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Zhou A, Ding Y, Zhang X, Zhou Y, Liu Y, Li T, Xiao L. Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-white goat prolificacya. Anim Biotechnol 2024; 35:2258166. [PMID: 37729465 DOI: 10.1080/10495398.2023.2258166] [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: 09/22/2023]
Abstract
In this study, we evaluated the copy number variation in the genomes of two groups of Beichuan-white goat populations with large differences in litter size by FST method, and identified 1739 genes and 485 missense mutations in the genes subject to positive selection. Through functional enrichment, ITGAV, LRP4, CDH23, TPRN, RYR2 and CELSR1 genes, involved in embryonic morphogenesis, were essential for litter size trait, which received intensive attention. In addition, some mutation sites of these genes have been proposed (ITGAV: c.38C > T; TPRN: c.133A > T, c.1192A > G, c.1250A > C; CELSR1: c.7640T > C), whose allele frequencies were significantly changed in the high fecundity goat group. Besides, we found that new mutations at these sites altered the hydrophilicity and 3D structure of the protein. Candidate genes related to litter size in this study and their missense mutation sites were identified. These candidate genes are helpful to understand the genetic mechanism of fecundity in Beichuan white goat, and have important significance for future goat breeding.
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Affiliation(s)
- Aimin Zhou
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
| | - Yi Ding
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
| | - Xiaohui Zhang
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Yugang Zhou
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Yadong Liu
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Tingjian Li
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Long Xiao
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
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2
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Wang R, Wang X, Qi Y, Li Y, Na Q, Yuan H, Rong Y, Ao X, Guo F, Zhang L, Liu Y, Shang F, Zhang Y, Wang Y. Genetic diversity analysis of Inner Mongolia cashmere goats (Erlangshan subtype) based on whole genome re-sequencing. BMC Genomics 2024; 25:698. [PMID: 39014331 PMCID: PMC11253418 DOI: 10.1186/s12864-024-10485-x] [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: 03/07/2024] [Accepted: 05/30/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND Inner Mongolia cashmere goat (IMCG), renowned for its superior cashmere quality, is a Chinese indigenous goat breed that has been developed through natural and artificial selection over a long period. However, recently, the genetic resources of IMCGs have been significantly threatened by the introduction of cosmopolitan goat breeds and the absence of adequate breed protection systems. RESULTS In order to assess the conservation effectiveness of IMCGs and efficiently preserve and utilize the purebred germplasm resources, this study analyzed the genetic diversity, kinship, family structure, and inbreeding of IMCGs utilizing resequencing data from 225 randomly selected individuals analyzed using the Plink (v.1.90), GCTA (v.1.94.1), and R (v.4.2.1) software. A total of 12,700,178 high-quality SNPs were selected through quality control from 34,248,064 SNP sites obtained from 225 individuals. The average minor allele frequency (MAF), polymorphic information content (PIC), and Shannon information index (SHI) were 0.253, 0.284, and 0.530, respectively. The average observed heterozygosity (Ho) and the average expected heterozygosity (He) were 0.355 and 0.351, respectively. The analysis of the identity by state distance matrix and genomic relationship matrix has shown that most individuals' genetic distance and genetic relationship are far away, and the inbreeding coefficient is low. The family structure analysis identified 10 families among the 23 rams. A total of 14,109 runs of homozygosity (ROH) were identified in the 225 individuals, with an average ROH length of 1014.547 kb. The average inbreeding coefficient, calculated from ROH, was 0.026 for the overall population and 0.027 specifically among the 23 rams, indicating a low level of inbreeding within the conserved population. CONCLUSIONS The IMCGs exhibited moderate polymorphism and a low level of kinship with inbreeding occurring among a limited number of individuals. Simultaneously, it is necessary to prevent the loss of bloodline to guarantee the perpetuation of the IMCGs' germplasm resources.
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Affiliation(s)
- Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Xinle Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yunpeng Qi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yanbo Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Qin Na
- Inner Mongolia Autonomous Region Agricultural and Animal Husbandry Technology Extension Center, Hohhot, 010010, China
| | - Huiping Yuan
- Bayannur Forestry and Grassland Career Development Center, Bayannur, 015006, China
| | - Youjun Rong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Xiaofang Ao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Furong Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lifei Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yan Liu
- College of Vocational and Technical, Inner Mongolia Agricultural University, Baotou, 014109, China
| | - Fangzheng Shang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, 010018, China.
- Key Laboratory of Goat and Sheep Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, 010018, China.
- Northern Agriculture and Livestock Husbandry Technology Innovation Center, Hohhot, 010018, China.
| | - Yu Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010018, China.
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Kang KM, Kim HY. Effects of Sous-vide Cooking Temperature on Triceps Brachii of Black Goats. Food Sci Anim Resour 2024; 44:861-872. [PMID: 38974722 PMCID: PMC11222698 DOI: 10.5851/kosfa.2024.e23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/03/2024] [Accepted: 03/12/2024] [Indexed: 07/09/2024] Open
Abstract
The aim of this study was to determine the effects of sous-vide cooking temperature on the triceps brachii of black goats. Triceps brachii of black goats (12 months) were sous-vide cooked at 55°C, 60°C, and 65°C. The samples were examined for color, scanning electron microscope photographs, sarcomere length, fiber cross-sectional area, cooking yield, shear force, sensory evaluation, and aromatic profile. The results showed that CIE a*, CIE b*, and chroma increased with increasing sous-vide cooking temperature. However, the cooking yield significantly decreased with increasing sous-vide cooking temperature, and the shear forces of the 60°C and 65°C samples showed no significant differences. For sensory evaluation, the 60°C sample showed the highest scores for flavor, texture, and off-flavor. Furthermore, the 60°C sample showed the significantly lowest value of octadienone (aroma characteristics of metallic) intensity (p<0.05). Therefore, sous-vide cooking of triceps brachii of black goats at 60°C is effective in reducing off-flavor and improving tenderness.
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Affiliation(s)
- Kyu-Min Kang
- Department of Animal Resources Science,
Kongju National University, Yesan 32439, Korea
| | - Hack-Youn Kim
- Department of Animal Resources Science,
Kongju National University, Yesan 32439, Korea
- Resource Science Research Institute,
Kongju National University, Yesan 32439, Korea
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4
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Belay S, Belay G, Nigussie H, Ahbara AM, Tijjani A, Dessie T, Tarekegn GM, Jian-Lin H, Mor S, Woldekiros HS, Dobney K, Lebrasseur O, Hanotte O, Mwacharo JM. Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats. Sci Rep 2024; 14:14908. [PMID: 38942813 PMCID: PMC11213886 DOI: 10.1038/s41598-024-65303-x] [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: 04/12/2023] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. FST, XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes.
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Affiliation(s)
- Shumuye Belay
- Tigray Agricultural Research Institute, Mekelle, Ethiopia.
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia.
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Helen Nigussie
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abulgasim M Ahbara
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Department of Zoology, Misurata University, Misurata, Libya
| | - Abdulfatai Tijjani
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Getinet M Tarekegn
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Institute of Biotechnology (IoB), Addis Ababa University, Addis Ababa, Ethiopia
| | - Han Jian-Lin
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Beijing, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Siobhan Mor
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Helina S Woldekiros
- Department of Anthropology, Washington University in St. Louis, St. Louis, USA
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- University of Sydney, Sydney, Australia
| | - Ophelie Lebrasseur
- Palaeogenomics and Bioarchaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joram M Mwacharo
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia.
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5
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Gebreselase HB, Nigussie H, Wang C, Luo C. Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing. Animals (Basel) 2024; 14:307. [PMID: 38254476 PMCID: PMC10812714 DOI: 10.3390/ani14020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Goats belong to a group of animals called small ruminants and are critical sources of livelihood for rural people. Genomic sequencing can provide information ranging from basic knowledge about goat diversity and evolutionary processes that shape genomes to functional information about genes/genomic regions. In this study, we exploited a whole-genome sequencing data set to analyze the genetic diversity, population structure and selection signatures of 44 individuals belonging to 5 Ethiopian goat populations: 12 Aberegalle (AB), 5 Afar (AF), 11 Begait (BG), 12 Central highlands (CH) and 5 Meafure (MR) goats. Our results revealed the highest genetic diversity in the BG goat population compared to the other goat populations. The pairwise genetic differentiation (FST) among the populations varied and ranged from 0.011 to 0.182, with the closest pairwise value (0.003) observed between the AB and CH goats and a distant correlation (FST = 0.182) between the BG and AB goats, indicating low to moderate genetic differentiation. Phylogenetic tree, ADMIXTURE and principal component analyses revealed a classification of the five Ethiopian goat breeds in accordance with their geographic distribution. We also found three top genomic regions that were detected under selection on chromosomes 2, 5 and 13. Moreover, this study identified different candidate genes related to milk characteristics (GLYCAM1 and SRC), carcass (ZNF385B, BMP-7, PDE1B, PPP1R1A, FTO and MYOT) and adaptive and immune response genes (MAPK13, MAPK14, SCN7A, IL12A, EST1 DEFB116 and DEFB119). In conclusion, this information could be helpful for understanding the genetic diversity and population structure and selection scanning of these important indigenous goats for future genetic improvement and/or as an intervention mechanism.
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Affiliation(s)
- Haile Berihulay Gebreselase
- State Key Laboratory of Swine and Poultry Breeding Industry Guangdong Key Laboratory of Animal Breeding and Nutrition Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Department of Biotechnology, College of Natural and Computational Science, Aksum University, Aksum 1010, Tigray, Ethiopia
| | | | - Changfa Wang
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng 252000, China;
| | - Chenglong Luo
- State Key Laboratory of Swine and Poultry Breeding Industry Guangdong Key Laboratory of Animal Breeding and Nutrition Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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6
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Sood V, Rodas-González A, Valente TS, Virtuoso MCS, Li C, Lam S, López-Campos Ó, Segura J, Basarab J, Juárez M. Genome-wide association study for primal cut lean traits in Canadian beef cattle. Meat Sci 2023; 204:109274. [PMID: 37437385 DOI: 10.1016/j.meatsci.2023.109274] [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: 02/28/2023] [Revised: 06/07/2023] [Accepted: 07/02/2023] [Indexed: 07/14/2023]
Abstract
This study identified genomic variants and underlying candidate genes related to the whole carcass and individual primal cut lean content in Canadian commercial crossbred beef cattle. Genotyping information of 1035 crossbred beef cattle were available alongside estimated and actual carcass lean meat yield and individual primal cut lean content in all carcasses. Significant fixed effects and covariates were identified and included in the animal model. Genome-wide association analysis were implemented using the weighted single-step genomic best linear unbiased prediction (WssGBLUP). A number of candidate genes identified linked to lean tissue production were unrelated to estimated lean meat yield and were specific to the actual lean traits. Among these, 41 genes were common for actual lean traits, on specific regions of BTA4, BTA13 and BTA25 indicating potential involvement in lean mass synthesis. Therefore, the results suggested the inclusion of primal cut lean traits as a selection objective in breeding programs with consideration of further functional studies of the identified genes could help in optimizing lean yield for maximal carcass value.
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Affiliation(s)
- Vipasha Sood
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada; Department of Food and Human Nutritional Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Argenis Rodas-González
- Department of Animal Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Tiago S Valente
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marcos Claudio S Virtuoso
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Changxi Li
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada; Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Stephanie Lam
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Óscar López-Campos
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Jose Segura
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - John Basarab
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Manuel Juárez
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.
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7
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Hu M, Jiang H, Lai W, Shi L, Yi W, Sun H, Chen C, Yuan B, Yan S, Zhang J. Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array. Animals (Basel) 2023; 13:ani13101717. [PMID: 37238146 DOI: 10.3390/ani13101717] [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: 03/08/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.
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Affiliation(s)
- Mingyue Hu
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Hao Jiang
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Wenfeng Yi
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Hao Sun
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Chengzhen Chen
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Bao Yuan
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Jiabao Zhang
- College of Animal Science, Jilin University, Changchun 130062, China
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8
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Du X, Liu Y, He X, Tao L, Fang M, Chu M. Uterus proliferative period ceRNA network of Yunshang black goat reveals candidate genes on different kidding number trait. Front Endocrinol (Lausanne) 2023; 14:1165409. [PMID: 37251683 PMCID: PMC10213787 DOI: 10.3389/fendo.2023.1165409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Pregnancy loss that occurs in the uterus is an important and widespread problem in humans and farm animals and is also a key factor affecting the fecundity of livestock. Understanding the differences in the fecundity of goats may be helpful in guiding the breeding of goats with high fecundity. In this study, we performed RNA sequencing and bioinformatics analysis to study the uterus of Yunshang black goats with high and low fecundity in the proliferative period. We identified mRNAs, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) by analyzing the uterine transcriptomes. The target genes of the identified miRNAs and lncRNAs were predicted, and miRNA-mRNA interaction and competitive endogenous RNA (ceRNA) networks were constructed. By comparisons between low- and high-fecundity groups, we identified 1,674 differentially expressed mRNAs (914 were upregulated, and 760 were downregulated), 288 differentially expressed lncRNAs (149 were upregulated, and 139 were downregulated), and 17 differentially expressed miRNAs (4 were upregulated, and 13 were downregulated). In addition, 49 miRNA-mRNA pairs and 45 miRNA-lncRNA pairs were predicted in the interaction networks. We successfully constructed a ceRNA interaction network with 108 edges that contained 19 miRNAs, 11 mRNAs, and 73 lncRNAs. Five candidate genes (PLEKHA7, FAT2, FN1, SYK, and ITPR2) that were annotated as cell adhesion or calcium membrane channel protein were identified. Our results provide the overall expression profiles of mRNAs, lncRNAs, and miRNAs in the goat uterus during the proliferative period and are a valuable reference for studies into the mechanisms associated with the high fecundity, which may be helpful to guide goat to reduce pregnancy loss.
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Affiliation(s)
- Xiaolong Du
- 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, China
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, Ministry of Agriculture and Rural Affairs (MARA) PRC Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yufang Liu
- 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, China
| | - Xiaoyun 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, China
| | - Lin 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, China
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, Ministry of Agriculture and Rural Affairs (MARA) PRC Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Mingxing 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, China
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9
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Kour A, Deb SM, Nayee N, Niranjan SK, Raina VS, Mukherjee A, Gupta ID, Patil CS. Novel insights into genome-wide associations in Bos indicus reveal genetic linkages between fertility and growth. Anim Biotechnol 2023; 34:39-55. [PMID: 34120566 DOI: 10.1080/10495398.2021.1932520] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bos indicus breed Sahiwal, famous for its optimum performance, has so far been genetically improved for performance traits based on phenotypic records and the genomic knowhow regarding genes, regions and biological processes underlying the complex quantitative traits is lacking. In this context, a Genome-wide Association Study was performed for fertility and growth traits in Sahiwal cattle to shed light on its genomic profile. A total of 46 SNPs were found associated with the traits at genome-wide suggestive threshold of P ≤ 10-4. USP32, LRPPRC, PLA2G10, RRN3 and ASAP1 were identified as putative candidate genes for body weight at different ages. However, several genes mapped for growth traits like GREB1, PLA2G10, RAD51C, BIRC6, TEX14 and PEBP4 had significant physiological underpinnings in determining fertility of the animals. Moreover, Quantitative trait loci (QTL) identification revealed potential overlaps with the already reported QTLs for both fertility and growth for most of the traits. Further, candidate SNP enrichment analysis revealed an enriched biological process for birth weight with a significant reproductive role. Based on the findings, genetic linkages underlying fertility and growth could be discerned in Sahiwal population and may be utilized for improving fertility traits in future.
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Affiliation(s)
- Aneet Kour
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | | | - Nilesh Nayee
- National Dairy Development Board, Anand, Gujarat, India
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10
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Xiong J, Bao J, Hu W, Shang M, Zhang L. Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat. Front Genet 2023; 13:1044017. [PMID: 36685859 PMCID: PMC9852865 DOI: 10.3389/fgene.2022.1044017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.
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Selionova M, Aibazov M, Mamontova T, Malorodov V, Sermyagin A, Zinovyeva N, Easa AA. Genome-wide association study of live body weight and body conformation traits in young Karachai goats. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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12
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Saleh AA, Rashad AMA, Hassanine NNAM, Sharaby MA, Zhao Y. Assessment of hair and cashmere properties and their genetic background of several goat breeds in Southwest China. Sci Rep 2022; 12:11135. [PMID: 35778400 PMCID: PMC9249783 DOI: 10.1038/s41598-022-14441-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/07/2022] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to determine the properties and quality characteristics of hair and cashmere fibres of three goat breeds raised in Southwest China, namely; Dazu black goat (DBG, n = 203; ♂99, ♀104), Inner Mongolia cashmere goat (IMCG, n = 65; 21♂, 44♀) and their first cross (F1, n = 79; 39♂, 40♀). Totals of 5219, 2130 and 2981 fibre samples, from the three breeds respectively, were taken prior to shearing at 32.5 ± 01.25 months of age from four body sites; shoulder, side-portion, abdomen and leg. Breed effect was significant (P < 0.01) for most hair and cashmere properties. IMCG and F1 hair lengths were longer (P < 0.001) with less variable lengths than DBG. Shoulder hair diameters of the three breeds were not different (P > 0.05) but biggest of the side-portion and abdomen sites of DBG were bigger (P > 0.01), however, the biggest (P < 0.001) hair diameter was recorded for the leg site of F1 and the smallest (P > 0.01) for IMCG. IMCG recorded the longest value for cashmere lengths followed by DBG, while F1 recorded the lowest (P = 0.001), whilst F1 recorded the biggest (P = 0.001) diameter whereas no differences existed between parents' breeds. The cortical cell lengths of IMCG and DBG were 94.57 and 86.85 μm without significant difference detected between breeds. Differences between hair length and diameter for body sites of the studied goat breeds were significant (P < 0.01) but between whiteness, cashmere diameter and diameter of cortical cells were not. Sex had no significant effect on all hair/cashmere properties. Quality characteristics of cashmere fibres from IMCG and F1 were better (P < 0.001) than from DBG. Leg hair diameter, curl recovery rate and cashmere diameter were superior in the crossbred F1 compared to pure breed parents, and DBG was superior to IMCG for fibre elasticity and intensity traits. FGF-5 gene was detected as a candidate gene for hair and cashmere traits in IMCG breed. Whilst, KIT gene was found to be associated with coat colour in the studied breeds. Extra investigations to examine more cashmere goat breeds and crosses are needed to discover genetic variability in cashmere production locally and worldwide.
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Affiliation(s)
- Ahmed A Saleh
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City, 11865, Egypt.
| | - Amr M A Rashad
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City, 11865, Egypt
| | - Nada N A M Hassanine
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing, 400715, People's Republic of China
| | - Mahmoud A Sharaby
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City, 11865, Egypt
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing, 400715, People's Republic of China
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13
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Duarte INH, Bessa AFDO, Rola LD, Genuíno MVH, Rocha IM, Marcondes CR, Regitano LCDA, Munari DP, Berry DP, Buzanskas ME. Cross-population selection signatures in Canchim composite beef cattle. PLoS One 2022; 17:e0264279. [PMID: 35363779 PMCID: PMC8975110 DOI: 10.1371/journal.pone.0264279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
Analyses of livestock genomes have been used to detect selection signatures, which are genomic regions associated with traits under selection leading to a change in allele frequency. The objective of the present study was to characterize selection signatures in Canchim composite beef cattle using cross-population analyses with the founder Nelore and Charolais breeds. High-density single nucleotide polymorphism genotypes were available on 395 Canchim representing the target population, along with genotypes from 809 Nelore and 897 Charolais animals representing the reference populations. Most of the selection signatures were co-located with genes whose functions agree with the expectations of the breeding programs; these genes have previously been reported to associate with meat quality, as well as reproductive traits. Identified genes were related to immunity, adaptation, morphology, as well as behavior, could give new perspectives for understanding the genetic architecture of Canchim. Some selection signatures identified genes that were recently introduced in Canchim, such as the loci related to the polled trait.
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Affiliation(s)
| | | | - Luciana Diniz Rola
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
| | | | - Iasmin Marques Rocha
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
| | | | | | - Danísio Prado Munari
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Donagh Pearse Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy Co. Cork., Ireland
| | - Marcos Eli Buzanskas
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
- * E-mail:
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Qiao G, Xu P, Guo T, Wu Y, Lu X, Zhang Q, He X, Zhu S, Zhao H, Lei Z, Sun W, Yang B, Yue Y. Genetic Basis of Dorper Sheep ( Ovis aries) Revealed by Long-Read De Novo Genome Assembly. Front Genet 2022; 13:846449. [PMID: 35480318 PMCID: PMC9035736 DOI: 10.3389/fgene.2022.846449] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Dorper sheep (Ovis aries) (DPS), developed in the 1930s by crossing Dorset Horn and Blackhead Persian sheep in South Africa, is a world-famous composite breed for mutton production. The genetic basis underlying this breed is yet to be elucidated. Here, we report the sequencing and assembly of a highly contiguous Dorper sheep genome via integration of Oxford Nanopore Technology (ONT) sequencing and Hi-C (chromatin conformation capture) approaches. The assembled genome was around 2.64 Gb with a contig N50 of 73.33 Mb and 140 contigs in total. More than 99.5% of the assembled sequences could be anchored to 27 chromosomes and they were annotated with 20,450 protein-coding genes. Allele-specific expression (ASE) genes of Dorper sheep were revealed through ASE analysis and they were involved in the immune system, lipid metabolism, and environmental adaptation. A total of 5,701 and 456 allelic sites were observed in the SNP and indels loci identified from relevant whole-genome resequencing data. These allelic SNP and INDEL sites were annotated in 1,002 and 294 genes, respectively. Moreover, we calculated the number of variant sites and related genes derived from the maternal and paternal ancestors, revealing the genetic basis of outstanding phenotypic performance of Dorper sheep. In conclusion, this study reports the first reference genome of Dorper sheep and reveals its genetic basis through ASE. This study also provides a pipeline for mining genetic information of composite breeds, which has an implication for future hybrid-breeding practices.
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Affiliation(s)
- Guoyan Qiao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, 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
| | - Pan Xu
- 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
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, 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
| | - Yi Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, 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
| | - Xiaofang Lu
- Tianjin Aoqun Animal Husbandry Pty., Ltd., Tianjin, China
- The Enterprises Key Laboratory of Tianjin Meat-Type-Sheep Genetics and Breeding, Tianjin, China
| | - Qingfeng Zhang
- Tianjin Aoqun Animal Husbandry Pty., Ltd., Tianjin, China
- The Enterprises Key Laboratory of Tianjin Meat-Type-Sheep Genetics and Breeding, Tianjin, China
| | - Xue He
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shaohua Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, 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
| | - Hongchang Zhao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, 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
| | - Zhihui Lei
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, 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
| | - Weibo Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, 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
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, 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
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, 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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15
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Gu B, Sun R, Fang X, Zhang J, Zhao Z, Huang D, Zhao Y, Zhao Y. Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats. Animals (Basel) 2022; 12:ani12050548. [PMID: 35268118 PMCID: PMC8908837 DOI: 10.3390/ani12050548] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Body conformation traits are economically important in the goat meat industry. Good growth performance in goats, including an accelerated growth rate, can improve carcass weight and meat yield. The identification of genetic variants associated with these traits provides a basis for the genetic improvement of growth performance. In this study, we measured six body conformation traits, including body height, body length, cannon circumference, chest depth, chest width, and heart girth. By a genome-wide association study of a Chinese meat goat breed, 53 significant single nucleotide polymorphisms and 42 candidate genes associated with these traits were detected. These findings improve our understanding of the genetic basis of body conformation traits in goats. Abstract Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats (DBGs), a Chinese indigenous goat breed. In particular, 150 DBGs were genotyped by whole-genome sequencing, and six body conformation traits, including body height (BH), body length (BL), cannon circumference (CC), chest depth (CD), chest width (CW), and heart girth (HG), were examined. In total, 53 potential SNPs were associated with these body conformation traits. A bioinformatics analysis was performed to evaluate the genes located close to the significant SNPs. Finally, 42 candidate genes (e.g., PSTPIP2, C7orf57, CCL19, FGF9, SGCG, FIGN, and SIPA1L) were identified as components of the genetic architecture underlying body conformation traits. Our results provide useful biological information for the improvement of growth performance and have practical applications for genomic selection in goats.
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Affiliation(s)
- Bowen Gu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Ruifan Sun
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Xingqiang Fang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Jipan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Zhongquan Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Deli Huang
- Tengda Animal Husbandry Co., Ltd., Chongqing 402360, China;
| | - Yuanping Zhao
- Dazu County Agriculture and Rural Committee, Chongqing 402360, China;
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
- Correspondence:
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16
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Ma J, Gao X, Li J, Gao H, Wang Z, Zhang L, Xu L, Gao H, Li H, Wang Y, Zhu B, Cai W, Wang C, Chen Y. Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array. Animals (Basel) 2021; 11:ani11123469. [PMID: 34944246 PMCID: PMC8698132 DOI: 10.3390/ani11123469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.
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Affiliation(s)
- Jun Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Zezhao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Han Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Hongwei Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Yahui Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Bo Zhu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Congyong Wang
- Beijing Lianyu Beef Cattle Breeding Technology Limited Company, Beijing 100193, China;
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
- Correspondence:
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17
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Tsartsianidou V, Sánchez-Molano E, Kapsona VV, Basdagianni Z, Chatziplis D, Arsenos G, Triantafyllidis A, Banos G. A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep. Genet Sel Evol 2021; 53:90. [PMID: 34856922 PMCID: PMC8641236 DOI: 10.1186/s12711-021-00682-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 02/07/2023] Open
Abstract
Background The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change. Results We detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h2 = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response. Conclusions Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00682-7.
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Affiliation(s)
- Valentina Tsartsianidou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
| | - Enrique Sánchez-Molano
- Division of Genetics and Genomics, School of Veterinary Studies, The Roslin Institute and Royal (Dick), University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Vanessa Varvara Kapsona
- Department of Animal and Veterinary Sciences, Scotland's Rural College, Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, UK
| | - Zoitsa Basdagianni
- Department of Animal Production, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dimitrios Chatziplis
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agriculture, International Hellenic University, Alexander Campus, 57400, Sindos, Greece
| | - Georgios Arsenos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Georgios Banos
- Department of Animal and Veterinary Sciences, Scotland's Rural College, Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, UK.,Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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18
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Detection of 15-bp Deletion Mutation within PLAG1 Gene and Its Effects on Growth Traits in Goats. Animals (Basel) 2021; 11:ani11072064. [PMID: 34359192 PMCID: PMC8300177 DOI: 10.3390/ani11072064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Goats have always served as an important domesticated livestock. PLAG1 is a major gene that affects the stature and growth of animals. Body size traits are very important for goats as it directly affects the economic characteristics of meat and cashmere production. This study showed that the 15-base pair (bp) InDel (rs637141549) can significantly affect growth traits such as body weight, height, height at hip cross, chest circumference, hip width and body index of goats through the detection of large samples (n = 1581) in four indigenous breeds. Accordingly, it is suggested that the deletion mutation can be used as a potential molecular marker that significantly affects goat growth traits. Moreover, the 15bp deletion mutation can be used as a potential molecular marker, which significantly affects the growth traits of goats and plays an important role in animal husbandry production. Abstract Stature and weight are important growth and development traits for animals, which also significantly affect the productivity of livestock. Polymorphic adenoma gene 1 (PLAG1) is located in the growth-related quantitative trait nucleotides (QTN), and its variation has been determined to significantly affect the body stature of bovines. This study found that novel 15-bp InDel could significantly influence important growth traits in goats. The frequencies of genotypes of the 15-bp mutation and relationship with core growth traits such as body weight, body height, height at hip cross, chest circumference, hip width and body index were explored in 1581 individuals among 4 Chinese native goat breeds. The most frequent genotypes of Shaanbei white Cashmere goat (SWCG), Inner Mongolia White Cashmere goat (IMCG) and Guanzhong Dairy goat (GZDG) were II genotypes (insertion/insertion), and the frequency of ID genotype (insertion/deletion) was found to be slightly higher than that of II genotype in Hainan Black goat (HNBG), showing that the frequency of the I allele was higher than that of the D allele. In adult goats, there were significant differences between 15-bp variation and body weight, chest circumference and body height traits in SWCG (p < 0.05). Furthermore, the locus was also found to be significantly correlated with the body index of HNBG (p = 0.044) and hip width in GZDG (p = 0.002). In regard to lambs, there were significant differences in height at the hip cross of SWCG (p = 0.036) and hip width in IMWC (p = 0.005). The corresponding results suggest that the 15-bp InDel mutation of PLAG1 is associated with the regulation of important growth characteristics of both adult and lamb of goats, which may serve as efficient molecular markers for goat breeding.
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Bao Z, Li C, Guo C, Xiang Z. Convergent Evolution of Himalayan Marmot with Some High-Altitude Animals through ND3 Protein. Animals (Basel) 2021; 11:ani11020251. [PMID: 33498455 PMCID: PMC7909448 DOI: 10.3390/ani11020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 11/16/2022] Open
Abstract
The Himalayan marmot (Marmota himalayana) mainly lives on the Qinghai-Tibet Plateau and it adopts multiple strategies to adapt to high-altitude environments. According to the principle of convergent evolution as expressed in genes and traits, the Himalayan marmot might display similar changes to other local species at the molecular level. In this study, we obtained high-quality sequences of the CYTB gene, CYTB protein, ND3 gene, and ND3 protein of representative species (n = 20) from NCBI, and divided them into the marmot group (n = 11), the plateau group (n = 8), and the Himalayan marmot (n = 1). To explore whether plateau species have convergent evolution on the microscale level, we built a phylogenetic tree, calculated genetic distance, and analyzed the conservation and space structure of Himalayan marmot ND3 protein. The marmot group and Himalayan marmots were in the same branch of the phylogenetic tree for the CYTB gene and CYTB protein, and mean genetic distance was 0.106 and 0.055, respectively, which was significantly lower than the plateau group. However, the plateau group and the Himalayan marmot were in the same branch of the phylogenetic tree, and the genetic distance was only 10% of the marmot group for the ND3 protein, except Marmota flaviventris. In addition, some sites of the ND3 amino acid sequence of Himalayan marmots were conserved from the plateau group, but not the marmot group. This could lead to different structures and functional diversifications. These findings indicate that Himalayan marmots have adapted to the plateau environment partly through convergent evolution of the ND3 protein with other plateau animals, however, this protein is not the only strategy to adapt to high altitudes, as there may have other methods to adapt to this environment.
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Affiliation(s)
| | | | - Cheng Guo
- Correspondence: (C.G.); (Z.X.); Tel.: +86-731-5623392 (C.G. & Z.X.); Fax: +86-731-5623498 (C.G. & Z.X.)
| | - Zuofu Xiang
- Correspondence: (C.G.); (Z.X.); Tel.: +86-731-5623392 (C.G. & Z.X.); Fax: +86-731-5623498 (C.G. & Z.X.)
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Whole Genome Sequencing Reveals the Effects of Recent Artificial Selection on Litter Size of Bamei Mutton Sheep. Animals (Basel) 2021; 11:ani11010157. [PMID: 33445473 PMCID: PMC7827510 DOI: 10.3390/ani11010157] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Bamei mutton sheep is a Chinese domestic sheep breed developed by crossing German Mutton Merino sheep and indigenous Mongolian sheep for meat production. There is large variation in the reproductive abilities of Bamei mutton sheep. After recent artificial selection, the average lambing rate of the Bamei mutton nucleus group was over 150%. We used the FST (Fixation Index) and XP-EHH (The Cross-Population Extended Haplotype Homozygosity) statistical approach to detect the selective sweeps between high- and low-fecundity Bamei mutton sheep groups. JUN (JUN proto-oncogene, AP-1 transcription factor subunit), ITPR3 (inositol 1,4,5-trisphosphate receptor type 3, PLCB2 (phospholipase C beta 2), HERC5 (HECT and RLD domain containing E3 ubiquitin protein ligase 5), and KDM4B (lysine demethylase 4B) were detected that are potential responsible for litter size. These observations provide a new opportunity to research the genetic variation influencing fecundity traits within a population evolving under artificial selection. Abstract Bamei mutton sheep is a Chinese domestic sheep breed developed by crossing German Mutton Merino sheep and indigenous Mongolian sheep for meat production. Here, we focused on detecting candidate genes associated with the increasing of the litter size in this breeds under recent artificial selection to improve the efficiency of mutton production. We selected five high- and five low-fecundity Bamei mutton sheep for whole-genome resequencing to identify candidate genes for sheep prolificacy. We used the FST and XP-EHH statistical approach to detect the selective sweeps between these two groups. Combining the two selective sweep methods, the reproduction-related genes JUN, ITPR3, PLCB2, HERC5, and KDM4B were detected. JUN, ITPR3, and PLCB2 play vital roles in GnRH (gonadotropin-releasing hormone), oxytocin, and estrogen signaling pathway. Moreover, KDM4B, which had the highest FST value, exhibits demethylase activity. It can affect reproduction by binding the promoters of estrogen-regulated genes, such as FOXA1 (forkhead box A1) and ESR1 (estrogen receptor 1). Notably, one nonsynonymous mutation (p.S936A) specific to the high-prolificacy group was identified at the TUDOR domain of KDM4B. These observations provide a new opportunity to research the genetic variation influencing fecundity traits within a population evolving under artificial selection. The identified genomic regions that are responsible for litter size can in turn be used for further selection.
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Wang K, Liu X, Qi T, Hui Y, Yan H, Qu L, Lan X, Pan C. Whole-genome sequencing to identify candidate genes for litter size and to uncover the variant function in goats (Capra hircus). Genomics 2020; 113:142-150. [PMID: 33276007 DOI: 10.1016/j.ygeno.2020.11.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/28/2020] [Accepted: 11/26/2020] [Indexed: 01/23/2023]
Abstract
To select candidate genes for goat prolificacy, we managed six multi- and six single-kid female goats at the same feeding level and in the same management mode over a 4-year period. These goats showed stable differences in litter size over five continuous parturition records. Whole-genome re-sequencing was used in all 12 to select candidate genes, namely, AURKA, ENDOG, SOX2, RORA, GJA10, RXFP2, CDC25C, and NANOS3, by the strength of their differentiation signals. Most of the selected genes were enriched in the coiled coil process and ovarian development, which suggests that the coiled coil process has a potential regulatory effect on fecundity. Detection of the distribution of variants and association analyses with litter size in 400 goats showed that NANOS3 exon mutations may lead to a transformation of the protein structure. The variation in CDC25C, ENDOG, and NANOS3 showed a significant association with litter size. These results can contribute to the improvement of reproduction traits in the artificial breeding of goats.
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Affiliation(s)
- Ke Wang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China
| | - Xinfeng Liu
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China
| | - Tang Qi
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China
| | - Yiqing Hui
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China
| | - Hailong Yan
- Department of Neurology, Institute of Brain Science, Medical School, Shanxi Datong University, Datong 037000, China
| | - Lei Qu
- Life Science Research Center, Yulin University, Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin 719000, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China.
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China.
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Genetic Signatures of Selection for Cashmere Traits in Chinese Goats. Animals (Basel) 2020; 10:ani10101905. [PMID: 33080940 PMCID: PMC7603090 DOI: 10.3390/ani10101905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cashmere goats are a unique husbandry resource in China. These goats are well known for producing the highest cashmere yield and best fiber quality in the world. Although cashmere is highly valued and also known as “fiber gem” and “soft gold”, few studies have examined the genetic basis of cashmere traits in cashmere goats. Here, we identified selection signals by comparing Fst and XP-EHH (the cross population extend haplotype homozygosity test) of a non-cashmere breed (Huanghuai goat) with those of two cashmere breeds (Inner Mongolia and Liaoning cashmere goats). Two genes (WNT10A and CSN3) were potentially associated with cashmere traits. This information may be valuable for studying the genetic uniqueness of cashmere goats and elucidating the mechanisms underlying cashmere traits in cashmere goats. Abstract Inner Mongolia and Liaoning cashmere goats in China are well-known for their cashmere quality and yield. Thus, they are great models for identifying genomic regions associated with cashmere traits. Herein, 53 Inner Mongolia cashmere goats, Liaoning cashmere goats and Huanghuai goats were genotyped, and 53,347 single-nucleotide polymorphisms (SNPs) were produced using the Illumina Caprine 50K SNP chip. Additionally, we identified some positively selected SNPs by analyzing Fst and XP-EHH. The top 5% of SNPs had selection signatures. After gene annotation, 222 and 173 candidate genes were identified in Inner Mongolia and Liaoning cashmere goats, respectively. Several genes were related to hair follicle development, such as TRPS1, WDR74, LRRC14, SPTLC3, IGF1R, PADI2, FOXP1, WNT10A and CSN3. Gene enrichment analysis of these cashmere trait-associated genes related 67 enriched signaling pathways that mainly participate in hair follicle development and stem cell pluripotency regulation. Furthermore, we identified 20 overlapping genes that were selected in both cashmere goat breeds. Among these overlapping genes, WNT10A and CSN3, which are associated with hair follicle development, are potentially involved in cashmere production. These findings may improve molecular breeding of cashmere goats in the future.
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Tao L, He XY, Jiang YT, Lan R, Li M, Li ZM, Yang WF, Hong QH, Chu MX. Combined approaches to reveal genes associated with litter size in Yunshang black goats. Anim Genet 2020; 51:924-934. [PMID: 32986880 DOI: 10.1111/age.12999] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 01/25/2023]
Abstract
Intensive artificial selection has been imposed in Yunshang black goats, the first black specialist mutton goat breed in China, with a breeding object of improving reproductive performance, which has contributed to reshaping of the genome including the characterization of SNP, ROH and haplotype. However, variation in reproductive ability exists in the present population. A WGS was implemented in two subpopulations (polytocous group, PG, and monotocous group, MG) with evident differences of litter size. Following the mapping to reference genome, and SNP calling and pruning, three approaches - GWAS, ROH analysis and detection of signatures of selection - were employed to unveil candidate genes responsible for litter size. Consequently, 12 candidate genes containing OSBPL8 with the minimum P-value were uncovered by GWAS. Differences were observed in the pattern of ROH between two subpopulations that shared similar low inbreeding coefficients. Two ROH hotspots and 12 corresponding genes emerged from ROH pool association analysis. Based on the nSL statistic, 15 and 61 promising genes were disclosed under selection for MG and PG respectively. Of them, some promising genes participate in ovarian function (PPP2R5C, CDC25A, ESR1, RPS26 and SERPINBs), seasonal reproduction (DIO3, BTG1 and CRYM) and metabolism (OSBPL8, SLC39A5 and SERPINBs). Our study pinpointed some novel promising genes influencing litter size, provided a comprehensive insight into genetic makeup of litter size and might facilitate selective breeding in goats.
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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
| | - Y T Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, China
| | - R Lan
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, China
| | - M Li
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Z M Li
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - W F Yang
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Q H Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, 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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Conservation Assessment of the State Goat Farms by Using SNP Genotyping Data. Genes (Basel) 2020; 11:genes11060652. [PMID: 32545749 PMCID: PMC7349881 DOI: 10.3390/genes11060652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/10/2023] Open
Abstract
Conservation of genetic resources is of great concern globally to maintain genetic diversity for sustainable food security. Comprehensive identification of the breed composition, estimation of inbreeding and effective population size are essential for the effective management of farm animal genetic resources and to prevent the animals from genetic erosion. The Zhongwei male (ZWM), Arbas Cashmere male (ACM) and Jining Grey male (JGM) goats are conserved in three different state goat farms in China but their family information, level of inbreeding and effective population size are unknown. We investigated the genomic relationship, inbreeding coefficient and effective population size in these three breeds from three state goat farms using the Illumina goat SNP50 BeadChip. Genomic relationships and phylogenetic analysis revealed that the breeds are clearly separated and formed separate clusters based on their genetic relationship. We obtained a high proportion of informative SNPs, ranging from 91.8% in the Arbas Cashmere male to 96.2% in the Jining Grey male goat breeds with an average mean of 96.8%. Inbreeding, as measured by FROH, ranged from 1.79% in ZWM to 8.62% in ACM goat populations. High FROH values, elevated genomic coverage of very long ROH (>30 Mb) and severe decline in effective population size were recorded in ACM goat farm. The existence of a high correlation between FHOM and FROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. The Ne estimates 13 generations ago were 166, 69 and 79 for ZWM, ACM and JGM goat farm, respectively indicating that these goat breeds were strongly affected by selection pressure or genetic drift. This study provides insight into the genomic relationship, levels of inbreeding and effective population size in the studied goat populations conserved in the state goat farms which will be valuable in prioritizing populations for conservation and for developing suitable management practices for further genetic improvement of these Chinese male goats.
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Genome-wide association analysis reveals the genetic locus for high reproduction trait in Chinese Arbas Cashmere goat. Genes Genomics 2020; 42:893-899. [PMID: 32506265 DOI: 10.1007/s13258-020-00937-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Litter size is the most important reproductive trait which plays a crucial role in goat production. Therefore, improvement of litter size trait has been of increasing interest in goat industry as small improvement in litter size may lead to large profit. The recent Cashmere goat breeding program produced a high-reproductive genetic line of Arbas Cashmere goat. But the genetic mechanism of high reproduction rate remains largely unknown in this Chinese native goat breed. To address this question, we performed a genome-wide association studies (GWAS) using two groups of goats varying in fecundity. OBJECTIVES Our study was aimed to investigate the significant SNPs and genes associated with high reproduction trait in Inner Mongolia Arbas Cashmere Goat. METHODS We used logistic model association to perform GWAS using 47 goats from high fecundity group (~ 190%) and 314 goats from low fecundity group (~ 130%) of the Arbas Cashmere goat breed. RESULTS We identified 66 genomic regions associated with genome wide significant level wherein six loci were found to be associated with reproduction traits. Further analysis showed that five key candidate genes including KISS1, KHDRBS2, WNT10B, SETDB2 and PPP3CA genes are involved in goat fecundity trait. Gene ontology enrichment analysis revealed that several biological pathways could be involved in the variation of fecundity in female goats. CONCLUSIONS The identified significant SNPs or genes provide useful information about the underlying genetic control of fecundity trait which will be helpful to use them in goat breeding programs for improving the reproductive efficiency of goats.
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Chen Q, Wang Z, Sun J, Huang Y, Hanif Q, Liao Y, Lei C. Identification of Genomic Characteristics and Selective Signals in a Du'an Goat Flock. Animals (Basel) 2020; 10:E994. [PMID: 32517248 PMCID: PMC7341327 DOI: 10.3390/ani10060994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/21/2022] Open
Abstract
The Du'an goat is one of the most important farm animals in the Guangxi Autonomous Region of China, but the genetic basis underlying its adaptive traits has still not been investigated. Firstly, in this study, the genomes of 15 Du'an goats from a breeding farm were sequenced (mean depth: 9.50X) to analyze the patterns of genetic variation. A comparable diversity (17.3 million single nucleotide polymorphisms and 2.1 million indels) was observed to be associated with a lower runs of homozygosity-based inbreeding coefficient and smaller effective population size in comparison with other breeds. From selective sweep and gene set enrichment analyses, we revealed selective signals related to adaptive traits, including immune resistance (serpin cluster, INFGR1, TLR2, and immune-related pathways), body size (HMGA2, LCOR, ESR1, and cancer-related pathways) and heat tolerance (MTOR, ABCG2, PDE10A, and purine metabolism pathway). Our findings uncovered the unique diversity at the genomic level and will provide the opportunities for improvement of productivity in the Du'an goat.
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Affiliation(s)
- Qiuming Chen
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (Q.C.); (Z.W.); (J.S.); (Y.H.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China;
| | - Zihao Wang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (Q.C.); (Z.W.); (J.S.); (Y.H.)
| | - Junli Sun
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (Q.C.); (Z.W.); (J.S.); (Y.H.)
| | - Yingfei Huang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (Q.C.); (Z.W.); (J.S.); (Y.H.)
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad 577, Pakistan;
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan
| | - Yuying Liao
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; (Q.C.); (Z.W.); (J.S.); (Y.H.)
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China;
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Pick JL, Hatakeyama M, Ihle KE, Gasparini J, Haussy C, Ishishita S, Matsuda Y, Yoshimura T, Kanaoka MM, Shimizu‐Inatsugi R, Shimizu KK, Tschirren B. Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation. Evol Lett 2020; 4:200-211. [PMID: 32547781 PMCID: PMC7293072 DOI: 10.1002/evl3.166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/23/2020] [Accepted: 02/18/2020] [Indexed: 11/06/2022] Open
Abstract
The trade-off between reproduction and self-maintenance is a cornerstone of life history theory, yet its proximate underpinnings are elusive. Here, we used an artificial selection approach to create replicated lines of Japanese quail (Coturnix japonica) that differ genetically in their reproductive investment. Whole transcriptome sequencing revealed that females from lines selected for high reproductive output show a consistent upregulation of genes associated with reproduction but a simultaneous downregulation of immune genes. Concordant phenotypic differences in immune function (i.e., specific antibody response against keyhole limpet hemocyanin) were observed between the selection lines, even in males who do not provide parental care. Our findings demonstrate the key role of obligate transcriptional constraints in the maintenance of life history variation. These constraints set fundamental limits to productivity and health in natural and domestic animal populations.
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Affiliation(s)
- Joel L. Pick
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich8057Switzerland
- School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyAustralia
- Current Address: Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUnited Kingdom
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich8057Switzerland
- Functional Genomics Center ZurichZurich8057Switzerland
| | - Kate E. Ihle
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich8057Switzerland
| | - Julien Gasparini
- Laboratoire Ecologie and Evolution UMR 7625Université Pierre et Marie Curie CNRS ENSParisFrance
| | - Claudy Haussy
- Laboratoire Ecologie and Evolution UMR 7625Université Pierre et Marie Curie CNRS ENSParisFrance
| | - Satoshi Ishishita
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoya464–8602Japan
| | - Yoichi Matsuda
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoya464–8602Japan
| | - Takashi Yoshimura
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoya464–8602Japan
| | | | - Rie Shimizu‐Inatsugi
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich8057Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich8057Switzerland
- Kihara Institute for Biological ResearchYokohama City UniversityYokohama244–0813Japan
| | - Barbara Tschirren
- Centre for Ecology and ConservationUniversity of ExeterPenrynTR10 9FEUnited Kingdom
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Wang JJ, Zhang T, Chen QM, Zhang RQ, Li L, Cheng SF, Shen W, Lei CZ. Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat. Front Genet 2020; 11:286. [PMID: 32273886 PMCID: PMC7113370 DOI: 10.3389/fgene.2020.00286] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/09/2020] [Indexed: 12/28/2022] Open
Abstract
Litter size (LS), an important economic trait in livestock, is so complicate that involves many aspects of reproduction, the underlying mechanism of which particularly in goat has always been scanty. To uncover the genetic basis of LS, the genomic sequence of Jining Gray goat groups (one famous breed for high prolificacy in China) with LS 1, 2, and 3 for firstborn was analyzed, obtaining 563.67 Gb sequence data and a total of 31,864,651 high-quality single nucleotide polymorphisms loci were identified. Particularly, the increased heterozygosity in higher LS groups, and large continuous homozygous segments associated with lower LS group had been uncovered. Through an integrated analysis of three popular methods for detecting selective sweeps (Fst, nucleotide diversity, and Tajima’s D statistic), 111 selected regions and 42 genes associated with LS were scanned genome wide. The candidate genes with highest selective signatures included KIT, KCNH7, and KMT2E in LS2 and PAK1, PRKAA1, and SMAD9 in LS3 group, respectively. Meanwhile, functional terms of programmed cell death involved in cell development and regulation of insulin receptor signaling pathway were mostly enriched with 42 candidate genes, which also included reproduction related terms of steroid metabolic process and cellular response to hormone stimulus. In conclusion, our study identified novel candidate genes involving in regulation of LS in goat, which expand our understanding of genetic fundament of reproductive ability, and the novel insights regarding to LS would be potentially applied to improve reproductive performance.
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Affiliation(s)
- Jun-Jie Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Teng Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Qiu-Ming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Rui-Qian Zhang
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lan Li
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Shun-Feng Cheng
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Wei Shen
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chu-Zhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Guo J, Zhong J, Li L, Zhong T, Wang L, Song T, Zhang H. Comparative genome analyses reveal the unique genetic composition and selection signals underlying the phenotypic characteristics of three Chinese domestic goat breeds. Genet Sel Evol 2019; 51:70. [PMID: 31771503 PMCID: PMC6880376 DOI: 10.1186/s12711-019-0512-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/15/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND As one of the important livestock species around the world, goats provide abundant meat, milk, and fiber to fulfill basic human needs. However, the genetic loci that underlie phenotypic variations in domestic goats are largely unknown, particularly for economically important traits. In this study, we sequenced the whole genome of 38 goats from three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) and downloaded the genome sequence data of 30 goats from five other breeds (four non-Chinese and one Chinese breed) and 21 Bezoar ibexes to investigate the genetic composition and selection signatures of the Chinese goat breeds after domestication. RESULTS Based on population structure analysis and FST values (average FST = 0.22), the genetic composition of Chengdu Brown goats differs considerably from that of Bezoar ibexes as a result of geographic isolation. Strikingly, the genes under selection that we identified in Tibetan Cashmere goats were significantly enriched in the categories hair growth and bone and nervous system development, possibly because they are involved in adaptation to high-altitude. In particular, we found a large difference in allele frequency of one novel SNP (c.-253G>A) in the 5'-UTR of FGF5 between Cashmere goats and goat breeds with short hair. The mutation at this site introduces a start codon that results in the occurrence of a premature FGF5 protein and is likely a natural causal variant that is involved in the long hair phenotype of cashmere goats. The haplotype tagged with the AGG-allele in exon 12 of DSG3, which encodes a cell adhesion molecule that is expressed mainly in the skin, was almost fixed in Tibetan Cashmere goats, whereas this locus still segregates in the lowland goat breeds. The pigmentation gene KITLG showed a strong signature of selection in Tibetan Cashmere goats. The genes ASIP and LCORL were identified as being under positive selection in Jintang Black goats. CONCLUSIONS After domestication, geographic isolation of some goat breeds has resulted in distinct genetic structures. Furthermore, our work highlights several positively selected genes that likely contributed to breed-related traits in domestic goats.
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Affiliation(s)
- Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jie Zhong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Tao Zhong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Linjie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Tianzeng Song
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850009 China
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
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30
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E G, Zhou D, Yang B, Duan X, Na R, Han Y, Zeng Y. Association analysis of sixty‐seven single nucleotide polymorphisms with litter size in Dazu Black goats. Anim Genet 2019; 51:151-152. [DOI: 10.1111/age.12879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Guang‐Xin E
- College of Animal Science and Technology Southwest University No. 2 Tiansheng Road Chongqing 400715 China
| | - Dong‐Ke Zhou
- College of Animal Science and Technology Southwest University No. 2 Tiansheng Road Chongqing 400715 China
| | - Bai‐Gao Yang
- College of Animal Science and Technology Southwest University No. 2 Tiansheng Road Chongqing 400715 China
| | - Xing‐Hai Duan
- College of Animal Science and Technology Southwest University No. 2 Tiansheng Road Chongqing 400715 China
| | - Ri‐Su Na
- College of Animal Science and Technology Southwest University No. 2 Tiansheng Road Chongqing 400715 China
| | - Yan‐Guo Han
- College of Animal Science and Technology Southwest University No. 2 Tiansheng Road Chongqing 400715 China
| | - Yan Zeng
- College of Animal Science and Technology Southwest University No. 2 Tiansheng Road Chongqing 400715 China
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31
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Abstract
Genome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. In this study, we identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. The sizes of ROH events varied considerably ranging from 0.5 to 66 Mb, with an average length of 1.22 Mb. The highest average proportion of the genome covered by ROH (~11.54% of the cattle genome) was found in Nanda cattle (NDC) from South China, whereas the lowest average proportion (~3.1%) was observed in Yanhuang cattle (YHC). The average estimated FROH ranged from 0.03 in YHC to 0.12 in NDC. For each of three ROH classes with different sizes (Small 0.5-1 Mb, Medium 1-5 Mb and Large >5 Mb), the numbers and total lengths of ROH per individual showed considerable differences across breeds. Moreover, we obtained 993 to 3603 ROH hotspots (which were defined where ROH frequency at a SNP within each breed exceeded the 1% threshold) among eight cattle breeds. Our results also revealed several candidate genes embedded with ROH hotspots which may be related to environmental conditions and local adaptation. In conclusion, we generated baselines for homozygosity patterns in diverse Chinese cattle breeds. Our results suggested that selection has, at least partially, played a role with other factors in shaping the genomic patterns of ROH in Chinese local cattle and might provide valuable insights for understanding the genetic basis of economic and adaptive traits.
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32
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Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds. Genes (Basel) 2019; 10:genes10110938. [PMID: 31744198 PMCID: PMC6895971 DOI: 10.3390/genes10110938] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/09/2019] [Accepted: 11/13/2019] [Indexed: 11/16/2022] Open
Abstract
Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.
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33
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Ling YH, Zheng Q, Li YS, Sui MH, Wu H, Zhang YH, Chu MX, Ma YH, Fang FG, Xu LN. Identification of lncRNAs by RNA Sequencing Analysis During in Vivo Pre-Implantation Developmental Transformation in the Goat. Front Genet 2019; 10:1040. [PMID: 31708972 PMCID: PMC6823246 DOI: 10.3389/fgene.2019.01040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/30/2019] [Indexed: 11/15/2022] Open
Abstract
Pre-implantation development is a dynamic, complex and precisely regulated process that is critical for mammalian development. There is currently no description of the role of the long noncoding RNAs (lncRNAs) during the pre-implantation stages in the goat. The in vivo transcriptomes of oocytes (n = 3) and pre-implantation stages (n=19) at seven developmental stages in the goat were analyzed by RNA sequencing (RNA-Seq). The major zygotic gene activation (ZGA) event was found to occur between the 8- and 16-cell stages in the pre-implantation stages. We identified 5,160 differentially expressed lncRNAs (DELs) in developmental stage comparisons and functional analyses of the major and minor ZGAs. Fourteen lncRNA modules were found corresponding to specific pre-implantation developmental stages by weighted gene co-expression network analysis (WGCNA). A comprehensive analysis of the lncRNAs at each developmental transition of high correlation modules was done. We also identified lncRNA-mRNA networks and hub-lncRNAs for the high correlation modules at each stage. The extensive association of lncRNA target genes with other embryonic genes suggests an important regulatory role for lncRNAs in embryonic development. These data will facilitate further exploration of the role of lncRNAs in the developmental transformation in the pre-implantation stage.
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Affiliation(s)
- Ying-Hui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei, China
| | - Qi Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei, China
| | - Yun-Sheng Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei, China
| | - Meng-Hua Sui
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei, China
| | - Hao Wu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei, China
| | - Yun-Hai Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei, China
| | - Ming-Xing Chu
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue-Hui Ma
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fu-Gui Fang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei, China
| | - Li-Na Xu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
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34
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E GX, Duan XH, Zhang JH, Huang YF, Zhao YJ, Na RS, Zhao ZQ, Ma YH, Chu MX, Basang WD, Zhu YB, An TW, Luo XL, Han YG, Zeng Y. Genome-wide selection signatures analysis of litter size in Dazu black goats using single-nucleotide polymorphism. 3 Biotech 2019; 9:336. [PMID: 31475088 DOI: 10.1007/s13205-019-1869-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 08/12/2019] [Indexed: 11/24/2022] Open
Abstract
Litter size is considered to be the most important index for estimating domestic animal productivity. The number of indigenous goats in China with higher litter sizes than those of commercial breeds in other countries may be helpful for accelerating genetic improvements in goat breeding. We performed a genome-wide selective sweep analysis of 31 Dazu black goats with extreme standard deviation in litter size within the third fetus to identify significant genomic regions and candidate genes through different analyses. The analysis identified a total of 33,917,703 variants, including 32,262,179 SNPs and 1,655,524 indels. In addition, two novel candidate genes (LRP1B and GLRB), which are related to litter size, were obtained with π, Tajima's D, πA/πB, and F ST at the individual level with a 95% threshold for each parameter. These two genes were annotated in five GO terms (localization, binding, macromolecular complex, membrane part, and membrane) and two pathways (long-term depression and neuroactive ligand-receptor interaction pathway). Regarding the result of linkage disequilibrium (LD) analysis, in LRP1B and GRID2, the high-yield Dazu black goats exhibit significantly different LD patterns from low-yield goats. Litter size variability has low heritability and is related to multiple complex factors found in domestic animals. Obtaining a clear explanation and significant signal by genome-wide selective sweep analysis with a small sample size is difficult. However, we investigated some candidate genes, particularly LRP1B and GLRB, which may provide useful information for further research.
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Affiliation(s)
- Guang-Xin E
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xing-Hai Duan
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Jia-Hua Zhang
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yong-Fu Huang
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yong-Ju Zhao
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Ri-Su Na
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Zhong-Quan Zhao
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yue-Hui Ma
- 2Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193 China
| | - Ming-Xing Chu
- 2Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193 China
| | - Wang-Dui Basang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husandry Science, Lasa, 850009 China
| | - Yan-Bin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husandry Science, Lasa, 850009 China
| | - Tian-Wu An
- 4Sichuan Academy of Grassland Sciences, Chengdu, 611731 Sichuan China
| | - Xiao-Lin Luo
- 4Sichuan Academy of Grassland Sciences, Chengdu, 611731 Sichuan China
| | - Yan-Guo Han
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yan Zeng
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
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35
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Jiang L, Bi D, Ding H, Ren Q, Wang P, Kan X. Identification and comparative profiling of gonadal microRNAs in the adult pigeon ( Columba livia). Br Poult Sci 2019; 60:638-648. [PMID: 31343256 DOI: 10.1080/00071668.2019.1639140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1. MicroRNAs are small noncoding RNA molecules that play crucial roles in gene expression. However, the comparative profiling of testicular and ovarian microRNAs in birds are rarely reported, particularly in pigeon.2. In this study, Illumina next-generation sequencing technology was used to sequence miRNA libraries of the gonads from six healthy adult utility pigeons. A total of 344 conserved known miRNAs and 32 novel putative miRNAs candidates were detected. Compared with those of ovaries, 130 differentially expressed (DE) miRNAs were identified in the testes. Among them, 70 miRNAs showed down-regulation in the ovaries, while another 60 miRNAs were up-regulated.3. Combining the results of the expression of target gene measurements and pathway enrichment analyses, it was revealed that some DEmiRNAs from the gonad samples involved in sexual differentiation and development (such as cli-miR-210-3p and cli-miR-214-3p) could down-regulate AR (androgen receptor). Cli-miR-181b-5p, cli-miR-9622-3p and cli-miR-145-5p were highly expressed in both the ovaries and testes, which could co-target HOXC9, and were related to regulation of primary metabolic processes. KEGG enrichment analysis showed that DEmiRNAs may play biological and sex-related roles in pigeon gonads.4. The expression profiles of testicular and ovarian miRNA in adult pigeon gonads are presented for the first time, and the findings may contribute to a better understanding of gonadal expression in poultry.
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Affiliation(s)
- L Jiang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - D Bi
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - H Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Q Ren
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - P Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - X Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
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36
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Kim JY, Jeong S, Kim KH, Lim WJ, Lee HY, Kim N. Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds. Front Genet 2019; 10:699. [PMID: 31440273 PMCID: PMC6694180 DOI: 10.3389/fgene.2019.00699] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 07/03/2019] [Indexed: 12/16/2022] Open
Abstract
Indigenous breeds develop their own genomic characteristics by adapting to local environments or cultures over long periods of time. Most of them are not particularly productive in commercial terms, but they have abilities to survive in harsh environments or tolerate to specific diseases. Their adaptive characteristics play an important role as genetic materials for improving commercial breeds. As a step toward this goal, we analyzed the genome of Korean indigenous goats within 10 goat breeds. We collected 136 goat individuals by sequencing 46 new goats and employing 90 publicly available goats. Our whole-genome data was comprised of three indigenous breeds (Korean indigenous goat, Iranian indigenous goat, and Moroccan indigenous goat; n = 29, 18, 20), six commercial breeds (Saanen, Boer, Anglo-Nubian, British Alpine, Alpine, and Korean crossbred; n = 16, 11, 5, 5, 2, 13), and their ancestral species (Capra aegagrus; n = 17). We identified that the Iranian indigenous goat and the Moroccan indigenous goat have relatively similar genomic characteristics within a large category of genomic diversity but found that the Korean indigenous goat has unique genomic characteristics distinguished from the other nine breeds. Through population analysis, we confirmed that these characteristics have resulted from a near-isolated environment with strong genetic drift. The Korean indigenous goat experienced a severe genetic bottleneck upon entering the Korean Peninsula about 2,000 years ago, and has subsequently rarely experienced genetic interactions with other goat breeds. From selection analysis and gene-set enrichment analysis, we revealed selection signals for Salmonella infection and cardiomyopathy in the genome of the Korean indigenous goat. These adaptive characteristics were further identified with genomic-based evidence. We uncovered genomic regions of selective sweeps in the LBP and BPI genes (Salmonella infection) and the TTN and ITGB6 genes (cardiomyopathy), among several candidate genes. Our research presents unique genomic characteristics and distinctive selection signals of the Korean indigenous goat based on the extensive comparison. Although the adaptive traits require further validation through biological experiments, our findings are expected to provide a direction for future biodiversity conservation strategies and to contribute another option to genomic-based breeding programmes for improving the viability of Capra hircus.
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Affiliation(s)
- Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Seongmun Jeong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Ho-Yeon Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
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37
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Berihulay H, Islam R, Jiang L, Ma Y. Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel. Animals (Basel) 2019; 9:ani9060350. [PMID: 31200540 PMCID: PMC6617254 DOI: 10.3390/ani9060350] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/20/2019] [Accepted: 05/30/2019] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Information on linkage disequilibrium (LD) and the extent of effective population size (Ne) has important implications for exploring the degree of biological diversity, for predicting underlying selection pressure, and for designing animal breeding programs. In this study, we assessed LD, Ne, and the distribution of minor allele frequency in six goat populations. Accordingly, the results of LD and Ne using a single nucleotide polymorphism (SNP) panel (Caprine SNP 50K BeadChip, Lincoln, NE, USA) are helpful for the sustainable conservation, proper management, and utilization of Chinese goat populations. Abstract Genome-wide linkage disequilibrium is a useful parameter to study quantitative trait locus (QTL) mapping and genetic selection. In many genomic methodologies, effective population size is an important genetic parameter because of its relationship to the loss of genetic variation, increases in inbreeding, the accumulation of mutations, and the effectiveness of selection. In this study, a total of 193 individuals were genotyped to assess the extent of LD and Ne in six Chinese goat populations using the SNP 50K BeadChip. Across the determined autosomal chromosomes, we found an average of 0.02 and 0.23 for r2 and D’ values, respectively. The average r2 between all the populations varied little and ranged from 0.055 r2 for the Jining Grey to 0.128 r2 for the Guangfeng, with an overall mean of 0.083. Across the 29 autosomal chromosomes, minor allele frequency (MAF) was highest on chromosome 1 (0.321) and lowest on chromosome 25 (0.309), with an average MAF of 0.317, and showing the lowest (25.5% for Louping) and highest (28.8% for Qingeda) SNP proportions at MAF values > 0.3. The inbreeding coefficient ranged from 0.064 to 0.085, with a mean of 0.075 for all the autosomes. The Jining Grey and Qingeda populations showed higher Ne estimates, highlighting that these animals could have been influenced by artificial selection. Furthermore, a declining recent Ne was distinguished for the Arbas Cashmere and Guangfeng populations, and their estimated values were closer to 64 and 95, respectively, 13 generations ago, which indicates that these breeds were exposed to strong selection. This study provides an insight into valuable genetic information and will open up the opportunity for further genomic selection analysis of Chinese goat populations.
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Affiliation(s)
- Haile Berihulay
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Rabiul Islam
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
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38
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Guan D, Mármol-Sánchez E, Cardoso TF, Such X, Landi V, Tawari NR, Amills M. Genomic analysis of the origins of extant casein variation in goats. J Dairy Sci 2019; 102:5230-5241. [PMID: 30928270 DOI: 10.3168/jds.2018-15281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 02/05/2019] [Indexed: 12/29/2022]
Abstract
The variation in the casein genes has a major impact on the milk composition of goats. Even though many casein polymorphisms have been identified so far, we do not know yet whether they are evolutionarily ancient (i.e., they existed before domestication) or young (i.e., they emerged after domestication). Herewith, we identified casein polymorphisms in a data set of 106 caprine whole-genome sequences corresponding to bezoars (Capra aegagrus, the ancestor of domestic goats) and 4 domestic goat (Capra hircus) populations from Europe, Africa, the Far East, and the Near East. Domestic and wild goat populations shared a substantial number of casein SNP, from 36.1% (CSN2) to 55.1% (CSN1S2). The comparison of casein variation among bezoars and the 4 domestic goat populations demonstrated that more than 50% of the casein SNP are shared by 2 or more populations, and 18 to 44% are shared by all populations. Moreover, the majority of casein alleles reported in domestic goats also segregate in the bezoar, including several alleles displaying significant associations with milk composition (e.g., the A/B alleles of the CSN1S1 and CSN3 genes, the A allele of the CSN2 gene). We conclude that much of the current diversity of the caprine casein genes comes from ancient standing variation segregating in the ancestor of modern domestic goats.
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Affiliation(s)
- D Guan
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - E Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - T F Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; CAPES Foundation, Ministry of Education of Brazil, Brasilia D.F., 70.040-020 Brazil
| | - X Such
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - V Landi
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - N R Tawari
- Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672
| | - M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Berihulay H, Li Y, Liu X, Gebreselassie G, Islam R, Liu W, Jiang L, Ma Y. Genetic diversity and population structure in multiple Chinese goat populations using a SNP panel. Anim Genet 2019; 50:242-249. [PMID: 30883837 DOI: 10.1111/age.12776] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2019] [Indexed: 11/30/2022]
Abstract
Information about genetic diversity and population structure among goat breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of goat breeds. Here, we measured genetic diversity and population structure in multiple Chinese goat populations, namely, Nanjiang, Qinggeda, Arbas Cashmere, Jining Grey, Luoping Yellow and Guangfeng goats. A total of 193 individuals were genotyped for about 47 401 autosomal single nucleotide polymorphisms (SNPs). We found a high proportion of informative SNPs, ranging from 69.5% in the Luoping Yellow to 93.9% in the Jining Grey goat breeds with an average mean of 84.7%. Diversity, as measured by expected heterozygosity, ranged from 0.371 in Luoping Yellow to 0.405 in Jining Grey goat populations. The average estimated pair-wise genetic differentiation (FST ) among the populations was 8.6%, ranging from 0.2% to 16% and indicating low to moderate genetic differentiation. Principal component analysis, genetic structure and phylogenetic tree analysis revealed a clustering of six Chinese goat populations according to geographic distribution. The results from this study can contribute valuable genetic information and can properly assist with within-breed diversity, which provides a good opportunity for sustainable utilization of and maintenance of genetic resource improvements in the Chinese goat populations.
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Affiliation(s)
- H Berihulay
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Y Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - X Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - G Gebreselassie
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - R Islam
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - W Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - L Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Y Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
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40
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Cao Y, Xu H, Li R, Gao S, Chen N, Luo J, Jiang Y. Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids. Front Genet 2019; 10:145. [PMID: 30891061 PMCID: PMC6411798 DOI: 10.3389/fgene.2019.00145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 02/12/2019] [Indexed: 01/18/2023] Open
Abstract
Chinese Yunling black goats and African Nubian goats are divergent breeds showing significant differences in body size, milk production, and environmental adaptation. However, the genetic mechanisms underlying these phenotypic differences remain to be elucidated. In this report, we provide a detailed portrait of allele-specific expression (ASE) from 54 RNA-Seq analyses across six tissues from nine F1 hybrid offspring generated by crossing the two breeds combined with 13 genomes of the two breeds. We identified a total of 524 genes with ASE, which are involved in bone development, muscle cell differentiation, and the regulation of lipid metabolic processes. We further found that 38 genes with ASE were also under directional selection by comparing 13 genomes of the two breeds; these 38 genes play important roles in metabolism, immune responses, and the adaptation to hot and humid environments. In conclusion, our study shows that the exploration of genes with ASE in F1 hybrids provides an efficient way to understand the genetic basis underlying the phenotypic differences of two diverse goat breeds.
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Affiliation(s)
- Yanhong Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Guangxi Key Laboratory of Livestock Genetic Improvement, The Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Han Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 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, China
| | - Shan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jun Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Bertolini F, Servin B, Talenti A, Rochat E, Kim ES, Oget C, Palhière I, Crisà A, Catillo G, Steri R, Amills M, Colli L, Marras G, Milanesi M, Nicolazzi E, Rosen BD, Van Tassell CP, Guldbrandtsen B, Sonstegard TS, Tosser-Klopp G, Stella A, Rothschild MF, Joost S, Crepaldi P. Signatures of selection and environmental adaptation across the goat genome post-domestication. Genet Sel Evol 2018; 50:57. [PMID: 30449276 PMCID: PMC6240954 DOI: 10.1186/s12711-018-0421-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. RESULTS Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. CONCLUSIONS These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.
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Affiliation(s)
- Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), 2800 Lyngby, Denmark
| | - Bertrand Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
| | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Claire Oget
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Isabelle Palhière
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Alessandra Crisà
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Gennaro Catillo
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Roberto Steri
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
| | - Gabriele Marras
- Fondazione Parco Tecnologico Padano (PTP), 26900 Lodi, Italy
| | - Marco Milanesi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, Brazil
| | | | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD 20705 USA
| | | | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | | | - Gwenola Tosser-Klopp
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Alessandra Stella
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
| | - 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
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
| | - the AdaptMap consortium
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), 2800 Lyngby, Denmark
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Recombinetics Inc, St Paul, 55104 MN USA
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- Fondazione Parco Tecnologico Padano (PTP), 26900 Lodi, Italy
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, Brazil
- Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD 20705 USA
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
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N’Diaye A, Haile JK, Nilsen KT, Walkowiak S, Ruan Y, Singh AK, Clarke FR, Clarke JM, Pozniak CJ. Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height. FRONTIERS IN PLANT SCIENCE 2018; 9:1589. [PMID: 30455711 PMCID: PMC6230583 DOI: 10.3389/fpls.2018.01589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/15/2018] [Indexed: 05/21/2023]
Abstract
Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirby T. Nilsen
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Fran R. Clarke
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - John M. Clarke
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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Peripolli E, Metzger J, de Lemos MVA, Stafuzza NB, Kluska S, Olivieri BF, Feitosa FLB, Berton MP, Lopes FB, Munari DP, Lôbo RB, Magnabosco CDU, Di Croce F, Osterstock J, Denise S, Pereira ASC, Baldi F. Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits. BMC Genomics 2018; 19:680. [PMID: 30223795 PMCID: PMC6142381 DOI: 10.1186/s12864-018-5060-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022] Open
Abstract
Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. Electronic supplementary material The online version of this article (10.1186/s12864-018-5060-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Marcos Vinícius Antunes de Lemos
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Sabrina Kluska
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Bianca Ferreira Olivieri
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fabieli Louise Braga Feitosa
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Mariana Piatto Berton
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fernando Brito Lopes
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Raysildo Barbosa Lôbo
- Associação Nacional de Criadores e Pesquisadores (ANCP), Ribeirão Preto, 14020-230, Brazil
| | | | | | | | | | | | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
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Guo J, Tao H, Li P, Li L, Zhong T, Wang L, Ma J, Chen X, Song T, Zhang H. Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds. Sci Rep 2018; 8:10405. [PMID: 29991772 PMCID: PMC6039503 DOI: 10.1038/s41598-018-28719-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
Comparative population genomics analysis is an effective approach to identify selection signatures in farm animals. In this study, we systematically investigated the selection signatures in six phenotypically diverse goat breeds using SNPs obtained from pooled whole-genome resequencing data. More than 95.5% of 446–642 million clean reads were mapped to the latest reference goat genome, which generated a sequencing depth ranging from 22.30 to 31.75-fold for each breed. A total of 5,802,307, 6,794,020, 7,562,312, 5,325,119, 8,764,136, and 9,488,057 putative SNPs were detected in Boer, Meigu, Jintang Black, Nanjiang Yellow, Tibetan, and Tibetan cashmere goats, respectively. Based on the genome-wide FST and expected heterozygosity scores along 100-kb sliding windows, 68, 89, 44, 44, 19, and 35 outlier windows were deemed as the selection signatures in the six goat breeds. After genome annotation, several genes within the selection signals were found to be possibly associated with important traits in goats, such as coat color (IRF4, EXOC2, RALY, EIF2S2, and KITLG), high-altitude adaptation (EPAS1), growth (LDB2), and reproduction traits (KHDRBS2). In summary, we provide an improved understanding of the genetic diversity and the genomic footprints under positive selection or the adaptations to the local environments in the domestic goat genome.
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Affiliation(s)
- Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Haixi Tao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Pengfei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Tao Zhong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Linjie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Jinying Ma
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, 850009, China
| | - Xiaoying Chen
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, 850009, China
| | - Tianzeng Song
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, 850009, China.
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China.
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Li X, Su R, Wan W, Zhang W, Jiang H, Qiao X, Fan Y, Zhang Y, Wang R, Liu Z, Wang Z, Liu B, Ma Y, Zhang H, Zhao Q, Zhong T, Di R, Jiang Y, Chen W, Wang W, Dong Y, Li J. Identification of selection signals by large-scale whole-genome resequencing of cashmere goats. Sci Rep 2017; 7:15142. [PMID: 29123196 PMCID: PMC5680388 DOI: 10.1038/s41598-017-15516-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/27/2017] [Indexed: 01/14/2023] Open
Abstract
Inner Mongolia and Liaoning cashmere goats are two outstanding Chinese multipurpose breeds that adapt well to the semi-arid temperate grassland. These two breeds are characterized by their soft cashmere fibers, thus making them great models to identify genomic regions that are associated with cashmere fiber traits. Whole-genome sequencing of 70 cashmere goats produced more than 5.52 million single-nucleotide polymorphisms and 710,600 short insertions and deletions. Further analysis of these genetic variants showed some population-specific molecular markers for the two cashmere goat breeds that are otherwise phenotypically similar. By analyzing FST and θπ outlier values, we identified 135 genomic regions that were associated with cashmere fiber traits within the cashmere goat populations. These selected genomic regions contained genes, which are potential involved in the production of cashmere fiber, such as FGF5, SGK3, IGFBP7, OXTR, and ROCK1. Gene ontology enrichment analysis of identified short insertions and deletions also showed enrichment in keratinocyte differentiation and epidermal cell differentiation. These findings demonstrate that this genomic resource will facilitate the breeding of cashmere goat and other Capra species in future.
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Affiliation(s)
- Xiaokai Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Wenting Wan
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Huaizhi Jiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Xian Qiao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Yixing Fan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Bin Liu
- Institute of Animal Husbandry, Academy of Agriculture and Stockbreeding Sciences, Hohhot, Inner Mongolia, 010030, China
| | - Yuehui Ma
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianjun Zhao
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ran Di
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Wei Chen
- College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan, 650504, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, Yunnan, 650201, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
| | - Yang Dong
- College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan, 650504, China. .,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. .,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, Yunnan, 650201, China.
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. .,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. .,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. .,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
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