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Nisa FU, Kaul H, Asif M, Amin I, Mrode R, Mansoor S, Mukhtar Z. Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale. Mamm Genome 2023; 34:602-614. [PMID: 37804434 DOI: 10.1007/s00335-023-10019-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/13/2023] [Indexed: 10/09/2023]
Abstract
Linkage disequilibrium (LD) affects genomic studies accuracy. High-density genotyping platforms identify SNPs across animal genomes, increasing LD evaluation resolution for accurate analysis. This study aimed to evaluate the decay and magnitude of LD in a cohort of 81 crossbred dairy cattle using the GGP_HDv3_C Bead Chip. After quality control, 116,710 Single Nucleotide Polymorphisms (SNPs) across 2520.241 Mb of autosomes were retained. LD extent was assessed between autosomal SNPs within a 10 Mb range using the r2 statistics. LD value declined as inter-marker distance increased. The average r2 value was 0.24 for SNP pairs < 10 kb apart, decreasing to 0.13 for 50-100 kb distances. Minor allele frequency (MAF) and sample size significantly impact LD. Lower MAF thresholds result in smaller r2 values, while higher thresholds show increased r2 values. Additionally, smaller sample sizes exhibit higher average r2 values, especially for larger physical distance intervals (> 50 kb) between SNP pairs. Effective population size and inbreeding coefficient were 150 and 0.028 for the present generation, indicating a decrease in genetic diversity over time. These findings imply that the utilization of high-density SNP panels and customized/breed-specific SNP panels represent a highly favorable approach for conducting genome-wide association studies (GWAS) and implementing genomic selection (GS) in the Bos indicus cattle breeds, whose genomes are still largely unexplored. Furthermore, it is imperative to devise a meticulous breeding strategy tailored to each herd, aiming to enhance desired traits while simultaneously preserving genetic diversity.
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Affiliation(s)
- Fakhar Un Nisa
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Haiba Kaul
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Raphael Mrode
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, UK
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan.
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Mdyogolo S, MacNeil MD, Neser FWC, Scholtz MM, Makgahlela ML. Assessing accuracy of genotype imputation in the Afrikaner and Brahman cattle breeds of South Africa. Trop Anim Health Prod 2022; 54:90. [PMID: 35133512 DOI: 10.1007/s11250-022-03102-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
Abstract
Imputation may be used to rescue genomic data from animals that would otherwise be eliminated due to a lower than desired call rate. The aim of this study was to compare the accuracy of genotype imputation for Afrikaner, Brahman, and Brangus cattle of South Africa using within- and multiple-breed reference populations. A total of 373, 309, and 101 Afrikaner, Brahman, and Brangus cattle, respectively, were genotyped using the GeneSeek Genomic Profiler 150 K panel that contained 141,746 markers. Markers with MAF ≤ 0.02 and call rates ≤ 0.95 or that deviated from Hardy Weinberg Equilibrium frequency with a probability of ≤ 0.0001 were excluded from the data as were animals with a call rate ≤ 0.90. The remaining data included 99,086 SNPs and 360 Afrikaner, 75,291 SNPs and 288 animals Brahman, and 97,897 SNPs and 99 Brangus animals. A total of 7986, 7002, and 7000 SNP from 50 Afrikaner and Brahman and 30 Brangus cattle, respectively, were masked and then imputed using BEAGLE v3 and FImpute v2. The within-breed imputation yielded accuracies ranging from 89.9 to 96.6% for the three breeds. The multiple-breed imputation yielded corresponding accuracies from 69.21 to 88.35%. The results showed that population homogeneity and numerical representation for within and across breed strategies, respectively, are crucial components for improving imputation accuracies.
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Affiliation(s)
- S Mdyogolo
- Department of Animal Breeding and Genetics, Agricultural Research Council, Irene, South Africa.
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa.
| | - M D MacNeil
- Department of Animal Breeding and Genetics, Agricultural Research Council, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
- Delta G, Miles City, MT, USA
| | - F W C Neser
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - M M Scholtz
- Department of Animal Breeding and Genetics, Agricultural Research Council, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - M L Makgahlela
- Department of Animal Breeding and Genetics, Agricultural Research Council, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
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Verardo LL, E Silva FF, Machado MA, do Carmo Panetto JC, de Lima Reis Faza DR, Otto PI, de Almeida Regitano LC, da Silva LOC, do Egito AA, do Socorro Maués Albuquerque M, Zanella R, da Silva MVGB. Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil. Front Genet 2021; 12:702822. [PMID: 34386042 PMCID: PMC8353373 DOI: 10.3389/fgene.2021.702822] [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: 04/30/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022] Open
Abstract
Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (Ne), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, Ne, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low Ne values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.
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Affiliation(s)
- Lucas Lima Verardo
- Animal Breeding Lab, Department of Animal Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brazil
| | | | | | | | | | - Pamela Itajara Otto
- Department of Animal Science, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | | | | | | | | | - Ricardo Zanella
- Department of Veterinary Medicine, Universidade de Passo Fundo, Passo Fundo, Brazil
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Fabbri MC, Dadousis C, Bozzi R. Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds. Animals (Basel) 2020; 10:ani10061034. [PMID: 32545850 PMCID: PMC7341513 DOI: 10.3390/ani10061034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = 100) were used. All cattle were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. The genotype quality control for each breed was conducted separately, and SNPs with call rate < 0.95 and minor allele frequency (MAF) > 1% were used for the analysis. LD extent was estimated in PLINK v1.9 using the squared correlation between pairs of loci (r2) across autosomes. Moreover, r2 values were used to calculate historical and contemporary effective population size (Ne) in each breed. Average r2 was similar in Calvana and Mucca Pisana (~0.14) and higher in Pontremolese (0.17); Limousin presented the lowest LD extent (0.07). LD up to 0.11-0.15 was persistent in the local breeds up to 0.75 Mbp, while in Limousin, it showed a more rapid decay. Variation of different LD levels across autosomes was observed in all the breeds. The results demonstrated a rapid decrease in Ne across generations for local breeds, and the contemporary population size observed in the local breeds, ranging from 41.7 in Calvana to 17 in Pontremolese, underlined the demographic alarming situation.
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Jahuey-Martínez FJ, Parra-Bracamonte GM, Garrick DJ, López-Villalobos N, Martínez-González JC, Sifuentes-Rincón AM, López-Bustamante LA. Accuracies of direct genomic breeding values for birth and weaning weights of registered Charolais cattle in Mexico. ANIMAL PRODUCTION SCIENCE 2020. [DOI: 10.1071/an18363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Genomic prediction is now routinely used in many livestock species to rank individuals based on genomic breeding values (GEBV).
Aims
This study reports the first assessment aimed to evaluate the accuracy of direct GEBV for birth (BW) and weaning (WW) weights of registered Charolais cattle in Mexico.
Methods
The population assessed included 823 animals genotyped with an array of 77000 single nucleotide polymorphisms. Genomic prediction used genomic best linear unbiased prediction (GBLUP), Bayes C (BC), and single-step Bayesian regression (SSBR) methods in comparison with a pedigree-based BLUP method.
Key results
Our results show that the genomic prediction methods provided low and similar accuracies to BLUP. The prediction accuracy of GBLUP and BC were identical at 0.31 for BW and 0.29 for WW, similar to BLUP. Prediction accuracies of SSBR for BW and WW were up to 4% higher than those by BLUP.
Conclusions
Genomic prediction is feasible under current conditions, and provides a slight improvement using SSBR.
Implications
Some limitations on reference population size and structure were identified and need to be addressed to obtain more accurate predictions in liveweight traits under the prevalent cattle breeding conditions of Mexico.
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Relationship of runs of homozygosity with adaptive and production traits in a paternal broiler line. Animal 2017; 12:1126-1134. [PMID: 29065939 DOI: 10.1017/s1751731117002671] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (N e ), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The N e of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.
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Linkage disequilibrium and haplotype block structure in Limousin, Simmental and native Polish Red cattle. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Niu H, Zhu B, Guo P, Zhang W, Xue J, Chen Y, Zhang L, Gao H, Gao X, Xu L, Li J. Estimation of linkage disequilibrium levels and haplotype block structure in Chinese Simmental and Wagyu beef cattle using high-density genotypes. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Zanella R, Peixoto JO, Cardoso FF, Cardoso LL, Biegelmeyer P, Cantão ME, Otaviano A, Freitas MS, Caetano AR, Ledur MC. Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data. Genet Sel Evol 2016; 48:24. [PMID: 27029213 PMCID: PMC4812646 DOI: 10.1186/s12711-016-0203-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/15/2016] [Indexed: 12/16/2022] Open
Abstract
Background Genetic improvement in livestock populations can be achieved without significantly affecting genetic diversity if mating systems and selection decisions take genetic relationships among individuals into consideration. The objective of this study was to examine the genetic diversity of two commercial breeds of pigs. Genotypes from 1168 Landrace (LA) and 1094 Large White (LW) animals from a commercial breeding program in Brazil were obtained using the Illumina PorcineSNP60 Beadchip. Inbreeding estimates based on pedigree (Fx) and genomic information using runs of homozygosity (FROH) and the single nucleotide polymorphisms (SNP) by SNP inbreeding coefficient (FSNP) were obtained. Linkage disequilibrium (LD), correlation of linkage phase (r) and effective population size (Ne) were also estimated. Results Estimates of inbreeding obtained with pedigree information were lower than those obtained with genomic data in both breeds. We observed that the extent of LD was slightly larger at shorter distances between SNPs in the LW population than in the LA population, which indicates that the LW population was derived from a smaller Ne. Estimates of Ne based on genomic data were equal to 53 and 40 for the current populations of LA and LW, respectively. The correlation of linkage phase between the two breeds was equal to 0.77 at distances up to 50 kb, which suggests that genome-wide association and selection should be performed within breed. Although selection intensities have been stronger in the LA breed than in the LW breed, levels of genomic and pedigree inbreeding were lower for the LA than for the LW breed. Conclusions The use of genomic data to evaluate population diversity in livestock animals can provide new and more precise insights about the effects of intense selection for production traits. Resulting information and knowledge can be used to effectively increase response to selection by appropriately managing the rate of inbreeding, minimizing negative effects of inbreeding depression and therefore maintaining desirable levels of genetic diversity.
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Affiliation(s)
- Ricardo Zanella
- Embrapa Swine and Poultry National Research Center, Animal Breeding and Genetics, Concordia, SC, Brazil.,Faculdade de Agronomia e Medicina Veterinária (FAMV), University of Passo Fundo, Passo Fundo, RS, Brazil
| | - Jane O Peixoto
- Embrapa Swine and Poultry National Research Center, Animal Breeding and Genetics, Concordia, SC, Brazil
| | - Fernando F Cardoso
- Embrapa Southern Region Animal Husbandry, Bagé, RS, Brazil.,Programa de pós-graduação em Zootecnia/UFPel, Pelotas, RS, Brazil
| | | | | | - Maurício E Cantão
- Embrapa Swine and Poultry National Research Center, Animal Breeding and Genetics, Concordia, SC, Brazil
| | | | | | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.,Programa de pós-graduação em Ciências Animais/Universidade de Brasília, Brasília, DF, Brazil
| | - Mônica C Ledur
- Embrapa Swine and Poultry National Research Center, Animal Breeding and Genetics, Concordia, SC, Brazil. .,Programa de pós-graduação em Zootecnia/Campus UDESC Oeste, Universidade do Estado de Santa Catarina, Chapecó, SC, Brazil.
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Karimi K, Esmailizadeh Koshkoiyeh A, Gondro C. Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2015; 57:47. [PMID: 26705480 PMCID: PMC4690407 DOI: 10.1186/s40781-015-0080-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/22/2015] [Indexed: 12/15/2022]
Abstract
BACKGROUND Knowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data. RESULTS A total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the r(2) criterion were computed by grouping all syntenic SNP pairwises for inter-marker distances from 0 Kb up to 1 Mb using three distance sets. Average r(2) above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations. CONCLUSIONS A wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.
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Affiliation(s)
- Karim Karimi
- />Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133 Iran
- />Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, PB 76169-133 Iran
| | - Ali Esmailizadeh Koshkoiyeh
- />Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133 Iran
| | - Cedric Gondro
- />School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
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Edea Z, Dadi H, Dessie T, Lee SH, Kim KS. Genome-wide linkage disequilibrium analysis of indigenous cattle breeds of Ethiopia and Korea using different SNP genotyping BeadChips. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0304-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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