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.

Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats

Background:In this study,we aimed to investigate the molecular basis of lactation as well as to identify the genetic factors that influence milk yield and composition in goats.To achieve these two goals,we have analyzed how the mRNA profile of the mammary gland changes in seven Murciano-Granadina goats at each of three different time points,i.e.78 d(T1,early lactation),216 d(T2,late lactation)and 285 d(T3,dry period)after parturition.Moreover,we have performed a genome-wide association study(GWAS)for seven dairy traits recorded in the 1st lactation of 822 Murciano-Granadina goats.Results:The expression profiles of the mammary gland in the early(T1)and late(T2)lactation were quite similar(42 differentially expressed genes),while strong transcriptomic differences(more than one thousand differentially expressed genes)were observed between the lactating(T1/T2)and non-lactating(T3)mammary glands.A large number of differentially expressed genes were involved in pathways related with the biosynthesis of amino acids,cholesterol,triglycerides and steroids as well as with glycerophospholipid metabolism,adipocytokine signaling,lipid binding,regulation of ion transmembrane transport,calcium ion binding,metalloendopeptidase activity and complement and coagulation cascades.With regard to the second goal of the study,the performance of the GWAS allowed us to detect 24 quantitative trait loci(QTLs),including three genome-wide significant associations:QTL1(chromosome 2,130.72-131.01 Mb)for lactose percentage,QTL6(chromosome 6,78.90-93.48 Mb)for protein percentage and QTL17(chromosome 17,11.20 Mb)for both protein and dry matter percentages.Interestingly,QTL6 shows positional coincidence with the casein genes,which encode 80%of milk proteins.Conclusions:The abrogation of lactation involves dramatic changes in the expression of genes participating in a broad array of physiological processes such as protein,lipid and carbohydrate metabolism,calcium homeostasis,cell death and tissue remodeling,as well as immunity.We also conclude that genetic variation at the casein genes has a major impact on the milk protein content of Murciano-Granadina goats.