Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds

Crum, Tamar E.; Schnabel, Robert D.; Decker, Jared E.; Taylor, Jeremy F.

doi:10.3389/fgene.2021.758394

Cited by 6Genetic and phenotypic traits in livestockGenetic Mapping and Diversity in Plants and AnimalsLivestock Farming and Management

Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds

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Crum, Tamar E., Schnabel, Robert D., Decker, Jared E., Taylor, Jeremy F.·2021·Frontiers in Genetics

DOI 10.3389/fgene.2021.758394PMC PMC8558500

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Abstract

Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.

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To enhance productivity, particularly heat tolerance and disease resistance, zebu breeds such as Kankrej, Ongole, and Gir were introduced from 1813 onwards, later yielding the Brahman favoured in tropical regions and indicine × taurine crossbreds such as the Beefmaster.
“To enhance productivity, particularly heat tolerance and disease resistance, zebu breeds such as Kankrej, Ongole, and Gir were introduced from 1813 onwards, later yielding the Brahman favoured in tropical regions and indicine × taurine crossbreds such as the Beefmaster [59,68].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [68]
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A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle
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Whole Genome Scan to Detect Chromosomal Regions Affecting Multiple Traits in Dairy Cattle
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Detection of Quantitative Trait Loci in Danish Holstein Cattle Affecting Clinical Mastitis, Somatic Cell Score, Udder Conformation Traits, and Assessment of Associated Effects on Milk Yield
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A Gene-Set Enrichment and Protein–Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle
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Local and Global Ancestry Inference and Applications to Genetic Association Analysis for Admixed Populations
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A QTL for the degree of spotting in cattle shows synteny with the KIT locus on chromosome 6
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The Polled Locus Maps to BTA1 in a Bos indicus x Bos taurus Cross
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A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23
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Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility
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Whole‐genome scan for quantitative trait loci associated with birth weight, gestation length and passive immune transfer in a Holstein × Jersey crossbred population
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Mapping of quantitative trait loci controlling tick [Riphicephalus (Boophilus) microplus] resistance on bovine chromosomes 5, 7 and 14
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A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo
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Identification of the ABCC4, IER3, and CBFA2T2 candidate genes for resistance to paratuberculosis from sequence-based GWAS in Holstein and Normande dairy cattle
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Putative quantitative trait loci associated with the probability of contracting infectious bovine keratoconjunctivitis1,2
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Genome-wide association study for female fertility in Nordic Red cattle
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Mapping of Multiple Quantitative Trait Loci Affecting Bovine Spongiform Encephalopathy
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Genome scan for postmortem carcass traits in Nellore cattle
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Genome‐wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle
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Genomic regions influencing coat color saturation and facial markings in Fleckvieh cattle
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Detection of quantitative trait loci for maternal traits using high-density genotypes of Blonde d’Aquitaine beef cattle
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Candidate genes for male and female reproductive traits in Canchim beef cattle
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Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle
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Analyzes of genome-wide association follow-up study for calving traits in dairy cattle
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Gene set enrichment analysis of SNP data in dairy and beef cattle with bovine respiratory disease
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Genome scan detects quantitative trait loci affecting female fertility traits in Danish and Swedish Holstein cattle
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Tag SNP selection for prediction of tick resistance in Brazilian Braford and Hereford cattle breeds using Bayesian methods
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Identification of Loci and Pathways Associated with Heifer Conception Rate in U.S. Holsteins
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A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits
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Evidence of positive selection towards Zebuine haplotypes in the BoLA region of Brangus cattle
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Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers1,2
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Dynamics of genomic architecture during composite breed development in cattle
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Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle
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A quantitative trait locus for live weight maps to bovine Chromosome 23
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Brief communication. The 'spotted' locus maps to bovine chromosome 6 in Hereford-cross population
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Genome‐wide association studies pathway‐based meta‐analysis for residual feed intake in beef cattle
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Genome-Wide Association Analysis Reveals QTL and Candidate Mutations Involved in White Spotting in Cattle
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Variance components for bovine tuberculosis infection and multi-breed genome-wide association analysis using imputed whole genome sequence data
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Fifty Years of Progress in Breeding Beef Cattle
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Genomewide association study of reproductive efficiency in female cattle1,2,3,4
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Quantitative trait loci for fertility traits in Finnish Ayrshire cattle
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Comparative genomics between fly, mouse, and cattle identifies genes associated with sire conception rate
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The Molecular Effects of a Polymorphism in the 5′UTR of Solute Carrier Family 44, Member 5 that Is Associated with Birth Weight in Holsteins
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Identification of loci associated with conception rate in primiparous Holstein cows
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Need for sharp phenotypes in QTL detection for calving traits in dairy cattle
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A genome-wide association study of direct gestation length in US Holstein and Italian Brown populations
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Population Structure and Genomic Breed Composition in an Angus–Brahman Crossbred Cattle Population
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Genome‐wide association study for age at puberty in young Nelore bulls
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Quantitative trait loci for organ weights and adipose fat composition in Jersey and Limousin back‐cross cattle finished on pasture or feedlot
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Short Communication: Quantitative Trait Loci Analysis on 17 Nonproduction Traits in the New Zealand Dairy Population
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Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle
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Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle
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Genome scan for the degree of white spotting in dairy cattle
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Genome-Wide Association Study in Mexican Holstein Cattle Reveals Novel Quantitative Trait Loci Regions and Confirms Mapped Loci for Resistance to Bovine Tuberculosis
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Genome screen for twinning rate QTL in four North American Holstein families
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Polymorphisms in the bovine ghrelin precursor (GHRL) and Syndecan-1 (SDC1) genes that are associated with growth traits in cattle
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Quantitative Trait Loci Associated with the Immune Response to a Bovine Respiratory Syncytial Virus Vaccine
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Overlapping chromosomal regions for fertility traits and production traits in the Danish Holstein population
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Analysis of early survival of Holstein-Friesian heifers of diverse sire origins on commercial dairy farms in Kenya
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A putative quantitative trait locus on chromosome 20 associated with bovine pathogenic disease incidence1,2
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Genetic association between NOD 2 polymorphism and infection status by M ycobacterium avium ssp. paratuberculosis in G erman H olstein cattle
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Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo)
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A genome‐wide association study for the incidence of persistent bovine viral diarrhea virus infection in cattle
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Associations between single nucleotide polymorphisms and carcass traits in Nellore cattle using high-density panels
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CRUMBLER: A tool for the prediction of ancestry in cattle
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Genome-wide association study on growth traits in Colombian creole breeds and crossbreeds with Zebu cattle
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CARD15 Gene Polymorphisms Are Associated with Tuberculosis Susceptibility in Chinese Holstein Cows
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Genomewide association study of liver abscess in beef cattle1,2
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RAPID COMMUNICATION: Multi-breed validation study unraveled genomic regions associated with puberty traits segregating across tropically adapted breeds1
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THE SANTA GERTRUDIS BREED
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Genome‐wide scan for signatures of selection in the Brangus cattle genome
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Genome‐wide scan for signatures of selection in the Brangus cattle genome
Cecco, P. Á., Rogberg‐Muñoz, A., Balbi, M., Bonamy, M., Munilla, S., Forneris, N. S., García, P. P., Cantet, R. J. C., Giovambattista, G., & Fernández, M. E. (2022) · Journal of Animal Breeding and Genetics · doi:10.1111/jbg.12733 · Cited by 8 · see citing works
Breed Composition and Heterozygosity in Brangus and Braford Composite Cattle Breeds
Cruz, D. J., Munilla, S., Villalba, P. V., Toledo-Alvarado, H. O., & Rogberg‐Muñoz, A. (2026) · Animal Genetics · doi:10.1002/age.70217
A look under the hood of genomic-estimated breed compositions for brangus cattle: What have we learned?
Li, Z., He, J., Yang, F. W., Yin, S., Gao, Z., Chen, W., Sun, C., Tait, R. G., Bauck, S. W., Guo, W., et al. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1080279 · Cited by 8 · see citing works
Dynamics of genomic architecture during composite breed development in cattle
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Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil
Verardo, L. L., Silva, F. F. E., Machado, M. A., Panetto, J. C. D. C., Faza, D. R. D. L. R., Otto, P. I., Regitano, L. C. D. A., da Silva, L. O. C., do Egito, A. A., Albuquerque, M. S. M., et al. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.702822 · Cited by 23 · see citing works

Authors: Crum, T. E., Schnabel, R. D., Decker, J. E., & Taylor, J. F.
Affiliations: University of Missouri (US)
Corresponding author: Crum, Tamar E.
Taylor, Jeremy F.
ORCID: Crum, Tamar E.
Schnabel, Robert D.
Decker, Jared E.
Taylor, Jeremy F.
Venue: Frontiers in Genetics
Publisher: Frontiers Media SA
Published: 2021-10-18
Volume: 12
Pages: 758394-758394
ISSN: 1664-8021 (ISSN-L)
DOI: 10.3389/fgene.2021.758394
PMC: PMC8558500
OpenAlex: W3207783846
Cited by: 6
References: 158
Citations by year: 2026: 3 · 2025: 2 · 2022: 1
FWCI: 0.14
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: Frontiers in Genetics (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, other-oa)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: U.S. Department of Agriculture
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Livestock Farming and Management
Keywords: local ancestry, admixture, Brangus, Santa Gertrudis, adaptive traits, haplotype effects, SNP genotypes

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Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds

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