Reproduction

Detection of novel and known recessive haplotypes and their association with reproductive performance in South African Afrikaner and Brahman beef cattle

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Abstract

Lethal haplotypes represent a hidden genetic burden on livestock populations, reducing reproductive success through early embryonic losses, prenatal lethality, or compromised survival. Genomic tools facilitate discovery of deleterious haplotypes that may harbor recessive lethal alleles, offering new insights into candidate genes, their biological pathways and known phenotypes such as embryonic lethality. Knowledge of lethal haplotypes is essential for developing genomic selection strategies that minimize their frequency in the population. This study aims to identify and characterize both novel and known recessive haplotypes and their association with reproductive performance traits. Performance data consisted of 12825 and 91287 records for the Afrikaner and Brahman cattle, respectively. Genotyped animals were 456 for Afrikaner and 399 for Brahman, both genotyped for 141716 SNP markers. Genotype data were first edited using PLINK, followed by phasing in BEAGLE. Putative lethal haplotypes were identified using R software, and overlapping genes within haplotypes were characterized. Gene annotations and associated phenotypes were retrieved from Ensembl, while known QTL were identified using the Cattle QTL database. Association analyses between identified haplotypes and reproductive performance traits were conducted using sommer package in R. In the Afrikaner, four putative lethal haplotypes were identified on a single chromosome, overlapping the genes 5S_rRNA and BRAF, which have been associated with embryonic lethality in mouse. In the Brahman, eight putative lethal haplotypes were detected across several chromosomes, including 6, 9, 10, 17, 21, and 26. These haplotypes overlapped with multiple candidate genes such as MAP1A, SORCS3, C1QTNF7, CC2D2A, CATSPER2, STRC, PDIA3, MTG1, and PAOX; underlying prenatal lethality and abnormal sperm physiology. In Afrikaner cattle, association analysis indicated that carriers of allele 0 tended to calve earlier (33.74 days) and exhibited a longer inter-calving period (ICP) (472 days) compared to non-carriers (35.5 days and 420 days, respectively), whereas allele 1 showed no significant effect on either age at first calving (AFC) or ICP. In Brahman cattle, association analysis revealed weak but directionally consistent effects of several candidate haplotypes on age at first calving (AFC), with effect sizes ranging from −2.16 to +4.50 days. For ICP, multiple haplotypes exhibited significant associations, the strongest signal occurring on chromosome 21, where carriers had markedly longer ICP compared to non-carriers (470 vs. 391 days; β = +78.74, P < 0.001). In contrast, the haplotype on chromosome 6 showed a trend toward shorter ICP (426 vs. 526 days; β = −100), although this effect did not reach statistical significance (P=0.07). This study identified putative lethal haplotypes overlapping genes associated with embryonic lethality, prenatal loss, and reproductive dysfunction. Several haplotypes exhibited measurable effects on reproductive traits, underscoring their potential influence on herd fertility and the importance of integrating lethal haplotype screening into mating and breeding strategies

Keywords: 2026

How to Cite:

Kgari, R., Dzama, K. & Makgahlela, M., (2026) “Detection of novel and known recessive haplotypes and their association with reproductive performance in South African Afrikaner and Brahman beef cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286964. doi: https://doi.org/10.31274/wcgalp.24181

Rights: 1