Birth weight (BW) and days to 100 kg (D100) are important economic traits that are both affected by polygenes.  However, the genetic architecture of these quantitative traits is still elusive.  Genotyping-by-sequencing (GBS) data containing a large number of single nucleotide polymorphisms (SNPs) have become a powerful tool in genomic analysis.  To better understand their complex genetic structure, a total of 600 Yorkshire pigs were sequenced using GBS technology.  After quality control, 279 787 SNPs were generated for subsequent genome-wide association study (GWAS).  A total of 30 genome-wide SNPs (P<1.79E–07) were identified for D100.  Furthermore, a total of 22 and 2 suggestive SNPs (P<3.57E–06) were detected for D100 and BW, respectively.  Of these, one locus located on SSC12 (position: 46 226 512 bp) were evaluated to affect both BW and D100 in Yorkshire pigs, indicating the pleiotropism in different traits.  Considering the function of candidate genes, two genes, NSRP1 and DOCK7, were suggested as the most promising candidate genes involved in growth traits.  Thus, use of GBS is able to identify novel variants and potential candidate genes for BW and D100, and provide an opportunity for improving pig growth traits using genomic selection in pigs.

 

We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs.  Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST (Z(FST)) method, and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity (ZHp) method.  The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism, disease resistance, cellular processes, and biochemical signals, and several were related to body morphology and organs.  They included PPP3CA, which plays an essential role in the transduction of intracellular Ca²⁺-mediated signals, and WWTR1, which plays a pivotal role in organ size control and tumor suppression.  These results suggest that genes associated with body morphology were subject to selection pressure during domestication, whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding.  Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.