0691 Translational genomics for improving sow reproductive longevity

Abstract

Listen

Translate article

Approximately 50% of sows are culled annually with more than one-third due to poor fertility. Age at puberty, the earliest prebreeding 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 it 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 a UNL resource population (n > 1,700 gilts) were integrated with genomewide 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 SNP 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 SNP from major 1-Mb windows with one based on SNP with the largest estimated effect. The model based on all SNP from the major windows explained more of the phenotypic variance compared with the model based on large effect SNP (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 with 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 165 bp with a depth that varied from 16.2x to 29.7x. A substantial proportion (38%) of the total SNP discovered (140,000) were located in known genes. Transcriptome profile was evaluated by RNA sequencing of the microdissected arcuate nucleus (ARC) in pre-/postpubertal 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 Agriculture and Food Research Initiative Competitive Grant number 2013-68004-20370 from the USDA–National Institute of Food and Agriculture. The USDA is an equal opportunity provider and employer.