Genome wide association study and genomic prediction of sow resilience based on reproductive traits

AbstractRobust animals, who are generally less susceptible to disease and require fewer medications, have greater resilience. As big data collection technologies have progressed, discovering new indicators of resilience by examining longitudinal data has become feasible. Environmental factor-induced variability in reproductive traits may be related to an animal's capacity to adapt to changing environmental circumstances. However, no documented studies have used variations in reproductive traits to assess resilience in pigs. We here gathered data on the reproductive traits of 16 383 pigs, including 11 321 Yorkshire pigs, 3 317 Landrace pigs, and 1 745 Duroc pigs. Regarding reproductive traits, we computed the environmental standard deviation () for each reproductive trait. The heritability of the resilience traits ranged from 0.02 to 0.61 across three breeds. In total, 9 171 sows were conducted the individual genotyping with three chips, KPS® Zhongxin-1 Porcine Breeding ChipV2 (1 133 Yorkshire, 176 Landrace, and 116 Duroc pigs) and Chip_plus (2 815 Yorkshire, 1 107 Landrace, and 663 Duroc pigs), and CAU50K (2 287 Yorkshire, 614 Landrace, and 350 Duroc pigs). After quality control, 46 358 single nucleotide polymorphisms (SNPs) and 9 171 individuals were used for the subsequent genome-wide association study (GWAS) and genomic selection prediction. GWAS was conducted onof reproductive traits across three breeds, thereby identifying 130 significant SNPs and 3 259 candidate genes. We performed breeding value estimation reliability forof reproductive traits using the best linear unbiased prediction (BLUP) and revealed that the reliability varied from 0.05 to 0.49. When the genomic BLUP (GBLUP) and single-step GBLUP (ssGBLUP) were used, the average genomic prediction reliability increased by 0.02 (range: −0.02 to 0.09) and 0.04 (range: −0.01 to 0.08) for Yorkshire and Duroc pigs, respectively. Forof ten reproductive traits and their original traits, the phenotypic correlations (|0.01| to |0.90|) and genetic correlations (|0.00| to |0.99|) were observed. Considering results comprehensively,of litter weight, andof survival rate could be used as the indicators of resilience across the three breeds. In addition,of number of mummies,of number born weak, andof number of stillbirth, could be as the resilience traits for Yorkshire and Duroc pigs, andof number born healthy could be used for resilience evolution in Landrace pigs. Across the three breeds, high-resilience individuals exhibited higher reproductive performance than their low-resilience counterparts. These findings expanded the scope of molecular markers used for assessing pig reproductive capabilities and disease resistance, and also provided the basis for incorporating resilience into breeding practices.