Litter size is one of the most important reproductive traits of sheep, which has pronounced effects on the profit of husbandry enterprises and enthusiasm of breeders. Despite the importance of litter size, the underlying genetic mechanisms have not been entirely elucidated. Therefore, based on a high-density SNP chip, genome-wide comparative analysis was performed between two groups with different fecundity to reveal candidate genes linked to litter size via detection of homozygosity and selection signatures in Luzhong mutton sheep. Consequently, nine promising genes were identified from six runs of homozygosity islands, and functionally linked to reproduction (ACTL7A, ACTL7B, and ELP1), embryonic development (KLF5 and PIBF1), and cell cycle (DACH1, BORA, DIS3, and MZT1). A total of 128 genes were observed under selection, of which HECW1 and HTR1E were related to total lambs born, GABRG3, LRP1B, and MACROD2 to teat number, and AGBL1 to reproductive seasonality. Additionally, the presence of inbreeding depression implies the urgency of reasonable mating system to increase litter size in the present herd. These findings provide a comprehensive insight to the genetic makeup of litter size, and also contribute to implementation of marker-assisted selection in sheep.
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Affiliation(s)
- L Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - X Y He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - F Y Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - L X Pan
- Ji'nan Laiwu Yingtai Agriculture and Animal Husbandry Technology Co., Ltd, Ji'nan, Shandong, 271114, China
| | - X Y Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - S Q Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang, 832000, China
| | - R Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - M X Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Ghoreishifar SM, Rochus CM, Moghaddaszadeh-Ahrabi S, Davoudi P, Salek Ardestani S, Zinovieva NA, Deniskova TE, Johansson AM. Shared Ancestry and Signatures of Recent Selection in Gotland Sheep. Genes (Basel) 2021; 12:genes12030433. [PMID: 33802939 PMCID: PMC8002741 DOI: 10.3390/genes12030433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/01/2021] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (~50%), Karakul (~30%), Romanov (~20%), and Fjällnäs (~10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation FST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the FST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep.
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Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 31587-11167, Iran;
| | - Christina Marie Rochus
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands;
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz 5157944533, Iran;
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N5E3, Canada; (P.D.); (S.S.A.)
| | - Siavash Salek Ardestani
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N5E3, Canada; (P.D.); (S.S.A.)
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (N.A.Z.); (T.E.D.)
| | - Tatiana E. Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (N.A.Z.); (T.E.D.)
| | - Anna M. Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
- Correspondence:
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Gorlov IF, Shirokova NV, Anisimova EY, Slozhenkina MI, Kolosov YA, Natyrov AK, Kolosov AY, Mosolova NI, Kolosova MA, Tarchokov TT, Mosolov AA, Mosolova DA, Karpenko EV. MC4R gene polymorphism and its association with meat traits of Karachai sheep grown in Russian Federation. JOURNAL OF APPLIED ANIMAL RESEARCH 2021. [DOI: 10.1080/09712119.2021.1883624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Ivan Fiodorovich Gorlov
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Volgograd State Technical University, Volgograd, Russian Federation
| | - Nadezhda Vasilievna Shirokova
- Don State Agrarian University, Laboratory of Molecular Diagnostics and Biotechnology of Farm Animals, Persianovsky, Russian Federation
| | - Elena Yurievna Anisimova
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Volgograd State University, Volgograd, Russian Federation
| | - Marina Ivanovna Slozhenkina
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Volgograd State Technical University, Volgograd, Russian Federation
| | - Yuriy Anatolievich Kolosov
- Don State Agrarian University, Laboratory of Molecular Diagnostics and Biotechnology of Farm Animals, Persianovsky, Russian Federation
| | | | - Anatoliy Yurievich Kolosov
- Don State Agrarian University, Laboratory of Molecular Diagnostics and Biotechnology of Farm Animals, Persianovsky, Russian Federation
| | - Natalia Ivanovna Mosolova
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Volgograd State Technical University, Volgograd, Russian Federation
| | - Maria Anatolievna Kolosova
- Don State Agrarian University, Laboratory of Molecular Diagnostics and Biotechnology of Farm Animals, Persianovsky, Russian Federation
| | | | - Aleksandr Anatolievich Mosolov
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
| | - Daria Aleksandrovna Mosolova
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Plekhanov Russian University of Economics, Moscow, Russian Federation
| | - Ekaterina Vladimirovna Karpenko
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Volgograd State Technical University, Volgograd, Russian Federation
- Volgograd State University, Volgograd, Russian Federation
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Eydivandi S, Roudbar MA, Karimi MO, Sahana G. Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia. Sci Rep 2021; 11:2834. [PMID: 33531649 PMCID: PMC7854752 DOI: 10.1038/s41598-021-82625-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/22/2021] [Indexed: 01/30/2023] Open
Abstract
The performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated population genetic diversity and selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. To detect genetic diversity and population structure, we used principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of homozygosity. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, nine overlapping candidate genes were detected by these four tests, especially TNIK, DOCK1, USH2A, and TYW1B which associate with resistance to diseases and climate adaptation. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.
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Affiliation(s)
- Sirous Eydivandi
- Department of Animal Science, Behbahan Branch, Islamic Azad University, Behbahan, Iran.
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark.
| | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful, Iran
| | - Mohammad Osman Karimi
- Department of Animal Science, Faculty of Agriculture, Herat University, Herat, Afghanistan
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark
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42
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Eydivandi S, Roudbar MA, Ardestani SS, Momen M, Sahana G. A selection signatures study among Middle Eastern and European sheep breeds. J Anim Breed Genet 2021; 138:574-588. [PMID: 33453096 DOI: 10.1111/jbg.12536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/25/2020] [Accepted: 12/26/2020] [Indexed: 01/26/2023]
Abstract
Selection, both natural and artificial, leaves patterns on the genome during domestication of animals and leads to changes in allele frequencies among populations. Detecting genomic regions influenced by selection in livestock may assist in understanding the processes involved in genome evolution and discovering genomic regions related to traits of economic and ecological interests. In the current study, genetic diversity analyses were conducted on 34,206 quality-filtered SNP positions from 450 individuals in 15 sheep breeds, including six indigenous breeds from the Middle East, namely Iranian Balouchi, Afshari, Moghani, Qezel, Karakas and Norduz, and nine breeds from Europe, namely East Friesian Sheep, Ile de France, Mourerous, Romane, Swiss Mirror, Spaelsau, Suffolk, Comisana and Engadine Red Sheep. The SNP genotype data generated by the Illumina OvineSNP50 Genotyping BeadChip array were used in this analysis. We applied two complementary statistical analyses, FST (fixation index) and xp-EHH (cross-population extended haplotype homozygosity), to detect selection signatures in Middle Eastern and European sheep populations. FST and xp-EHH detected 629 and 256 genes indicating signatures of selection, respectively. Genomic regions identified using FST and xp-EHH contained the CIDEA, HHATL, MGST1, FADS1, RTL1 and DGKG genes, which were reported earlier to influence a number of economic traits. Both FST and xp-EHH approaches identified 60 shared genes as the signatures of selection, including four candidate genes (NT5E, ADA2, C8A and C8B) that were enriched for two significant Gene Ontology (GO) terms associated with the adenosine metabolic procedure. Knowledge about the candidate genomic regions under selective pressure in sheep breeds may facilitate identification of the underlying genes and enhance our understanding on these genes role in local adaptation.
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Affiliation(s)
- Sirous Eydivandi
- Department of Animal Science, Behbahan Branch, Islamic Azad University, Behbahan, Iran.,Faculty of Technical Sciences, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Dezful, Iran
| | | | - Mehdi Momen
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Goutam Sahana
- Faculty of Technical Sciences, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
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43
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Association of TMEM8B and SPAG8 with Mature Weight in Sheep. Animals (Basel) 2020; 10:ani10122391. [PMID: 33333720 PMCID: PMC7765121 DOI: 10.3390/ani10122391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 01/08/2023] Open
Abstract
Simple Summary Domestication and the subsequent selection of animals for either economic or morphological features can impact the legacy genome of a population in myriad ways. In sheep, the rs426272889 single nucleotide polymorphism (SNP) was identified as the peak of a signature of selection. We examined phenotypic data and identified associations for the Transmembrane protein 8B (TMEM8B) rs426272889 SNP and its genetically linked Sperm-associated antigen 8 (SPAG8) rs160159557 SNP with ewe mature weight in four sheep breeds. These data provided the first production-relevant phenotypes, as well as the first organism-level (as opposed to cellular or tumor-derived) phenotypes, associated with TMEM8B, and in so doing, improved the annotation of this gene and genomic region by adding body weight implications. Once validated, these data can be applied in genetic or genomic selection aiming to achieve desired mature body weight. Abstract Signature of selection studies have identified many genomic regions with known functional importance and some without verified functional roles. Multiple studies have identified Transmembrane protein 8B (TMEM8B)rs426272889 as having been recently under extreme selection pressure in domesticated sheep, but no study has provided sheep phenotypic data clarifying a reason for extreme selection. We tested rs426272889 for production trait association in 770 U.S. Rambouillet, Targhee, Polypay, and Suffolk sheep. TMEM8Brs426272889 was associated with mature weight at 3 and 4 years (p < 0.05). This suggested selection for sheep growth and body size might explain the historical extreme selection pressure in this genomic region. We also tested Sperm-associated antigen 8 (SPAG8) rs160159557 encoding a G493C substitution. While this variant was associated with mature weights at ages 3 and 4, it was not as strongly associated as TMEM8Brs426272889. Transmembrane protein 8B has little functional information except as an inhibitor of cancer cell proliferation. To our knowledge, this is the first study linking TMEM8B to whole organism growth and body size under standard conditions. Additional work will be necessary to identify the underlying functional variant(s). Once identified, such variants could be used to improve sheep production through selective breeding.
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Sweet-Jones J, Yurchenko AA, Igoshin AV, Yudin NS, Swain MT, Larkin DM. Resequencing and signatures of selection scan in two Siberian native sheep breeds point to candidate genetic variants for adaptation and economically important traits. Anim Genet 2020; 52:126-131. [PMID: 33107621 DOI: 10.1111/age.13015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2020] [Indexed: 12/12/2022]
Abstract
Russian sheep breeds represent an important economic asset by providing meat and wool, whilst being adapted to extreme climates. By resequencing two Russian breeds from Siberia: Tuva (n = 20) and Baikal (n = 20); and comparing them with a European (UK) sheep outgroup (n = 14), 41 million variants were called, and signatures of selection were identified. High-frequency missense mutations on top of selection peaks were found in genes related to immunity (LOC101109746) in the Baikal breed and wool traits (IDUA), cell differentiation (GLIS1) and fat deposition (AADACL3) in the Tuva breed. In addition, genes found under selection owing to haplotype frequency changes were related to wool traits (DSC2), parasite resistance (CLCA1), insulin receptor pathway (SOCS6) and DNA repair (DDB2) in the Baikal breed, and vision (GPR179) in the Tuva breed. Our results present candidate genes and SNPs for future selection programmes, which are necessary to maintain and increase socioeconomic gain from Siberian breeds.
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Affiliation(s)
- J Sweet-Jones
- Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - A A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, 630090, Russia
| | - A V Igoshin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, 630090, Russia
| | - N S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, 630090, Russia
| | - M T Swain
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, SY23 3DA, UK
| | - D M Larkin
- Royal Veterinary College, University of London, London, NW1 0TU, UK.,The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, 630090, Russia
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Posbergh CJ, Huson HJ. All sheeps and sizes: a genetic investigation of mature body size across sheep breeds reveals a polygenic nature. Anim Genet 2020; 52:99-107. [PMID: 33089531 PMCID: PMC7821113 DOI: 10.1111/age.13016] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2020] [Indexed: 02/02/2023]
Abstract
Mature body size is genetically correlated with growth rate, an important economic trait in the sheep industry. Mature body size has been studied extensively in humans as well as cattle and other domestic animal populations but not in sheep. Six‐hundred and sixteen ewes, across 22 breeds, were measured for 28 linear measurements representing various skeletal parts. PCA from these measures generated principal components 1 and 2 which represented 66 and 7% of the phenotypic variation respectively. Two‐hundred and twenty sheep were genotyped on the Illumina Ovine HD beadchip for a GWAS investigating mature body size and linear body measurements. Forty‐six (Bonferroni P < 0.05) SNP associations across 14 chromosomes were identified utilizing principal component 1, representing overall body size, revealing mature body size to have fewer loci of large effect than other domestic species such as dogs and horses. Genome‐wide associations for individual linear measures identified major quantitative trait loci for withers height and ear length. Withers height was associated (Bonferroni P < 0.05) with 12 SNPs across six chromosomes whereas ear length was associated with a single locus on chromosome 3, containing MSRB3. This analysis identified several loci known to be associated with mature body size in other species such as NCAPG, LCORL, and HMGA2. Mature body size is more polygenic in sheep than other domesticated species, making the development of genomic selection for the trait the most efficient option for maintaining or reducing mature body size in sheep.
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Affiliation(s)
- C J Posbergh
- Department of Animal Science, Cornell University, Ithaca, NY, 14853, USA
| | - H J Huson
- Department of Animal Science, Cornell University, Ithaca, NY, 14853, USA
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Ghoreishifar SM, Eriksson S, Johansson AM, Khansefid M, Moghaddaszadeh-Ahrabi S, Parna N, Davoudi P, Javanmard A. Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds. Genet Sel Evol 2020; 52:52. [PMID: 32887549 PMCID: PMC7487911 DOI: 10.1186/s12711-020-00571-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/21/2020] [Indexed: 02/01/2023] Open
Abstract
Background Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C). Conclusions We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.
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Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden.
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Majid Khansefid
- AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | - Nahid Parna
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N5E3, Canada
| | - Arash Javanmard
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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Rovelli G, Ceccobelli S, Perini F, Demir E, Mastrangelo S, Conte G, Abeni F, Marletta D, Ciampolini R, Cassandro M, Bernabucci U, Lasagna E. The genetics of phenotypic plasticity in livestock in the era of climate change: a review. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1809540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Giacomo Rovelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Francesco Perini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Eymen Demir
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Giuseppe Conte
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, University of Pisa, Pisa, Italy
| | - Fabio Abeni
- Centro di ricerca Zootecnia e Acquacoltura, Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), Lodi, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | | | - Martino Cassandro
- Dipartimento di Agronomia, Animali, Alimenti, Risorse naturali e Ambiente, University of Padova, Legnaro, Italy
| | - Umberto Bernabucci
- Dipartimento di Scienze Agrarie e Forestali, Università della Tuscia, Viterbo, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
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Dettori ML, Pazzola M, Petretto E, Vacca GM. Association Analysis between SPP1, POFUT1 and PRLR Gene Variation and Milk Yield, Composition and Coagulation Traits in Sarda Sheep. Animals (Basel) 2020; 10:E1216. [PMID: 32708940 PMCID: PMC7401589 DOI: 10.3390/ani10071216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 01/02/2023] Open
Abstract
Many studies focus on the identification of genomic regions that undergo selective processes, where evidence of selection is revealed and positional candidate genes are identified. The aim of the research was to evaluate the association between positional candidate genes, namely secreted phosphoprotein 1 (SPP1, sheep chromosome Ovis aries OAR6, 36.651-36.658 Mb), protein O-fucosyltransferase 1 (POFUT1, OAR13, 61.006-61.027 Mb) and prolactin receptor (PRLR, OAR16, 38.969-39.028 Mb) with milk yield, composition and coagulation traits. Eight single nucleotide polymorphisms (SNPs) mapping to the three genes were genotyped in 380 Sarda dairy sheep. Statistical analysis revealed an association between SNP rs161844011 at SPP1 (chromosome position Oar_v3 OAR6:36651870, gene region exon 7) and somatic cell score, while POFUT1 SNP rs424501869 (OAR13:61007495, intron 1) was associated with curd firmness both 45 and 60 min after rennet addition (p = 0.015 and p = 0.007, respectively). SNP rs400874750 at PRLR gene (OAR16:39004070, intron 2) had a significant association with lactose content (p = 0.020), somatic cell score (p = 0.038), rennet coagulation time (p = 0.018) and curd firming time (p = 0.047). The outcome of this research confirmed predictions based on genomic studies, producing new information regarding the SPP1, POFUT1 and PRLR genes, which may be useful for future breeding schemes.
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Affiliation(s)
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (M.L.D.); (E.P.); (G.M.V.)
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Stefos GC, Theodorou G, Politis I. DNA G-quadruplexes: functional significance in plant and farm animal science. Anim Biotechnol 2019; 32:262-271. [PMID: 31642375 DOI: 10.1080/10495398.2019.1679823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
G-quadruplexes (G4s) are non-canonical structures that can be formed in DNA and RNA sequences which carry four short runs of guanines. They are distributed in the whole genome but are enriched in gene promoter regions, gene UTRs and chromosome telomeres. The whole array of their functional roles is not fully explored yet but there is solid evidence supporting their implication in a number of processes like regulation of transcription, replication and telomere organization, among others. During the last decade, there is an increased research interest for G4s that has resulted in a better understanding of their role in several physiological and pathological conditions. On the other hand, these structures are poorly studied in plant species and animals of agricultural interest. Here, we summarize the current methods that are used for studying G4s, we review the studies concerning plants and farm animals and we discuss the advantages of a more thorough inclusion of G4s research in the agricultural sciences.
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Affiliation(s)
- Georgios C Stefos
- Independent researcher, Agricultural University of Athens, Athens, Greece
| | - Georgios Theodorou
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Athens, Greece
| | - Ioannis Politis
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Athens, Greece
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Yudin N, Larkin DM. Shared Signatures of Selection Related to Adaptation and Acclimation in Local Cattle and Sheep Breeds from Russia. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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