[Association of microsatellite genomic heterozygosity with inbred pig performance under successive inbreeding]

Genomic scanning using microsatellites was carried out in a pig family that has undergone 5 successive generations of inbreeding. A total of 56 microsatellite markers were utilized, which were derived from swine chromosome 01, 02, 11, 13, 17, 18 and gave a considerable coverage of these chromosomes. Genomic heterozygosity was estimated as an average of marker heterozygosity over all 6 chromosomes. Analysis of variance using a generalized linear model indicated that genomic heterozygosity was positively and significantly associated with slaughter weight (SWT) and average daily slaughter gain (ADSG), but inconsistently and non-significantly associated with backfat depth (BFDP). Association effects of GH on SWT and ADSG increased from generation 1 to generation 2, and, then, reduced gradually with generations while levels of inbreeding accumulated. The maximum effect was observed in generation 2, which was estimated to be 22.43 kg for SWT and 0.132 kg/d for ADSG. The effect of marker heterozygosity on SWT and ASDG differed dramatically from chromosome to chromosome: the largest effect was observed with chromosome 13 (i.e. 6.306 kg for SWT and 0.032 kg/d for ADSG), followed by chromosome 01, 17, 18, 02 and 11. Marker heterozygosity was not found to be significantly associated with BFDP for all chromosomes. These results give rise to three implications. First, genes (e.g. QTL) contributing to traits of economic importance are not equally distributed among these chromosomes, which represents the difference in determination of quantitative traits across chromosomes or at DNA level. Second, the association of genomic or marker heterozygosity with pig performance varies from chromosome to chromosome, or with generations of inbreeding. This phenomenon provides an evidence that heterozygosity-performance association is not straight-forward, but rather complex as a result of complicated gene actions and interactions, and sometimes may even be much more complicated when confounded and misled by inabequate or improper markers utilized. Last, decreased heterozygous advantage or heterozygous disadvantage, in some cases, is very much likely as a result of the high linkage disequilibrium under high levels of inbreeding, where one or several deleterious alleles might be linked with neutural markers in much high probability.