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Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle ( Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers. Int J Mol Sci 2023; 24:ijms24055061. [PMID: 36902492 PMCID: PMC10003406 DOI: 10.3390/ijms24055061] [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: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
Abstract
Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.
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Falchi L, Cesarani A, Mastrangelo S, Senczuk G, Portolano B, Pilla F, Macciotta NPP. Analysis of runs of homozygosity of cattle living in different climate zones. J Anim Sci 2023; 101:skad061. [PMID: 36802370 PMCID: PMC10066727 DOI: 10.1093/jas/skad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.
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Affiliation(s)
- Laura Falchi
- Dipartimento di Agraria, University of Sassari, 07100 Sassari, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, 07100 Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, 30602 Athens, USA
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
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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: 5] [Impact Index Per Article: 2.5] [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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Toro Ospina AM, Aguilar I, Vargas de Oliveira MH, Cruz Dos Santos Correia LE, Vercesi Filho AE, Albuquerque LG, de Vasconcelos Silva JAI. Assessing the accuracy of imputation in the Gyr breed using different SNP panels. Genome 2021; 64:893-899. [PMID: 34057850 DOI: 10.1139/gen-2020-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to evaluate the accuracy of imputation in a Gyr population using two medium-density panels (Bos taurus - Bos indicus) and to test whether the inclusion of the Nellore breed increases the imputation accuracy in the Gyr population. The database consisted of 289 Gyr females from Brazil genotyped with the GGP Bovine LDv4 chip containing 30 000 SNPs and 158 Gyr females from Colombia genotyped with the GGP indicus chip containing 35 000 SNPs. A customized chip was created that contained the information of 9109 SNPs (9K) to test the imputation accuracy in Gyr populations; 604 Nellore animals with information of LD SNPs tested in the scenarios were included in the reference population. Four scenarios were tested: LD9K_30KGIR, LD9K_35INDGIR, LD9K_30KGIR_NEL, and LD9K_35INDGIR_NEL. Principal component analysis (PCA) was computed for the genomic matrix and sample-specific imputation accuracies were calculated using Pearson's correlation (CS) and the concordance rate (CR) for imputed genotypes. The results of PCA of the Colombian and Brazilian Gyr populations demonstrated the genomic relationship between the two populations. The CS and CR ranged from 0.88 to 0.94 and from 0.93 to 0.96, respectively. Among the scenarios tested, the highest CS (0.94) was observed for the LD9K_30KGIR scenario. The present results highlight the importance of the choice of chip for imputation in the Gyr breed. However, the variation in SNPs may reduce the imputation accuracy even when the chip of the Bos indicus subspecies is used.
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Affiliation(s)
| | - Ignacio Aguilar
- Instituto Nacional de Investigación Agropecuaria, INIA, Montevideo, Uruguay
| | | | | | | | - Lucia Galvão Albuquerque
- Faculdade de Ciências Agrárias e Veterinárias - Unesp, CEP 14.884-900, Jaboticabal, São Paulo, Brasil
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Malomane DK, Weigend S, Schmitt AO, Weigend A, Reimer C, Simianer H. Genetic diversity in global chicken breeds in relation to their genetic distances to wild populations. Genet Sel Evol 2021; 53:36. [PMID: 33853523 PMCID: PMC8048360 DOI: 10.1186/s12711-021-00628-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 03/30/2021] [Indexed: 12/03/2022] Open
Abstract
Background Migration of a population from its founder population is expected to cause a reduction of its genetic diversity and facilitates differentiation between the population and its founder population, as predicted by the theory of genetic isolation by distance. Consistent with that theory, a model of expansion from a single founder predicts that patterns of genetic diversity in populations can be explained well by their geographic expansion from their founders, which is correlated with genetic differentiation. Methods To investigate this in chicken, we estimated the relationship between the genetic diversity of 160 domesticated chicken populations and their genetic distances to wild chicken populations. Results Our results show a strong inverse relationship, i.e. 88.6% of the variation in the overall genetic diversity of domesticated chicken populations was explained by their genetic distance to the wild populations. We also investigated whether the patterns of genetic diversity of different types of single nucleotide polymorphisms (SNPs) and genes are similar to that of the overall genome. Among the SNP classes, the non-synonymous SNPs deviated most from the overall genome. However, genetic distance to the wild chicken still explained more variation in domesticated chicken diversity across all SNP classes, which ranged from 83.0 to 89.3%. Conclusions Genetic distance between domesticated chicken populations and their wild relatives can predict the genetic diversity of the domesticated populations. On the one hand, genes with little genetic variation across populations, regardless of the genetic distance to the wild population, are associated with major functions such as brain development. Changes in such genes may be detrimental to the species. On the other hand, genetic diversity seems to change at a faster rate within genes that are associated with e.g. protein transport and protein and lipid metabolic processes. In general, such genes may be flexible to changes according to the populations’ needs. These results contribute to the knowledge of the evolutionary patterns of different functional genomic regions in the chicken. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00628-z.
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Affiliation(s)
- Dorcus Kholofelo Malomane
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany. .,Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.
| | - Steffen Weigend
- Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Armin Otto Schmitt
- Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Breeding Informatics Group, Department of Animal Sciences, Georg August-Universität Goettingen, Goettingen, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
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Kierkegaard LS, Groeneveld LF, Kettunen A, Berg P. The status and need for characterization of Nordic animal genetic resources. ACTA AGR SCAND A-AN 2020. [DOI: 10.1080/09064702.2020.1722216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | | | - Anne Kettunen
- Farm Animal Section, NordGen – The Nordic Genetic Resource Center, Ås, Norway
- Nofima AS, Ås, Norway
| | - Peer Berg
- Farm Animal Section, NordGen – The Nordic Genetic Resource Center, Ås, Norway
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
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Utsunomiya YT, Milanesi M, Fortes MRS, Porto-Neto LR, Utsunomiya ATH, Silva MVGB, Garcia JF, Ajmone-Marsan P. Genomic clues of the evolutionary history of Bos indicus cattle. Anim Genet 2019; 50:557-568. [PMID: 31475748 DOI: 10.1111/age.12836] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2019] [Indexed: 01/08/2023]
Abstract
Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.
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Affiliation(s)
- Y T Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Bld, 68 Cooper Rd, Brisbane, 4072, Qld, Australia
| | - L R Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia QLD, Brisbane, 4067, Qld, Australia
| | - A T H Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M V G B Silva
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Gado de Leite, Juiz de Fora, MG, 360381330, Brazil
| | - J F Garcia
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Brazil
| | - P Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA and BioDNA, Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, Piacenza, 29122, Italy
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Iqbal N, Liu X, Yang T, Huang Z, Hanif Q, Asif M, Khan QM, Mansoor S. Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan. PLoS One 2019; 14:e0215065. [PMID: 30973947 PMCID: PMC6459497 DOI: 10.1371/journal.pone.0215065] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/26/2019] [Indexed: 12/30/2022] Open
Abstract
The primary goal of cattle genomics is the identification of genome-wide polymorphism associated with economically important traits. The bovine genome sequencing project was completed in 2009. Since then, using massively parallel sequencing technologies, a large number of Bos taurus cattle breeds have been resequenced and scanned for genome-wide polymorphisms. As a result, a substantial number of single nucleotide polymorphisms (SNPs) have been discovered across European Bos taurus genomes, whereas extremely less number of SNPs are cataloged for Bos indicus breeds. In this study, we performed whole-genome resequencing, reference-based mapping, functional annotation and gene enrichment analysis of 20 sires representing eleven important Bos indicus (indicine) breeds of Pakistan. The breeds sequenced here include: Sahiwal, Red Sindhi, Tharparkar and Cholistani (tropically adapted dairy and dual purpose breeds), Achai, Bhagnari, Dajal and Lohani (high altitude adapted dual and drought purpose breeds); Dhanni, Hisar Haryana and Gabrali (dairy and light drought purpose breeds). A total of 17.4 billion QC passed reads were produced using BGISEQ-500 next generation sequencing platform to generate 9 to 27-fold genome coverage (average ~16×) for each of the 20 sequenced sires. A total of 67,303,469 SNPs were identified, of which 3,850,365 were found novel and 1,083,842 insertions-deletions (InDels) were detected across the whole sequenced genomes (491,247 novel). Comparative analysis using coding region SNPs revealed a close relationship between the best milking indicine breeds; Red Sindhi and Sahiwal. On the other hand, Bhagnari and Tharparkar being popular for their adaptation to dry and extremely hot climates were found to share the highest number of SNPs. Functional annotation identified a total of 3,194 high-impact (disruptive) SNPs and 745 disruptive InDels (in 275 genes) that may possibly affect economically important dairy and beef traits. Functional enrichment analysis was performed and revealed that high or moderate impact variants in wingless-related integration site (Wnt) and vascular smooth muscle contraction (VSMC) signaling pathways were significantly over-represented in tropically adapted heat tolerant Pakistani-indicine breeds. On the other hand, vascular endothelial growth factor (VEGF) and hypoxia-inducible factor 1 (HIF-1) signaling pathways were found over-represented in highland adapted Pakistani-indicine breeds. Similarly, the ECM-receptor interaction and Jak-STAT signaling pathway were significantly enriched in dairy and beef purpose Pakistani-indicine cattle breeds. The Toll-like receptor signaling pathway was significantly enriched in most of the Pakistani-indicine cattle. Therefore, this study provides baseline data for further research to investigate the molecular mechanisms of major traits and to develop potential genomic markers associated with economically important breeding traits, particularly in indicine cattle.
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Affiliation(s)
- Naveed Iqbal
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
- Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Department of Biotechnology & Informatics, Faculty of life Sciences, Baluchistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Baluchistan, Pakistan
| | - Xin Liu
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
| | - Ting Yang
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
| | - Ziheng Huang
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Qaiser Mahmood Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
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Zhao J, Li T, Xu Z, Wang Z, Yang S, Chen A. AFLP markers for meat traceability of cattle in the Chinese market. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.04.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Nayee N, Sahana G, Gajjar S, Sudhakar A, Trivedi K, Lund MS, Guldbrandtsen B. Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses. J Anim Breed Genet 2018; 135:432-441. [PMID: 30117205 DOI: 10.1111/jbg.12356] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 01/06/2023]
Abstract
Bos indicus cattle breeds are genetically distinct from Bos taurus breeds. We examined the performance of three SNP arrays, the Illumina BovineHD BeadChip (777k; Illumina Inc.), the Illumina BovineSNP50 BeadChip (50k) and the GeneSeek 70k Indicus chip (75Ki; GeneSeek) in four B. indicus breeds (Gir, Kankrej, Sahiwal and Red Sindhi) and their B. taurus crosses, along with two B. taurus breeds, Holstein and Jersey. More SNPs on both Illumina SNP chips were monomorphic in B. indicus breeds (average 20.3%-29.3% on the 777k chip, 35.5%-45.5% on the 50k chip) than in Holstein (19.7% on the 777k chip, 17.1% on the 50k chip). The proportion of monomorphic SNPs on the 75Ki chip was much lower, 4% (2.8%-7%) in B. indicus breeds, while it was 33.5% in Holstein. With on average 164,357 heterozygous loci in B. indicus breeds, the 777k SNP chip has sufficient heterozygous loci to design a chip customized for B. indicus breeds. Principal component analysis clearly differentiated B. indicus from B. taurus breeds. Differentiation among B. indicus breeds was only achieved by plotting the third and fifth principal components using 777k genotype data. Admixture analysis showed that many B. indicus animals, previously believed to be of pure origin, are in fact had mixed ancestry. The extent of linkage disequilibrium showed comparatively higher effective population sizes in four B. indicus breeds compared to two B. taurus breeds. The results of admixture analyses show that it is important to assess the genomic composition of a bull before using it in a breeding programme.
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Affiliation(s)
- Nilesh Nayee
- National Dairy Development Board, Gujarat, India
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | | | | | | | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
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11
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A PLAG1 mutation contributed to stature recovery in modern cattle. Sci Rep 2017; 7:17140. [PMID: 29215042 PMCID: PMC5719367 DOI: 10.1038/s41598-017-17127-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 11/22/2017] [Indexed: 01/06/2023] Open
Abstract
The recent evolution of cattle is marked by fluctuations in body size. Height in the Bos taurus lineage was reduced by a factor of ~1.5 from the Neolithic to the Middle Ages, and increased again only during the Early Modern Ages. Using haplotype analysis, we found evidence that the bovine PLAG1 mutation (Q) with major effects on body size, weight and reproduction is a >1,000 years old derived allele that increased rapidly in frequency in Northwestern European B. taurus between the 16th and 18th centuries. Towards the 19th and 20th centuries, Q was introgressed into non-European B. taurus and Bos indicus breeds. These data implicate a major role of Q in recent changes in body size in modern cattle, and represent one of the first examples of a genomic sweep in livestock that was driven by selection on a complex trait.
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12
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Stafuzza NB, Zerlotini A, Lobo FP, Yamagishi MEB, Chud TCS, Caetano AR, Munari DP, Garrick DJ, Machado MA, Martins MF, Carvalho MR, Cole JB, Barbosa da Silva MVG. Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. PLoS One 2017; 12:e0173954. [PMID: 28323836 PMCID: PMC5360315 DOI: 10.1371/journal.pone.0173954] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/01/2017] [Indexed: 11/18/2022] Open
Abstract
Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | | | | | | | - Tatiane Cristina Seleguim Chud
- Departamento de Ciências Exatas, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | | | - Danísio Prado Munari
- Departamento de Ciências Exatas, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Dorian J. Garrick
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | | | | | - Maria Raquel Carvalho
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - John Bruce Cole
- United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, United States of America
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13
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Upadhyay MR, Chen W, Lenstra JA, Goderie CRJ, MacHugh DE, Park SDE, Magee DA, Matassino D, Ciani F, Megens HJ, van Arendonk JAM, Groenen MAM. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle. Heredity (Edinb) 2016; 118:169-176. [PMID: 27677498 PMCID: PMC5234481 DOI: 10.1038/hdy.2016.79] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 01/10/2023] Open
Abstract
The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.
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Affiliation(s)
- M R Upadhyay
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish Institute of Agricultural Sciences, Uppsala, Sweden
| | - W Chen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, CM Utrecht, The Netherlands
| | | | - D E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - S D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre, Dublin 2, Ireland
| | - D A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - D Matassino
- Consortium for Experimentation, Dissemination and application of Innovative Biotechniques, ConSDABI NFP, I FAO-GS AnGR, Benevento, Italy
| | - F Ciani
- Consortium for Experimentation, Dissemination and application of Innovative Biotechniques, ConSDABI NFP, I FAO-GS AnGR, Benevento, Italy
| | - H-J Megens
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - J A M van Arendonk
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - M A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
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14
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Biegelmeyer P, Gulias-Gomes CC, Caetano AR, Steibel JP, Cardoso FF. Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle. BMC Genet 2016; 17:32. [PMID: 26832943 PMCID: PMC4736111 DOI: 10.1186/s12863-016-0339-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/20/2016] [Indexed: 11/25/2022] Open
Abstract
Background The existence of moderate to high levels of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) affecting traits of interest is fundamental for the success of genome-wide association (GWAS) and genomic selection (GS) studies. Knowledge about the extent and the pattern of LD in livestock populations is essential to determine the density of single nucleotide polymorphisms (SNP) required for accurate GWAS and GS. Moreover, observed LD is related to historical effective population sizes (Ne), and can provide insights into the genetic diversity history of populations. Estimates of the consistency of linkage phase across breeds (RH,B) can be used to determine if there is sufficient relationship to use pooled reference populations in multi-breed GS programs. The objective of this study was to estimate LD levels, persistence of phase and effective population size in Hereford and Braford cattle populations sampled in Brazil. Results Mean LD estimates, measured using the squared correlation of alleles at two loci (r2), obtained between adjacent SNP across all chromosomes were 0.21 ± 0.27 for Herefords (391 samples with 41,241 SNP) and 0.16 ± 0.22 for Brafords (2044 samples and 41,207 SNP). Estimated r2 was > 0.2 and 0.3, respectively, for 34 and 25 % of adjacent markers in Herefords, and 26 and 17 % in Brafords. Estimated Ne for Brafords and Herefords at the current generation was 220 and 153 individuals, respectively. The two breeds demonstrated moderate to strong persistence of phase at all distances (RH,B = 0.53 to 0.97). The largest phase correlations were found in the 0 to 50 Kb bins (RH,B = 0.92 to 0.97). Estimated LD decreased rapidly with increasing distance between SNP, however, useful linkage for GWAS and GS (r2 > 0.2) was found spanning to ~50 Kb. Conclusions Panels containing about 50,000 and 150,000 SNP markers are necessary to detect minimal levels of LD between adjacent markers that would be useful for GWAS and GS studies to Hereford and Braford breeds, respectively. Markers are expected to be linked to the same QTL alleles in distances < 50 Kb in both populations due to observed high persistence of phase levels.
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Affiliation(s)
- Patrícia Biegelmeyer
- Programa de Pós-Graduação em Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil.
| | | | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. .,Programa de Pós-Graduação em Ciências Animais, Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Brasília, Distrito Federal, Brazil. .,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, Distrito Federal, Brazil.
| | | | - Fernando F Cardoso
- Programa de Pós-Graduação em Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil. .,Embrapa Pecuária Sul, Bagé, Rio Grande do Sul, Brazil. .,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, Distrito Federal, Brazil.
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15
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Hartati H, Utsunomiya YT, Sonstegard TS, Garcia JF, Jakaria J, Muladno M. Evidence of Bos javanicus x Bos indicus hybridization and major QTLs for birth weight in Indonesian Peranakan Ongole cattle. BMC Genet 2015; 16:75. [PMID: 26141727 PMCID: PMC4491226 DOI: 10.1186/s12863-015-0229-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/10/2015] [Indexed: 11/10/2022] Open
Abstract
Background Peranakan Ongole (PO) is a major Indonesian Bos indicus breed that derives from animals imported from India in the late 19th century. Early imports were followed by hybridization with the Bos javanicus subspecies of cattle. Here, we used genomic data to partition the ancestry components of PO cattle and map loci implicated in birth weight. Results We found that B. javanicus contributes about 6-7 % to the average breed composition of PO cattle. Only two nearly fixed B. javanicus haplotypes were identified, suggesting that most of the B. javanicus variants are segregating under drift or by the action of balancing selection. The zebu component of the PO genome was estimated to derive from at least two distinct ancestral pools. Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle. Conclusions This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization. Additionally, previously described loci implicated in body size in worldwide beef cattle breeds also affect birth weight in PO cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0229-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hartati Hartati
- Beef Cattle Research Station, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Jln. Pahlawan no. 2 Grati, Pasuruan, East Java, 16784, Indonesia.
| | - Yuri Tani Utsunomiya
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil.
| | - Tad Stewart Sonstegard
- ARS-USDA - Agricultural Research Service - United States Department of Agriculture, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA.
| | - José Fernando Garcia
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil. .,Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, 16050-680, Brazil.
| | - Jakaria Jakaria
- Faculty of Animal Science, Bogor Agriculture University, Jln. Agatis kampus IPB Dramaga, Bogor, 16680, Indonesia.
| | - Muladno Muladno
- Faculty of Animal Science, Bogor Agriculture University, Jln. Agatis kampus IPB Dramaga, Bogor, 16680, Indonesia.
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16
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Boison S, Santos D, Utsunomiya A, Carvalheiro R, Neves H, O’Brien A, Garcia J, Sölkner J, da Silva M. Strategies for single nucleotide polymorphism (SNP) genotyping to enhance genotype imputation in Gyr (Bos indicus) dairy cattle: Comparison of commercially available SNP chips. J Dairy Sci 2015; 98:4969-89. [DOI: 10.3168/jds.2014-9213] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/22/2015] [Indexed: 01/15/2023]
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O'Brien AMP, Höller D, Boison SA, Milanesi M, Bomba L, Utsunomiya YT, Carvalheiro R, Neves HHR, da Silva MVB, VanTassell CP, Sonstegard TS, Mészáros G, Ajmone-Marsan P, Garcia F, Sölkner J. Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations. Genet Sel Evol 2015; 47:31. [PMID: 25928250 PMCID: PMC4404172 DOI: 10.1186/s12711-015-0109-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 02/27/2015] [Indexed: 11/10/2022] Open
Abstract
Background Nelore and Gir are the two most important indicine cattle breeds for production of beef and milk in Brazil. Historical records state that these breeds were introduced in Brazil from the Indian subcontinent, crossed to local taurine cattle in order to quickly increase the population size, and then backcrossed to the original breeds to recover indicine adaptive and productive traits. Previous investigations based on sparse DNA markers detected taurine admixture in these breeds. High-density genome-wide analyses can provide high-resolution information on the genetic composition of current Nelore and Gir populations, estimate more precisely the levels and nature of taurine introgression, and shed light on their history and the strategies that were used to expand these breeds. Results We used the high-density Illumina BovineHD BeadChip with more than 777 K single nucleotide polymorphisms (SNPs) that were reduced to 697 115 after quality control filtering to investigate the structure of Nelore and Gir populations and seven other worldwide populations for comparison. Multidimensional scaling and model-based ancestry estimation clearly separated the indicine, European taurine and African taurine ancestries. The average level of taurine introgression in the autosomal genome of Nelore and Gir breeds was less than 1% but was 9% for the Brahman breed. Analyses based on the mitochondrial SNPs present in the Illumina BovineHD BeadChip did not clearly differentiate taurine and indicine haplotype groupings. Conclusions The low level of taurine ancestry observed for both Nelore and Gir breeds confirms the historical records of crossbreeding and supports a strong directional selection against taurine haplotypes via backcrossing. Random sampling in production herds across the country and subsequent genotyping would be useful for a more complete view of the admixture levels in the commercial Nelore and Gir populations. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0109-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana M Perez O'Brien
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Daniela Höller
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Solomon A Boison
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Marco Milanesi
- Università Cattolica del Sacro Cuore di Piacenza, Institute of Zootechnica and Biodiversity and Ancient DNA Research Center - BioDNA, Piacenza, Italy.
| | - Lorenzo Bomba
- Università Cattolica del Sacro Cuore di Piacenza, Institute of Zootechnica and Biodiversity and Ancient DNA Research Center - BioDNA, Piacenza, Italy.
| | - Yuri T Utsunomiya
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil.
| | - Roberto Carvalheiro
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil.
| | - Haroldo H R Neves
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil.
| | - Marcos V B da Silva
- Empresa Brasileira de Pesquisa Agropecuária - Embrapa Gado de Leite, Juiz de Fora, MG, Brazil.
| | - Curtis P VanTassell
- United States Department of Agriculture - Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, USA.
| | - Tad S Sonstegard
- United States Department of Agriculture - Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD, USA.
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Paolo Ajmone-Marsan
- Università Cattolica del Sacro Cuore di Piacenza, Institute of Zootechnica and Biodiversity and Ancient DNA Research Center - BioDNA, Piacenza, Italy.
| | - Fernando Garcia
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrária e Veterinárias, Jaboticabal, SP, Brazil. .,Universidade Estadual Paulista (UNESP) - Faculdade de Medicina Veterinária de Araçatuba, Araçatuba, SP, Brazil.
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
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18
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Biscarini F, Nicolazzi EL, Stella A, Boettcher PJ, Gandini G. Challenges and opportunities in genetic improvement of local livestock breeds. Front Genet 2015; 6:33. [PMID: 25763010 PMCID: PMC4340267 DOI: 10.3389/fgene.2015.00033] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/25/2015] [Indexed: 11/29/2022] Open
Abstract
Sufficient genetic variation in livestock populations is necessary both for adaptation to future changes in climate and consumer demand, and for continual genetic improvement of economically important traits. Unfortunately, the current trend is for reduced genetic variation, both within and across breeds. The latter occurs primarily through the loss of small, local breeds. Inferior production is a key driver for loss of small breeds, as they are replaced by high-output international transboundary breeds. Selection to improve productivity of small local breeds is therefore critical for their long term survival. The objective of this paper is to review the technology options available for the genetic improvement of small local breeds and discuss their feasibility. Most technologies have been developed for the high-input breeds and consequently are more favorably applied in that context. Nevertheless, their application in local breeds is not precluded and can yield significant benefits, especially when multiple technologies are applied in close collaboration with farmers and breeders. Breeding strategies that require cooperation and centralized decision-making, such as optimal contribution selection, may in fact be more easily implemented in small breeds.
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Affiliation(s)
| | | | - Alessandra Stella
- Parco Tecnologico Padano , Lodi, Italy ; Institute of Agricultural Biology and Biotechnology, National Research Council , Milan, Italy
| | - Paul J Boettcher
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations , Rome, Italy
| | - Gustavo Gandini
- Department of Veterinary Sciences and Public Health, University of Milan , Milan, Italy
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19
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Zavarez LB, Utsunomiya YT, Carmo AS, Neves HHR, Carvalheiro R, Ferenčaković M, Pérez O'Brien AM, Curik I, Cole JB, Van Tassell CP, da Silva MVGB, Sonstegard TS, Sölkner J, Garcia JF. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Front Genet 2015; 6:5. [PMID: 25688258 PMCID: PMC4310349 DOI: 10.3389/fgene.2015.00005] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/07/2015] [Indexed: 11/18/2022] Open
Abstract
The use of relatively low numbers of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, which affects conservation of genetic resources and sustainability of this breed. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH (>1 Mb) was lower than previously reported for other cattle breeds (4.58%). In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of Brazilian Nellore cattle. The putative signatures of selection on chromosomes 4, 7, and 12 may be involved in resistance to infectious diseases and fertility, and should be subject of future investigation.
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Affiliation(s)
- Ludmilla B Zavarez
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Yuri T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Adriana S Carmo
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Haroldo H R Neves
- GenSys Consultores Associados Porto Alegre, Rio Grande do Sul, Brazil ; Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Roberto Carvalheiro
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil
| | - Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Ana M Pérez O'Brien
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - John B Cole
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Marcos V G B da Silva
- Bioinformatics and Animal Genomics Laboratory, Embrapa Dairy Cattle Juiz de Fora, Minas Gerais, Brazil
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria
| | - José F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil ; Laboratório de Bioquímica e Biologia Molecular Animal, Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista Araçatuba, São Paulo, Brazil
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