Utilization Of Microsatellite Markers To Analyze Molecular Genetics Of SPF Breeding Bird

The National Center on Experimental Poultry Genetic Resources hosted by Haerbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences preserves the BWEL-SPF chicken and duck populations. A rotational mating scheme was applied to the BWEL-SPF chicken families from F1 to F14 generations and a maximum non-inbred mating scheme has been adopted since F15 generation in eight chicken families in 2007. For the SPF ducks, two families were established according to their egg shell colors and they are in F3 generation. In this study, microsatellite loci were used to characterize the BWEL-SPF chickens of F16 generation and ducks of both F2 and F3 generations. A microsatellite located within the MHC-B region was also genotyped to understand the immunological background of the BWEL-SPF chickens. We aim at investigating the genetic variation and inbreeding within the families and the genetic relationships between the families. The findings provide baseline information for standard management and breeding of the SPF chickens and ducks, in particular the establishment of specific families of genetic resistance/susceptibility to certain pathogens. We obtained the following results:The genetic diversity of SPF ducks in F2 and F3 generations were assessed using 18 microsatellite loci. A total of 80 alleles were detected in F2 and F3 HBK-B and HBK-Q duck populations. The average PIC values for each of the 18 loci were all greater than 0.49. The heterzygosity at single loci ranged between 0.321 and 0.760 with an average of 0.571 in the pooled population and between 0.311 and 0.752 with an average of 0.565 in the sub-populations. The expected heterzygosity of HBK-B and HBK-Q ducks were between 0.560 and 0.618 and between 0.570 and 0.591, respectively. These data indicated a high genetic diversity present in HBK-SPF ducks.Significant tests for inbreeding levels(FST) within HBK-B and HBK-Q ducks detected some loci significantly deviated from zero(P < 0.05), an indication of the presence of a high level of inbreeding in HBK-SPF ducks, therefore appropriate measures have to be taken in controlling while utilizing present high level of inbreeding.Significant tests for the pairwise FST estimates revealed significant genetic differentiations between HBK-B and HBK-Q ducks in both generations(P < 0.001).χ2 tests for allelic frequency in both HBK-B and HBK-Q ducks between the F2 and F3 generations showed significant differences(P < 0.01)at six and eleven loci, respectively. These results meant that the selection according to egg shell colors has resulted in some degree of genetic differentiation between the two populations, but the genetic stability within populations have to be enhanced through increasing the effective population sizes.Using 14 microsatellite loci, we analyzed the genetic variation of SPF chickens in F15 generation. The results showed that, due to the inbreeding over 14 generations of mating within families, a number of loci(35.7%; 5/14)have been fixed with single alleles or approaching to fixation with single predominant alleles (> 0.9) with allele variations in general being reduced significantly within the population. However, the change of breeding scheme in mating from within families to between families since the F15 generation has converted the positive inbreeding FIS values to negative out-breeding FIS estimates in most of the families(7/8)with four of them significantly deviated from zero (P < 0.05), indicating a considerable compromise in inbreeding within the families.Significant tests for the pairwise FST estimates still indicated significant genetic differentiations between the eight families (P < 0.01). There was 12.9% of the total genetic variation present among the families, implying the presence of significant genetic differentiation once present among the families over 14 generations within-family selection and breeding.By comparing the pattern of allele distributions between the SPF chickens and other chicken breeds from different genetic background, we found that, apart from a few loci being fixed or approaching fixation, majority of loci( 64.3%, 9/14) still maintained two or three dominant alleles in the SPF chickens through inbreeding over 14 generations. This phenomenon urges the need for examination of the intrinsic genetics of different ancestral populations that have been or are used to establish the inbreeding lines when the microsatellite markers are employed to assess their inbreeding and genetic purity.By genotyping LEI0258, we were able to select homozygotes at this locus as fundamental birds to establish inbred lines with specific MHC genotypes that may lead to different disease resistance or susceptibility.