NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock

Abstract

University of Liège (B34), 4000-Liège, BelgiumWe herein report the result of a large-scale, next generation sequencing (NGS)-based screen for embryonic lethal (EL) mutations in Belgian beef and New Zealand dairy cattle. We estimated by simulation that cattle might carry, on average, ∼0.5 recessive EL mutations. We mined exome sequence data from >600 animals, and identified 1377 stop-gain, 3139 frame-shift, 1341 splice-site, 22,939 disruptive missense, 62,399 benign missense, and 92,163 synonymous variants. We show that cattle have a comparable load of loss-of-function (LoF) variants (defined as stop-gain, frame-shift, or splice-site variants) as humans despite having a more variable exome. We genotyped >40,000 animals for up to 296 LoF and 3483 disruptive missense, breed-specific variants. We identified candidate EL mutations based on the observation of a significant depletion in homozygotes. We estimated the proportion of EL mutations at 15% of tested LoF and 6% of tested disruptive missense variants. We confirmed the EL nature of nine candidate variants by genotyping 200 carrier × carrier trios, and demonstrating the absence of homozygous offspring. The nine identified EL mutations segregate at frequencies ranging from 1.2% to 6.6% in the studied populations and collectively account for the mortality of ∼0.6% of conceptuses. We show that EL mutations preferentially affect gene products fulfilling basic cellular functions. The resulting information will be useful to avoid atrisk matings, thereby improving fertility.

Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle

“…Embryonic lethality has become a challenge to cattle breeders, especially for dairy cattle where a limited number of bulls were extensively used in breeding for fast genetic progress in economic traits like milk and protein yield 1 . An estimated yearly loss of ∼$10.74 million is attributed to known recessive lethals in four dairy cattle breeds from USA only, where Holstein accounts for ∼70% of the total losses, followed by Jersey, Brown Swiss, and Ayrshire 2 .…”

Genotype disclosure in the genomics era: roles and responsibilities

“…6 Thousands of animals can be surveyed in genetic panel screening studies using DNA microarray chips. The total mutational load for loss-offunction (LoF) variants is similar in humans and cattle, despite higher overall genetic variation in cattle, 8 but, as noted by Lyons et al, almost 200 proven pathogenic sequence variations of the acidic alpha-glucosidase (GAA) gene have been identified in humans to date, 12 but only 3 such variations in cattle. 11 Large-scale next-generation sequencing can identify multiple EL mutations (detected by depletion of homozygotes in the population) that can collectively account for significant mortality in all conceptuses in a breed.…”

“…Efficient WGS and bioinformatics can characterise the mutational load of several breeds in a single study. 8 Pompe disease provides an indication of the potential mutational load still to be discovered. 11 A single study can identify several different causal alleles for one recognised phenotype (locus heterogeneity), as well as additional breeds affected by known mutations.…”

“…14 Nine EL mutations in cattle segregating at frequencies of 1.2-6.6% and accounting for 0.6% mortality in all conceptuses were identified in one recent study, 8 with evidence of many more EL alleles segregating at frequencies of > 2%, raising the possibility that fertility can be improved by avoiding carrier matings. A recent study indicated domestic cattle are, on average, heterozygous for 51 (range 25-82) and homozygous for 7 (range 0-21) LoF variants (excluding large deletions), of which 15% are probably EL, 8 supporting the idea that all individuals carry several EL alleles.…”

“…LoF and disruptive missense mutations therefore do not all have the same practical importance in animal breeding; 15% of LoF mutations are EL, 8 but most have less severe phenotypes, some innocuous. Some non-lethal phenotypes are nonetheless economically more important than EL phenotypes.…”