Reproduction

Screening for novel causative mutation candidates for the Trio allele.

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Abstract

Increased ovulation rate leads to increased opportunity for birth of multiple calves, which is potentially beneficial to beef producers. A region on BTA10 was previously identified as the location harboring a major gene for ovulation rate. This allele ("Trio allele") causes ~ 3-fold greater ovulation rate in Trio allele carriers compared to non-carriers. The objective of this study was to identify candidates for the causative mutation responsible for the Trio allele phenotype using genomic sequence data generated from two Trio allele homozygotes with genome-wide 150 bp paired-end reads to a 40X read depth and Oxford Nanopore long-reads to a 14.8X read depth, respectively. Initially, the breed haplotype associated with the Trio allele on BTA10 was determined using Bovine HapMap data. The haplotype containing the Trio allele was observed in six of 134 breeds with a frequency in Herefords ≥ 3-fold greater compared with other breeds represented by five or more individuals. The occurrence of the Trio allele in a Hereford background facilitated identification of potential causative variants by comparison of sequence data with the reference genome which was based on a Hereford cow. The 1.2 Mb positional candidate region on BTA 10 was screened for variants by identifying those which were homozygous in the Trio allele homozygotes and differing from the reference genome. Putative variants which were potentially novel were identified by comparison with the 1000 Bull Genomes project data. Comparing variant overlap between the two homozygous individuals showed only one SNP to be in both individuals and within the 1.2 Mb region of interest. The SNP is located 206 kb distal to SMAD6, the gene which is approximately 9-fold overexpressed in Trio allele carriers and strongly implicated as the basis for the Trio allele phenotype. Genotyping of this SNP showed 100% correspondence with the inferred Trio allele genotypes of 111 individuals. Additionally, this variant was absent in two non-Trio populations (Hereford, n= 104; USDA-MARC Twinner, n=83) thought to be the most likely outside the Trio family to possess the allele. The SNP is located within a long non-coding RNA gene and LINE element L1M3. The long-read assembly also identified a 2.2 Mb inversion 84 kb proximal to SMAD6. Like the SNP, the inversion allele was absent in the Hereford and MARC-Twinner samples. However, the inversion is outside the previously identified candidate region. The SNP is a strong variant for further testing as the potential connection to SMAD6 overexpression remains unknown.

Keywords: 2026

How to Cite:

Lett, B., Sanders, D., Garcia-Guerra, A., Monson, R., Wiltbank, M. & Kirkpatrick, B., (2026) “Screening for novel causative mutation candidates for the Trio allele.”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286911. doi: https://doi.org/10.31274/wcgalp.24160

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