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Gebrehiwot NZ, Aliloo H, Strucken EM, Marshall K, Al Kalaldeh M, Missohou A, Gibson JP. Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations. Front Genet 2021; 12:584355. [PMID: 33841491 PMCID: PMC8025404 DOI: 10.3389/fgene.2021.584355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 02/22/2021] [Indexed: 11/24/2022] Open
Abstract
Several studies have evaluated computational methods that infer the haplotypes from population genotype data in European cattle populations. However, little is known about how well they perform in African indigenous and crossbred populations. This study investigates: (1) global and local ancestry inference; (2) heterozygosity proportion estimation; and (3) genotype imputation in West African indigenous and crossbred cattle populations. Principal component analysis (PCA), ADMIXTURE, and LAMP-LD were used to analyse a medium-density single nucleotide polymorphism (SNP) dataset from Senegalese crossbred cattle. Reference SNP data of East and West African indigenous and crossbred cattle populations were used to investigate the accuracy of imputation from low to medium-density and from medium to high-density SNP datasets using Minimac v3. The first two principal components differentiated Bos indicus from European Bos taurus and African Bos taurus from other breeds. Irrespective of assuming two or three ancestral breeds for the Senegalese crossbreds, breed proportion estimates from ADMIXTURE and LAMP-LD showed a high correlation (r ≥ 0.981). The observed ancestral origin heterozygosity proportion in putative F1 crosses was close to the expected value of 1.0, and clearly differentiated F1 from all other crosses. The imputation accuracies (estimated as correlation) between imputed and the real data in crossbred animals ranged from 0.142 to 0.717 when imputing from low to medium-density, and from 0.478 to 0.899 for imputation from medium to high-density. The imputation accuracy was generally higher when the reference data came from the same geographical region as the target population, and when crossbred reference data was used to impute crossbred genotypes. The lowest imputation accuracies were observed for indigenous breed genotypes. This study shows that ancestral origin heterozygosity can be estimated with high accuracy and will be far superior to the use of observed individual heterozygosity for estimating heterosis in African crossbred populations. It was not possible to achieve high imputation accuracy in West African crossbred or indigenous populations based on reference data sets from East Africa, and population-specific genotyping with high-density SNP assays is required to improve imputation.
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Affiliation(s)
- Netsanet Z Gebrehiwot
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Hassan Aliloo
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Eva M Strucken
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Karen Marshall
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
| | - Mohammad Al Kalaldeh
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Ayao Missohou
- L'École Inter-États des Sciences et Médecine Vétérinaires de Dakar (EISMV), Dakar, Senegal
| | - John P Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
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Michel-Regalado NG, Ayala-Valdovinos MÁ, Galindo-García J, Duifhuis-Rivera T, Sánchez-Chiprés DR, Valencia-Posadas M. Effect of COQ9 and STAT5A polymorphisms on reproductive performance in a Holstein cow herd in Mexico. Anim Reprod 2020; 17:e20200039. [PMID: 33029215 PMCID: PMC7534564 DOI: 10.1590/1984-3143-ar2020-0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Coenzyme Q9 (COQ9), a coenzyme Q (CoQ) precursor, is an essential component of the mitochondrial electron transport chain that drives adenosine triphosphate production. COQ9 polymorphism 18:25527339 is characterized by substitution of guanine (allele G) for adenine (allele A), which modifies the function of the protein encoded by the gene. In Holsteins, allele A has been associated with better reproductive performance in terms of the conception rate, number of services per conception (SPC) and days open (DO). The signal transducer and activator of transcription (STAT) protein is a transcription factor activated in the presence of cytokines and growth factors. STAT5A polymorphism 19:42407732 in exon 8 has been associated with higher fertility and embryonic survival rates. The objective of this study was to determine the relationship of COQ9 and STAT5A polymorphisms with reproductive parameters [calving to first heat interval (CFHI), DO and SPC]. Blood samples were taken from 112 lactating Holstein from a herd in México for allele genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). To estimate the association between reproductive parameters and genotypes, a linear mixed-effect model was performed. The COQ9 AG genotype was associated significantly with lower SPC (P<0.05) but not with DO or CFHI. No significant association with any reproductive parameter was found for STAT5A. Our findings suggest that the COQ9 18:25527339 polymorphism is a useful molecular marker for improvement of reproductive performance in dairy herds.
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Affiliation(s)
- Néstor Gerardo Michel-Regalado
- Departamento de Producción Animal, División de Ciencias Veterinarias, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Jalisco, México
| | - Miguel Ángel Ayala-Valdovinos
- Departamento de Producción Animal, División de Ciencias Veterinarias, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Jalisco, México
| | - Jorge Galindo-García
- Departamento de Producción Animal, División de Ciencias Veterinarias, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Jalisco, México
| | - Theodor Duifhuis-Rivera
- Departamento de Producción Animal, División de Ciencias Veterinarias, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Jalisco, México
| | - David Román Sánchez-Chiprés
- Departamento de Producción Animal, División de Ciencias Veterinarias, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Jalisco, México
| | - Mauricio Valencia-Posadas
- Departamento de Veterinaria y Zootecnia, División de Ciencias de la Vida, Universidad de Guanajuato, Campus Irapuato Salamanca, Irapuato, Guanajuato, México
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Khayatzadeh N, Mészáros G, Utsunomiya YT, Schmitz-Hsu F, Seefried F, Schnyder U, Ferenčaković M, Garcia JF, Curik I, Sölkner J. Genome-wide mapping of the dominance effects based on breed ancestry for semen traits in admixed Swiss Fleckvieh bulls. J Dairy Sci 2019; 102:11217-11224. [PMID: 31548062 DOI: 10.3168/jds.2019-16899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/01/2019] [Indexed: 11/19/2022]
Abstract
Heterosis is the beneficial deviation of crossbred progeny from the average of parental lines for a particular trait. Heterosis is due to nonadditive genetic effects with dominance and epistatic components. Recent advances in genotyping technology have encouraged researchers to estimate and scan heterosis components for a range of traits in crossbred populations, applying various definitions of such components. In this study, we defined the intralocus (dominance) component of heterosis using local genetic ancestry and performed genome-wide association analysis for admixed Swiss Fleckvieh bulls and their parental populations, Red Holstein Friesian and Swiss Simmental, for semen traits. A linear mixed model for 41,824 SNP, including SNP additive genetic, breed additive, and breed dominance effects on 1,178 bulls (148 Red Holstein Friesian, 213 Swiss Simmental, and 817 Swiss Fleckvieh) with a total of 43,782 measurements was performed. In total, 19 significant regions for breed dominance were identified for volume (2 regions on Bos taurus autosome 10 and 22) and percentage of live spermatozoa (17 regions on Bos taurus autosome 3, 4, 5, 7, 13, 14, and 17), and genes associated with spermatogenesis, sperm motility, and male fertility traits were located there. No significant region for breed dominance was detected for total number of spermatozoa. The signals for breed dominance were relatively wide, most likely due to limited numbers of recombination events in a small number of generations (10-15 generations) of crossbreeding in the recent Swiss Fleckvieh composite.
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Affiliation(s)
- N Khayatzadeh
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Strasse 33, A-1180 Vienna, Austria.
| | - G Mészáros
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Strasse 33, A-1180 Vienna, Austria
| | - Y T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Cinêcias Agrárias Veterinárias, UNESP-Univ Estadual Paulista, Araçatuba, São Paulo, Brazil 16050-680
| | - F Schmitz-Hsu
- Swissgenetics, Meielenfeldweg 12, Postfach, 3052 Zollikofen, Switzerland
| | - F Seefried
- Qualitas AG, Chamerstrasse 56, Ch-6300, Zug, Switzerland
| | - U Schnyder
- Qualitas AG, Chamerstrasse 56, Ch-6300, Zug, Switzerland
| | - M Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - J F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Cinêcias Agrárias Veterinárias, UNESP-Univ Estadual Paulista, Araçatuba, São Paulo, Brazil 16050-680; Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Araçatuba, São Paulo, Brazil 16050-680
| | - I Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - J Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Strasse 33, A-1180 Vienna, Austria
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