Translational genomics for improving sow reproductive longevity

Abstract Text: Approximately 50% of sows are culled annually with more than one third due to poor fertility. Age at puberty, the earliest pre-breeding indicator of reproductive longevity, can be measured early in life, and has a moderate heritability. Selection for age at puberty is challenging due to labor-intensive phenotyping. Genomic selection for this trait would be a more viable option because could increase accuracy and selection response. This study aims to identify DNA markers that will predict, at weaning, gilts with early age at puberty and superior reproductive longevity. Our hypothesis is that genetic sources that affect age at puberty also explain variation in sow reproductive longevity. To test the hypothesis, data and tissues from UNL resource population (n>1,700 gilts) were integrated with genome-wide association analyses, genome/RNA sequencing and polymorphism discovery to uncover DNA variants that could predict age at puberty and reproductive longevity. A BeadArray panel of 56,424 SNPs explained 25.2% of the phenotypic variation in age at puberty in a training set (n=820). In an evaluation data set consisting of subsequent batches of similar genetics (n=412), we compared a model based on all SNPs from major 1 Mb-windows with one based on SNPs with the largest estimated effect. The model based on all SNPs from the major windows explained more of the phenotypic variance compared to the model based on large effect SNPs (12.3 to 36.8% vs. 6.5 to 23.7%). One major pleiotropic region included AVPR1A, for which the favorable genotype was associated with higher probability of the gilts to produce the first parity compared to the other genotypes (P<0.05). Genome sequencing of 20 sires using Proton technology provided sources of genetic variation outside the limited capability of the BeadArray. Sequencing reads averaged 165bp with a depth that varied from 16.2 to 29.7X. A substantial proportion (38%) of the total SNPs discovered (140K) were located in known genes. Transcriptome profile was evaluated by RNA sequencing of the micro-dissected Arcuate Nucleus (ARC) in pre/post- pubertal gilts (n=12) subjected to different dietary treatments. Using a combination of Tophat and local Bowtie the majority of the reads were aligned to the reference genome/transcriptome (>93%). This integrated knowledge accompanied by economic modeling will be evaluated in commercial populations to understand and improve expression of puberty and sow reproductive potential through genomic selection. This project is supported by AFRI Competitive Grant no. 2013-68004-20370 from the USDA-NIFA. USDA is an equal opportunity provider and employer.

Keywords: age at puberty, genomic selection, reproductive longevity.