Genomic patterns of homozygosity and inbreeding depression in MurcianoGranadina goats

Background:Inbreeding depression can adversely affect traits related to fitness,reproduction and productive performance.Although current research suggests that inbreeding levels are generally low in most goat breeds,the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data.Results:We genotyped 1040 goats with the Goat SNP50 BeadChip.This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns.We detected38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1,2,4,6,14,16 and 17.Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes.Four regions on chromosomes 8 and 25were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count.Notably,these regions contain several genes related with immunity,such as SYK,IL27,CCL19 and CCL21.Moreover,one region on chromosome 2 was significantly associated with inbreeding depression for milk yield.Conclusions:Although genomic inbreeding levels are low in Murciano-Granadina goats,significant evidence of inbreeding depression for the logarithm of the somatic cell count,a phenotype closely associated with udder health and milk yield,have been detected in this population.Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis,which is one of the main causes of dairy goat culling.

Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations

A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 （SD 0.00） and 0.19 （SD 0.03） for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by： a） estimation of the recombination fraction and LD in consecutive SNPs using family information, b） linkage analyses between fragments, c） phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual （sire level）. SNPs for which the sire and calf were heterozygotes became informative （over 90%） after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes （with at least 20 SNP） in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.

Proteomic analysis of F_(1)hybrids and intermediate variants in a Littorina saxatilis hybrid zone

Proteomic analysis was carried out on the Crab(upper-shore)and Wave(lower-shore)ecotypes of Littorina saxatilis from a hybrid zone at Silleiro Cape,Spain.Proteome profiles of individual snails were obtained.Protein expression in F_(1)hybrid snails bred in the laboratory and snails with intermediate shell phenotypes collected from the mid-shore were compared with Crab and Wave ecotypes using analytical approaches used to study dominance.Multivariate analysis over many protein spots showed that the F_(1)snails are distinct from both ecotypes but closer to the Wave ecotype.The intermediate snails are highly variable,some closer to the Crab and others to the Wave ecotype.Considered on a protein by protein basis,some proteins are significantly closer in expression to the Crab and others to the Wave ecotype for both F_(1)and intermediate snails.Furthermore,a significant majority of proteins were closer in expression to the Wave ecotype for the F_(1),consistent with the multivariate analysis.No such significant majority toward either the Crab or Wave ecotype was observed for the intermediate snails.The closer similarity of F_(1)and Wave ecotype expression patterns could be the result of similar selective pressures in the similar mid-shore and low-shore environments.For a significantly larger number of proteins,intermediate snails were closer in expression to the ecotype having the lower expression,for both Crab and Wave ecotypes.This is somewhat unexpected as lower expression might be expected to be an indication of impairment of function and lower fitness.Proteomic analysis could be important for the identification of candidate proteins useful for gaining improved understanding of adaptation and barriers to gene flow in hybrid zones.