Discovering Genomic Regions Associated with Reproductive Traits and Frame Score in Mexican Simmental and Simbrah Cattle Using Individual SNP and Haplotype Markers

Reproductive efficiency stands as a critical determinant of profitability within beef production systems. The incorporation of molecular markers can expedite advancements in reproductive performance. While the use of SNPs in association analysis is prevalent, approaches centered on haplotypes can of...

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Bibliographic Details
Published in:Genes 2023-10, Vol.14 (11), p.2004
Main Authors: Calderón-Chagoya, René, Vega-Murillo, Vicente Eliezer, García-Ruiz, Adriana, Ríos-Utrera, Ángel, Martínez-Velázquez, Guillermo, Montaño-Bermúdez, Moisés
Format: Article
Language:English
Subjects:
Analysis
Animals
Association analysis
Bayes Theorem
Bayesian analysis
Beef
Beef industry
Cattle
Cattle - genetics
Economics
Efficiency
Female
Fertility
Genes
Genetic aspects
Genomes
Genomics
Haplotypes
Haplotypes - genetics
Linkage disequilibrium
Mathematical models
Phenotype
Phenotypes
Polymorphism, Single Nucleotide
Quality control
Quality management
Single-nucleotide polymorphism
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Summary:Reproductive efficiency stands as a critical determinant of profitability within beef production systems. The incorporation of molecular markers can expedite advancements in reproductive performance. While the use of SNPs in association analysis is prevalent, approaches centered on haplotypes can offer a more comprehensive insight. The study used registered Simmental and Simbrah cattle genotyped with the GGP Bovine 150 k panel. Phenotypes included scrotal circumference (SC), heifer fertility (HF), stayability (STAY), and frame score (FS). After quality control, 105,129 autosomal SNPs from 967 animals were used. Haplotype blocks were defined based on linkage disequilibrium. Comparison between haplotypes and SNPs for reproductive traits and FS was conducted using Bayesian and frequentist models. 23, 13, 7, and 2 SNPs exhibited associations with FS, SC, HF, and STAY, respectively. In addition, seven, eight, seven, and one haplotypes displayed associations with FS, SC, HF, and STAY, respectively. Within these delineated genomic segments, potential candidate genes were associated.
ISSN:2073-4425
2073-4425
DOI:10.3390/genes14112004