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Yang R, Han Z, Zhou W, Li X, Zhang X, Zhu L, Wang J, Li X, Zhang CL, Han Y, Li L, Liu S. Population structure and selective signature of Kirghiz sheep by Illumina Ovine SNP50 BeadChip. PeerJ 2024; 12:e17980. [PMID: 39308831 PMCID: PMC11416764 DOI: 10.7717/peerj.17980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/06/2024] [Indexed: 09/25/2024] Open
Abstract
Objective By assessing the genetic diversity and associated selective traits of Kirghiz sheep (KIR), we aim to uncover the mechanisms that contribute to sheep's adaptability to the Pamir Plateau environment. Methods This study utilized Illumina Ovine SNP50 BeadChip data from KIR residing in the Pamir Plateau, Qira Black sheep (QBS) inhabiting the Taklamakan Desert, and commonly introduced breeds including Dorper sheep (DOR), Suffolk sheep (SUF), and Hu sheep (HU). The data was analyzed using principal component analysis, phylogenetic analysis, population admixture analysis, kinship matrix analysis, linkage disequilibrium analysis, and selective signature analysis. We employed four methods for selective signature analysis: fixation index (Fst), cross-population extended homozygosity (XP-EHH), integrated haplotype score (iHS), and nucleotide diversity (Pi). These methods aim to uncover the genetic mechanisms underlying the germplasm resources of Kirghiz sheep, enhance their production traits, and explore their adaptation to challenging environmental conditions. Results The test results unveiled potential selective signals associated with adaptive traits and growth characteristics in sheep under harsh environmental conditions, and annotated the corresponding genes accordingly. These genes encompass various functionalities such as adaptations associated with plateau, cold, and arid environment (ETAA1, UBE3D, TLE4, NXPH1, MAT2B, PPARGC1A, VEGFA, TBX15 and PLXNA4), wool traits (LMO3, TRPS1, EPHA5), body size traits (PLXNA2, EFNA5), reproductive traits (PPP3CA, PDHA2, NTRK2), and immunity (GATA3). Conclusion Our study identified candidate genes associated with the production traits and adaptation to the harsh environment of the Pamir Plateau in Kirghiz sheep. These findings provide valuable resources for local sheep breeding programs. The objective of this study is to offer valuable insights for the sustainable development of the Kirghiz sheep industry.
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Affiliation(s)
- Ruizhi Yang
- College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Xinjiang Production and Construction Corps, Key Laboratory of Tarim Animal Husbandry Science and Technology, Alar, Xinjiang, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Xinjiang Production and Construction Corps, Key Laboratory of Tarim Animal Husbandry Science and Technology, Alar, Xinjiang, China
| | - Xuejiao Li
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Xuechen Zhang
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Xinjiang Production and Construction Corps, Key Laboratory of Tarim Animal Husbandry Science and Technology, Alar, Xinjiang, China
| | - Lijun Zhu
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Xinjiang Production and Construction Corps, Key Laboratory of Tarim Animal Husbandry Science and Technology, Alar, Xinjiang, China
| | - Jieru Wang
- College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Cheng-long Zhang
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Yahui Han
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Lianrui Li
- College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Xinjiang Production and Construction Corps, Key Laboratory of Tarim Animal Husbandry Science and Technology, Alar, Xinjiang, China
- Xinjiang Production and Construction Corps, Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Alar, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Xinjiang Production and Construction Corps, Key Laboratory of Tarim Animal Husbandry Science and Technology, Alar, Xinjiang, China
- Xinjiang Production and Construction Corps, Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Alar, Xinjiang, China
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Han ZP, Yang RZ, Zhou W, Zhang LL, Wang JR, Liu CJ, Liu SD. Population structure and selection signal analysis of indigenous sheep from the southern edge of the Taklamakan Desert. BMC Genomics 2024; 25:681. [PMID: 38982349 PMCID: PMC11232224 DOI: 10.1186/s12864-024-10581-y] [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: 08/29/2023] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
Analyzing the genetic diversity and selection characteristics of sheep (Ovis aries) holds significant value in understanding their environmental adaptability, enhancing breeding efficiency, and achieving effective conservation and rational utilization of genetic resources. In this study, we utilized Illumina Ovine SNP 50 K BeadChip data from four indigenous sheep breeds from the southern margin of the Taklamakan Desert (Duolang sheep: n = 36, Hetian sheep: n = 74, Kunlun sheep: n = 27, Qira black sheep: n = 178) and three foreign meat sheep breeds (Poll Dorset sheep: n = 105, Suffolk sheep: n = 153, Texel sheep: n = 150) to investigate the population structure, genetic diversity, and genomic signals of positive selection within the indigenous sheep. According to the Principal component analysis (PCA), the Neighbor-Joining tree (NJ tree), and Admixture, we revealed distinct clustering patterns of these seven sheep breeds based on their geographical distribution. Then used Cross Population Extended Haplotype Homozygosity (XP-EHH), Fixation Index (FST), and Integrated Haplotype Score (iHS), we identified a collective set of 32 overlapping genes under positive selection across four indigenous sheep breeds. These genes are associated with wool follicle development and wool traits, desert environmental adaptability, disease resistance, reproduction, and high-altitude adaptability. This study reveals the population structure and genomic selection characteristics in the extreme desert environments of native sheep breeds from the southern edge of the Taklimakan Desert, providing new insights into the conservation and sustainable use of indigenous sheep genetic resources in extreme environments. Additionally, these findings offer valuable genetic resources for sheep and other mammals to adapt to global climate change.
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Affiliation(s)
- Zhi-Peng Han
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Rui-Zhi Yang
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Lu-Lu Zhang
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Jie-Ru Wang
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Chun-Jie Liu
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Shu-Dong Liu
- College of Animal Science and Technology, Tarim University, Alar, 843300, China.
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China.
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Cui W, Wang H, Li J, Lv D, Xu J, Liu M, Yin G. Sheep litter size heredity basis using genome-wide selective analysis. Reprod Domest Anim 2024; 59:e14689. [PMID: 39044628 DOI: 10.1111/rda.14689] [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: 03/22/2024] [Revised: 06/19/2024] [Accepted: 07/12/2024] [Indexed: 07/25/2024]
Abstract
Sheep are important herbivorous domestic animal globally, and the Chinese indigenous sheep breed has a multitude of economically significant variations due to the diverse geographical and ecological conditions. In particular, certain native breeds exhibit a visible high litter size phenotype due to the selection pressure of natural and artificial for thousands of years, offering an ideal animal model for investigating sheep's fecundity. In this study, selective signal analysis was performed on public whole-genome sequencing data from 60 sheep across eight breeds to identify candidate genes related to litter size. Results revealed that a total of 34,065,017 single-nucleotide polymorphisms (SNPs) were identified from all sheep, and 65 candidate genes (CDGs) were pinpointed from the top 1% of interacted windows and SNPs between the pairwise fixation index (FST, >0.149543) and cross-population extended haplotype homozygosity (XP-EHH, >0.701551). A total of 41 CDGs (e.g. VRTN, EYA2 and MCPH1) were annotated to 576 GO terms, of which seven terms were directly linked to follicular and embryonic development (e.g. TBXT, BMPR1B, and BMP2). In addition, 73 KEGG pathways were enriched by 21 CDGs (e.g. ENTPD5, ABCD4 and RXFP2), mainly related to Hippo (TCF4, BMPR1B and BMP2), TGF-β (BMPR1B and BMP2), PI3K-Akt (ITGB4, IL4R and PPP2R5A) and Jak-STAT signalling pathways (IL20RA and IL4R). Notably, a series of CDGs was under strong selection in sheep with high litter size traits. These findings result could improve the comprehension of the genetic underpinnings of sheep litter size. Furthermore, it provides valuable CDGS for future molecular breeding.
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Affiliation(s)
- Weiguo Cui
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hechuan Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jingchun Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dongyu Lv
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jiayi Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mengyu Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Guoan Yin
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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4
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Anaya G, Laseca N, Granero A, Ziadi C, Arrebola F, Domingo A, Molina A. Genomic Characterization of Quality Wool Traits in Spanish Merino Sheep. Genes (Basel) 2024; 15:795. [PMID: 38927731 PMCID: PMC11203093 DOI: 10.3390/genes15060795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The native Spanish Merino breed was the founder of all the other Merino and Merino-derived breeds worldwide. Despite the fact that this breed was created and improved to produce the highest quality fine wool, the global wool market crisis led to the wholescale crossing of most of the herds with breeds for meat purposes. Nevertheless, there are still some purebred animals with a high potential for producing quality wool. The objective of this study was to characterize the current wool quality of the breed and identify genes associated with these parameters. To achieve this, over 12,800 records from the most representative animals of the breed (registered in the herd book) were analyzed using the Australian OFDA 2000 system, for parameters such as fiber diameter (FD), standard deviation (SD), coefficient of variation (CV), fibers over 15 microns (>15%), staple length (SL), and comfort factor (CRV). Additionally, animals with the most extreme FD values were whole-genome sequenced using NGS. Genome-wide association studies (GWAS) determined the association of 74 variants with the different traits studied, which were located in 70 different genes. Of these genes, EDN2, COL18A1, and LRP1B, associated with fibers over 15%, and FGF12 and ADAM17, associated with SL, play a key role in hair follicle growth and development. Our study reveals the great potential for recovering this breed for fine wool production, and identifies five candidate genes whose understanding may aid in that selection process.
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Affiliation(s)
- Gabriel Anaya
- MERAGEM Research Group, Department of Genetics, University of Córdoba, CN IV KM 396, 17071 Córdoba, Spain; (G.A.); (C.Z.)
| | - Nora Laseca
- MERAGEM Research Group, Department of Genetics, University of Córdoba, CN IV KM 396, 17071 Córdoba, Spain; (G.A.); (C.Z.)
| | - Antonio Granero
- National Association of Merino Sheep Breeders (ACME), 28007 Madrid, Spain
| | - Chiraz Ziadi
- MERAGEM Research Group, Department of Genetics, University of Córdoba, CN IV KM 396, 17071 Córdoba, Spain; (G.A.); (C.Z.)
| | - Francisco Arrebola
- Agriculture, Livestock and Fisheries Research Institute (IFAPA), 14270 Cordoba, Spain
| | - Andrés Domingo
- Center of Selection and Reproduction Animals (CENSYRA), 06007 Badajoz, Spain
| | - Antonio Molina
- MERAGEM Research Group, Department of Genetics, University of Córdoba, CN IV KM 396, 17071 Córdoba, Spain; (G.A.); (C.Z.)
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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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Sun X, Guo J, Li R, Zhang H, Zhang Y, Liu GE, Emu Q, Zhang H. Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep. Animals (Basel) 2024; 14:444. [PMID: 38338087 PMCID: PMC10854784 DOI: 10.3390/ani14030444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/12/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2-an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher's exact test, p < 2.2 × 10-16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.
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Affiliation(s)
- Xueliang Sun
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Huanhuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yifei Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Quzhe Emu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, No. 7, Niusha Road, Chengdu 610066, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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Lv X, Chen W, Wang S, Cao X, Yuan Z, Getachew T, Mwacharo JM, Haile A, Sun W. Whole-genome resequencing of Dorper and Hu sheep to reveal selection signatures associated with important traits. Anim Biotechnol 2023; 34:3016-3026. [PMID: 36200839 DOI: 10.1080/10495398.2022.2127409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Dorper and Hu sheep exhibit different characteristics in terms of reproduction, growth, and meat quality. Comparison of the genomes of two breeds help to reveal important genomic information. In this study, whole genome resequencing of 30 individuals (Dorper, DB and Hu sheep, HY) identified 15,108,125 single nucleotide polymorphisms (SNPs). Population differentiation (Fst) and cross population extended haplotype homozygosity (XP-EHH) were performed for selective signal analysis. In total, 106 and 515 overlapped genes were present in both the Fst results and XP-EHH results in HY vs DB and in DB vs HY, respectively. In HY vs DB, 106 genes were enriched in 12 GO terms and 83 KEGG pathways, such as ATP binding (GO:0005524) and PI3K-Akt signaling pathway (oas04151). In DB vs HY, 515 genes were enriched in 109 GO terms and 215 KEGG pathways, such as skeletal muscle cell differentiation (GO:0035914) and MAPK signaling pathway (oas04010). According to the annotation results, we identified a series of candidate genes associated with reproduction (UNC5C, BMPR1B, and GLIS1), meat quality (MECOM, MEF2C, and MYF6), and immunity (GMDS, GALK1, and ITGB4). Our investigation has uncovered genomic information for important traits in sheep and provided a basis for subsequent studies of related traits.
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Affiliation(s)
- Xiaoyang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
| | - Weihao Chen
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shanhe Wang
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
| | - Tesfaye Getachew
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Aynalem Haile
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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8
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Zhang Y, Qin Y, Gu M, Xu Y, Dou X, Han D, Lin G, Wang L, Wang Z, Wang J, Sun Y, Wu Y, Chen R, Qiao Y, Zhang Q, Li Q, Wang X, Xu Z, Cong Y, Chen J, Wang Z. Association between the cashmere production performance, milk production performance, and body size traits and polymorphism of COL6A5 and LOC102181374 genes in Liaoning cashmere goats. Anim Biotechnol 2023; 34:4415-4429. [PMID: 36527393 DOI: 10.1080/10495398.2022.2155177] [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: 12/23/2022]
Abstract
The purpose of this study was to analyze the relationship between COL6A5 (collagen type VI alpha 5 chain) and LOC102181374 (alcohol dehydrogenase 1) genes and the production performance of Liaoning cashmere goats by single nucleotide polymorphism (SNP). We have searched for SNP loci of COL6A5 and LOC102181374 genes through sequence alignment and PCR experiments, and have used SPSS and SHEsis software to analyze production data. We obtained five SNP loci in total, including three SNP loci (G50985A, G51140T, G51175A) in COL6A5 gene and two SNP loci (A10067G, T10108C) in LOC102181374 gene. The genotypes G50985A (AG), G51140T (GT), G51175A (AA), A10067G (AA), and T10108C (CC) of these loci have certain advantages in improving the production performance of Liaoning cashmere goats. The haplotype combinations that can improve production performance in COL6A5 gene were H1H5:AGGGAG, H4H4:GGGGAA, and H4H4:GGGGAA. H3H3:GGCC and H2H4:AGTT were the dominant combinations in LOC102181374 gene. At G51175A and A10067G loci, we found that H1H2:AAAG and H1H3:AGAA have dominant effects. These results may provide some support for the molecular breeding of production traits in Liaoning cashmere goats.
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Affiliation(s)
- Yu Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuting Qin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ming Gu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xingtang Dou
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Di Han
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Guangyu Lin
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Lingling Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Zhanhong Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Jiaming Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Yinggang Sun
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanjun Qiao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qiu Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qian Li
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaowei Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhiguo Xu
- Dalian Modern Agricultural Production Development Service Center, Dalian, China
| | - Yuyan Cong
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jing Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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9
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Zhou F, Wang S, Qin H, Zeng H, Ye J, Yang J, Cai G, Wu Z, Zhang Z. Genome-wide association analysis unveils candidate genes and loci associated with aplasia cutis congenita in pigs. BMC Genomics 2023; 24:701. [PMID: 37990155 PMCID: PMC10664689 DOI: 10.1186/s12864-023-09803-6] [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: 08/06/2023] [Accepted: 11/11/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Aplasia cutis congenita (ACC) is a rare genetic disorder characterized by the localized or widespread absence of skin in humans and animals. Individuals with ACC may experience developmental abnormalities in the skeletal and muscular systems, as well as potential complications. Localized and isolated cases of ACC can be treated through surgical and medical interventions, while extensive cases of ACC may result in neonatal mortality. The presence of ACC in pigs has implications for animal welfare. It contributes to an elevated mortality rate among piglets at birth, leading to substantial economic losses in the pig farming industry. In order to elucidate candidate genetic loci associated with ACC, we performed a Genome-Wide Association Study analysis on 216 Duroc pigs. The primary goal of this study was to identify candidate genes that associated with ACC. RESULTS This study identified nine significant SNPs associated with ACC. Further analysis revealed the presence of two quantitative trait loci, 483 kb (5:18,196,971-18,680,098) on SSC 5 and 159 kb (13:20,713,440-207294431 bp) on SSC13. By annotating candidate genes within a 1 Mb region surrounding the significant SNPs, a total of 11 candidate genes were identified on SSC5 and SSC13, including KRT71, KRT1, KRT4, ITGB7, CSAD, RARG, SP7, PFKL, TRPM2, SUMO3, and TSPEAR. CONCLUSIONS The results of this study further elucidate the potential mechanisms underlying and genetic architecture of ACC and identify reliable candidate genes. These results lay the foundation for treating and understanding ACC in humans.
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Affiliation(s)
- Fuchen Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Shenghui Wang
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Haojun Qin
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Haiyu Zeng
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Jian Ye
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China.
| | - Zebin Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.
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10
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More M, Veli E, Cruz A, Gutiérrez JP, Gutiérrez G, Ponce de León FA. Genome-Wide Association Study of Fiber Diameter in Alpacas. Animals (Basel) 2023; 13:3316. [PMID: 37958071 PMCID: PMC10648856 DOI: 10.3390/ani13213316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (-log10(p-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray.
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Affiliation(s)
- Manuel More
- Facultad de Agronomía y Zootecnia, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, Peru;
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
| | - Eudosio Veli
- Centro Experimental La Molina, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru;
| | - Alan Cruz
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
- Estación Científica de Pacomarca, Inca Tops S.A., Arequipa 04007, Peru
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - Gustavo Gutiérrez
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
- Instituto de Investigación de Bioquímica y Biología Molecular, Universidad Nacional Agraria La Molina, Lima 15024, Peru
| | - F. Abel Ponce de León
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
- Department of Animal Science, University of Minnesota, Minneapolis, MN 55108, USA
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11
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Xie S, Isaacs K, Becker G, Murdoch BM. A computational framework for improving genetic variants identification from 5,061 sheep sequencing data. J Anim Sci Biotechnol 2023; 14:127. [PMID: 37779189 PMCID: PMC10544426 DOI: 10.1186/s40104-023-00923-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 08/01/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND Pan-genomics is a recently emerging strategy that can be utilized to provide a more comprehensive characterization of genetic variation. Joint calling is routinely used to combine identified variants across multiple related samples. However, the improvement of variants identification using the mutual support information from multiple samples remains quite limited for population-scale genotyping. RESULTS In this study, we developed a computational framework for joint calling genetic variants from 5,061 sheep by incorporating the sequencing error and optimizing mutual support information from multiple samples' data. The variants were accurately identified from multiple samples by using four steps: (1) Probabilities of variants from two widely used algorithms, GATK and Freebayes, were calculated by Poisson model incorporating base sequencing error potential; (2) The variants with high mapping quality or consistently identified from at least two samples by GATK and Freebayes were used to construct the raw high-confidence identification (rHID) variants database; (3) The high confidence variants identified in single sample were ordered by probability value and controlled by false discovery rate (FDR) using rHID database; (4) To avoid the elimination of potentially true variants from rHID database, the variants that failed FDR were reexamined to rescued potential true variants and ensured high accurate identification variants. The results indicated that the percent of concordant SNPs and Indels from Freebayes and GATK after our new method were significantly improved 12%-32% compared with raw variants and advantageously found low frequency variants of individual sheep involved several traits including nipples number (GPC5), scrapie pathology (PAPSS2), seasonal reproduction and litter size (GRM1), coat color (RAB27A), and lentivirus susceptibility (TMEM154). CONCLUSION The new method used the computational strategy to reduce the number of false positives, and simultaneously improve the identification of genetic variants. This strategy did not incur any extra cost by using any additional samples or sequencing data information and advantageously identified rare variants which can be important for practical applications of animal breeding.
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Affiliation(s)
- Shangqian Xie
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID, USA
| | | | - Gabrielle Becker
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID, USA.
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12
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Zhang W, Jin M, Li T, Lu Z, Wang H, Yuan Z, Wei C. Whole-Genome Resequencing Reveals Selection Signal Related to Sheep Wool Fineness. Animals (Basel) 2023; 13:2944. [PMID: 37760343 PMCID: PMC10526036 DOI: 10.3390/ani13182944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Wool fineness affects the quality of wool, and some studies have identified about forty candidate genes that affect sheep wool fineness, but these genes often reveal only a certain proportion of the variation in wool thickness. We further explore additional genes associated with the fineness of sheep wool. Whole-genome resequencing of eight sheep breeds was performed to reveal selection signals associated with wool fineness, including four coarse wool and four fine/semi-fine wool sheep breeds. Multiple methods to reveal selection signals (Fst and θπ Ratio and XP-EHH) were applied for sheep wool fineness traits. In total, 269 and 319 genes were annotated in the fine wool (F vs. C) group and the coarse wool (C vs. F) group, such as LGR4, PIK3CA, and SEMA3C and NFIB, OPHN1, and THADA. In F vs. C, 269 genes were enriched in 15 significant GO Terms (p < 0.05) and 38 significant KEGG Pathways (p < 0.05), such as protein localization to plasma membrane (GO: 0072659) and Inositol phosphate metabolism (oas 00562). In C vs. F, 319 genes were enriched in 21 GO Terms (p < 0.05) and 16 KEGG Pathways (p < 0.05), such as negative regulation of focal adhesion assembly (GO: 0051895) and Axon guidance (oas 04360). Our study has uncovered genomic information pertaining to significant traits in sheep and has identified valuable candidate genes. This will pave the way for subsequent investigations into related traits.
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Affiliation(s)
- Wentao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Meilin Jin
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Taotao Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Zengkui Lu
- 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;
| | - Huihua Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Zehu Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China;
| | - Caihong Wei
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
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13
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Ma S, Long L, Huang X, Tian K, Tian Y, Wu C, Zhao Z. Transcriptome analysis reveals genes associated with wool fineness in merinos. PeerJ 2023; 11:e15327. [PMID: 37250719 PMCID: PMC10215774 DOI: 10.7717/peerj.15327] [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: 10/11/2022] [Accepted: 04/10/2023] [Indexed: 05/31/2023] Open
Abstract
Hair/wool usually plays an important role in maintaining animal physiological activities, and the economic value of wool cannot be ignored. At present, people set higher demands on wool fineness. Hence, improving wool fineness is the concern of fine wool sheep breeding. Using RNA-Seq to screen the potential candidate genes that associate with wool fineness can provide theoretical references for fine-wool sheep breeding, and also provide us new ideas for further understand the molecular regulation mechanism of hair growth. In this study, we compared the expression pattern difference of genome-wide genes between the skin transcriptomes of Subo and Chinese Merinos. The results showed that, 16 candidate differentially expressed genes (DEGs) (Included: CACNA1S, GP5, LOC101102392, HSF5, SLITRK2, LOC101104661, CREB3L4, COL1A1, PTPRR, SFRP4, LOC443220, COL6A6, COL6A5, LAMA1, LOC114115342 and LOC101116863 genes) that may associate with wool fineness were screened, and these genes were located in signaling pathways that regulate hair follicle development, cycle or hair growth. It is worth noting that, among the 16 DEGs, COL1A1 gene has the highest expression level in Merino skins, and the fold change of LOC101116863 gene is the highest, and the structures of these two genes are both highly conserved in different species. In conclusion, we speculate that these two genes may play a key role in regulating wool fineness and respectively have similar and conserved functions in different species.
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Affiliation(s)
- Shengchao Ma
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Li Long
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yuezhen Tian
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool Sheep and Cashmere-Goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Cuiling Wu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool Sheep and Cashmere-Goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Zhiwen Zhao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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14
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Arzik Y, Kizilaslan M, Behrem S, White SN, Piel LMW, Cinar MU. Genome-Wide Scan of Wool Production Traits in Akkaraman Sheep. Genes (Basel) 2023; 14:genes14030713. [PMID: 36980985 PMCID: PMC10048666 DOI: 10.3390/genes14030713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/26/2022] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The objective of this study was to uncover the genetic background of wool quality, a production trait, by estimating genomic heritability and implementing GWAS in Akkaraman sheep. The wool characteristics measured included fibre diameter (FD) and staple length (SL) at the age of 8 months and yearling fibre diameter (YFD), yearling staple length (YSL) and yearling greasy fleece weight (YGFW) at 18 months of age. Animals were genotyped using the Axiom 50 K Ovine Genotyping Array. Maximum likelihood estimations of a linear mixed model (LMM) were used to estimate genomic heritability, where GWAS was conducted following a score test of each trait. Genomic heritability estimates for the traits ranged between 0.22 and 0.63, indicating that phenotypes have a moderate range of heritability. One genome- and six chromosome-wide significant SNPs were associated with the wool traits in Akkaraman lambs. Accordingly, TRIM2, MND1, TLR2, RNF175, CEP290, TMTC3, RERE, SLC45A1, SOX2, MORN1, SKI, FAAP20, PRKCZ, GABRD, CFAP74, CALML6 and TMEM52 genes as well as nine uncharacterized regions (LOC101118971, LOC105609137, LOC105603067, LOC101122892, LOC106991694, LOC106991467, LOC106991455, LOC105616534 and LOC105609719) were defined as plausible candidates. The findings of this study shed light on the genetics of wool quality and yield for the Akkaraman breed and suggests targets for breeders during systematic breeding programmes.
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Affiliation(s)
- Yunus Arzik
- Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Türkiye
- International Center for Livestock Research and Training Center, Ministry of Agriculture and Forestry, 06852 Ankara, Türkiye
| | - Mehmet Kizilaslan
- Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Türkiye
- International Center for Livestock Research and Training Center, Ministry of Agriculture and Forestry, 06852 Ankara, Türkiye
- Correspondence: ; Tel.: +90-553-6725986
| | - Sedat Behrem
- Department of Animal Science, Faculty of Veterinary Medicine, Aksaray University, 68100 Aksaray, Türkiye
| | - Stephen N. White
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Lindsay M. W. Piel
- USDA-ARS Animal Disease Research 3003 ADBF, Washington State University, Pullman, WA 99164, USA
| | - Mehmet Ulas Cinar
- Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Türkiye
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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15
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Huang D, Ding H, Wang Y, Cheng G, Wang X, Leng T, Zhao H. Hair Follicle Transcriptome Analysis Reveals Differentially Expressed Genes That Regulate Wool Fiber Diameter in Angora Rabbits. BIOLOGY 2023; 12:biology12030445. [PMID: 36979137 PMCID: PMC10045444 DOI: 10.3390/biology12030445] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/15/2023]
Abstract
Wool fiber diameter (WFD) is an important index of wool traits and the main determinant of wool quality and value. However, the genetic determinants of fiber diameter have not yet been fully elucidated. Here, coarse and fine wool of Wan strain Angora rabbits and their hair follicle traits were characterized. The results indicated significant differences in the diameters of wool fibers and their hair follicles. The RNA sequencing (RNA-Seq) technique was used to identify differences in gene expression in hair follicles between coarse and fine wool. In total, 2574 differentially expressed genes (DEGs) were found between the two hair follicle groups. Transcription factors, keratin-associated protein (KAP) and keratin (KRT) families, and ECM-related genes may control the structure of fine fibers in rabbits. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that skin development, epidermal cell and keratinocyte differentiation, epithelium development, and Notch and ribosome signaling pathways were significantly enriched, respectively. GSEA further filtered six important pathways and related core genes. PPI analysis also mined functional DEGs associated with hair structure, including LEF1, FZD3, SMAD3, ITGB6, and BMP4. Our findings provide valuable information for researching the molecular mechanisms regulating wool fiber and could facilitate enhanced selection of super-fine wool rabbits through gene-assisted selection in the future.
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16
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Becker GM, Woods JL, Schauer CS, Stewart WC, Murdoch BM. Genetic association of wool quality characteristics in United States Rambouillet sheep. Front Genet 2023; 13:1081175. [PMID: 36755873 PMCID: PMC9901206 DOI: 10.3389/fgene.2022.1081175] [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: 10/26/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023] Open
Abstract
Introduction: Fine wool production is an important source of revenue, accounting for up to 13% of total revenue in extensively managed wool sheep production systems of the United States. The Rambouillet are a predominant breed that excels in wool quality characteristics. Understanding the genetic basis of wool quality characteristics would aid in the development of genomic breeding strategies to facilitate genetic improvement. Methods: Wool characteristics and DNA were collected for rams enrolled in the North Dakota State University and University of Wyoming annual central performance ram tests over a three-year period (2019-2021, N = 313). The relationships of wool quality characteristics including grease fleece weight adjusted 365 days (wt. 365 adj.), clean fleece wt. 365 adj., staple length 365 adj., average fiber diameter, face wool cover, amount of skin wrinkles and belly wool were evaluated through genome-wide association studies (GWAS), Pearson correlation and ANOVA. Results: The GWAS identified four genome-wide significant genetic markers (p-value <1.19e-06) and five chromosome-wide significant markers (p-value <1.13e-05) on chromosomes 1, 2, 4, 15, and 19. Significant markers were associated with genes notable for relevant wool biological functions, including the gene ABCC8 which codes for SUR1, an ATP-sensitive potassium channel known to affect hair growth and 60S ribosomal protein L17-like, previously found to be expressed during follicle formation. The strongest Pearson correlation coefficients were identified between clean fleece wt. 365 adj. and grease fleece wt. 365 adj. (r = 0.83) and between clean fleece wt. 365 adj. and staple length 365 adj. (r = 0.53). Additionally, clean fleece wt. 365 adj. was correlated with final body weight (r = 0.35) and scrotal circumference (r = 0.16). Staple length 365 adj. (p-value = 5e-04), average fiber diameter (p-value = .0053) and clean fleece wt. 365 adj. (p-value = .014) were significantly associated with belly wool score. Discussion: The results of this study provide important insight into the relationships between wool quality characteristics and report specific markers that Rambouillet sheep producers may use to help inform selection and breeding decisions for improved wool quality.
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Affiliation(s)
- Gabrielle M. Becker
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, United States
| | - Julia L. Woods
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, United States
| | - Christopher S. Schauer
- Hettinger Research Extension Center, North Dakota State University, Hettinger, ND, United States
| | - Whit C. Stewart
- Department of Animal Science, University of Wyoming, Laramie, WY, United States
| | - Brenda M. Murdoch
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, United States
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17
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Ramos Z, Garrick DJ, Blair HT, Vera B, Ciappesoni G, Kenyon PR. Genomic Regions Associated with Wool, Growth and Reproduction Traits in Uruguayan Merino Sheep. Genes (Basel) 2023; 14:167. [PMID: 36672908 PMCID: PMC9858812 DOI: 10.3390/genes14010167] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The aim of this study was to identify genomic regions and genes associated with the fiber diameter (FD), clean fleece weight (CFW), live weight (LW), body condition score (BCS), pregnancy rate (PR) and lambing potential (LP) of Uruguayan Merino sheep. Phenotypic records of approximately 2000 mixed-age ewes were obtained from a Merino nucleus flock. Genome-wide association studies were performed utilizing single-step Bayesian analysis. For wool traits, a total of 35 genomic windows surpassed the significance threshold (PVE ≥ 0.25%). The proportion of the total additive genetic variance explained by those windows was 4.85 and 9.06% for FD and CFW, respectively. There were 42 windows significantly associated with LWM, which collectively explained 43.2% of the additive genetic variance. For BCS, 22 relevant windows accounted for more than 40% of the additive genetic variance, whereas for the reproduction traits, 53 genomic windows (24 and 29 for PR and LP, respectively) reached the suggestive threshold of 0.25% of the PVE. Within the top 10 windows for each trait, we identified several genes showing potential associations with the wool (e.g., IGF-1, TGFB2R, PRKCA), live weight (e.g., CAST, LAP3, MED28, HERC6), body condition score (e.g., CDH10, TMC2, SIRPA, CPXM1) or reproduction traits (e.g., ADCY1, LEPR, GHR, LPAR2) of the mixed-age ewes.
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Affiliation(s)
- Zully Ramos
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
| | - Dorian J. Garrick
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
| | - Hugh T. Blair
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
| | - Brenda Vera
- National Research Program on Meat and Wool Production, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
| | - Gabriel Ciappesoni
- National Research Program on Meat and Wool Production, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
| | - Paul R. Kenyon
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
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18
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Wan X, Jing JN, Wang DF, Lv FH. Whole-genome selective scans detect genes associated with important phenotypic traits in goat ( Capra hircus). Front Genet 2023; 14:1173017. [PMID: 37144124 PMCID: PMC10151485 DOI: 10.3389/fgene.2023.1173017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. In this study, we focused on the worldwide goat breeds with outstanding traits and used whole-genome resequencing data in 361 samples from 68 breeds to detect genomic selection sweep regions. We identified 210-531 genomic regions with six phenotypic traits, respectively. Further gene annotation analysis revealed 332, 203, 164, 300, 205, and 145 candidate genes corresponding with dairy, wool, high prolificacy, poll, big ear, and white coat color traits. Some of these genes have been reported previously (e.g., KIT, KITLG, NBEA, RELL1, AHCY, and EDNRA), while we also discovered novel genes, such as STIM1, NRXN1, LEP, that may be associated with agronomic traits like poll and big ear morphology. Our study found a set of new genetic markers for genetic improvement in goats and provided novel insights into the genetic mechanisms of complex traits.
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Affiliation(s)
- Xing Wan
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jia-Nan Jing
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Feng-Hua Lv,
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19
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Addo S, Jung L. An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs. Front Genet 2022; 13:909986. [DOI: 10.3389/fgene.2022.909986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16–26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs.
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20
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Szalanczy AM, Goff E, Seshie O, Deal A, Grzybowski M, Klotz J, Chuang Key CC, Geurts AM, Solberg Woods LC. Keratinocyte-associated protein 3 plays a role in body weight and adiposity with differential effects in males and females. Front Genet 2022; 13:942574. [PMID: 36212147 PMCID: PMC9535360 DOI: 10.3389/fgene.2022.942574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
Despite the obesity crisis in the United States, the underlying genetics are poorly understood. Our lab previously identified Keratinocyte-associated protein 3, Krtcap3, as a candidate gene for adiposity through a genome-wide association study in outbred rats, where increased liver expression of Krtcap3 correlated with decreased fat mass. Here we seek to confirm that Krtcap3 expression affects adiposity traits. To do so, we developed an in vivo whole-body Krtcap3 knock-out (KO) rat model. Wild-type (WT) and KO rats were placed onto a high-fat (HFD) or low-fat diet (LFD) at 6 weeks of age and were maintained on diet for 13 weeks, followed by assessments of metabolic health. We hypothesized that Krtcap3-KO rats will have increased adiposity and a worsened metabolic phenotype relative to WT. We found that KO male and female rats have significantly increased body weight versus WT, with the largest effect in females on a HFD. KO females also ate more and had greater adiposity, but were more insulin sensitive than WT regardless of diet condition. Although KO males weighed more than WT under both diet conditions, there were no differences in eating behavior or fat mass. Interestingly, KO males on a HFD were more insulin resistant than WT. This study confirms that Krtcap3 plays a role in body weight regulation and demonstrates genotype- and sex-specific effects on food intake, adiposity, and insulin sensitivity. Future studies will seek to better understand these sex differences, the role of diet, and establish a mechanism for Krtcap3 in obesity.
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Affiliation(s)
- Alexandria M. Szalanczy
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Emily Goff
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Osborne Seshie
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Aaron Deal
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Michael Grzybowski
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jason Klotz
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Chia-Chi Chuang Key
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Aron M. Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Leah C. Solberg Woods
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
- *Correspondence: Leah C. Solberg Woods,
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21
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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22
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Oliveira RD, Mousel MR, Gonzalez MV, Durfee CJ, Davenport KM, Murdoch BM, Taylor JB, Neibergs HL, White SN. A high-density genome-wide association with absolute blood monocyte count in domestic sheep identifies novel loci. PLoS One 2022; 17:e0266748. [PMID: 35522671 PMCID: PMC9075649 DOI: 10.1371/journal.pone.0266748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 03/27/2022] [Indexed: 11/20/2022] Open
Abstract
Monocytes are a core component of the immune system that arise from bone marrow and differentiate into cells responsible for phagocytosis and antigen presentation. Their derivatives are often responsible for the initiation of the adaptive immune response. Monocytes and macrophages are central in both controlling and propagating infectious diseases such as infection by Coxiella burnetii and small ruminant lentivirus in sheep. Genotypes from 513 Rambouillet, Polypay, and Columbia sheep (Ovis aries) were generated using the Ovine SNP50 BeadChip. Of these sheep, 222 animals were subsequently genotyped with the Ovine Infinium® HD SNP BeadChip to increase SNP coverage. Data from the 222 HD genotyped sheep were combined with the data from an additional 258 unique sheep to form a 480-sheep reference panel; this panel was used to impute the low-density genotypes to the HD genotyping density. Then, a genome-wide association analysis was conducted to identify loci associated with absolute monocyte counts from blood. The analysis used a single-locus mixed linear model implementing EMMAX with age and ten principal components as fixed effects. Two genome-wide significant peaks (p < 5x10-7) were identified on chromosomes 9 and 1, and ten genome-wide suggestive peaks (p < 1x10-5) were identified on chromosomes 1, 2, 3, 4, 9, 10, 15, and 16. The identified loci were within or near genes including KCNK9, involved into cytokine production, LY6D, a member of a superfamily of genes, some of which subset monocyte lineages, and HMGN1, which encodes a chromatin regulator associated with myeloid cell differentiation. Further investigation of these loci is being conducted to understand their contributions to monocyte counts. Investigating the genetic basis of monocyte lineages and numbers may in turn provide information about pathogens of veterinary importance and elucidate fundamental immunology.
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Affiliation(s)
- Ryan D. Oliveira
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, Washington, United States of America
| | - Michelle R. Mousel
- USDA-ARS Animal Disease Research, Pullman, Washington, United States of America
- Allen School for Global Animal Health, Washington State University, Pullman, Washington, United States of America
| | - Michael V. Gonzalez
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Codie J. Durfee
- USDA-ARS Animal Disease Research, Pullman, Washington, United States of America
| | - Kimberly M. Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, United States of America
| | - Brenda M. Murdoch
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, United States of America
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - J. Bret Taylor
- USDA-ARS Range Sheep Production Efficiency Research, Dubois, Idaho, United States of America
| | - Holly L. Neibergs
- Department of Animal Sciences, Washington State University, Pullman, WA, United States of America
| | - Stephen N. White
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, Washington, United States of America
- USDA-ARS Animal Disease Research, Pullman, Washington, United States of America
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
- * E-mail:
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23
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Wang C, Yuan Z, Hu R, Li F, Yue X. Association of SNPs within PTPN3 gene with wool production and growth traits in a dual-purpose sheep population. Anim Biotechnol 2022:1-7. [PMID: 35192431 DOI: 10.1080/10495398.2022.2029465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Protein tyrosine phosphatase non-receptor type 3 (PTPN3), a member of the membrane-associated non-receptor protein tyrosine phosphatase (PTP) family, plays significant roles in the cytoplasm and affects the development and growth of skin and hair. A recent study identified the PTPN3 as the potential gene related to sheep wool quality. To detect single-nucleotide polymorphisms (SNPs) of PTPN3 and elucidate its association with wool production and growth traits in fine wool sheep a total of 644 healthy SG (South African mutton merino♂ × Gansu alpine fine-wool sheep♀, SG) and SSG (South African mutton merino♂ × SG♀, SSG) hybrid sheep were selected. Pooled-DNA sequencing and SNPscan methods were used to scan and genotype SNPs within PTPN3. Association analyses between SNPs and wool production and growth traits were implemented. Consequently, the results revealed that PTPN3 has six SNPs (two missense mutations, one synonymous mutation, and three intron mutations), of which four loci (SNP2, SNP3, SNP4, and SNP5) were significantly positively correlated with growth and wool traits (p < 0.05). SNP4 was significantly (p < 0.05) linked with thigh wool length, and SNP6 was significantly (p < 0.05) associated with abdomen wool length. Moreover, one strongly linked SNP block was identified to be correlated with wool production and growth traits (body weight and body size). The significant SNPs founded by this study could serve as useful genetic markers for breeding fine-wool sheep.®.
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Affiliation(s)
- Chong Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Ruixue Hu
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fadi Li
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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24
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Mohamadipoor Saadatabadi L, Mohammadabadi M, Amiri Ghanatsaman Z, Babenko O, Stavetska R, Kalashnik O, Kucher D, Kochuk-Yashchenko O, Asadollahpour Nanaei H. Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds. BMC Vet Res 2021; 17:369. [PMID: 34861880 PMCID: PMC8641187 DOI: 10.1186/s12917-021-03077-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sheep were among the first animals to be domesticated. They are raised all over the world and produce a major scale of animal-based protein for human consumption and play an important role in agricultural economy. Iran is one of the important locations for sheep genetic resources in the world. Here, we compared the Illumina Ovine SNP50 BeadChip data of three Iranian local breeds (Moghani, Afshari and Gezel), as a population that does not undergone artificial breeding programs as yet, and five other sheep breeds namely East Friesian white, East Friesian brown, Lacaune, DorsetHorn and Texel to detect genetic mechanisms underlying economical traits and daptation to harsh environments in sheep. RESULTS To identify genomic regions that have been targeted by positive selection, we used fixation index (Fst) and nucleotide diversity (Pi) statistics. Further analysis indicated candidate genes involved in different important traits such as; wool production included crimp of wool (PTPN3, NBEA and KRTAP20-2 genes), fiber diameter (PIK3R4 gene), hair follicle development (LHX2 gene), the growth and development of fiber (COL17A1 gene)), adaptation to hot arid environments (CORIN gene), adaptive in deficit water status (CPQ gene), heat stress (PLCB4, FAM107B, NBEA, PIK3C2B and USP43 genes) in sheep. CONCLUSIONS We detected several candidate genes related to wool production traits and adaptation to hot arid environments in sheep that can be applicable for inbreeding goals. Our findings not only include the results of previous researches, but also identify a number of novel candidate genes related to studied traits. However, more works will be essential to acknowledge phenotype- genotype relationships of the identified genes in our study.
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Affiliation(s)
| | | | - Zeinab Amiri Ghanatsaman
- Department of Animal Science, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Shiraz, Iran
| | - Olena Babenko
- Department of Animal Science, Bila Tserkva National Agrarian University, Soborna, Bila Tserkva, Kyivska Oblast, Ukraine
| | - Ruslana Stavetska
- Department of Animal Science, Bila Tserkva National Agrarian University, Soborna, Bila Tserkva, Kyivska Oblast, Ukraine
| | - Oleksandr Kalashnik
- Department of Animal Science, Sumy National Agrarian University, Sumy, Ukraine
| | - Dmytro Kucher
- Department of Breeding, Animal Genetics and Biotechnology, Polissia National University, Zhytomyr, Ukraine
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25
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Zhu S, Guo T, Yuan C, Liu J, Li J, Han M, Zhao H, Wu Y, Sun W, Wang X, Wang T, Liu J, Tiambo CK, Yue Y, Yang B. Evaluation of Bayesian alphabet and GBLUP based on different marker density for genomic prediction in Alpine Merino sheep. G3 (BETHESDA, MD.) 2021; 11:6310012. [PMID: 34849779 PMCID: PMC8527494 DOI: 10.1093/g3journal/jkab206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/01/2021] [Indexed: 01/20/2023]
Abstract
The marker density, the heritability level of trait and the statistical models adopted are critical to the accuracy of genomic prediction (GP) or selection (GS). If the potential of GP is to be fully utilized to optimize the effect of breeding and selection, in addition to incorporating the above factors into simulated data for analysis, it is essential to incorporate these factors into real data for understanding their impact on GP accuracy, more clearly and intuitively. Herein, we studied the GP of six wool traits of sheep by two different models, including Bayesian Alphabet (BayesA, BayesB, BayesCπ, and Bayesian LASSO) and genomic best linear unbiased prediction (GBLUP). We adopted fivefold cross-validation to perform the accuracy evaluation based on the genotyping data of Alpine Merino sheep (n = 821). The main aim was to study the influence and interaction of different models and marker densities on GP accuracy. The GP accuracy of the six traits was found to be between 0.28 and 0.60, as demonstrated by the cross-validation results. We showed that the accuracy of GP could be improved by increasing the marker density, which is closely related to the model adopted and the heritability level of the trait. Moreover, based on two different marker densities, it was derived that the prediction effect of GBLUP model for traits with low heritability was better; while with the increase of heritability level, the advantage of Bayesian Alphabet would be more obvious, therefore, different models of GP are appropriate in different traits. These findings indicated the significance of applying appropriate models for GP which would assist in further exploring the optimization of GP.
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Affiliation(s)
- Shaohua Zhu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.,Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Tingting Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.,Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chao Yuan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.,Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.,Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianye Li
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.,Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Mei Han
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.,Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Hongchang Zhao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.,Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yi Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.,Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Weibo Sun
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.,Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xijun Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan 734400, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan 734400, China
| | - Jigang Liu
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan 734400, China
| | - Christian Keambou Tiambo
- Centre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute, Nairobi 00100, Kenya
| | - Yaojing Yue
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bohui Yang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
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26
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Passamonti MM, Somenzi E, Barbato M, Chillemi G, Colli L, Joost S, Milanesi M, Negrini R, Santini M, Vajana E, Williams JL, Ajmone-Marsan P. The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. Animals (Basel) 2021; 11:2833. [PMID: 34679854 PMCID: PMC8532622 DOI: 10.3390/ani11102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Affiliation(s)
- Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Elisa Somenzi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Licia Colli
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Research Center on Biodiversity and Ancient DNA—BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - Marco Milanesi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Monia Santini
- Impacts on Agriculture, Forests and Ecosystem Services (IAFES) Division, Fondazione Centro Euro-Mediterraneo Sui Cambiamenti Climatici (CMCC), Viale Trieste 127, 01100 Viterbo, Italy;
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center—PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
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Zhao H, Zhu S, Guo T, Han M, Chen B, Qiao G, Wu Y, Yuan C, Liu J, Lu Z, Sun W, Wang T, Li F, Zhang Y, Hou F, Yue Y, Yang B. Whole-genome re-sequencing association study on yearling wool traits in Chinese fine-wool sheep. J Anim Sci 2021; 99:6319907. [PMID: 34255028 PMCID: PMC8418636 DOI: 10.1093/jas/skab210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 07/10/2021] [Indexed: 12/11/2022] Open
Abstract
To investigate single nucleotide polymorphism (SNP) loci associated with yearling wool traits of fine-wool sheep for optimizing marker-assisted selection and dissection of the genetic architecture of wool traits, we conducted a genome-wide association study (GWAS) based on the fixed and random model circulating probability unification (FarmCPU) for yearling staple length (YSL), yearling mean fiber diameter (YFD), yearling greasy fleece weight (YGFW), and yearling clean fleece rate (YCFR) by using the whole-genome re-sequenced data (totaling 577 sheep) from the following four fine-wool sheep breeds in China: Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Qinghai fine-wool sheep (QHS), and Aohan fine-wool sheep (AHS). A total of 16 SNPs were detected above the genome-wise significant threshold (P = 5.45E-09), and 79 SNPs were located above the suggestive significance threshold (P = 5.00E-07) from the GWAS results. For YFD and YGFW traits, 7 and 9 SNPs reached the genome-wise significance thresholds, whereas 10 and 12 SNPs reached the suggestive significance threshold, respectively. For YSL and YCFR traits, none of the SNPs reached the genome-wise significance thresholds, whereas 57 SNPs exceeded the suggestive significance threshold. We recorded 14 genes located at the region of ±50-kb near the genome-wise significant SNPs and 59 genes located at the region of ±50-kb near the suggestive significant SNPs. Meanwhile, we used the Average Information Restricted Maximum likelihood algorithm (AI-REML) in the “HIBLUP” package to estimate the heritability and variance components of the four desired yearling wool traits. The estimated heritability values (h2) of YSL, YFD, YGFW, and YCFR were 0.6208, 0.7460, 0.6758, and 0.5559, respectively. We noted that the genetic parameters in this study can be used for fine-wool sheep breeding. The newly detected significant SNPs and the newly identified candidate genes in this study would enhance our understanding of yearling wool formation, and significant SNPs can be applied to genome selection in fine-wool sheep breeding.
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Affiliation(s)
- Hongchang Zhao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Shaohua Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Mei Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Bowen Chen
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Guoyan Qiao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Yi Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Weibo Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Fanwen Li
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Yajun Zhang
- Xinjiang Gongnaisi Breeding Sheep Farm, Xinyuan, 835808, China
| | - Fujun Hou
- Aohan Banner Breeding Sheep Farm, Chifeng, 024300, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
- Corresponding author:
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Zhao H, Hu R, Li F, Yue X. Two strongly linked blocks within the KIF16B gene significantly influence wool length and greasy yield in fine wool sheep (Ovis aries). ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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29
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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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Zhao B, Luo H, Huang X, Wei C, Di J, Tian Y, Fu X, Li B, Liu GE, Fang L, Zhang S, Tian K. Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep. Genet Sel Evol 2021; 53:56. [PMID: 34193030 PMCID: PMC8247193 DOI: 10.1186/s12711-021-00649-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). RESULTS Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from - 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. CONCLUSIONS Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.
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Affiliation(s)
- Bingru Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hanpeng Luo
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Chen Wei
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jiang Di
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Yuezhen Tian
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Bingjie Li
- Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, EH25 9RG, UK
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
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Shen X, Song C, Wu T. Effects of Nano-copper on Antioxidant Function in Copper-Deprived Guizhou Black Goats. Biol Trace Elem Res 2021; 199:2201-2207. [PMID: 32812170 DOI: 10.1007/s12011-020-02342-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 08/09/2020] [Indexed: 12/12/2022]
Abstract
Guizhou black goats are essential to the production system in the Wumeng prairie in the Western China. This study aimed to determine the influence of nano-copper on antioxidant system in copper-deprived Guizhou black goats. We analyzed mineral contents in soil, forage, and goats' tissues. Blood parameters were also determined. The results showed that copper concentrations in soil and forage were significantly lower, and the iron content was significantly higher in affected compared with healthy area (P < 0.01). Copper concentrations in animal tissues (blood, liver, and hair) were significantly lower and iron content was significantly higher in affected compared with healthy goats (P < 0.01). After supplementation of nano-copper or copper sulfate, copper concentration in blood was significantly increased and iron content was significantly lower (P < 0.01). Compared with nano-copper group, the effect of copper sulfate was slower. Hemoglobin levels, erythrocyte count, and packed cell volume from nano-copper and copper sulfate groups were significantly higher than those in copper-deprived goats (P < 0.01). Compared with the copper-deprived Guizhou black goats, serum ceruloplasmin levels in nano-copper and copper sulfate groups were significantly increased, while serum lactate dehydrogenase, aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, and creatinine were significantly decreased (P < 0.01). Compared with the copper-deprived animals, serum superoxide dismutase, glutathione peroxidase, catalase, and total antioxidant capacity in nano-copper and copper sulfate groups were significantly higher, while serum malondialdehyde content was significantly lower (P < 0.01). The effect of copper sulfate group was significantly lower than that in nano-copper group (P < 0.01). Consequently, nano-copper could not only markedly increase the copper content in blood in copper-deprived Guizhou black goats but also much improves the antioxidant capacity.
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Affiliation(s)
- Xiaoyun Shen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.
- State Engineering Technology Institute for Karst Desertification Control, Guizhou Normal University, Guiyang, 550025, China.
- World Bank Poverty Alleviation Project Office in Guizhou, Southwest China, Guiyang, 550004, China.
| | - Chunjie Song
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Ting Wu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
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Cortellari M, Barbato M, Talenti A, Bionda A, Carta A, Ciampolini R, Ciani E, Crisà A, Frattini S, Lasagna E, Marletta D, Mastrangelo S, Negro A, Randi E, Sarti FM, Sartore S, Soglia D, Liotta L, Stella A, Ajmone-Marsan P, Pilla F, Colli L, Crepaldi P. The climatic and genetic heritage of Italian goat breeds with genomic SNP data. Sci Rep 2021; 11:10986. [PMID: 34040003 PMCID: PMC8154919 DOI: 10.1038/s41598-021-89900-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including > 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo-political situation preceding the country unification around two centuries ago. We leveraged the remarkable genetic and geographical diversity of the Italian goat populations and performed landscape genomics analysis to disentangle the relationship between genotype and environment, finding 64 SNPs intercepting genomic regions linked to growth, circadian rhythm, fertility, and inflammatory response. Lastly, we calculated the hypothetical future genotypic frequencies of the most relevant SNPs identified through landscape genomics to evaluate their long-term effect on the genetic structure of the Italian goat populations. Our results provide an insight into the past and the future of the Italian local goat populations, helping the institutions in defining new conservation strategy plans that could preserve their diversity and their link to local realities challenged by climate change.
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Affiliation(s)
- Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - Mario Barbato
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti and BioDNA Centro di ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Andrea Talenti
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy.
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - Antonello Carta
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, Università di Pisa, Viale delle Piagge 2, 56124, Pisa, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, Università degli Studi di Bari, Via Orabona 4, 70126, Bari, Italy
| | - Alessandra Crisà
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015, Monterotondo, Rome, Italy
| | - Stefano Frattini
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Donata Marletta
- Department of Agriculture, Food and Environment, University of Catania, Via Valdisavoia 5, 95123, Catania, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Alessio Negro
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - Ettore Randi
- Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Francesca M Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Stefano Sartore
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, largo Braccini 2, 10095, Grugliasco, Italy
| | - Dominga Soglia
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, largo Braccini 2, 10095, Grugliasco, Italy
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Messina, Italy
| | - Alessandra Stella
- Institute of Biology and Biotechnology in Agriculture, National Research Council (CNR), Milan, Italy
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti and BioDNA Centro di ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti Universitá degli Studi del Molise, 86100, Campobasso, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti and BioDNA Centro di ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
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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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Sutera AM, Moscarelli A, Mastrangelo S, Sardina MT, Di Gerlando R, Portolano B, Tolone M. Genome-Wide Association Study Identifies New Candidate Markers for Somatic Cells Score in a Local Dairy Sheep. Front Genet 2021; 12:643531. [PMID: 33828586 PMCID: PMC8019815 DOI: 10.3389/fgene.2021.643531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
In the Mediterranean basin countries, the dairy sheep production is usually based on local breeds, which are very well-adapted to their production systems and environments and can indeed guarantee income, employment, and economic viability in areas where production alternatives are scarce or non-existent. Mastitis is still one of the greatest problems affecting commercial milk production. However, genetic evaluation of mastitis is particularly difficult because of its low heritability and the categorical nature of the trait. The aim of this study was to identify genomic regions putatively associated with somatic cells count (SCC) in the local economically important Valle del Belice sheep breed using of deregressed breeding values (DEBV) as response variables. All the samples were genotyped using the Illumina OvineSNP50K BeadChip. Genome-wide association analysis was carried out based on regression of DEBV. A total of eight markers were found to be significantly associated with log-transformed SCC. Several candidate genes associated with SCC were identified related to immunity system and udder conformation. The results can help improving the competitiveness of the local Valle del Belìce breed. Further studies considering a higher sample size or independent population will be needed to confirm our results.
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Affiliation(s)
- Anna Maria Sutera
- Dipartimento Scienze Veterinarie, University of Messina, Messina, Italy
| | - Angelo Moscarelli
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Marco Tolone
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
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Zhao H, Guo T, Lu Z, Liu J, Zhu S, Qiao G, Han M, Yuan C, Wang T, Li F, Zhang Y, Hou F, Yue Y, Yang B. Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep. BMC Genomics 2021; 22:127. [PMID: 33602144 PMCID: PMC7893944 DOI: 10.1186/s12864-021-07399-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. In this study, we used the Illumina HiSeq X Ten platform to re-sequence 460 sheep belonging to four different fine-wool sheep breeds, namely, Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Aohan fine-wool sheep (AHS) and Qinghai fine-wool sheep (QHS). Eight wool traits, including fiber diameter (FD), fiber diameter coefficient of variance (FDCV), fiber diameter standard deviation (FDSD), staple length (SL), greasy fleece weight (GFW), clean wool rate (CWR), staple strength (SS) and staple elongation (SE) were examined. A genome-wide association study (GWAS) was performed to detect the candidate genes for the eight wool traits. RESULTS A total of 8.222 Tb of raw data was generated, with an average of approximately 8.59X sequencing depth. After quality control, 12,561,225 SNPs were available for analysis. And a total of 57 genome-wide significant SNPs and 30 candidate genes were detected for the desired wool traits. Among them, 7 SNPs and 6 genes are related to wool fineness indicators (FD, FDCV and FDSD), 10 SNPs and 7 genes are related to staple length, 13 SNPs and 7 genes are related to wool production indicators (GFW and CWR), 27 SNPs and 10 genes associated with staple elongation. Among these candidate genes, UBE2E3 and RHPN2 associated with fiber diameter, were found to play an important role in keratinocyte differentiation and cell proliferation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results, revealed that multitude significant pathways are related to keratin and cell proliferation and differentiation, such as positive regulation of canonical Wnt signaling pathway (GO:0090263). CONCLUSION This is the first GWAS on the wool traits by using re-sequencing data in Chinese fine-wool sheep. The newly detected significant SNPs in this study can be used in genome-selective breeding for the fine-wool sheep. And the new candidate genes would provide a good theoretical basis for the fine-wool sheep breeding.
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Affiliation(s)
- Hongchang Zhao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Shaohua Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Guoyan Qiao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Mei Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Fanwen Li
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Yajun Zhang
- Xinjiang Gongnaisi Breeding Sheep Farm, Xinyuan, 835808, China
| | - Fujun Hou
- Aohan Banner Breeding Sheep Farm, Chifeng, 024300, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
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Yuan C, Lu Z, Guo T, Yue Y, Wang X, Wang T, Zhang Y, Hou F, Niu C, Sun X, Zhao H, Zhu S, Liu J, Yang B. A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing. BMC Genomics 2021; 22:78. [PMID: 33485316 PMCID: PMC7825165 DOI: 10.1186/s12864-021-07387-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/13/2021] [Indexed: 12/13/2022] Open
Abstract
Background Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing. Results A total of 1,747,604 CNVs were detected in this study, and 7228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4307.17 bp. “Deletion” events took place more frequently than “duplication” or “both” events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39–55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective sweep of CNVRs, and it was found that the relaxin family peptide receptor 2 (RXFP2) gene was strongly influenced by selection. Conclusions In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07387-7.
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Affiliation(s)
- Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Xijun Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Yajun Zhang
- Xinjiang Gongnaisi Breeding Sheep Farm, Xinyuan, 835808, China
| | - Fujun Hou
- Aohan Banner Breeding Sheep Farm, Chifeng, 024300, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Xiaopin Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Hongchang Zhao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Shaohua Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China.
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China.
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Krivoruchko AY, Yatsyk OA, Safaryan EY. Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed. Vavilovskii Zhurnal Genet Selektsii 2020; 24:836-843. [PMID: 35087996 PMCID: PMC8763718 DOI: 10.18699/vj20.681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/15/2020] [Accepted: 10/29/2020] [Indexed: 11/23/2022] Open
Abstract
Genome-wide association studies allow identification of loci and polymorphisms associated with the formation of relevant phenotypes. When conducting a full genome analysis of sheep, particularly promising is the study
of individuals with outstanding productivity indicators – exhibition animals, representatives of the super-elite class.
The aim of this study was to identify new candidate genes for economically valuable traits based on the search for
single nucleotide polymorphisms (SNPs) associated with belonging to different evaluation classes in rams of the Russian meat merino breed. Animal genotyping was performed using Ovine Infinium HD BeadChip 600K DNA, association search was performed using PLINK v. 1.07 software. Highly reliable associations were found between animals
belonging to different evaluation classes and the frequency of occurrence of individual SNPs on chromosomes 2, 6,
10, 13, and 20. Most of the substitutions with high association reliability are concentrated on chromosome 10 in the
region 10: 30859297–31873769. To search for candidate genes, 15 polymorphisms with the highest association reliability were selected (–log10(р) > 9). Determining the location of the analyzed SNPs relative to the latest annotation
Oar_rambouillet_v1.0 allowed to identify 11 candidate genes presumably associated with the formation of a complex
of phenotypic traits of animals in the exhibition group: RXFP2, ALOX5AP, MEDAG, OPN5, PRDM5, PTPRT, TRNAS-GGA,
EEF1A1, FRY, ZBTB21-like, and B3GLCT-like. The listed genes encode proteins involved in the control of the cell cycle and
DNA replication, regulation of cell proliferation and apoptosis, lipid and carbohydrate metabolism, the development
of the inflammatory process and the work of circadian rhythms. Thus, the candidate genes under consideration can
influence the formation of exterior features and productive qualities of sheep. However, further research is needed
to confirm the influence of genes and determine the exact mechanisms for implementing this influence on the phenotype.
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Affiliation(s)
- A. Y. Krivoruchko
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
| | - O. A. Yatsyk
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
| | - E. Y. Safaryan
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
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Zhu S, Guo T, Zhao H, Qiao G, Han M, Liu J, Yuan C, Wang T, Li F, Yue Y, Yang B. Genome-Wide Association Study Using Individual Single-Nucleotide Polymorphisms and Haplotypes for Erythrocyte Traits in Alpine Merino Sheep. Front Genet 2020; 11:848. [PMID: 32849829 PMCID: PMC7411260 DOI: 10.3389/fgene.2020.00848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/13/2020] [Indexed: 11/13/2022] Open
Abstract
Adaptation to high-altitude hypoxia is essential for domestic animals, such as yak, Tibetan chicken, and Tibetan sheep, living on high plateaus, as it ensures efficient oxygen absorption and utilization. Red blood cells are the primary medium for transporting oxygen in the blood. However, little is known about the genetic mechanism of erythrocyte traits. Genome-wide association studies (GWASs) based on single markers or haplotypes have identified potential mechanisms for genetic variation and quantitative traits. To identify loci associated with erythrocyte traits, we performed a GWAS based on the method of the single marker and haplotype in 498 Alpine Merino sheep for six erythrocyte traits: red blood cell count (RBC), hemoglobin (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and RBC volume distribution width coefficient of variation (RWD_CV). Forty-two significant single-nucleotide polymorphisms (SNPs) associated with the six erythrocyte traits were detected by means of a single-marker GWAS, and 34 significant haplotypes associated with five erythrocyte traits were detected by means of haplotype analysis. We identified six genes (DHCR24, SPATA9, FLI1, PLCB1, EFNB2, and SH2B3) as potential genes of interest via gene function annotations, location, and expression variation. In particular, FLI1 and PLCB1 were associated with hematopoiesis and erythropoiesis, respectively. These results provide a theoretical basis for analyzing erythrocyte traits and high-altitude hypoxia adaptation in Alpine Merino sheep and will be a useful reference for future studies of plateau-dwelling livestock.
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Affiliation(s)
- Shaohua Zhu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tingting Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hongchang Zhao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guoyan Qiao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mei Han
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianbin Liu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chao Yuan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, China
| | - Fanwen Li
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, China
| | - Yaojing Yue
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bohui Yang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
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Li X, Yang J, Shen M, Xie XL, Liu GJ, Xu YX, Lv FH, Yang H, Yang YL, Liu CB, Zhou P, Wan PC, Zhang YS, Gao L, Yang JQ, Pi WH, Ren YL, Shen ZQ, Wang F, Deng J, Xu SS, Salehian-Dehkordi H, Hehua E, Esmailizadeh A, Dehghani-Qanatqestani M, Štěpánek O, Weimann C, Erhardt G, Amane A, Mwacharo JM, Han JL, Hanotte O, Lenstra JA, Kantanen J, Coltman DW, Kijas JW, Bruford MW, Periasamy K, Wang XH, Li MH. Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. Nat Commun 2020; 11:2815. [PMID: 32499537 PMCID: PMC7272655 DOI: 10.1038/s41467-020-16485-1] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/04/2020] [Indexed: 01/15/2023] Open
Abstract
Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.
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Affiliation(s)
- Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Guang-Jian Liu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Ya-Xi Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Yong-Lin Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 256600, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Deng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- 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
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Ondřej Štěpánek
- Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Christina Weimann
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, Germany
| | - Georg Erhardt
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, Germany
| | - Agraw Amane
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Center for Tropical Livestock Genetics and Health (CTLGH), the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600, Jokioinen, Finland
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - James W Kijas
- CSIRO Livestock Industries, St Lucia, Brisbane, QLD, Australia
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, Wales, UK
- Sustainable Places Research Institute, Cardiff University, CF10 3BA, Cardiff, Wales, UK
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Liu G, Li S, Liu H, Zhu Y, Bai L, Sun H, Gao S, Jiang W, Li F. The functions of ocu-miR-205 in regulating hair follicle development in Rex rabbits. BMC DEVELOPMENTAL BIOLOGY 2020; 20:8. [PMID: 32321445 PMCID: PMC7178635 DOI: 10.1186/s12861-020-00213-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 04/13/2020] [Indexed: 12/03/2022]
Abstract
BACKGROUND Hair follicles are an appendage of the vertebrate epithelium in the skin that arise from the embryonic ectoderm and regenerate cyclically during adulthood. Dermal papilla cells (DPCs) are the key dermal component of the hair follicle that directly regulate hair follicle development, growth and regeneration. According to recent studies, miRNAs play an important role in regulating hair follicle morphogenesis and the proliferation, differentiation and apoptosis of hair follicle stem cells. RESULTS The miRNA expression profile of the DPCs from Rex rabbits with different hair densities revealed 240 differentially expressed miRNAs (|log2(HD/LD)| > 1.00 and Q-value≤0.001). Among them, ocu-miR-205-5p was expressed at higher levels in DPCs from rabbits with low hair densities (LD) than in rabbits with high hair densities (HD), and it was expressed at high levels in the skin tissue from Rex rabbits (P < 0.05). Notably, ocu-miR-205 increased cell proliferation and the cell apoptosis rate, altered the progression of the cell cycle (P < 0.05), and modulated the expression of genes involved in the PI3K/Akt, Wnt, Notch and BMP signalling pathways in DPCs and skin tissue from Rex rabbits. It also inhibited the phosphorylation of the CTNNB1 and GSK-3β proteins, decreased the level of the noggin (NOG) protein, and increased the level of phosphorylated Akt (P < 0.05). A significant change in the primary follicle density was not observed (P > 0.05), but the secondary follicle density and total follicle density (P < 0.05) were altered upon interference with ocu-miR-205-5p expression, and the secondary/primary ratio (S/P) in the ocu-miR-205-5p interfered expression group increased 14 days after the injection (P < 0.05). CONCLUSIONS In the present study, ocu-miR-205 promoted the apoptosis of DPCs, altered the expression of genes and proteins involved in the PI3K/Akt, Wnt, Notch and BMP signalling pathways in DPCs and skin from Rex rabbits, promoted the transition of hair follicles from the growth phase to the regression and resting phase, and altered the hair density of Rex rabbits.
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Affiliation(s)
- Gongyan Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, 271018, People's Republic of China
- Animal Husbandry and Veterinary Institute, Shandong Academy of Agricultural Sciences, Jinan, 251000, People's Republic of China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, 251000, People's Republic of China
| | - Shu Li
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, 271018, People's Republic of China
| | - Hongli Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, 271018, People's Republic of China
| | - Yanli Zhu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, 271018, People's Republic of China
| | - Liya Bai
- Animal Husbandry and Veterinary Institute, Shandong Academy of Agricultural Sciences, Jinan, 251000, People's Republic of China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, 251000, People's Republic of China
| | - Haitao Sun
- Animal Husbandry and Veterinary Institute, Shandong Academy of Agricultural Sciences, Jinan, 251000, People's Republic of China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, 251000, People's Republic of China
| | - Shuxia Gao
- Animal Husbandry and Veterinary Institute, Shandong Academy of Agricultural Sciences, Jinan, 251000, People's Republic of China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, 251000, People's Republic of China
| | - Wenxue Jiang
- Animal Husbandry and Veterinary Institute, Shandong Academy of Agricultural Sciences, Jinan, 251000, People's Republic of China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, 251000, People's Republic of China
| | - Fuchang Li
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, 271018, People's Republic of China.
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Wei C, Luo H, Zhao B, Tian K, Huang X, Wang Y, Fu X, Tian Y, Di J, Xu X, Wu W, Tulafu H, Yasen M, Zhang Y, Zhao W. The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep. Animals (Basel) 2020; 10:ani10040569. [PMID: 32231053 PMCID: PMC7222387 DOI: 10.3390/ani10040569] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 01/06/2023] Open
Abstract
Simple Summary Genetic improvement of wool production and quality traits in fine-wool sheep is an appealing option for enhancing the market value of wool products. We estimated genetic parameters and the accuracies of estimated breeding values for various wool production and quality traits in fine-wool sheep using pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) strategies. ssGBLUP performed slightly better than PBLUP for the studied traits. Therefore, the single-step genetic evaluation method could be successfully implemented in genomic evaluations of fine-wool sheep and the prediction of future breeding values in young Merino sheep as part of an early preselection strategy in the near future. Abstract Genomic evaluations are a method for improving the accuracy of breeding value estimation. This study aimed to compare estimates of genetic parameters and the accuracy of breeding values for wool traits in Merino sheep between pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) using Bayesian inference. Data were collected from 28,391 yearlings of Chinese Merino sheep (classified in 1992–2018) at the Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, China. Subjectively-assessed wool traits, namely, spinning count (SC), crimp definition (CRIM), oil (OIL), and body size (BS), and objectively-measured traits, namely, fleece length (FL), greasy fleece weight (GFW), mean fiber diameter (MFD), crimp number (CN), and body weight pre-shearing (BWPS), were analyzed. The estimates of heritability for wool traits were low to moderate. The largest h2 values were observed for FL (0.277) and MFD (0.290) with ssGBLUP. The heritabilities estimated for wool traits with ssGBLUP were slightly higher than those obtained with PBLUP. The accuracies of breeding values were low to moderate, ranging from 0.362 to 0.573 for the whole population and from 0.318 to 0.676 for the genotyped subpopulation. The correlation between the estimated breeding values (EBVs) and genomic EBVs (GEBVs) ranged from 0.717 to 0.862 for the whole population, and the relative increase in accuracy when comparing EBVs with GEBVs ranged from 0.372% to 7.486% for these traits. However, in the genotyped population, the rank correlation between the estimates obtained with PBLUP and ssGBLUP was reduced to 0.525 to 0.769, with increases in average accuracy of 3.016% to 11.736% for the GEBVs in relation to the EBVs. Thus, genomic information could allow us to more accurately estimate the relationships between animals and improve estimates of heritability and the accuracy of breeding values by ssGBLUP.
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Affiliation(s)
- Chen Wei
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Hanpeng Luo
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Bingru Zhao
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kechuan Tian
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
- Correspondence: (K.T.); (X.H.); (Y.W.); Tel.: +86-1590-900-1963 (K.T.); +86-1399-999-6861 (X.H.); +86-1580-159-5851 (Y.W.)
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
- Correspondence: (K.T.); (X.H.); (Y.W.); Tel.: +86-1590-900-1963 (K.T.); +86-1399-999-6861 (X.H.); +86-1580-159-5851 (Y.W.)
| | - Yachun Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Correspondence: (K.T.); (X.H.); (Y.W.); Tel.: +86-1590-900-1963 (K.T.); +86-1399-999-6861 (X.H.); +86-1580-159-5851 (Y.W.)
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Yuezhen Tian
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Jiang Di
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Xinming Xu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Weiwei Wu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Hanikezi Tulafu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Maerziya Yasen
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi 830011, China (J.D.)
| | - Yajun Zhang
- Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, Ili Kazak Autonomous Prefecture 835800, China
| | - Wensheng Zhao
- Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, Ili Kazak Autonomous Prefecture 835800, China
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Gebreselassie G, Berihulay H, Jiang L, Ma Y. Review on Genomic Regions and Candidate Genes Associated with Economically Important Production and Reproduction Traits in Sheep ( Ovies aries). Animals (Basel) 2019; 10:E33. [PMID: 31877963 PMCID: PMC7022721 DOI: 10.3390/ani10010033] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/24/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022] Open
Abstract
Sheep (Ovis aries) is one of the most economically, culturally, and socially important domestic animals. They are reared primarily for meat, milk, wool, and fur production. Sheep were reared using natural selection for a long period of time to offer these traits. In fact, this production system has been slowing the productivity and production potential of the sheep. To improve production efficiency and productivity of this animal through genetic improvement technologies, understanding the genetic background of traits such as body growth, weight, carcass quality, fat percent, fertility, milk yield, wool quality, horn type, and coat color is essential. With the development and utilization of animal genotyping technologies and gene identification methods, many functional genes and genetic variants associated with economically important phenotypic traits have been identified and annotated. This is useful and presented an opportunity to increase the pace of animal genetic gain. Quantitative trait loci and genome wide association study have been playing an important role in identifying candidate genes and animal characterization. This review provides comprehensive information on the identified genomic regions and candidate genes associated with production and reproduction traits, and gene function in sheep.
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Affiliation(s)
- Gebremedhin Gebreselassie
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Department of Agricultural Biotechnology, Biotechnology Center, Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa 1000, Ethiopia
| | - Haile Berihulay
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lin Jiang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yuehui Ma
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
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Megdiche S, Mastrangelo S, Ben Hamouda M, Lenstra JA, Ciani E. A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds. Front Genet 2019; 10:1025. [PMID: 31708969 PMCID: PMC6824410 DOI: 10.3389/fgene.2019.01025] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/24/2019] [Indexed: 12/24/2022] Open
Abstract
Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical FST-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested via the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, with non-Merino breeds from the same geographic area were tested via the FST-outlier method. Signals observed using both methods were compared with genome-wide patterns of distribution of runs of homozygosity (ROH) islands. Novel and known selection signatures were detected. The most reliable signals were observed on OAR 3 (MSRB3 and LEMD3), OAR10 (FRY and RXFP2), OAR 13 (RALY), OAR17 (FAM101A), and OAR18 (NFKBIA, SEC23A, and PAX9). All the above overlapped with known QTLs for wool traits, and evidences from the literature of their involvement in skin/hair/wool biology, as well as gene network analysis, further corroborated these results. The signal on OAR10 also contains well known evidence for association with horn morphology and polledness. More elusive biological evidences of association with the Merino phenotype were observed for a number of other genes, notably LOC101120019 and TMEM132B (OAR17), LOC105609948 (OAR3), LOC101110773 (OAR10), and EIF2S2 (OAR17). Taken together, the above results further contribute to decipher the genetic basis underlying the Merino phenotype.
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Affiliation(s)
- Sami Megdiche
- Départment des Ressources Animales, Agroalimentaire et Développement Rural, Institut Supérieur Agronomique de Chott-Mariem, Université de Sousse, Sousse, Tunisia
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | | | | | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
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Mattucci F, Galaverni M, Lyons LA, Alves PC, Randi E, Velli E, Pagani L, Caniglia R. Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations. Sci Rep 2019; 9:11612. [PMID: 31406125 PMCID: PMC6691104 DOI: 10.1038/s41598-019-48002-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 07/25/2019] [Indexed: 12/22/2022] Open
Abstract
The survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priority. We analyzed 63k cat Single Nucleotide Polymorphisms (SNPs) with multivariate, Bayesian and gene-search tools to better evaluate admixture levels between domestic and wild cats collected in Europe, timing and ancestry proportions of their hybrids and backcrosses, and track the origin (wild or domestic) of the genomic blocks carried by admixed cats, also looking for possible deviations from neutrality in their inheritance patterns. Small domestic ancestry blocks were detected in the genomes of most admixed cats, which likely originated from hybridization events occurring from 6 to 22 generations in the past. We identified about 1,900 outlier coding genes with excess of wild or domestic ancestry compared to random expectations in the admixed individuals. More than 600 outlier genes were significantly enriched for Gene Ontology (GO) categories mainly related to social behavior, functional and metabolic adaptive processes (wild-like genes), involved in cognition and neural crest development (domestic-like genes), or associated with immune system functions and lipid metabolism (parental-like genes). These kinds of genomic ancestry analyses could be reliably applied to unravel the admixture dynamics in European wildcats, as well as in other hybridizing populations, in order to design more efficient conservation plans.
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Affiliation(s)
- Federica Mattucci
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy.
| | | | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, USA
| | - Paulo C Alves
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBio - Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, USA
| | - Ettore Randi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Edoardo Velli
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy
| | - Luca Pagani
- Dipartimento di Biologia, Università degli Studi di Padova, Padua, Italy
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Romolo Caniglia
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy
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Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 2019; 20:294. [PMID: 32039702 PMCID: PMC7227232 DOI: 10.1186/s12864-019-5537-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- 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
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, 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.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Timur N Khamiruev
- Research Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences, Chita, Russia
| | - Marina I Selionova
- All-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian Center, Stavropol, 355017, Russia
| | - Sergey V Egorov
- Siberian Research Institute of Animal Husbandry, Krasnoobsk, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, UK.
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Di Gerlando R, Sutera AM, Mastrangelo S, Tolone M, Portolano B, Sottile G, Bagnato A, Strillacci MG, Sardina MT. Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep. PLoS One 2019; 14:e0215204. [PMID: 31013280 PMCID: PMC6478285 DOI: 10.1371/journal.pone.0215204] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 03/28/2019] [Indexed: 11/19/2022] Open
Abstract
Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits.
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Affiliation(s)
- Rosalia Di Gerlando
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Anna Maria Sutera
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Salvatore Mastrangelo
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Marco Tolone
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Baldassare Portolano
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Gianluca Sottile
- Università degli Studi di Palermo, Dipartimento di Scienze Economiche, Aziendali e Statistiche, Italy
| | - Alessandro Bagnato
- Università degli Studi di Milano, Dipartimento di Medicina Veterinaria, Italy
| | | | - Maria Teresa Sardina
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
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Bai L, Jiang W, Wang W, Gao S, Sun H, Yang L, Hu H. Optimum wool harvest interval of angora rabbits under organised farm conditions in East China. WORLD RABBIT SCIENCE 2019. [DOI: 10.4995/wrs.2019.10838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The present study was conducted to evaluate the commercial lifespan and optimum wool harvest interval of Angora rabbits. One hundred shorn Angora rabbits were housed in an organised farm to describe the wool production curve. It showed that the optimum wool harvest interval was 75 d, when fibre length reached 55.0 mm. Wool production was lower from the 3<sup>rd</sup> to the 6<sup>th</sup> mo (young stage) than from 7<sup>th</sup> to 28<sup>th</sup> mo and rapidly decreased from 28<sup>th</sup> to 31<sup>st</sup> mo and was the lowest from 31<sup>st</sup> to 33<sup>rd</sup> mo of age. Feed intake-to-wool production ratio was higher from 3<sup>rd</sup> to 4<sup>th</sup> and from 7<sup>th</sup> to 9<sup>th</sup> mo of age than during the adult stage, and increased from 31<sup>st</sup> to 33<sup>rd</sup> mo of age. Daily weight gain was significantly higher from 3<sup>rd</sup> to 4<sup>th</sup> mo of age than in any other periods of the adult stage, and was negative from 23<sup>rd</sup> to 33<sup>rd</sup> mo of age. Therefore, the study reveals that the commercial lifespan of Angora rabbits was approximately 28 mo. Furthermore, wool production was higher in spring and winter than in autumn, and was the lowest in summer. Concomitantly, feed intake-to-wool production ratio was lower in spring than in autumn and winter, and was the highest in summer. Finally, daily weight gain was higher in spring and autumn than in winter, and was the lowest in summer. This indicates that wool production was depending on the season, and decreased significantly in summer. Moreover, the spring provided the best conditions for Angora rabbits.
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48
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New world goat populations are a genetically diverse reservoir for future use. Sci Rep 2019; 9:1476. [PMID: 30728441 PMCID: PMC6365549 DOI: 10.1038/s41598-019-38812-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/30/2018] [Indexed: 01/02/2023] Open
Abstract
Western hemisphere goats have European, African and Central Asian origins, and some local or rare breeds are reported to be adapted to their environments and economically important. By-in-large these genetic resources have not been quantified. Using 50 K SNP genotypes of 244 animals from 12 goat populations in United States, Costa Rica, Brazil and Argentina, we evaluated the genetic diversity, population structure and selective sweeps documenting goat migration to the "New World". Our findings suggest the concept of breed, particularly among "locally adapted" breeds, is not a meaningful way to characterize goat populations. The USA Spanish goats were found to be an important genetic reservoir, sharing genomic composition with the wild ancestor and with specialized breeds (e.g. Angora, Lamancha and Saanen). Results suggest goats in the Americas have substantial genetic diversity to use in selection and promote environmental adaptation or product driven specialization. These findings highlight the importance of maintaining goat conservation programs and suggest an awaiting reservoir of genetic diversity for breeding and research while simultaneously discarding concerns about breed designations.
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49
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Pompanon F. Des signatures génomiques de domestication homologues chez la chèvre et le mouton. Med Sci (Paris) 2018; 34:916-919. [DOI: 10.1051/medsci/2018229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Convergent genomic signatures of domestication in sheep and goats. Nat Commun 2018; 9:813. [PMID: 29511174 PMCID: PMC5840369 DOI: 10.1038/s41467-018-03206-y] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/29/2018] [Indexed: 12/15/2022] Open
Abstract
The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species. The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.
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