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Vostry L, Vostra-Vydrova H, Moravcikova N, Kasarda R, Margetin M, Rychtarova J, Drzaic I, Shihabi M, Cubric-Curik V, Sölkner J, Curik I. Genomic analysis of conservation status, population structure and admixture in local Czech and Slovak dairy goat breeds. J Dairy Sci 2024:S0022-0302(24)00937-8. [PMID: 38908686 DOI: 10.3168/jds.2023-24607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/30/2024] [Indexed: 06/24/2024]
Abstract
While dairy goat production, characterized by traditional production on small farms, is an important source of income in the Czech Republic and Slovakia, locally adapted breeds have not been fully consolidated over the last 100 years due to large fluctuations in population size and inconsistent breeding programs that allowed for different crossbreeding strategies. Our main objective in this study was therefore to assess the conservation status of 4 Czech (Alpine Goat, White Shorthair, Brown Shorthair and Czech Landrace) and one Slovak (Slovak White Shorthair) local goat breeds, to analyze their population structure and admixture, and to estimate their relatedness to several neighboring breeds. Our analyses included 142 goats belonging to 5 local breeds genotyped with the Illumina 50K BeadChip and 618 previously genotyped animals representing 15 goat breeds from Austria and Switzerland (all analyses based on 46,862 autosomal SNPs and 760 animals). In general, the conservation status of the Czech and Slovak local goat breeds was satisfactory, with the exception of the Brown Shorthair goat, as the analyzed parameters (heterozygosity, haplotype richness, ROH-based inbreeding and effective population size) were mostly above the median of 20 breeds. However, for all 5 Czech and Slovakian breeds, an examination of historical effective population size indicated a substantial decline about 8 to 22 generations ago. In addition, our study revealed that the Czech and Slovakian breeds are not fully consolidated; for instance, White Shorthair and Brown Shorthair were not clearly distinguishable. Considerable admixture, especially in Czech Landrace (effective number of parental clusters equal to 4.2), and low but numerous migration rates from other Austrian and Swiss breeds were found. These results provide valuable insights for future breeding programs and genetic diversity management of local Czech and Slovak goat breeds.
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Affiliation(s)
- Lubos Vostry
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic.
| | - Hana Vostra-Vydrova
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Nina Moravcikova
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Radovan Kasarda
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Milan Margetin
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Jana Rychtarova
- Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic
| | - Ivana Drzaic
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Mario Shihabi
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Vlatka Cubric-Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Johan Sölkner
- University of Natural Resources & Life Sciences Vienna, Gregor-Mendel-Strasse 33, 1180 Vienna, Austria
| | - Ino Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia; Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary.
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2
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Le SV, de Las Heras-Saldana S, Alexandri P, Olmo L, Walkden-Brown SW, van der Werf JHJ. Genetic diversity, population structure and origin of the native goats in Central Laos. J Anim Breed Genet 2024. [PMID: 38520124 DOI: 10.1111/jbg.12862] [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: 11/15/2023] [Revised: 02/14/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024]
Abstract
Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011-0.043) and negligible inbreeding coefficients (FIS: -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.
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Affiliation(s)
- Sang V Le
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Sara de Las Heras-Saldana
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Panoraia Alexandri
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Luisa Olmo
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Stephen W Walkden-Brown
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Julius H J van der Werf
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
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Arenas-Báez P, Torres-Hernández G, Castillo-Hernández G, Hernández-Rodríguez M, Sánchez-Gutiérrez RA, Vargas-López S, González-Maldonado J, Domínguez-Martínez PA, Granados-Rivera LD, Maldonado-Jáquez JA. Coat Color in Local Goats: Influence on Environmental Adaptation and Productivity, and Use as a Selection Criterion. BIOLOGY 2023; 12:929. [PMID: 37508360 PMCID: PMC10376610 DOI: 10.3390/biology12070929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/16/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
This paper aims to review, systematically synthesize, and analyze fragmented information about the importance of coat color in local goats and its relationship with productivity and other important traits. Topics on current research on color expression are addressed, the relationship that has as a mechanism of environmental adaptation, its relationship with the production of meat, milk, and derivates, and the economic value of this characteristic. The use of this attribute as a tool to establish selection criteria in breeding programs based on results reported in the scientific literature is significant, particularly for low-income production systems, where the implementation of classic genetic improvement schemes is limited due to the lack of productive information, which is distinctive of extensive marginal or low scaled production systems around the world.
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Affiliation(s)
- Pablo Arenas-Báez
- Unidad Regional Universitaria de Zonas Áridas, Universidad Autónoma Chapingo, Bermejillo, Durango 35230, Mexico
| | | | - Gabriela Castillo-Hernández
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54714, Mexico
| | | | - Ricardo Alonso Sánchez-Gutiérrez
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Zacatecas, Calera, Zacatecas 98500, Mexico
| | | | - Juan González-Maldonado
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Mexicali 21750, Mexico
| | - Pablo Alfredo Domínguez-Martínez
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Valle del Guadiana, Durango 34170, Mexico
| | - Lorenzo Danilo Granados-Rivera
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Genera Terán, General Terán 67400, Mexico
| | - Jorge Alonso Maldonado-Jáquez
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental La Laguna, Matamoros 27440, Mexico
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4
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Teissier M, Brito LF, Schenkel FS, Bruni G, Fresi P, Bapst B, Robert-Granie C, Larroque H. Genetic Characterization and Population Connectedness of North American and European Dairy Goats. Front Genet 2022; 13:862838. [PMID: 35783257 PMCID: PMC9247305 DOI: 10.3389/fgene.2022.862838] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/03/2022] [Indexed: 12/26/2022] Open
Abstract
Genomic prediction of breeding values is routinely performed in several livestock breeding programs around the world, but the size of the training populations and the genetic structure of populations evaluated have, in many instances, limited the increase in the accuracy of genomic estimated breeding values. Combining phenotypic, pedigree, and genomic data from genetically related populations can be a feasible strategy to overcome this limitation. However, the success of across-population genetic evaluations depends on the pedigree connectedness and genetic relationship among individuals from different populations. In this context, this study aimed to evaluate the genetic connectedness and population structure of Alpine and Saanen dairy goats from four countries involved in the European project SMARTER (SMAll RuminanTs Breeding for Efficiency and Resilience), including Canada, France, Italy, and Switzerland. These analyses are paramount for assessing the potential feasibility of an across-country genomic evaluation in dairy goats. Approximately, 9,855 genotyped individuals (with 51% French genotyped animals) and 6,435,189 animals included in the pedigree files were available across all four populations. The pedigree analyses indicated that the exchange of breeding animals was mainly unilateral with flows from France to the other three countries. Italy has also imported breeding animals from Switzerland. Principal component analyses (PCAs), genetic admixture analysis, and consistency of the gametic phase revealed that French and Italian populations are more genetically related than the other dairy goat population pairs. Canadian dairy goats showed the largest within-breed heterogeneity and genetic differences with the European populations. The genetic diversity and population connectedness between the studied populations indicated that an international genomic evaluation may be more feasible, especially for French and Italian goats. Further studies will investigate the accuracy of genomic breeding values when combining the datasets from these four populations.
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Affiliation(s)
- Marc Teissier
- GenPhySE, Université de Toulouse, Toulouse, France
- *Correspondence: Marc Teissier,
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
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Genetic Differentiation among Livestock Breeds—Values for Fst. Animals (Basel) 2022; 12:ani12091115. [PMID: 35565543 PMCID: PMC9103131 DOI: 10.3390/ani12091115] [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: 04/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary The degree of relationship among livestock breeds can be quantified by the Fst statistic, which measures the extent of genetic differentiation between them. An Fst value of 0.1 has often been taken as indicating that two breeds are indeed genetically distinct, but this concept has not been evaluated critically. Here, Fst values have been collated for the six major livestock species: cattle, sheep, goats, pigs, horses, and chickens. These values are remarkably variable both within and between species, demonstrating that Fst > 0.1 is not a reliable criterion for breed distinctiveness. However, the large body of Fst data accumulated in the last 20–30 years represents an untapped database that could contribute to the development of interdisciplinary research involving livestock breeds. Abstract (1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06–0.12, SNP 0.08–0.15; sheep: microsatellite 0.06–0.10, SNP 0.06–0.17; horses: microsatellite 0.04–0.11, SNP 0.08–0.12; goats: microsatellite 0.04–0.14, SNP 0.08–0.16; pigs: microsatellite 0.06–0.27, SNP 0.15–0.22; chickens: microsatellite 0.05–0.28, SNP 0.08–0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world’s livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.
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Serranito B, Cavalazzi M, Vidal P, Taurisson-Mouret D, Ciani E, Bal M, Rouvellac E, Servin B, Moreno-Romieux C, Tosser-Klopp G, Hall SJG, Lenstra JA, Pompanon F, Benjelloun B, Da Silva A. Local adaptations of Mediterranean sheep and goats through an integrative approach. Sci Rep 2021; 11:21363. [PMID: 34725398 PMCID: PMC8560853 DOI: 10.1038/s41598-021-00682-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022] Open
Abstract
Small ruminants are suited to a wide variety of habitats and thus represent promising study models for identifying genes underlying adaptations. Here, we considered local Mediterranean breeds of goats (n = 17) and sheep (n = 25) from Italy, France and Spain. Based on historical archives, we selected the breeds potentially most linked to a territory and defined their original cradle (i.e., the geographical area in which the breed has emerged), including transhumant pastoral areas. We then used the programs PCAdapt and LFMM to identify signatures of artificial and environmental selection. Considering cradles instead of current GPS coordinates resulted in a greater number of signatures identified by the LFMM analysis. The results, combined with a systematic literature review, revealed a set of genes with potentially key adaptive roles in relation to the gradient of aridity and altitude. Some of these genes have been previously implicated in lipid metabolism (SUCLG2, BMP2), hypoxia stress/lung function (BMPR2), seasonal patterns (SOX2, DPH6) or neuronal function (TRPC4, TRPC6). Selection signatures involving the PCDH9 and KLH1 genes, as well as NBEA/NBEAL1, were identified in both species and thus could play an important adaptive role.
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Affiliation(s)
- Bruno Serranito
- INRA, EA7500, USC1061 GAMAA, Univ. Limoges, 87000, Limoges, France
- CRESCO, Museum National d'Histoire Naturelle (MNHN), 35800, Dinard, France
| | | | - Pablo Vidal
- Universidad Catolica de Valencia, Valencia, Spain
| | - Dominique Taurisson-Mouret
- GEOLAB, UMR 6042, Univ. Limoges, Limoges, France
- CNRS, UMR 5815, Dynamiques du droit, Université de Montpellier, Montpellier, France
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Marie Bal
- GEOLAB, UMR 6042, Univ. Limoges, Limoges, France
| | | | - Bertrand Servin
- GenPhySE, INRAE, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | | | | | - Stephen J G Hall
- Estonian University of Life Sciences, Kreutzwaldi 5, 51014, Tartu, Estonia
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM, Utrecht, The Netherlands
| | - François Pompanon
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
| | - Badr Benjelloun
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
- National Institute of Agronomic Research (INRA), Regional Centre of Agronomic Research, Beni-Mellal, Morocco
| | - Anne Da Silva
- INRA, EA7500, USC1061 GAMAA, Univ. Limoges, 87000, Limoges, France.
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Selionova MI, Aibazov AMM, Mamontova TV, Stolpovsky IA, Beketov SV, Petrov SN, Kharzinova VR, Dotsev AV, Zinovieva NA. Characteristics of the Allele Pool and the Genetic Differentiation of Goats of Different Breeds and their Wild Relatives by Str-Markers. ARCHIVES OF RAZI INSTITUTE 2021; 76:1351-1362. [PMID: 35355766 PMCID: PMC8934102 DOI: 10.22092/ari.2021.355684.1709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/29/2021] [Indexed: 06/14/2023]
Abstract
Based on 16 STR-loci, the allele pool and interbreed differentiation of goat breeds of Russian and foreign breeding were investigated in this study. These breeds included Karachai (KRCH-K, n=73, mountain zone; KRCH-Z, n=33, foothill zone), Dagestan Downy (DAGD, n=30), Dagestan Wool (DAGW, n=30), Soviet Wool (SOVW, n=30), Saanen (SAAN, n=34), Murciano-Granadina (MURS, n=37), as well as wild goats, represented by three species of mountain goats (n=52): Siberian Capricorn (Capra sibirica) of Altai (CSIB-S, n=6), Tajikistan (CSIB-T, n=4), Kyrgyzstan (CSIB-K, n=6), and the Himalayas (CSIB-H, n=4); Bezoar goat (Capa aegagrus) of Turkey (CAEG, n=3) and Pakistan (CAEG-S, n=3); West Caucasian tur (Capra caucasica): western Caucasian (Kuban, CCAU-K, n=10), central Caucasian (CCAU-M, n=8), and eastern Caucasian (Dagestan, CCAU-D, n=8). The highest genetic diversity was observed in the North Caucasus breeds, such as Karachai, Dagestan Downy, and Dagestan Wool. The mean numbers of alleles per locus and allelic diversity were 7.385-9.154 and 7.353-7.713, respectively. The genetic proximity of Caucasian breeds was confirmed by cluster analysis, and they formed a common branch with the highest genetic affinity, while the Orenburg and Soviet Wool breeds formed another branch, and the third branch with the least affinity was the dairy breed of foreign selection.The analysis of the phylogenetic tree of domestic and wild species established the formation of three clusters formed by the subspecies of the West Caucasian tur, Siberian ibex, and breeds of domestic goats. At the same time, populations of the Bezoar goats were localized at the root of the last cluster, which confirmed their role as the ancestors of domestic goats.
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Affiliation(s)
- M I Selionova
- Federal State Budgetary Educational Institution of Higher Education, Russian State Agrarian University, Moscow Timiryazev Agricultural Academy, Moscow, 127550, Russia
| | - A-M M Aibazov
- All-Russian Research Institute of Sheep and Goat Breeding, Branch of the Federal State Budgetary Scientific Institution, North Caucasian Federal Scientific Agrarian Center, Stavropol, 355017, Russia
| | - T V Mamontova
- All-Russian Research Institute of Sheep and Goat Breeding, Branch of the Federal State Budgetary Scientific Institution, North Caucasian Federal Scientific Agrarian Center, Stavropol, 355017, Russia
| | - Iu A Stolpovsky
- Institute of General Genetics, N.I. Vavilov Russian Academy of Sciences, Moscow, 119991, Russia
| | - S V Beketov
- Institute of General Genetics, N.I. Vavilov Russian Academy of Sciences, Moscow, 119991, Russia
| | - S N Petrov
- Federal State Budgetary Scientific Institution, L.K. Ernst Federal Research Center for Animal Husbandry, Moscow region, Podolsk, settlement of Dubrovitsy, 142132, Russia
| | - V R Kharzinova
- Federal State Budgetary Scientific Institution, L.K. Ernst Federal Research Center for Animal Husbandry, Moscow region, Podolsk, settlement of Dubrovitsy, 142132, Russia
| | - A V Dotsev
- Federal State Budgetary Scientific Institution, L.K. Ernst Federal Research Center for Animal Husbandry, Moscow region, Podolsk, settlement of Dubrovitsy, 142132, Russia
| | - N A Zinovieva
- Federal State Budgetary Scientific Institution, L.K. Ernst Federal Research Center for Animal Husbandry, Moscow region, Podolsk, settlement of Dubrovitsy, 142132, Russia
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Pogorevc N, Simčič M, Khayatzadeh N, Sölkner J, Berger B, Bojkovski D, Zorc M, Dovč P, Medugorac I, Horvat S. Post-genotyping optimization of dataset formation could affect genetic diversity parameters: an example of analyses with alpine goat breeds. BMC Genomics 2021; 22:546. [PMID: 34273960 PMCID: PMC8285797 DOI: 10.1186/s12864-021-07802-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/13/2021] [Indexed: 12/05/2022] Open
Abstract
Background Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, and five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters. Results Distinct genetic origin of the Drežnica goat was demonstrated as having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning. Conclusions Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of breeding and management programs and are therefore important for preserving genetic variability and uniqueness of local rare breeds. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07802-z.
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Affiliation(s)
- Neža Pogorevc
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Mojca Simčič
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Negar Khayatzadeh
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Gregor Mendel Str. 33, A-1180, Vienna, Austria
| | - Johann Sölkner
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Gregor Mendel Str. 33, A-1180, Vienna, Austria
| | - Beate Berger
- Department Animal Genetic Resources, AREC Raumberg-Gumpenstein, Institute of Organic Farming and Biodiversity of Farm Animals, 4601 Thalheim b., Wels, Austria
| | - Danijela Bojkovski
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Minja Zorc
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Peter Dovč
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Lena-Christ-Straβe 48, 8215, Martinsried/Planegg, Germany
| | - Simon Horvat
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia.
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9
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An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds. Animals (Basel) 2021; 11:ani11072016. [PMID: 34359144 PMCID: PMC8300386 DOI: 10.3390/ani11072016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The number of local farm animal breeds is declining worldwide. However, these breeds have different degrees of genetic diversity. Measuring genetic diversity is important for the development of conservation strategies and, therefore, various genomic analysis techniques are available. The aim of the present work was to shed light on the use of these techniques in diversity studies of local breeds. In summary, a total of 133 worldwide studies that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that over time, almost all available genomic techniques were used and various diversity parameters were calculated. Therefore, the present results provide a comprehensive overview of the application of these techniques in the field of local breeds. This can provide helpful insights into the advancement of the conservation of breeds with high genetic diversity. Abstract Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds.
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Guan D, Martínez A, Luigi-Sierra MG, Delgado JV, Landi V, Castelló A, Fernández Álvarez J, Such X, Jordana J, Amills M. Detecting the footprint of selection on the genomes of Murciano-Granadina goats. Anim Genet 2021; 52:683-693. [PMID: 34196982 DOI: 10.1111/age.13113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 01/14/2023]
Abstract
Artificial selection is one of the major forces modifying the genetic composition of livestock populations. Identifying genes under selection could be useful to elucidate their impact on phenotypic variation. We aimed to identify genomic regions targeted by selection for dairy and pigmentation traits in Murciano-Granadina goats. Performance of a selection scan based on the integrated haplotype score test in a population of 1183 Murciano-Granadina goats resulted in the identification of 77 candidate genomic regions/SNPs. The most significant selective sweeps mapped to chromosomes 1 (69.86 Mb), 4 (41.80-49.95 Mb), 11 (65.74 Mb), 12 (31.24 and 52.51 Mb), 17 (34.76-37.67 Mb), 22 (31.75 Mb), and 26 (26.69-31.05 Mb). By using previously generated RNA-Seq data, we built a catalogue of 6414 genes that are differentially expressed across goat lactation (i.e. 78 days post-partum, early lactation; 216 days post-partum, late lactation; 285 days post-partum, dry period). Interestingly, 183 of these genes mapped to selective sweeps and several of them display functions related with lipid, protein, and carbohydrate metabolism, insulin signaling, cell proliferation, as well as mammary development and involution. Of particular interest are the CSN3 and CSN1S2 genes, which encode two major milk proteins. Additionally, we found three pigmentation genes (GLI3, MC1R, and MITF) co-localizing with selective sweeps. Performance of a genome-wide association study and Sanger sequencing and TaqMan genotyping experiments revealed that the c.801C>G (p.Cys267Trp) polymorphism in the melanocortin 1 receptor (MC1R) gene is the main determinant of the black (GG or GC genotypes) and brown (CC genotypes) colorations of Murciano-Granadina goats.
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Affiliation(s)
- D Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - A Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain
| | - M G Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - J V Delgado
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain
| | - V Landi
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain.,Department of Veterinary Medicine, University of Bari "Aldo Moro", SP. 62 per Casamassima km. 3, Valenzano, 70010, Italy
| | - A Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - J Fernández Álvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), Fuente Vaqueros, Granada, 18340, Spain
| | - X Such
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Spain
| | - J Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - M Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 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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Exploring genetic diversity and population structure of Punjab goat breeds using Illumina 50 K SNP bead chip. Trop Anim Health Prod 2021; 53:368. [PMID: 34169364 DOI: 10.1007/s11250-021-02825-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/18/2021] [Indexed: 10/21/2022]
Abstract
Pakistan has 35 goat breeds. Moreover, the province of Punjab has highest goat population constituting 37% of country's total population with seven goat breeds including Beetal, Daira Deen Panah, Nachi, Barbari, Teddi, Pahari, and Pothwari. The diversity study of breeds warrants the documentation of breeds particularly using genome wide panel of markers, i.e., SNP chip. The objective of the current study was to fill this gap of information. Therefore, in current study we collected total of 879 unrelated goat blood samples along with data on body weight measurements; genomic DNA was extracted, and genotyping was carried out using 50 K SNP bead chip. Quality control measures were performed in Plink 1.07. Genetic diversity was observed among studied populations using heterozygosity and pairwise FST estimates, principal component analysis, admixture analysis in Plink software with visualization in Clumpak, and constructing phylogenetic tree in Mega 7 software. Moderate to high level of heterozygosity was observed among the studied populations. Coefficient of inbreeding varied from 0.0186 ± 0.0327 in Pahari to 0.183 ± 0.0715 in Barbari. Barbari and Daira Deen Panah had quite higher level of inbreeding coefficient as compared to all other breeds with value of 0.183 ± 0.0715 and 0.1378 ± 0.0741, respectively. PCA identified three steps of subdividing the seven goat breeds at various levels of K. All the seven breeds made independent clusters at various levels of PCA. Admixture analysis revealed the distinctness of Teddi and Barbari breeds. Genetic sub-structuring was observed in the admixture patterns of Beetal breed. Moreover, high level of genetic admixture was observed in Nachi, Pahari, Pothwari, and Daira Deen Panah breeds. Admixture results were further interpreted by calculating pairwise FST values. Our results provided first insights about genetic diversity of Pakistani goat breeds based on genomic data. To conclude, the enriched goat breed diversity in Pakistan could provide valuable genetic reservoir for national breeding schemes.
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Eydivandi S, Roudbar MA, Karimi MO, Sahana G. Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia. Sci Rep 2021; 11:2834. [PMID: 33531649 PMCID: PMC7854752 DOI: 10.1038/s41598-021-82625-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/22/2021] [Indexed: 01/30/2023] Open
Abstract
The performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated population genetic diversity and selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. To detect genetic diversity and population structure, we used principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of homozygosity. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, nine overlapping candidate genes were detected by these four tests, especially TNIK, DOCK1, USH2A, and TYW1B which associate with resistance to diseases and climate adaptation. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.
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Affiliation(s)
- Sirous Eydivandi
- Department of Animal Science, Behbahan Branch, Islamic Azad University, Behbahan, Iran.
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark.
| | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful, Iran
| | - Mohammad Osman Karimi
- Department of Animal Science, Faculty of Agriculture, Herat University, Herat, Afghanistan
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark
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Martin SL, Benedict L, Wei W, Sauder CA, Beckie HJ, Hall LM. High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae). Sci Rep 2020; 10:18864. [PMID: 33139774 PMCID: PMC7608611 DOI: 10.1038/s41598-020-75345-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
Kochia, a major weed species, has evolved resistance to four herbicide modes of action. Herbicide resistance appears to spread quickly, which could result in diminished standing genetic variation, reducing the ability of populations to adapt further. Here we used double digest restriction enzyme associated sequencing to determine the level of gene flow among kochia populations and whether selection for glyphosate resistance reduces genetic variation. Canadian Prairie populations show little to no genetic differentiation (FST = 0.01) and no correlation between genetic and geographic distance (r2 = - 0.02 p = 0.56), indicating high gene flow and no population structure. There is some evidence that kochia populations are genetically depauperate compared to other weed species, but genetic diversity did not differ between glyphosate susceptible and resistant populations or individuals. The inbreeding coefficients suggest there are 23% fewer heterozygotes in these populations than expected with random mating, and no variation was found within the chloroplast. These results indicate that any alleles for herbicide resistance can be expected to spread quickly through kochia populations, but there is little evidence this spread will reduce the species' genetic variation or limit the species' ability to respond to further selection pressure.
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Affiliation(s)
- Sara L Martin
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, Canada.
| | - Leshawn Benedict
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, Canada
| | - Wei Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Connie A Sauder
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, Canada
| | - Hugh J Beckie
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, Australia
| | - Linda M Hall
- Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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Zhou Z, Fan Y, Wang G, Lai Z, Gao Y, Wu F, Lei C, Dang R. Detection of Selection Signatures Underlying Production and Adaptive Traits Based on Whole-Genome Sequencing of Six Donkey Populations. Animals (Basel) 2020; 10:ani10101823. [PMID: 33036357 PMCID: PMC7600737 DOI: 10.3390/ani10101823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 12/28/2022] Open
Abstract
Simple Summary After a long period of artificial selection, the donkey now presents a variety of body types and production performance values. In this experiment, we performed selective signal scanning on the second-generation resequencing data of six different varieties. The regions and candidate genes related to artificial selection were identified to provide reference for future breeding. Abstract Donkeys (Equus asinus) are an important farm animal. After long-term natural and artificial selection, donkeys now exhibit a variety of body sizes and production performance values. In this study, six donkey breeds, representing different regions and phenotypes, were used for second-generation resequencing. The sequencing results revealed more than seven million single nucleotide variants (SNVs), with an average of more than four million SNVs per species. We combined two methods, Z-transformed heterozygosity (ZHp) and unbiased estimates of pairwise fixation index (di) values, to analyze the signatures of selection. We mapped 11 selected regions and identified genes associated with coat color, body size, motion capacity, and high-altitude adaptation. These candidate genes included staining (ASIP and KITLG), body type (ACSL4, BCOR, CDKL5, LCOR, NCAPG, and TBX3), exercise (GABPA), and adaptation to low-oxygen environments (GLDC and HBB). We also analyzed the SNVs of the breed-specific genes for their potential functions and found that there are three varieties in the conserved regions with breed-specific mutation sites. Our results provide data to support the establishment of the donkey SNV chip and reference information for the utilization of the genetic resources of Chinese domestic donkeys.
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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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Kang X, Li M, Liu M, Liu S, Pan MG, Wiggans GR, Rosen BD, Liu GE. Copy number variation analysis reveals variants associated with milk production traits in dairy goats. Genomics 2020; 112:4934-4937. [PMID: 32898641 DOI: 10.1016/j.ygeno.2020.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 07/29/2020] [Accepted: 09/03/2020] [Indexed: 11/29/2022]
Abstract
Copy number variation (CNV) is a major type of genomic structural variation. We investigated their impacts on goat dairy traits using the CaprineSNP50 array. From 120 samples of five dairy goat breeds, we totally identified 42 CNVs ranging from 56,044 bp to 4,337,625 bp. We found significant associations between two CNVs (CNV5 and CNV25) and two milk production traits (mean of milk fat yield and mean of milk protein yield) after false discovery rate (FDR) correction (P < 0.05). CNV5 overlaps the ADAMTS20 gene, which is involved in the differentiation of mammary cell and plays a crucial role in lactogenic activity of bovine mammary epithelial cells. CNV25 overlaps with PAPPA2, which has been found to be associated with bovine reproduction and milk production traits. Our results revealed that CNVs overlapped with ADAMTS20 and PAPPA2 could be involved in goat dairy traits and function as candidate markers for further genetic selection.
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Affiliation(s)
- Xiaolong Kang
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, USA; College of Agriculture, Ningxia University, Yinchuan, China
| | - Mingxun Li
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, USA; College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Mei Liu
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, USA; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Michael G Pan
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, USA
| | | | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, USA.
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Barbato M, Reichel MP, Passamonti M, Low WY, Colli L, Tearle R, Williams JL, Ajmone Marsan P. A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel. PLoS One 2020; 15:e0231162. [PMID: 32271816 PMCID: PMC7145104 DOI: 10.1371/journal.pone.0231162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
In Hong Kong, there is a cattle population of ~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed ~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias ~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.
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Affiliation(s)
- Mario Barbato
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
| | - Michael P. Reichel
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Matilde Passamonti
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Wai Yee Low
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Licia Colli
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Rick Tearle
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - John L. Williams
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
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Gipson TA. Recent advances in breeding and genetics for dairy goats. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 32:1275-1283. [PMID: 31357268 PMCID: PMC6668855 DOI: 10.5713/ajas.19.0381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/03/2019] [Indexed: 12/27/2022]
Abstract
Goats (Capra hircus) were domesticated during the late Neolithic, approximately 10,500 years ago, and humans exerted minor selection pressure until fairly recently. Probably the largest genetic change occurring over the millennia happened via natural selection and random genetic drift, the latter causing genes to be fixed in small and isolated populations. Recent human-influenced genetic changes have occurred through biometrics and genomics. For the most part, biometrics has concentrated upon the refining of estimates of heritabilities and genetic correlations. Heritabilities are instrumental in the calculation of estimated breeding values and genetic correlations are necessary in the construction of selection indices that account for changes in multiple traits under selection at one time. Early genomic studies focused upon microsatellite markers, which are short tandem repeats of nucleic acids and which are detected using polymerase chain reaction primers flanking the microsatellite. Microsatellite markers have been very important in parentage verification, which can impact genetic progress. Additionally, microsatellite markers have been a useful tool in assessing genetic diversity between and among breeds, which is important in the conservation of minor breeds. Single nucleotide polymorphisms are a new genomic tool that have refined classical BLUP methodology (biometric) to provide more accurate genomic estimated breeding values, provided a large reference population is available.
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Affiliation(s)
- Terry A Gipson
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA
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