Riflessioni sulla globalizzazione

Excel file describing highly significant SNPs (genome-wise FDR ≤ 5 %, FDR ≤ 1% and genome-wise Bonferroni ≤ 5 %) resulting from GWAS using single SNP regression mixed linear model for milk production (MILK), fat production (FAT), fat deviation (FATD), protein production (PROT) and protein deviation (PROTD). (XLS 518 kb

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Excel file describing gene ontology biological process terms enriched among GWAS results for production traits; milk production (MILK), fat production (FAT), fat deviation (FATD), protein production (PROT) and protein deviation (PROTD). (XLS 803 kb

Estimation of genetic parameters for mid-infrared-predicted lactoferrin and milk fat globule size in Holstein cattle.

Lactoferrin (LF) and milk fat globule (MFG) are 2 biologically active components of milk with great economical and nutritional value in the dairy industry. The objectives of this study were to estimate (1) the heritability of mid-infrared (MIR)-predicted LF and MFG size (MFGS) and (2) the genetic correlations between predicted LF and MFGS with milk, fat, and protein yields, fat and protein percentages, and somatic cell score in first-parity Canadian Holstein cattle. A total of 109,029 test-day records from 22,432 cows and 1,572 farms for MIR-predicted LF and 109,212 test-day records from 22,424 cows and 1,559 farms for MIR-predicted MFGS were used in the analyses. Four separate 5-trait random regression test-day models were used. The models included days in milk, herd test date, and a polynomial regression on DIM nested in age-season of calving classes as fixed effects, random polynomial regressions on DIM nested in herd-year of calving, animal additive genetic and permanent environment classes, and a residual effect. Regression curves were modeled using orthogonal Legendre polynomials of order 4 for the fixed age-season of calving effect and of order 5 for the random effects. Moderate overall heritability estimates of 0.34 and 0.46 were estimated for the MIR-predicted LF and MIR-predicted MFGS, respectively. These heritability estimates were similar to the ones estimated for the direct measure of MFGS in a previous study. The genetic correlations between predicted MFGS and fat percentage (0.53) and between predicted LF and protein percentage (0.41) were both moderate and positive. Predicted LF and somatic cell score showed a weaker correlation (0.06) compared with other studies. The moderate genetic correlation between MIR-predicted MFGS and fat percentage and between MIR-predicted LF and protein percentage suggests that MIR predictions of MFGS and LF are not simply a function of the amount of fat and protein percentage, respectively, in the milk (i.e., the prediction equations are not simply predicting fat or protein percentages). Thus, these MIR-predicted values may provide additional information for selecting for fine milk components in Holstein cattle

Additional file 9: Table S4. of Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle

Excel file describing previously identified production or fertility trait QTL that overlap with the SNPs identified in this study for calving to first service interval (CTFS). (XLS 30 kb

Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

Abstract Background Our aim was to identify genomic regions via genome-wide association studies (GWAS) to improve the predictability of genetic merit in Holsteins for 10 calving and 28 body conformation traits. Animals were genotyped using the Illumina Bovine 50 K BeadChip and imputed to the Illumina BovineHD BeadChip (HD). GWAS were performed on 601,717 real and imputed single nucleotide polymorphism (SNP) genotypes using a single-SNP mixed linear model on 4841 Holstein bulls with breeding value predictions and followed by gene identification and in silico functional analyses. The association results were further validated using five scenarios with different numbers of SNPs. Results Seven hundred and eighty-two SNPs were significantly associated with calving performance at a genome-wise false discovery rate (FDR) of 5%. Most of these significant SNPs were on chromosomes 18 (71.9%), 17 (7.4%), 5 (6.8%) and 7 (2.4%) and mapped to 675 genes, among which 142 included at least one significant SNP and 532 were nearby one (100 kbp). For body conformation traits, 607 SNPs were significant at a genome-wise FDR of 5% and most of them were located on chromosomes 5 (30%), 18 (27%), 20 (13%), 6 (6%), 7 (5%), 14 (5%) and 13 (3%). SNP enrichment functional analyses for calving traits at a FDR of 1% suggested potential biological processes including musculoskeletal movement, meiotic cell cycle, oocyte maturation and skeletal muscle contraction. Furthermore, pathway analyses suggested potential pathways associated with calving performance traits including tight junction, oxytocin signaling, and MAPK signaling (P < 0.10). The prediction ability of the 1206 significant SNPs was between 78 and 83% of the prediction ability of the BovineSNP50 SNPs for calving performance traits and between 35 and 79% for body conformation traits. Conclusions Various SNPs that are significantly associated with calving performance are located within or nearby genes with potential roles in tight junction, oxytocin signaling, and MAPK signaling. Combining the significant SNPs or SNPs within or nearby gene(s) from the HD panel with the BovineSNP50 panel yielded a marginal increase in the accuracy of prediction of genomic estimated breeding values for all traits compared to the use of the BovineSNP50 panel alone

Additional file 2: Figure S2. of Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle

Genome-wide association analysis and quantile-quantile (Q-Q) of P-values of SNPs from single SNP regression mixed linear model for fertility traits: Panels A-C: The –log10 of the P-value for association with SNPs is plotted. Chromosome number is shown on the horizontal axis. The traits are shown as A. daughter fertility (DF); B. heifer first service to calving interval (FSTCh); C. days open (DO). The red line is the threshold for significant SNPs at 1 % FDR. The green line is the threshold for significant SNPs at 5 % FDR. Panels D-G: In the Q-Q plots the blue dots represent the –log10(P-values) to the expected distribution under the null hypothesis of no association. The traits are shown as D. daughter fertility (DF); E. heifer first service to calving interval (FSTCh); F. calving to first service interval (CTFS); G. days open (DO). The red line denotes the expected pattern under the null hypothesis. Deviations between the red line and blue dots indicate how the test statistics of loci deviate from the null hypothesis. (PPTX 3218 kb

MOESM2 of Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

Additional file 2: Figure S2. Distribution of 601,717 SNPs in the high-density panel across the bovine genome. Genomic coordinates of SNPs are displayed along the horizontal axis (Mb) and chromosome numbers are displayed on the vertical axi