SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

Abstract Background Understanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows. Methods Medium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny. Results For the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2. Conclusions The identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.

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Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

Livestock Science ◽

10.1016/j.livsci.2014.05.007 ◽

2014 ◽

Vol 166 ◽

pp. 121-132 ◽

Cited By ~ 36

Author(s):

Ana M. Pérez O’Brien ◽

Gábor Mészáros ◽

Yuri T. Utsunomiya ◽

Tad S. Sonstegard ◽

J. Fernando Garcia ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Allele Frequency ◽

Minor Allele Frequency ◽

Bos Taurus ◽

Bos Indicus ◽

High Density ◽

Minor Allele ◽

Frequency Distributions ◽

Chip Data ◽

Snp Chip

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Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers

Genes ◽

10.3390/genes11111312 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1312

Author(s):

Warren M. Snelling ◽

Jesse L. Hoff ◽

Jeremiah H. Li ◽

Larry A. Kuehn ◽

Brittney N. Keel ◽

...

Keyword(s):

Genomic Prediction ◽

Genomic Sequence ◽

Bos Taurus ◽

Low Cost ◽

Bos Indicus ◽

Snp Array ◽

Attractive Alternative ◽

Functional Variant ◽

Low Pass ◽

Low Coverage

Decreasing costs are making low coverage sequencing with imputation to a comprehensive reference panel an attractive alternative to obtain functional variant genotypes that can increase the accuracy of genomic prediction. To assess the potential of low-pass sequencing, genomic sequence of 77 steers sequenced to >10X coverage was downsampled to 1X and imputed to a reference of 946 cattle representing multiple Bos taurus and Bos indicus-influenced breeds. Genotypes for nearly 60 million variants detected in the reference were imputed from the downsampled sequence. The imputed genotypes strongly agreed with the SNP array genotypes (r¯=0.99) and the genotypes called from the transcript sequence (r¯=0.97). Effects of BovineSNP50 and GGP-F250 variants on birth weight, postweaning gain, and marbling were solved without the steers’ phenotypes and genotypes, then applied to their genotypes, to predict the molecular breeding values (MBV). The steers’ MBV were similar when using imputed and array genotypes. Replacing array variants with functional sequence variants might allow more robust MBV. Imputation from low coverage sequence offers a viable, low-cost approach to obtain functional variant genotypes that could improve genomic prediction.

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Candidate SNPs for carcass and meat traits in Nelore animals and in their crosses with Bos taurus

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2012000200019 ◽

2012 ◽

Vol 47 (2) ◽

pp. 294-301 ◽

Cited By ~ 6

Author(s):

Rogério Abdallah Curi ◽

Monique Marcondes Krauskopf ◽

Janaína Conte Hadlich ◽

Marina Rufino Salinas Fortes ◽

Dianne Margaret Vankan ◽

...

Keyword(s):

Allele Frequency ◽

Multiple Testing ◽

Bos Taurus ◽

Bos Indicus ◽

Total Sample ◽

Candidate Snps ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Fragmentation Index ◽

Allele Substitution

The objective of this work was to evaluate the effects of single-nucleotide polymorphisms (SNPs) in the genes IGF1 (AF_017143.1:g.198C>T), MSTN (AF_320998.1:g.433C>A), MYOD1 (NC_007313:g.1274A>G) and MYF5 (NC_007303:g.1911A>G) on carcass and meat traits in Nelore (Bos indicus) and Nelore x B. taurus. A total of 300 animals were genotyped and phenotyped for rib eye area (REA), backfat thickness (BT), intramuscular fat (IF), shear force (SF) and myofibrillar fragmentation index (MFI). The effects of allele substitution for each SNP were estimated by regression of the evaluated phenotypes on the number of copies of a particular allele using the general linear model. The polymorphism at IGF1 was non-informative in Nelore animals. In crossbred animals, the IGF1 C allele was associated with greater REA. However, this relation was not significant after Bonferroni correction for multiple testing. The A allele of the MSTN polymorphism was absent in Nelore cattle and was only found in two crossbred animals. The polymorphisms of MYOD1 and MYF5 were little informative in Nelore animals with G allele frequency of 0.097 and A allele frequency of 0.031, respectively. These markers show no association with the analyzed traits in the total sample of evaluated animals.

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Assessing accuracy of imputation in Gyr breed using different SNP panels

Genome ◽

10.1139/gen-2020-0081 ◽

2021 ◽

Author(s):

Alejandra Maria Toro Ospina ◽

Ignacio Aguilar ◽

Matheus Henrique Vargas de Oliveira ◽

Luiz eduardo Cruz dos Santos Correia ◽

Anibal Eugenio Vercesi Filho ◽

...

Keyword(s):

Principal Component Analysis ◽

Bos Taurus ◽

Imputation Accuracy ◽

Bos Indicus ◽

Principal Component ◽

Reference Population ◽

Medium Density ◽

Genomic Relationship ◽

Snp Panels ◽

Two Populations

The objective 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 9,109 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.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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Generating High Density, Low Cost Genotype Data in Soybean [Glycine max (L.) Merr.]

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400093 ◽

2019 ◽

Vol 9 (7) ◽

pp. 2153-2160 ◽

Cited By ~ 1

Author(s):

Mary M. Happ ◽

Haichuan Wang ◽

George L. Graef ◽

David L. Hyten

Keyword(s):

Glycine Max ◽

Low Cost ◽

High Density ◽

Genotype Data ◽

Glycine Max L

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Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations

Frontiers in Genetics ◽

10.3389/fgene.2021.584355 ◽

2021 ◽

Vol 12 ◽

Author(s):

Netsanet Z. Gebrehiwot ◽

Hassan Aliloo ◽

Eva M. Strucken ◽

Karen Marshall ◽

Mohammad Al Kalaldeh ◽

...

Keyword(s):

Reference Data ◽

Bos Taurus ◽

Imputation Accuracy ◽

West African ◽

High Density ◽

Genotype Imputation ◽

Indigenous Populations ◽

Medium Density ◽

Crossbred Cattle ◽

Ancestral Origin

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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Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽

10.1186/s12864-021-07653-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Cuili Pan ◽

Zhaoxiong Lei ◽

Shuzhe Wang ◽

Xingping Wang ◽

Dawei Wei ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Adipocyte Differentiation ◽

Bos Taurus ◽

Adipogenic Differentiation ◽

Critical Role ◽

Bos Indicus ◽

Specific Expression ◽

Genome Wide ◽

A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

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Expression of candidate genes for residual feed intake in tropically adapted Bos taurus and Bos indicus bulls under thermoneutral and heat stress environmental conditions

Journal of Thermal Biology ◽

10.1016/j.jtherbio.2021.102998 ◽

2021 ◽

pp. 102998

Author(s):

Bianca Vilela Pires ◽

Nedenia Bonvino Stafuzza ◽

Luara Afonso de Freitas ◽

Maria Eugênia Zerlotti Mercadante ◽

Ester Silveira Ramos ◽

...

Keyword(s):

Heat Stress ◽

Candidate Genes ◽

Feed Intake ◽

Environmental Conditions ◽

Bos Taurus ◽

Bos Indicus ◽

Residual Feed Intake

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Differences in copper and selenium metabolism between Angus (Bos taurus) and Brahman (Bos indicus) cattle

Journal of Animal Science ◽

10.1093/jas/skab048 ◽

2021 ◽

Author(s):

J Ranches ◽

R Alves ◽

M Vedovatto ◽

E Anne Palmer ◽

P Moriel ◽

...

Keyword(s):

Bos Taurus ◽

Bos Indicus ◽

First Trimester ◽

Beef Cows ◽

Experimental Unit ◽

University Of Florida ◽

Brahman Cattle ◽

Research And Education ◽

The University ◽

Se Status

Abstract A two-year study was conducted at the University of Florida – IFAS, Range Cattle Research and Education Center (Ona, FL) to evaluate differences in the metabolism of Cu and Se of Angus (Bos taurus) and Brahman (Bos indicus) cattle. Thirty-two pregnant beef cows (n = 8 Brahman and 8 Angus/year) were enrolled in the study in the first trimester of gestation. The study consisted of 3 phases: (1) restriction (d 0 to d 90); (2) supplementation (d 91 to 150), and (3) calving. During all 3 phases, cows were individually fed and housed in partially covered drylot pens. During the restriction and supplementation phases cows were provided a 1.5 kg/d of a grain-based concentrate supplement, which was fortified with flowers of S (50 g of supplemental S/cow daily; restriction phase) or Cu and Se (100 and 3 mg/d of Cu and Se, respectively; supplementation phase). Blood and liver samples were collected from all cows on 30 d intervals and from both cows and calves within 24 h of calving. Colostrum and milk samples were collected at calving and 7 d after birth. All data were analyzed using the MIXED procedure of SAS, where cow and calf were the experimental unit. During the restriction phase, a breed × day effect (P = 0.03) was observed where Brahman had greater liver Cu concentration than Angus cows in all sampling days. For liver Se concentration, a tendency (P = 0.07) for a breed effect was observed where Angus cows tended to have greater liver Se concentration than Brahman. During the supplementation phase, breed (P < 0.001) and day (P < 0.01) effects were observed, where Brahman cows had greater liver Cu concentration than Angus. For liver Se concentration, a day effect (P < 0.001) was observed, where liver Se concentration increased (P < 0.001) from d 90 to 120 and remained unchanged (P = 0.86) until d 150. At calving no effects of breed (P = 0.34) were observed for liver Cu concentration of cows, however, Brahman calves tended (P = 0.09) to have greater liver Cu concentration than Angus calves. For Se liver concentration at calving, Angus cows tended (P = 0.07) to have greater liver Se concentration than Brahman cows, however no breed differences (P = 0.70) were observed for liver Se concentration of calves at birth. In summary substantial differences in multiple indicators of Cu and Se status were observed between Angus and Brahman cattle, implying that Angus and Brahman cattle possibly have different mechanisms to maintain adequate Cu and Se status.

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