Abstract: The purpose of this study was to evaluate the inbreeding depression for TNB in Large White pigs with different genetic background after about 8 generations of selection. A total of 1 937 sows with phenotypic and pedigree records were genotyped with GeneSeek GGP Porcine HD chip. Out of them, 1 039 Large White pigs were from the Canadian line and 898 were from the French line. The pedigree of the two lines consisted of 3 086 Large White pigs. Inbreeding coefficients were estimated using 3 different measures based on pedigree data, SNPs and runs of homozygosity (ROH), respectively. Inbreeding depression of TNB was evaluated using an animal model in which the inbreeding coefficient was treated as a covariate. To fine mapping the genomic regions that lead to inbreeding depression of TNB, the inbreeding coefficients of each autosome and significant autosome segments were calculated and their effects were estimated. And then all the significant autosomes were divided into several segments with equal size and these genomic regions were further tested whether they were associated to inbreeding depression of TNB. In Canadian line, the average inbreeding coefficients of F_ROH, F_GRM and F_PED estimated were 0.124, 0.042 and 0.013, respectively. Among pairwise correlations between the different inbreeding coefficients across individuals, the highest correlation was between F_ROH and F_PED and the correlation coefficient was 0.358. In French line, the average inbreeding coefficients of F_ROH, F_GRMand F_PED estimated were 0.123, 0.052 and 0.007, respectively. The highest pairwise correlation was between F_ROH and F_GRM, and the correlation coefficient was 0.371. On the whole genome level, significant inbreeding depression was found for TNB in Canadian line using all 3 measures of inbreeding. Estimates of inbreeding depression were -0.571, -0.341 and -0.823 for TNB per 10% increase in F_ROH, F_GRMand F_PED, respectively. While in French line, only using F_ROH could detect significant inbreeding depression and a 10% increase in F_ROH resulted in a decrease of 0.690 for TNB. On the chromosome level, ROH-based inbreeding coefficient for each chromosome was used to perform inbreeding depression analysis. The results showed that chromosome 6, 7, 8 and 13 in the Canadian line were identified to be significant related to inbreeding depression for TNB, but in French line, no chromosome was associated to inbreeding depression. To narrow down the genomic regions causing inbreeding depression, the 4 significant chromosomes in Canadian lines were further divided into 2, 4, 6, 8 segments with equal size. When these 4 autosomes were divided into 8 segment, the segment lengths ranged from 15.1 to 25.8 Mb. Finally, one, two and three genomic segments on chromosome 6, 7 and 8 were found to be significantly associated with inbreeding depression, respectively. These regions harbored CUL7, MAPK14 and PPARD genes that were associated with placental development, and AREG and EREG genes involved in oocyte maturation. Three calculation measures of inbreeding coefficients were used to evaluate inbreeding depression for TNB in Large White pigs with different genetic background. At the genome level, significant inbreeding depression in Canadian line was detected for TNB using all 3 measures of inbreeding, but only the effect of F_ROH was significant in French lines. At the chromosome level, 4 autosomes showed significant effects. Use of ROH further identified the 4 chromosomes and 6 specific genomic segments that could lead to significant reduction in TNB of Canadian line. These specific genomic segments were annotated candidate genes related to reproduction. The study results not only provided a new sight into revealing the genetic mechanism of inbreeding depression, but also provided a reference for carrying out genomic selection and mating schemes in pigs.

Key words: Large White pigs, total number of piglets born, runs of homozygosity, inbreeding coefficient, inbreeding depression