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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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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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Wijayanti D, Zhang S, Bai Y, Pan C, Chen H, Qu L, Guo Z, Lan X. Investigation on mRNA expression and genetic variation within goat SMAD2 gene and its association with litter size. Anim Biotechnol 2023; 34:2111-2119. [PMID: 35584800 DOI: 10.1080/10495398.2022.2077214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The SMAD family member 2 (SMAD2), a member of the TGF-beta superfamily, executes a significant part in the oogenesis and ovulation process. A genome-wide selective sweep analysis also found SMAD2 was different in the fertility groups of Laoshan dairy goats; whether this gene was linked to litter size was unknown. Therefore, SMAD2 was chosen to study its effects on Shaanbei white cashmere goat reproduction and mRNA expression profile. Herein, the mRNA expression level of SMAD2 was firstly determined in female goat tissues, revealing significant differences in mRNA levels of different tissues (p < 0.05), including ovary tissue, indicating a potential role for SMAD2 in goat prolificacy. Then, using six pairs of primers, only one indel locus (P3-Del-12-bp) was found to be polymorphic in goat SMAD2 (n = 501). ANOVA also revealed that a P3-Del-12-bp deletion was significantly related to first-born litter size (p = 0.037). The Chi-square (χ2) test revealed that the ID genotype was significantly more prevalent in mothers with multiple lambs (p = 0.01), indicating that heterozygous individuals (ID) are more likely to produce multiple lambs. Our findings suggest that the SMAD2 gene's P3-Del-12-bp deletion could be used to improve goat breeds by assisting with litter size selection.
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Affiliation(s)
- Dwi Wijayanti
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Department of Animal Science, Perjuangan University of Tasikmalaya, Tasikmalaya, West Java, Indonesia
| | - Sihuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yangyang Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, PR China
| | - Zhengang Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Animal Husbandry and Veterinary Science of Bijie City, Guizhou, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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Sánchez-Ramos R, Trujano-Chavez MZ, Gallegos-Sánchez J, Becerril-Pérez CM, Cadena-Villegas S, Cortez-Romero C. Detection of Candidate Genes Associated with Fecundity through Genome-Wide Selection Signatures of Katahdin Ewes. Animals (Basel) 2023; 13:ani13020272. [PMID: 36670812 PMCID: PMC9854690 DOI: 10.3390/ani13020272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
One of the strategies to genetically improve reproductive traits, despite their low inheritability, has been the identification of candidate genes. Therefore, the objective of this study was to detect candidate genes associated with fecundity through the fixation index (FST) and runs of homozygosity (ROH) of selection signatures in Katahdin ewes. Productive and reproductive records from three years were used and the genotypes (OvineSNP50K) of 48 Katahdin ewes. Two groups of ewes were identified to carry out the genetic comparison: with high fecundity (1.3 ± 0.03) and with low fecundity (1.1 ± 0.06). This study shows for the first time evidence of the influence of the CNOT11, GLUD1, GRID1, MAPK8, and CCL28 genes in the fecundity of Katahdin ewes; in addition, new candidate genes were detected for fecundity that were not reported previously in ewes but that were detected for other species: ANK2 (sow), ARHGAP22 (cow and buffalo cow), GHITM (cow), HERC6 (cow), DPF2 (cow), and TRNAC-GCA (buffalo cow, bull). These new candidate genes in ewes seem to have a high expression in reproduction. Therefore, future studies are needed focused on describing the physiological basis of changes in the reproductive behavior influenced by these genes.
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Affiliation(s)
- Reyna Sánchez-Ramos
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
| | | | - Jaime Gallegos-Sánchez
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
| | - Carlos Miguel Becerril-Pérez
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
- Agroecosistemas Tropicales, Colegio de Postgraduados, Campus Veracruz, Carretera Xalapa-Veracruz Km. 88.5, Manlio Favio Altamirano, Veracruz 91690, Mexico
| | - Said Cadena-Villegas
- Producción Agroalimentaria en Trópico, Colegio de Postgraduados, Campus Tabasco, Periférico Carlos A. Molina, Ranchería Rio Seco y Montaña, Heroica Cárdenas 86500, Mexico
| | - César Cortez-Romero
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
- Innovación en Manejo de Recursos Naturales, Colegio de Postgraduados, Campus San Luis Potosí, Agustín de Iturbide No. 73, Salinas de Hidalgo, San Luis Potosí 78622, Mexico
- Correspondence: ; Tel.: +52-5959-520-200 (ext. 4000)
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Revealing Genetic Diversity and Population Structure of Endangered Altay White-Headed Cattle Population Using 100 k SNP Markers. Animals (Basel) 2022; 12:ani12223214. [PMID: 36428441 PMCID: PMC9686749 DOI: 10.3390/ani12223214] [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: 09/20/2022] [Revised: 10/17/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Understanding the genetic basis of native cattle populations that have adapted to the local environment is of great significance for formulating appropriate strategies and programs for genetic improvement and protection. Therefore, it is necessary to understand the genetic diversity and population structure of Altay white-headed cattle so as to meet the current production needs under various environments, carry out continuous genetic improvement, and promote rapid adaptation to changing environments and breeding objectives. A total of 46 individual samples of endangered Xinjiang Altay white-headed cattle were collected in this study, including nine bulls and 37 cows. To collect genotype data, 100 k SNP markers were used, and then studies of genetic diversity, genetic structure, inbreeding degree, and family analysis were carried out. A total of 101,220 SNP loci were detected, and the genotype detection rate for individuals was ≥90%. There were 85,993 SNP loci that passed quality control, of which 93.5% were polymorphic. The average effective allele number was 0.036, the Polymorphism Information Content was 0.304 and the minimum allele frequency was 0.309, the average observed heterozygosity was 0.413, and the average expected heterozygosity was 0.403. The average genetic distance of Idengtical By State (IBS) was 0.3090, there were 461 ROH (genome-length homozygous fragments), 76.1% of which were between 1 and 5 MB in length, and the average inbreeding coefficient was 0.016. The 46 Altay white-headed cattle were divided into their families, and the individual numbers of each family were obviously different. To sum up, the Altay white-headed cattle conservation population had low heterozygosity, a high inbreeding degree, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the follow-up seed conservation process, seed selection and matching should be carried out according to the divided families to ensure the long-term protection of Altay white-headed cattle genetic resources.
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Torres-Hernández G, Maldonado-Jáquez JA, Granados-Rivera LD, Salinas-González H, Castillo-Hernández G. Status quo of genetic improvement in local goats: a review. Arch Anim Breed 2022; 65:207-221. [PMID: 35693297 PMCID: PMC9176210 DOI: 10.5194/aab-65-207-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/14/2022] [Indexed: 11/26/2022] Open
Abstract
This review aims to summarize and synthesize the
fragmented information available on the genetic improvement of local goats
(criollo, indigenous, native) on the American and other continents, where
populations with these goats have an important role in food security and the
economy of rural communities, as well as in conservation of biodiversity and
productivity improvement. Topics such as the current state of goat
production globally, conservation programs, resistance to parasites and
diseases, use of phenotypical characteristics and genomic information, and
molecular markers for genetic improvement are addressed. The main
challenges, opportunities, and limitations described in recent literature
concerning local goats in the immediate future are discussed.
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Affiliation(s)
| | - Jorge Alonso Maldonado-Jáquez
- Colegio de Postgraduados-Campus Montecillo, 56230 Montecillo, Estado
de México, México
- Instituto Nacional de Investigaciones Forestales, Agrícolas y
Pecuarias, Centro de Investigación Regional Norte Centro, Campo
Experimental La Laguna, 27440 Matamoros, Coahuila, México
| | - Lorenzo Danilo Granados-Rivera
- Instituto Nacional de Investigaciones Forestales, Agrícolas y
Pecuarias, Centro de Investigación Regional Noreste, Campo Experimental
General Terán, 67400 General Terán, Nuevo León, México
| | | | - Gabriela Castillo-Hernández
- Colegio de Postgraduados-Campus Montecillo, 56230 Montecillo, Estado
de México, México
- Facultad de Estudios
Superiores Cuautitlán, Universidad Nacional Autónoma de México, 54714 Cuautitlán Izcalli, Estado de
México, México
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Passamonti MM, Somenzi E, Barbato M, Chillemi G, Colli L, Joost S, Milanesi M, Negrini R, Santini M, Vajana E, Williams JL, Ajmone-Marsan P. The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. Animals (Basel) 2021; 11:2833. [PMID: 34679854 PMCID: PMC8532622 DOI: 10.3390/ani11102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Affiliation(s)
- Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Elisa Somenzi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Licia Colli
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Research Center on Biodiversity and Ancient DNA—BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - Marco Milanesi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Monia Santini
- Impacts on Agriculture, Forests and Ecosystem Services (IAFES) Division, Fondazione Centro Euro-Mediterraneo Sui Cambiamenti Climatici (CMCC), Viale Trieste 127, 01100 Viterbo, Italy;
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center—PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
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Association of Breed of Sheep or Goats with Somatic Cell Counts and Total Bacterial Counts of Bulk-Tank Milk. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11167356] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The objective was to describe potential associations of somatic cell counts (SCC) and total bacterial counts (TBC) in bulk-tank milk from sheep and goat farms with breeds of these animals in Greece. In total, 325 dairy sheep flocks and 119 dairy goat herds were visited for the collection of milk; the breed of animals in farms was evaluated for a potential association with SCC or TBC. The most frequently seen sheep breeds were the Lacaune (95 flocks) and the Chios (44 flocks). The most frequently seen goat breeds were the indigenous Greek (Capra prisca) (50 herds) and the Murciano-Granadina (13 herds). In a multivariable analysis, the breed and the application of machine-milking in sheep flocks, and the breed and the management system in goat herds emerged as significant factors for increased SCC (>0.75 × 106 cells mL−1) in bulk-tank milk. Further, the month of lactation at sampling in sheep flocks emerged a significant factor for increased TBC (>1500 × 103 cfu mL−1) in bulk-tank milk.
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Deniskova TE, Dotsev AV, Selionova MI, Reyer H, Sölkner J, Fornara MS, Aybazov AMM, Wimmers K, Brem G, Zinovieva NA. SNP-Based Genotyping Provides Insight Into the West Asian Origin of Russian Local Goats. Front Genet 2021; 12:708740. [PMID: 34276802 PMCID: PMC8282346 DOI: 10.3389/fgene.2021.708740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Specific local environmental and sociocultural conditions have led to the creation of various goat populations in Russia. National goat diversity includes breeds that have been selected for down and mohair production traits as well as versatile local breeds for which pastoralism is the main management system. Effective preservation and breeding programs for local goat breeds are missing due to the lack of DNA-based data. In this work, we analyzed the genetic diversity and population structure of Russian local goats, including Altai Mountain, Altai White Downy, Dagestan Downy, Dagestan Local, Karachaev, Orenburg, and Soviet Mohair goats, which were genotyped with the Illumina Goat SNP50 BeadChip. In addition, we addressed genetic relationships between local and global goat populations obtained from the AdaptMap project. Russian goats showed a high level of genetic diversity. Although a decrease in historical effective population sizes was revealed, the recent effective population sizes estimated for three generations ago were larger than 100 in all studied populations. The mean runs of homozygosity (ROH) lengths ranged from 79.42 to 183.94 Mb, and the average ROH number varied from 18 to 41. Short ROH segments (<2 Mb) were predominant in all breeds, while the longest ROH class (>16 Mb) was the least frequent. Principal component analysis, Neighbor-Net graph, and Admixture clustering revealed several patterns in Russian local goats. First, a separation of the Karachaev breed from other populations was observed. Moreover, genetic connections between the Orenburg and Altai Mountain breeds were suggested and the Dagestan breeds were found to be admixed with the Soviet Mohair breed. Neighbor-Net analysis and clustering of local and global breeds demonstrated the close genetic relations between Russian local and Turkish breeds that probably resulted from past admixture events through postdomestication routes. Our findings contribute to the understanding of the genetic relationships of goats originating in West Asia and Eurasia and may be used to design breeding programs for local goats to ensure their effective conservation and proper management.
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Affiliation(s)
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Marina I Selionova
- Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | | | - Ali-Magomed M Aybazov
- All-Russian Research Institute of Sheep and Goat Breeding - Branch of the Federal State Budgetary Scientific Institution, North Caucasian Agrarian Center, Stavropol, Russia
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
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Kominakis A, Tarsani E, Hager-Theodorides AL, Mastranestasis I, Hadjigeorgiou I. Clustering patterns mirror the geographical distribution and genetic history of Lemnos and Lesvos sheep populations. PLoS One 2021; 16:e0247787. [PMID: 33657161 PMCID: PMC7928510 DOI: 10.1371/journal.pone.0247787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/16/2021] [Indexed: 12/18/2022] Open
Abstract
Elucidating the genetic variation and structure of Lemnos and Lesvos sheep is critical for maintaining local genetic diversity, ecosystem integrity and resilience of local food production of the two North Aegean islands. In the present study, we explored genetic diversity and differentiation as well as population structure of the Lemnos and Lesvos sheep. Furthermore, we sought to identify a small panel of markers with the highest discriminatory power to assign animals across islands. A total number of n = 424 (n = 307, Lemnos and n = 117, Lesvos) ewes, sampled from n = 24 herds dispersed at different geographic regions on the two islands, were genotyped with the 50K SNP array. Mean observed heterozygosity was higher (but not statistically significantly different) in Lesvos than in Lemnos population (0.384 vs. 0.377) while inbreeding levels were higher in Lemnos than Lesvos herds (0.065 vs. 0.031). Results of principal components along with that of admixture analysis and estimated genetic distances revealed genetic clusters corresponding to Lesvos and Lemnos origin and the existence of infrastructure within islands that were associated with geographical isolation and genetic history of the studied populations. In particular, genetic analyses highlighted three geographically isolated herds in Lemnos that are located at mountainous areas of the island and are characterized as representatives of the local sheep by historic data and reports. Admixture analysis also showed a shared genetic background between Lemnos and Lesvos sheep attributable to past gene flow. Little overall genetic differentiation was detected between the two island sheep populations, while 150 discriminatory SNPs could accurately assign animals to their origin. Present results are comparable with those reported in the worldwide sheep breeds, suggesting geography related genetic patterns across and within islands and the existence of the local Lemnos sheep.
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Affiliation(s)
- Antonios Kominakis
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | - Eirini Tarsani
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
- * E-mail:
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11
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Theodoridis G, Pechlivanis A, Thomaidis NS, Spyros A, Georgiou CA, Albanis T, Skoufos I, Kalogiannis S, Tsangaris GT, Stasinakis AS, Konstantinou I, Triantafyllidis A, Gkagkavouzis K, Kritikou AS, Dasenaki ME, Gika H, Virgiliou C, Kodra D, Nenadis N, Sampsonidis I, Arsenos G, Halabalaki M, Mikros E. FoodOmicsGR_RI. A Consortium for Comprehensive Molecular Characterisation of Food Products. Metabolites 2021; 11:74. [PMID: 33513809 PMCID: PMC7911248 DOI: 10.3390/metabo11020074] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
The national infrastructure FoodOmicsGR_RI coordinates research efforts from eight Greek Universities and Research Centers in a network aiming to support research and development (R&D) in the agri-food sector. The goals of FoodOmicsGR_RI are the comprehensive in-depth characterization of foods using cutting-edge omics technologies and the support of dietary/nutrition studies. The network combines strong omics expertise with expert field/application scientists (food/nutrition sciences, plant protection/plant growth, animal husbandry, apiculture and 10 other fields). Human resources involve more than 60 staff scientists and more than 30 recruits. State-of-the-art technologies and instrumentation is available for the comprehensive mapping of the food composition and available genetic resources, the assessment of the distinct value of foods, and the effect of nutritional intervention on the metabolic profile of biological samples of consumers and animal models. The consortium has the know-how and expertise that covers the breadth of the Greek agri-food sector. Metabolomics teams have developed and implemented a variety of methods for profiling and quantitative analysis. The implementation plan includes the following research axes: development of a detailed database of Greek food constituents; exploitation of "omics" technologies to assess domestic agricultural biodiversity aiding authenticity-traceability control/certification of geographical/genetic origin; highlighting unique characteristics of Greek products with an emphasis on quality, sustainability and food safety; assessment of diet's effect on health and well-being; creating added value from agri-food waste. FoodOmicsGR_RI develops new tools to evaluate the nutritional value of Greek foods, study the role of traditional foods and Greek functional foods in the prevention of chronic diseases and support health claims of Greek traditional products. FoodOmicsGR_RI provides access to state-of-the-art facilities, unique, well-characterised sample sets, obtained from precision/experimental farming/breeding (milk, honey, meat, olive oil and so forth) along with more than 20 complementary scientific disciplines. FoodOmicsGR_RI is open for collaboration with national and international stakeholders.
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Affiliation(s)
- Georgios Theodoridis
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.P.); (C.V.); (D.K.)
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
| | - Alexandros Pechlivanis
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.P.); (C.V.); (D.K.)
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
| | - Nikolaos S. Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis, Zografou, 15771 Athens, Greece; (N.S.T.); (A.S.K.); (M.E.D.)
| | - Apostolos Spyros
- Department of Chemistry, University of Crete, Voutes Campus, 71003 Heraklion, Greece;
| | - Constantinos A. Georgiou
- Chemistry Laboratory, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece;
| | - Triantafyllos Albanis
- Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (T.A.); (I.K.)
| | - Ioannis Skoufos
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, University of Ioannina, 47100 Arta, Greece;
| | - Stavros Kalogiannis
- Department of Nutritional Sciences & Dietetics, International Hellenic University, Sindos Campus, 57400 Thessaloniki, Greece; (S.K.); (I.S.)
| | - George Th. Tsangaris
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
| | | | - Ioannis Konstantinou
- Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (T.A.); (I.K.)
| | - Alexander Triantafyllidis
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia S. Kritikou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis, Zografou, 15771 Athens, Greece; (N.S.T.); (A.S.K.); (M.E.D.)
| | - Marilena E. Dasenaki
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis, Zografou, 15771 Athens, Greece; (N.S.T.); (A.S.K.); (M.E.D.)
| | - Helen Gika
- Department of Medicine, Laboratory of Forensic Medicine & Toxicology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Christina Virgiliou
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.P.); (C.V.); (D.K.)
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
| | - Dritan Kodra
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.P.); (C.V.); (D.K.)
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
| | - Nikolaos Nenadis
- Laboratory of Food Chemistry and Technology, School of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Ioannis Sampsonidis
- Department of Nutritional Sciences & Dietetics, International Hellenic University, Sindos Campus, 57400 Thessaloniki, Greece; (S.K.); (I.S.)
| | - Georgios Arsenos
- Department of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Maria Halabalaki
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, 15771 Athens, Greece; (M.H.); (E.M.)
| | - Emmanuel Mikros
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, 15771 Athens, Greece; (M.H.); (E.M.)
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12
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Saravanan KA, Panigrahi M, Kumar H, Parida S, Bhushan B, Gaur GK, Kumar P, Dutt T, Mishra BP, Singh RK. Genome-wide assessment of genetic diversity, linkage disequilibrium and haplotype block structure in Tharparkar cattle breed of India. Anim Biotechnol 2020; 33:297-311. [PMID: 32730141 DOI: 10.1080/10495398.2020.1796696] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (HO) and expected heterozygosity (HE) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by FROH, FHOM, FGRM and FUNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r2 was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations.
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Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Subhashree Parida
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - G K Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Pushpendra Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - B P Mishra
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - R K Singh
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
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13
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Guan D, Landi V, Luigi-Sierra MG, Delgado JV, Such X, Castelló A, Cabrera B, Mármol-Sánchez E, Fernández-Alvarez J, de la Torre Casañas JLR, Martínez A, Jordana J, Amills M. Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats. J Anim Sci Biotechnol 2020; 11:35. [PMID: 32175082 PMCID: PMC7065321 DOI: 10.1186/s40104-020-00435-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/17/2020] [Indexed: 12/19/2022] Open
Abstract
Background In this study, we aimed to investigate the molecular basis of lactation as well as to identify the genetic factors that influence milk yield and composition in goats. To achieve these two goals, we have analyzed how the mRNA profile of the mammary gland changes in seven Murciano-Granadina goats at each of three different time points, i.e. 78 d (T1, early lactation), 216 d (T2, late lactation) and 285 d (T3, dry period) after parturition. Moreover, we have performed a genome-wide association study (GWAS) for seven dairy traits recorded in the 1st lactation of 822 Murciano-Granadina goats. Results The expression profiles of the mammary gland in the early (T1) and late (T2) lactation were quite similar (42 differentially expressed genes), while strong transcriptomic differences (more than one thousand differentially expressed genes) were observed between the lactating (T1/T2) and non-lactating (T3) mammary glands. A large number of differentially expressed genes were involved in pathways related with the biosynthesis of amino acids, cholesterol, triglycerides and steroids as well as with glycerophospholipid metabolism, adipocytokine signaling, lipid binding, regulation of ion transmembrane transport, calcium ion binding, metalloendopeptidase activity and complement and coagulation cascades. With regard to the second goal of the study, the performance of the GWAS allowed us to detect 24 quantitative trait loci (QTLs), including three genome-wide significant associations: QTL1 (chromosome 2, 130.72-131.01 Mb) for lactose percentage, QTL6 (chromosome 6, 78.90-93.48 Mb) for protein percentage and QTL17 (chromosome 17, 11.20 Mb) for both protein and dry matter percentages. Interestingly, QTL6 shows positional coincidence with the casein genes, which encode 80% of milk proteins. Conclusions The abrogation of lactation involves dramatic changes in the expression of genes participating in a broad array of physiological processes such as protein, lipid and carbohydrate metabolism, calcium homeostasis, cell death and tissue remodeling, as well as immunity. We also conclude that genetic variation at the casein genes has a major impact on the milk protein content of Murciano-Granadina goats.
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Affiliation(s)
- Dailu Guan
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Vincenzo Landi
- 2Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
| | - María Gracia Luigi-Sierra
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | | | - Xavier Such
- 3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna Castelló
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Betlem Cabrera
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Emilio Mármol-Sánchez
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Javier Fernández-Alvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), 18340 Granada, Spain
| | | | - Amparo Martínez
- 2Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Jordi Jordana
- 3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marcel Amills
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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