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Cardona SJC, García-Baccino CA, Escobar-Restrepo CS, Cadavid HC, Álvarez JDC, Duarte JLG, Rogberg-Muñoz A. Genetic evaluations of dairy goats with few pedigree data: different approaches to use molecular information. Trop Anim Health Prod 2024; 56:109. [PMID: 38509383 DOI: 10.1007/s11250-024-03948-6] [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: 03/30/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
One of the limitations of implementing animal breeding programs in small-scale or extensive production systems is the lack of production records and genealogical records. In this context, molecular markers could help to gain information for the breeding program. This study addresses the inclusion of molecular data into traditional genetic evaluation models as a random effect by molecular pedigree reconstruction and as a fixed effect by Bayesian clustering. The methods were tested for lactation curve traits in 14 dairy goat herds with incomplete phenotypic data and pedigree information. The results showed an increment of 37.3% of the relationships regarding the originals with MOLCOAN and clustering into five genetic groups. Data leads to estimating additive variance, error variance, and heritability with four different models, including pedigree and molecular information. Deviance Information Criterion (DIC) values demonstrate a greater fitting of the models that include molecular information either as fixed (genetic clusters) or as random (molecular matrix) effects. The molecular information of simple markers can complement genetic improvement strategies in populations with little information.
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Affiliation(s)
- Samir Julián Calvo Cardona
- Universidad Tecnológica de Pereira, Facultad de Ciencias de La Salud, Programa de Medicina Veterinaria y Zootecnia, Grupo de Investigación BIOPEC, Carrera 27 # 10-02, Álamos, Pereira-Risaralda, Colombia
| | - Carolina Andrea García-Baccino
- Departamento de Producción, Facultad de Agronomía, Universidad de Buenos Aires, San Martín 4453 (1417), Ciudad Autónoma de Buenos Aires, Argentina
| | - Carlos Santiago Escobar-Restrepo
- Grupo de investigación en Agronomía y Zootecnia-GIAZ, Facultad de Ciencias Agropecuarias, Universidad Católica de Oriente, Sector 3, Carrera 46, no 40B-50, Rionegro, Colombia.
| | - Henry Cardona Cadavid
- Universidad de Antioquia UdeA, Facultad de Ciencias Agrarias, Grupo de Investigación Agrociencias, Biodiversidad y Territorio-GAMMA, Cl. 70 # 52-21, 050010, Medellín, Colombia
| | | | - José Luis Gualdrón Duarte
- Unit of Animal Genomics, GIGA-R, University of Liège, 11 Avenue de L'Hôpital (B34), 4000, Liège, Belgium
| | - Andres Rogberg-Muñoz
- Departamento de Producción, Facultad de Agronomía, Universidad de Buenos Aires, San Martín 4453 (1417), Ciudad Autónoma de Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires. Instituto de Investigaciones en Producción Animal (INPA), Buenos Aires, Argentina
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Huang C, Zhao Q, Chen Q, Su Y, Ma Y, Ye S, Zhao Q. Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China. Genes (Basel) 2024; 15:313. [PMID: 38540373 PMCID: PMC10970279 DOI: 10.3390/genes15030313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/25/2024] [Accepted: 02/25/2024] [Indexed: 06/14/2024] Open
Abstract
Runs of Homozygosity (ROH) are continuous homozygous DNA segments in diploid genomes, which have been used to estimate the genetic diversity, inbreeding levels, and genes associated with specific traits in livestock. In this study, we analyzed the resequencing data from 10 local goat breeds in Yunnan province of China and five additional goat populations obtained from a public database. The ROH analysis revealed 21,029 ROH segments across the 15 populations, with an average length of 1.27 Mb, a pattern of ROH, and the assessment of the inbreeding coefficient indicating genetic diversity and varying levels of inbreeding. iHS (integrated haplotype score) was used to analyze high-frequency Single-Nucleotide Polymorphisms (SNPs) in ROH regions, specific genes related to economic traits such as coat color and weight variation. These candidate genes include OCA2 (OCA2 melanosomal transmembrane protein) and MLPH (melanophilin) associated with coat color, EPHA6 (EPH receptor A6) involved in litter size, CDKAL1 (CDK5 regulatory subunit associated protein 1 like 1) and POMC (proopiomelanocortin) linked to weight variation and some putative genes associated with high-altitude adaptability and immune. This study uncovers genetic diversity and inbreeding levels within local goat breeds in Yunnan province, China. The identification of specific genes associated with economic traits and adaptability provides actionable insights for utilization and conservation efforts.
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Affiliation(s)
- Chang Huang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yinxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
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Vlaic BA, Vlaic A, Russo IR, Colli L, Bruford MW, Odagiu A, Orozco-terWengel P. Analysis of Genetic Diversity in Romanian Carpatina Goats Using SNP Genotyping Data. Animals (Basel) 2024; 14:560. [PMID: 38396528 PMCID: PMC10886219 DOI: 10.3390/ani14040560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Animal husbandry is one of man's oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country's goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (HE), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The Ne has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the Ne trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed.
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Affiliation(s)
- Bogdan Alin Vlaic
- Department of Animal Breeding, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur Street 3–5, 400372 Cluj-Napoca, Romania;
| | - Augustin Vlaic
- Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur Street 3–5, 400372 Cluj-Napoca, Romania;
| | - Isa-Rita Russo
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK; (I.-R.R.); (M.W.B.)
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti (DIANA), BioDNA Centro di ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense n. 84, 29122 Piacenza, PC, Italy;
| | - Michael William Bruford
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK; (I.-R.R.); (M.W.B.)
| | - Antonia Odagiu
- Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur Street 3–5, 400372 Cluj-Napoca, Romania
| | - Pablo Orozco-terWengel
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK; (I.-R.R.); (M.W.B.)
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Zhao P, Zhang L, Liu Y, Wang Z, Guo H, Li J, Wu S, Gao Z, Yuan H. Genetic diversity and phylogenetic relationship estimation of Shanxi indigenous goat breeds using microsatellite markers. Anim Biotechnol 2023; 35:2276717. [PMID: 37934003 DOI: 10.1080/10495398.2023.2276717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The objective of this study was to assess the genetic diversity, phylogenetic relationship and population structure of five goat breeds in Shanxi, China. High genetic diversities were found in the five populations, among which, Licheng big green goat (LCBG) has the highest genetic diversity, while Jinlan cashmere goat (JLCG) population has the lowest genetic diversity. Bottleneck analysis showed the absence of recent genetic bottlenecks in the five goat populations. Genetic differentiation analysis shows that the closest genetic relationship between LCBG and LLBG (Lvliang black goat) was found, and the genetic distance between JLCG and the other four populations is the largest. The population structure of JLCG is different from the other four populations with K = 2, while LCBG and LLBG have high similarity population structure as the K value changes. Knowledge about genetic diversity and population structure of indigenous goats is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of goat breeds.
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Affiliation(s)
- Peng Zhao
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Li Zhang
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Yin Liu
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Zhengkun Wang
- Shanxi Animal Husbandry Technology Popularization Service Center, Taiyuan, China
| | - Hongyu Guo
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Jun Li
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Shuai Wu
- Agriculture and Rural Bureau of Lvliang City, Lvliang, Shanxi Province, China
| | - Zefeng Gao
- Agriculture and Rural Bureau of Lvliang City, Lvliang, Shanxi Province, China
| | - Hao Yuan
- Animal Husbandry Center of Yangcheng County, Jincheng, Shanxi Province, China
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5
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Qin W, Chen D, Guo P, Hu L, Zheng X, Cheng J, Chen H. Ecogroups and maternal haplogroups reveal the ancestral origin of native Chinese goat populations based on the variation of mtDNA D-loop sequences. Ecol Evol 2023; 13:e10382. [PMID: 37554396 PMCID: PMC10405232 DOI: 10.1002/ece3.10382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/22/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
China is rich in goat breeding resources. Officially recognized local goat breeds are mainly distributed in agro-ecological regions. The population structure and matrilineal origin of native Chinese goats can be used to formulate protection and utilization strategies for these genetic resources. In this study, the genetic structure and maternal origin of native Chinese goats were investigated using mtDNA D-loop sequences. A total of 329 goat samples from 25 Chinese indigenous goat populations and five introduced goat breeds from abroad were collected; these populations were distributed in four ecogroups designated as Southwest, South-central, the North China Plain, and Foreign-ecogroup. A larger average number of nucleotide differences and richer nucleotide diversity were observed in South-central and Foreign-ecogroup, whereas these were lower in Southwest. The 216 haplotypes divided into several haplogroups, of which HapA contained 99 haplotypes distributed in Southwest, the North China Plain, and Foreign-ecogroup with high frequency (0.53-0.77), whereas the frequency of HapA in South-central was <0.09. HapB was mostly found in South-central (0.5538) and was distributed to the North China Plain (0.2667), while it was rare in Southwest (<0.08) and Foreign-ecogroup (<0.07). According to the estimation of kinship and ancestry, HapA had five ancestors (A2, A3, A5, A10, and A12), HapB had a single maternal ancestor (A8), and HapC had two maternal ancestors (A1 and A4). This study showed that native Chinese goat breeds were mainly divided into three haplogroups (HapA, HapB, and HapC) and goat populations have expanded in the ecological regions.
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Affiliation(s)
- Wenjuan Qin
- School of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding of Anhui ProvinceHefeiChina
- Animal Molecular Immunization Center of Anhui Agricultural UniversityHefeiChina
| | - Daosong Chen
- School of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Animal Molecular Immunization Center of Anhui Agricultural UniversityHefeiChina
| | - Panpan Guo
- School of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
| | - Lixing Hu
- School of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
| | - Xiaodong Zheng
- Department of DermatologyThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Jin Cheng
- College of Biological and Pharmaceutical EngineeringWest Anhui UniversityLuanChina
| | - Hongquan Chen
- School of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding of Anhui ProvinceHefeiChina
- Animal Molecular Immunization Center of Anhui Agricultural UniversityHefeiChina
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6
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The Profiles and Functions of RNA Editing Sites Associated with High-Altitude Adaptation in Goats. Int J Mol Sci 2023; 24:ijms24043115. [PMID: 36834526 PMCID: PMC9964554 DOI: 10.3390/ijms24043115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/08/2023] Open
Abstract
High-altitude environments dramatically influenced the genetic evolution of vertebrates. However, little is known about the role of RNA editing on high-altitude adaptation in non-model species. Here, we profiled the RNA editing sites (RESs) of heart, lung, kidney, and longissimus dorsi muscle from Tibetan cashmere goats (TBG, 4500 m) and Inner Mongolia cashmere goats (IMG, 1200 m) to reveal RNA editing-related functions of high-altitude adaptation in goats. We identified 84,132 high-quality RESs that were unevenly distributed across the autosomes in TBG and IMG, and more than half of the 10,842 non-redundant editing sites were clustered. The majority (62.61%) were adenosine-to-inosine (A-to-I) sites, followed by cytidine-to-uridine (C-to-U) sites (19.26%), and 32.5% of them had a significant correlation with the expression of catalytic genes. Moreover, A-to-I and C-to-U RNA editing sites had different flanking sequences, amino acid mutations, and alternative splicing activity. TBG had higher editing levels of A-to-I and C-to-U than IMG in the kidney, whereas a lower level was found in the longissimus dorsi muscle. Furthermore, we identified 29 IMG and 41 TBG population-specific editing sites (pSESs) and 53 population-differential editing sites (pDESs) that were functionally involved in altering RNA splicing or recoding protein products. It is worth noting that 73.3% population-differential, 73.2% TBG-specific, and 80% IMG-specific A-to-I sites were nonsynonymous sites. Moreover, the pSESs and pDESs editing-related genes play critical functions in energy metabolisms such as ATP binding molecular function, translation, and adaptive immune response, which may be linked to goat high-altitude adaptation. Our results provide valuable information for understanding the adaptive evolution of goats and studying plateau-related diseases.
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Gong Y, Guo Y, He YM, Yuan Y, Yang BG, Duan XH, Liu CL, Zhang JH, Hong QH, Ma YH, Na RS, Han YG, Zeng Y, Huang YF, Zhao YJ, Zhao ZQ, E G. Comparative analysis of the genetic diversity of the neutral microsatellite loci and second exon of the goat MHC-DQB1 gene. Anim Biotechnol 2023; 34:85-92. [PMID: 34289783 DOI: 10.1080/10495398.2021.1935980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
This study compared and analyzed the genetic diversity and population structure of exon 2 of the DQB1 gene and 13 autosomal neutral microsatellite markers from 14 Chinese goat breeds to explore the potential evolutionary mechanism of the major histocompatibility complex (MHC). A total of 287 haplotypes were constructed from MHC-DQB1 exon 2 from 14 populations, and 82 nucleotide polymorphic sites (SNPs, 31.78%) and 172 heterozygous individuals (79.12%) were identified. The FST values of the microsatellites and MHC-DQB ranged between 0.01831-0.26907 and 0.00892-0.38871, respectively. Furthermore, 14 goat populations showed rich genetic diversity in the microsatellite loci and MHC-DQB1 exon 2. However, the population structure and phylogenetic relationship represented by the two markers were different. Positive selection and Tajima's D test results showed the occurrence of a diversified selection mechanism, which was primarily based on a positive and balancing selection in goat DQB. This study also found that the DQB sequences of bovines exhibited trans-species polymorphism (TSP) among species and families. In brief, this study indicated that positive and balancing selection played a major role in maintaining the genetic diversity of DQB, and TSP of MHC in bovines was common, which enhanced the understanding of the MHC evolution.
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Affiliation(s)
- Ying Gong
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yi Guo
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yong-Meng He
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Ying Yuan
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Bai-Gao Yang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Xing-Hai Duan
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Cheng-Li Liu
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Jia-Hua Zhang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Qiong-Hua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yue-Hui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ri-Su Na
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yan-Guo Han
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yan Zeng
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yong-Fu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yong-Ju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Zhong-Quan Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Guangxin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
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8
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Wang X, Li G, Jiang Y, Tang J, Fan Y, Ren J. Genomic insights into the conservation and population genetics of two Chinese native goat breeds. J Anim Sci 2022; 100:skac274. [PMID: 35998083 PMCID: PMC9585554 DOI: 10.1093/jas/skac274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 08/20/2022] [Indexed: 11/14/2022] Open
Abstract
Chinese goats are an important group of goats worldwide. However, there are few studies on the conservation priority, genetic relationship, and potential gene flow between Chinese and global goat breeds. Here, we genotyped 239 goats from conservation populations of the Chinese Guangfeng and Ganxi breeds using the GoatSNP50 BeadChip. The conservation priority, population structure, selection signatures and introgression of these goats were analyzed in the context of 36 global goat breeds. First, we showed that Guangfeng and Ganxi goats had the largest effective population sizes across the global breeds 13 generations ago. Nevertheless, Ganxi goats have recently experienced a high degree of inbreeding, resulting in their conservation priority based on total gene and allelic diversities being lower than that of most other Chinese breeds (including Guangfeng goats). Population structure and admixture analyses showed that an average of 18% of Guangfeng genomic components were introgressed from Boer goats approximately 18-yr ago. Next, we reconstructed the subfamily structure of the core populations of Guangfeng and Ganxi goats, and proposed reasonable conservation strategies for inbreeding management. Moreover, a list of candidate genes under selection for fertility, immunity, growth, and meat quality were detected in Guangfeng and Ganxi goats. Finally, we identified some genes related to body development and reproduction, which were introgressed from Boer goats and may be beneficial for improving performance and productivity of Guangfeng goats. In conclusion, this study not only provides new insights into the conservation and utilization of Guangfeng and Ganxi goats but also enriches our understanding of artificial introgression from exotic goats into Chinese local goats.
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Affiliation(s)
- Xiaopeng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Guixin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yongchuang Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jianhong Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou 341000, China
| | - Yin Fan
- Department of Animal Science, Jiangxi Biotech Vocational College, Nanchang 330200, China
| | - Jun Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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9
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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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10
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Wang R, Wang Z, Wang X, Li Y, Qu L, Lan X. A novel 4-bp insertion within the goat CFAP43 gene and its association with litter size. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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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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12
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Jin M, Lu J, Fei X, Lu Z, Quan K, Liu Y, Chu M, Di R, Wei C, Wang H. Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet. Animals (Basel) 2020; 10:ani10091599. [PMID: 32911823 PMCID: PMC7552128 DOI: 10.3390/ani10091599] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022] Open
Abstract
Simple Summary In the process of domestication, goats have undergone long-term artificial and natural selection, leading to differences among goat breeds and leaving different selection traces on the genome. However, the genetic components underlying high-altitude adaptation remain largely unknown. Here, we genotyped four goat breeds using the Illumina Caprine 50K single nucleotide polymorphism (SNP) Chip. One highland breed (Tibetan goat) compared with three lowland breeds (Huanghuai goat, Taihang goat and Xinjiang goat) to identify the molecular basis of high-altitude adaptation. So, we investigated selection signatures using the di statistic of four goat breeds and some genes in Tibetan goats related to high-altitude adaptation were identified. In addition, q-PCR validated the gene expression level in Tibetan goats and Huanghuai goats. This information may be valuable for the study of the genetic uniqueness of Tibetan goats and increased understanding of the hypoxic adaptation mechanism of Tibetan goats on the plateau. Abstract Tibetan goat is an ancient breed, which inhabits the adverse conditions of the plateaus in China. To investigate the role of selection in shaping its genomes, we genotyped Tibetan goats (Nagqu Prefecture, above 4500 m) and three lowland populations (Xinjiang goats, Taihang goats and Huanghuai goats). The result of PCA, neighbor-joining (N-J) tree and model-based clustering showed that the genetic structure between the Tibetan goat and the three lowland populations has significant difference. As demonstrated by the di statistic, we found that some genes were related to the high-altitude adaptation of Tibetan goats. Functional analysis revealed that these genes were enriched in the VEGF (vascular endothelial growth factor) signaling pathway and melanoma, suggesting that nine genes (FGF2, EGFR, AKT1, PTEN, MITF, ENPEP, SIRT6, KDR, and CDC42) might have important roles in the high-altitude adaptation of Nagqu Tibetan goats. We also found that the LEPR gene was under the strongest selection (di value = 16.70), and it could induce upregulation of the hypoxic ventilatory response. In addition, five genes (LEPR, LDB1, EGFR, NOX4 and FGF2) with high di values were analyzed using q-PCR. Among them, we found that LEPR, LDB1 and FGF2 exhibited higher expression in the lungs of the Tibetan goats; LEPR, EGFR and LDB1 exhibited higher expression in the hearts of the Huanghuai goat. Our results suggest that LEPR, LDB1, EGFR and FGF2 genes may be related to the high-altitude adaptation of the goats. These findings improve our understanding of the selection of the high-altitude adaptability of the Nagqu Tibetan goats and provide new theoretical knowledge for the conservation and utilization of germplasm resources.
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Affiliation(s)
- Meilin Jin
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
| | - Jian Lu
- National Animal Husbandry Service, Beijing 100193, China;
| | - Xiaojuan Fei
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
| | - Yongbin Liu
- Inner Mongolia Academy of Animal Husbandry Science, Hohhot 010031, China;
| | - Mingxing Chu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
| | - Ran Di
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
| | - Caihong Wei
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
- Correspondence: (C.W.); (H.W.)
| | - Huihua Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
- Correspondence: (C.W.); (H.W.)
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13
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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14
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Association of single nucleotide polymorphism in NLRC3, NLRC5, HIP1, and LRP8 genes with fecal egg counts in goats naturally infected with Haemonchus contortus. Trop Anim Health Prod 2019; 52:1583-1598. [PMID: 31828571 DOI: 10.1007/s11250-019-02154-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
Abstract
Haemonchus contortus is a common, intractably pathogenic and economically important gastrointestinal nematode for goat producers worldwide, especially in tropical and subtropical regions. The objective of this study is to identify single nucleotide polymorphisms (SNPs) of 12 candidate goat genes mainly related to the innate immune response associated with fecal egg counts (FECs) of Haemonchus contortus in goat as an indicator of the level of parasite infection. Phenotypic data including FEC and blood traits were recorded in 189 native goats from China and 191 ones from Bangladesh, respectively. Bangladeshi goats had significantly (P < 0.01) lower FEC compared to that of Chinese goats, suggesting higher susceptible and infection rates in Chinese goat populations. FEC was significantly positive correlated with body weight (r = 0.64, P < 0.01) and hemoglobin (r = 0.49, P < 0.01) value, but negative with pack cell volume (r = - 0.63, P < 0.05) in goats. Genotyping of SNPs was performed using a matrix-assisted laser desorption ionization time of flight mass spectrometry assay and a generalized linear model was used to evaluate the association between each SNP and goat FEC trait. Eleven novel SNPs in the NLRC3, NLRC5, HIP1, and LRP8, out of 46 variants from these 12 genes, were significantly associated with FEC of goats with a nominal significance level of P < 0.05. Of these 11 SNPs, linkage disequilibrium were revealed among SNPs in LRP8 (r2 = 0.87 to 1), between SNPs in NLRC3, NLRC5, and HIP1 (r2 = 0.96 to 0.99), respectively. Further, haplotypes within NLRC3, NLRC5, and HIP1 were significantly associated (P < 0.001) with FEC. In artificial challenge trail, quantitative real-time PCR exposed that the relative expression of mRNA was higher in the resistant group for NLRC3 (P < 0.01), LRP8 and HIP1 (P < 0.001) but lower in the resistant group for NLRC5 (P < 0.0001), compared to the susceptible group. The possible SNP markers and genes identified in this study could be potentially used in marker-assisted selection for breeding local goats breeds resistant to gastrointestinal nematode parasite particularly for Haemonchus contortus, and then for improving health and productivity of goat.
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15
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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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16
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E G, Hong Q, Zhao Y, Ma Y, Chu M, Zhu L, Huang Y. Genetic diversity estimation of Yunnan indigenous goat breeds using microsatellite markers. Ecol Evol 2019; 9:5916-5924. [PMID: 31161008 PMCID: PMC6540658 DOI: 10.1002/ece3.5174] [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: 09/20/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND To assess the genetic diversity of seven Yunnan indigenous goat populations (Fengqing hornless goat, Mile red-bone goat, Longling goat, Ninglang black goat, Black-bone goat, Yunling black goat, and Zhaotong goat), their population structures were investigated using 20 microsatellite markers. RESULTS The results indicated that the genetic diversity of these goats was rich. The observed heterozygosity ranged from 0.4667 ± 0.0243 to 0.5793 ± 0.0230, and the mean number of alleles ranged from 4.80 ± 1.61 and 4.80 ± 1.64 to 6.20 ± 2.93. The population structure analysis showed that these seven goat populations were separated into two clusters, consistent with the results from phylogenetic networks, pairwise differences, and STRUCTURE analyses. We speculate that this may have been caused by natural geographical isolation, human migration and economic and cultural exchanges. We suggest removing CSRD247 and ILSTS005, two loci identified to be under positive selection in the present study, from the microsatellite evaluation system of goats. CONCLUSIONS The present study may provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.
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Affiliation(s)
- Guang‐Xin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Qiong‐Hua Hong
- Yunnan Animal Science and Veterinary InstituteKunmingChina
| | - Yong‐Ju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Yue‐Hui Ma
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Ming‐Xing Chu
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Lan Zhu
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yong‐Fu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
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17
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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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18
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Xue J, Zhang H, Ning X, Bu W, Yu X. Evolutionary history of a beautiful damselfly, Matrona basilaris, revealed by phylogeographic analyses: the first study of an odonate species in mainland China. Heredity (Edinb) 2018; 122:570-581. [PMID: 30356221 DOI: 10.1038/s41437-018-0158-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 09/18/2018] [Indexed: 11/09/2022] Open
Abstract
Matrona basilaris Selys, 1853 is a damselfly distributed mainly in mainland China. A total of 423 individuals from 48 populations covering almost the entire range were sampled to explore the genetic diversity, phylogeographic structure, and demographic dynamics of the species using sequences of three mitochondrial genes (COI, COII, and ND1) and a nuclear (ITS1 + 5.8 S + ITS2) gene. Phylogenetic tree, median-joining network, and BAPS analyses indicated a four-group division of the entire population, and the divergence event was estimated to have occurred in the middle Pleistocene. The diverse terrain of mainland China as well as past climatic oscillations were assumed to have shaped the current phylogeographic pattern of M. basilaris. Multiple lines of evidence supported population expansion in Group 1 and Group 2 but not in Group 3 or Group 4. The expansion times corresponded to the transition phase from the LIG (∼0.14-0.12 Mya) to the LGM (∼0.021-0.018 Mya). The pre-LGM expansion model reflected a different pattern affecting the historical dynamics of the population of East Asian species caused by Pleistocene climatic changes. Interestingly, Group 2 exhibited a disjunctive distribution pattern. The possible reasons were introgression caused by female-biased dispersal or human phoresy during construction of the Forbidden City during the Ming Dynasty of China.
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Affiliation(s)
- Junli Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Haiguang Zhang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Ning
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Yu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China. .,College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China.
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19
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E G, Zhao Y, Chen L, Ma Y, Chu M, Li X, Hong Q, Li L, Guo J, Zhu L, Han Y, Gao H, Zhang J, Jiang H, Jiang C, Wang G, Ren H, Jin M, Sun Y, Zhou P, Huang Y. Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA. Ecol Evol 2018; 8:5111-5123. [PMID: 29876086 PMCID: PMC5980450 DOI: 10.1002/ece3.4100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/21/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
The objective of this study was to assess the genetic diversity and population structure of goats in the Yangtze River region using microsatellite and mtDNA to better understand the current status of those goat genetic diversity and the effects of natural landscape in fashion of domestic animal genetic diversity. The genetic variability of 16 goat populations in the littoral zone of the Yangtze River was estimated using 21 autosomal microsatellites, which revealed high diversity and genetic population clustering with a dispersed geographical distribution. A phylogenetic analysis of the mitochondrial D-loop region (482 bp) was conducted in 494 goats from the Yangtze River region. In total, 117 SNPs were reconstructed, and 173 haplotypes were identified, 94.5% of which belonged to lineages A and B. Lineages C, D, and G had lower frequencies (5.2%), and lineage F haplotypes were undetected. Several high-frequency haplotypes were shared by different ecogeographically distributed populations, and the close phylogenetic relationships among certain low-frequency haplotypes indicated the historical exchange of genetic material among these populations. In particular, the lineage G haplotype suggests that some west Asian goat genetic material may have been transferred to China via Muslim migration.
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Affiliation(s)
- Guang‐Xin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Yong‐Ju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Li‐Peng Chen
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Yue‐Hui Ma
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Ming‐Xing Chu
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiang‐Long Li
- College of Animal Science and TechnologyHebei Normal University of Science & TechnologyQinghuangdaoChina
| | - Qiong‐Hua Hong
- Yunnan Animal Scinence and Veterinary InstituteKunmingChina
| | - Lan‐Hui Li
- College of Animal Science and TechnologyAgricultural University of HebeiBaoding, HebeiChina
| | - Ji‐Jun Guo
- Animal Husbandry Station of Qinghai ProvinceXining, QinghaiChina
| | - Lan Zhu
- Yunnan Animal Scinence and Veterinary InstituteKunmingChina
| | - Yan‐Guo Han
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Hui‐Jiang Gao
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Jia‐Hua Zhang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Huai‐Zhi Jiang
- Animal Science and Technology CollegeJilin Agriculture UniversityChangchun, JilinChina
| | - Cao‐De Jiang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Gao‐Fu Wang
- Chongqing Academy of Animal SciencesChongqingChina
| | | | - Mei‐Lan Jin
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Yuan‐Zhi Sun
- Wuhan Tianyi Huiyuan Bioscience & Technology IncWuhanChina
| | - Peng Zhou
- Chongqing Academy of Animal SciencesChongqingChina
| | - Yong‐Fu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
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20
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Abstract
Goats have played a key role as source of nourishment for humans in their expansion all over the world in long land and sea trips. This has guaranteed a place for this species in the important and rapid episode of livestock expansion triggered by Columbus' arrival in the Americas in the late 1400s. The aims of this study are to provide a comprehensive perspective on genetic diversity in American goat populations and to assess their origins and evolutionary trajectories. This was achieved by combining data from autosomal neutral genetic markers obtained in more than two thousand samples that encompass a wide range of Iberian, African and Creole goat breeds. In general, even though Creole populations differ clearly from each other, they lack a strong geographical pattern of differentiation, such that populations of different admixed ancestry share relatively close locations throughout the large geographical range included in this study. Important Iberian signatures were detected in most Creole populations studied, and many of them, particularly the Cuban Creole, also revealed an important contribution of African breeds. On the other hand, the Brazilian breeds showed a particular genetic structure and were clearly separated from the other Creole populations, with some influence from Cape Verde goats. These results provide a comprehensive characterisation of the present structure of goat genetic diversity, and a dissection of the Iberian and African influences that gave origin to different Creole caprine breeds, disentangling an important part of their evolutionary history. Creole breeds constitute an important reservoir of genetic diversity that justifies the development of appropriate management systems aimed at improving performance without loss of genomic diversity.
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Amills M, Capote J, Tosser-Klopp G. Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces. Anim Genet 2017; 48:631-644. [PMID: 28872195 DOI: 10.1111/age.12598] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2017] [Indexed: 12/23/2022]
Abstract
Domestic goats (Capra hircus) are spread across the five continents with a census of 1 billion individuals. The worldwide population of goats descends from a limited number of bezoars (Capra aegagrus) domesticated 10 000 YBP (years before the present) in the Fertile Crescent. The extraordinary adaptability and hardiness of goats favoured their rapid spread over the Old World, reaching the Iberian Peninsula and Southern Africa 7000 YBP and 2000 YBP respectively. Molecular studies have revealed one major mitochondrial haplogroup A and five less frequent haplogroups B, C, D, F and G. Moreover, the analysis of autosomal and Y-chromosome markers has evidenced an appreciable geographic differentiation. The implementation of new molecular technologies, such as whole-genome sequencing and genome-wide genotyping, allows for the exploration of caprine diversity at an unprecedented scale, thus providing new insights into the evolutionary history of goats. In spite of a number of pitfalls, the characterization of the functional elements of the goat genome is expected to play a key role in understanding the genetic determination of economically relevant traits. Genomic selection and genome editing also hold great potential, particularly for improving traits that cannot be modified easily by traditional selection.
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Affiliation(s)
- M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - J Capote
- Instituto Canario de Investigaciones Agrarias, La Laguna, 38108, Tenerife, Spain
| | - G Tosser-Klopp
- INRA-GenPhySE-Génétique, Physiologie et Systèmes d'Elevage-UMR1388, 24 Chemin de Borde Rouge-Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
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Scanning indels in the 5q22.1 region and identification of the TMEM232 susceptibility gene that is associated with atopic dermatitis in the Chinese Han population. Gene 2017; 617:17-23. [PMID: 28351738 DOI: 10.1016/j.gene.2017.03.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/21/2017] [Accepted: 03/24/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Atopic dermatitis (AD) is a chronic inflammatory skin disease. The 5q22.1 region was found to have an association with AD in our previous genome-wide association study (GWAS). OBJECTIVE To identify the AD susceptibility gene in 5q22.1 and observe its expression in AD tissues. METHODS Suggestive indels from the GWAS data were genotyped in 3013 AD patients and 5075 controls from the Chinese Han population with the SequenomMassArray system. Association, Bayesian and bioinformatics analyses were used to identify possible causal indels and genes in the 5q22.1 region. Immunohistochemistry (IHC) was performed to observe protein expression in the tissues. PLINK 1.07 software was used for all statistical analyses. RESULTS The genotyping and association analysis showed that six deletions and four SNPs were associated with AD (P<0.005). The rs11357450 (Pcombined=7.79E-04, OR=1.39, logBayes Factor=1.29) deletion located in TMEM232 was identified to be the strongest variant. Analysis of the genetic model revealed that the dominant model best described rs11357450 (P=1.96E-03, OR=1.22; 95% CI=1.07-1.37). IHC showed that the expression of TMEM232 decreased gradually from the granular layer to the basal layer in AD, but in normal tissues, this trend was reversed. Additionally, positive cytoplasm staining was found in lymphocytes around the blood vessels in AD. CONCLUSIONS The study indicates that TMEM232 in the 5q22.1 region is the causal gene for AD in the Chinese Han population.
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Periasamy K, Vahidi S, Silva P, Faruque M, Naqvi A, Basar M, Cao J, Zhao S, Thuy LT, Pichler R, Podesta MG, Shamsuddin M, Boettcher P, Garcia JF, Han JL, Marsan PA, Diallo A, Viljoen GJ. Mapping molecular diversity of indigenous goat genetic resources of Asia. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.12.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Du X, Cao J, Han X, Hao H, Yu M, Zhang G, Zhao S. Genetic diversity and population structure among eight Chinese indigenous goat breeds in the Yellow River valley. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.12.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Genetic Diversity of Eight Domestic Goat Populations Raised in Turkey. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2830394. [PMID: 27092309 PMCID: PMC4820616 DOI: 10.1155/2016/2830394] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 11/29/2022]
Abstract
The objective of this study was to determine the intra- and intergenetic diversities of eight different goat populations in Turkey including Hair, Angora, Kilis, Yayladag, Shami, Honamli, Saanen, and Alpine. A total of 244 DNA samples were genotyped using 11 microsatellites loci. The genetic differentiation between breeds was considerable as a result of the statistically significant (P < 0.001) pairwise FST values of each pair of breeds. Exceptionally, FST values calculated for Honamli and Hair breeds were statistically nonsignificant (P > 0.05). Heterozygosity values ranged between 0.62 and 0.73. According to the structure and assignment test, Angora and Yayladag goats were assigned to the breed they belong to, while other breeds were assigned to two or more different groups. Because this study for the first time presented genetic data on the Yayladag goat, results of structure analysis and assigned test suggest that further analyses are needed using additional and different molecular markers.
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Martínez AM, Gama LT, Delgado JV, Cañón J, Amills M, de Sousa CB, Ginja C, Zaragoza P, Manunza A, Landi V, Sevane N. The Southwestern fringe of Europe as an important reservoir of caprine biodiversity. Genet Sel Evol 2015; 47:86. [PMID: 26542127 PMCID: PMC4635977 DOI: 10.1186/s12711-015-0167-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/28/2015] [Indexed: 11/18/2022] Open
Abstract
Background Portugal and Spain, with six and 22 officially recognized caprine breeds, encompass 25 % of the European Union goat census. Many of these populations have suffered strong demographic declines because of competition with exotic breeds and the phasing-out of low income rural activities. In this study, we have investigated the consequences of these and other demographic processes on the genetic diversity, population structure and inbreeding levels of Iberian and Atlantic goats. Methods A sample of 975 individuals representing 25 officially recognized breeds from Portugal and Spain, two small populations not officially recognized (Formentera and Ajuí goats) and two ecotypes of the Tinerfeña and Blanca Celtibérica breeds were genotyped with a panel of 20 microsatellite markers. A wide array of population genetics methods was applied to make inferences about the genetic relationships and demography of these caprine populations. Results Genetic differentiation among Portuguese and Spanish breeds was weak but significant (FST = 0.07; P < 0.001), which is probably the consequence of their short splitting times and extensive gene flow due to transhumance. In contrast, Canarian goats were strongly differentiated because of prolonged geographic isolation. Most populations displayed considerable levels of diversity (mean He = 0.65). Conclusions High diversity levels and weak population structures are distinctive features of Portuguese and Spanish breeds. In general, these local breeds have a reduced census, but are still important reservoirs of genetic diversity. These findings reinforce the need for the implementation of management and breeding programs based on genetic data in order to minimize inbreeding, maintain overall genetic and allelic diversities and breed identities, while at the same time taking into account the within-breed genetic structure. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0167-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Luis T Gama
- CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal.
| | - Juan V Delgado
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain.
| | - Javier Cañón
- Departamento de Producción Animal, Universidad Complutense de Madrid, Madrid, Spain.
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UABUB), Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
| | - Carolina Bruno de Sousa
- Centro de Ciências do Mar, Universidade do Algarve, Instituto de Higiene e Medicina Tropical (UPMM), UNL, Lisbon, Portugal.
| | - Catarina Ginja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
| | - Pilar Zaragoza
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain.
| | - Arianna Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UABUB), Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain.
| | - Natalia Sevane
- Departamento de Producción Animal, Universidad Complutense de Madrid, Madrid, Spain.
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