Genomic Scanning of Inbreeding Depression for Litter Size in Two Varieties of Iberian Pigs

Inbreeding depression for litter size in two mice lines under divergent selection for environmental birth weight variability using genomic data

Inbreeding depression (ID) is usually observed as reduced survival and fertility and may have a variable impact in different populations. The aim of this study was to estimate ID from genomic and pedigree data in the litter size (LS) of the high variability (H-Line) and the low variability (L-Line) mice lines divergently selected for environmental birth weight variability. Of these, the L-Line performed better on traits related to robustness. A total of 1587 females from 26 selection generations were genotyped with a high-density SNP array. LS data of 732 L-Line and 648 of H-Line animals were used. The following were calculated: pedigree inbreeding coefficient (FPED), genomic inbreeding derived from different genomic matrices (FNEJ, FL&H,FVR1, FVR2, and FYAN), from runs of homozygosity (FROH) and from homozygosity by descent probabilities (FHBD). FROH were calculated in the 19 autosomes (CHR). FROH and FHBD were divided into nine lengths and age classes, respectively. All the inbreeding coefficients were standardized by the mean inbreeding coefficient of the 1st generation. Regression coefficients (m) obtained from genomic data were between -3.71 with FVR2 and -5.09 with FHBD in the H-Line, and that estimated from FPED was -5.67. In the L-Line the m obtained from genomic data were between -3.52 with FVR2 and -4.55 with FHBD, and that obtained with FPED was -4.08. Significant ID effects were detected in CHR13 in the H-Line and CHR1 and CHR9 in the L-Line. The m negative trended to be lower as the ROH length increased. The age of the homozygosity by descent segment performed differently in each line, for example FHBD raised 128 generations ago produced a significant positive effect only in the L-Line. The effect of global inbreeding coefficients on the LS was negative in both lines with a higher impact in the H-Line than in the L-Line, suggesting the L-Line having higher robustness. CHR 1, 9, and 13 were candidates for future gene search. In general, more recent FROH and FHBD presented negative effects on LS while older FROH and FHBD presented positive effects on LS in both selected lines.

Population dynamics of potentially harmful haplotypes: a pedigree analysis

BACKGROUND

The identification of low-frequency haplotypes, never observed in homozygous state in a population, is considered informative on the presence of potentially harmful alleles (candidate alleles), putatively involved in inbreeding depression. Although identification of candidate alleles is challenging, studies analyzing the dynamics of potentially harmful alleles are lacking. A pedigree of the highly endangered Gochu Asturcelta pig breed, including 471 individuals belonging to 51 different families with at least 5 offspring each, was genotyped using the Axiom PigHDv1 Array (658,692 SNPs). Analyses were carried out on four different cohorts defined according to pedigree depth and at the whole population (WP) level.

RESULTS

The 4,470 Linkage Blocks (LB) identified in the Base Population (10 individuals), gathered a total of 16,981 alleles in the WP. Up to 5,466 (32%) haplotypes were statistically considered candidate alleles, 3,995 of them (73%) having one copy only. The number of alleles and candidate alleles varied across cohorts according to sample size. Up to 4,610 of the alleles identified in the WP (27% of the total) were present in one cohort only. Parentage analysis identified a total of 67,742 parent-offspring incompatibilities. The number of mismatches varied according to family size. Parent-offspring inconsistencies were identified in 98.2% of the candidate alleles and 100% of the LB in which they were located. Segregation analyses informed that most potential candidate alleles appeared de novo in the pedigree. Only 17 candidate alleles were identified in the boar, sow, and paternal and maternal grandparents and were considered segregants.

CONCLUSIONS

Our results suggest that neither mutation nor recombination are the major forces causing the apparition of candidate alleles. Their occurrence is more likely caused by Allele-Drop-In events due to SNP calling errors. New alleles appear when wrongly called SNPs are used to construct haplotypes. The presence of candidate alleles in either parents or grandparents of the carrier individuals does not ensure that they are true alleles. Minimum Allele Frequency thresholds may remove informative alleles. Only fully segregant candidate alleles should be considered potentially harmful alleles. A set of 16 candidate genes, potentially involved in inbreeding depression, is described.