Abstract
Lethal recessive alleles that act prenatally may be detected from the absence of homozygous individuals in a population. However, these alleles may be maintained at relatively low frequencies in populations as heterozygotes. In pigs, they may reduce litter size. This study aimed to detect putative lethal variants in the Duroc breed. Phenotypes for the numbers of piglets born (TNB), born live (BA), alive at 24 h (L24), stillborn (SB), and born as mummified fetuses (MM) were available from 5340 recorded litters which resulted from mating of 192 genotyped boars with sows of unknown genotype (dataset 1). An additional 50 litters were produced from parents that were both genotyped (dataset 2). Imputed genotypes of 650K SNPs for 1359 Duroc boars were used in this study. One significant SNP (Bonferroni corrected P = 5.5E-06) was located on SSC14 with 45.3 homozygous individuals expected but none observed. This SNP was significant for mummified fetuses. One hundred fifty two haplotypes were also found to potentially harbor recessive lethal mutations. Twenty-one haplotypes had a significant harmful effect on at least one trait. Two regions, located on SSC8 (144.9–145.5 Mb) and SSC9 (19–19.4 Mb) had significant effects on fertility traits in both datasets. Additionally, regions on SSC1 (82.0–82.8 Mb), SSC3 (73.3–73.7 and 87.1–87.5 Mb) and SSC12 (35.8–36.2 and 50.0–50.5 Mb) had significant deleterious effects on TNB or BA or L24 in dataset 1. Finally, a region on SSC17 (28.7–29.3 Mb) had significant effects on TNB, BA and L24 in dataset 2. A few candidate genes identified within these regions were described as being involved in spermatogenesis and male fertility (TEX14, SEP4, and HSF5), or displayed recessive lethality (CYP26B1, SCD5, and PCF11) in other species. The putative loci detected in this study provide valuable information to potentially increase Duroc litter size by avoiding carrier-by-carrier matings in breeding programs. Further study of the identified candidate genes responsible for such lethal effects may lead to new insights into functions regulating pig fertility.
Highlights
Small litters are characteristic of the Duroc breed (Johnson, 1981; Sonderman and Luebbe, 2008)
Many factors may contribute to this loss and most work has focused on increasing litter size in the maternal lines based on Landrace and Large White breeds where high ovulation rates exist and litter size is relatively high and responds to selection (Sorensen et al, 2000; Noguera et al, 2002)
Under the assumptions that neither ovulation rate (Young et al, 1976) nor uterine capacity prior to fetal implantation are limiting in Duroc, we hypothesized that early embryonic mortality due to homozygosity of recessive lethal alleles may contribute to the production of relatively small litters by Duroc females
Summary
Small litters are characteristic of the Duroc breed (Johnson, 1981; Sonderman and Luebbe, 2008). With the generation of large amounts of genomic data this hypothesis can be tested where loci harboring lethal recessive alleles may be discovered from the absence of live animals that are homozygous. Precedent for this proposed mechanism is found in recent studies based on observations of missing homozygous haplotypes in cattle (VanRaden et al, 2011; Hoff et al, 2017; Howard et al, 2017). Under the assumptions that neither ovulation rate (Young et al, 1976) nor uterine capacity prior to fetal implantation are limiting in Duroc, we hypothesized that early embryonic mortality due to homozygosity of recessive lethal alleles may contribute to the production of relatively small litters by Duroc females. The third objective was to identify some candidate genes that might be involved in functional pathways of sow fertility
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
