Bayesian estimation of genetic variance and response to selection on linear or ratio traits of feed efficiency in dairy cattle

This study aimed to estimate genetic parameters of the linear trait genetic residual feed intake (RFI) and the ratio traits feed conversion ratio (FCR) and feed conversion efficiency (FCE) along with dry matter intake (DMI) and energy sink traits such as energy-corrected milk (ECM), body weight (BW), body condition score (BCS), and BW change (BWC) across different weeks in the first lactation of Danish Holstein cows. A second objective was to conduct a Bayesian analysis of direct and correlated superiority of the selected group when selecting on genetic RFI, FCR, or FCE. Feed intake and energy sink traits were recorded during wk 1 to 44 of lactation on 847 primiparous Danish Holstein cows. A Bayesian multivariate random regression animal model was used to analyze DMI, ECM, BW, and BCS in different weeks of lactation. Genetic RFI was obtained by conditioning DMI on ECM, BW, BCS, and BWC using genetic partial regression coefficients. The posterior distribution of the breeding values for FCR and FCE was derived from the posterior distribution of functions of "fixed" environmental effects and random additive genetic effects on DMI and ECM. Genetic superiority of the selected group was defined as the difference in additive genetic mean of the selected top individuals expected to be potential parents, and the total population after integrating genetic trends out of the posterior distribution of selection responses. Posterior means of heritability of genetic RFI ranged from 0.10 to 0.15, genetic variance of FCR and FCE ranged from 2.13 × 10-3 to 3.2 × 10-3 (kg2 DMI/kg2 ECM) and 6.11 × 10-3 to 2.4 × 10-2 (kg2 ECM/kg2 DMI), respectively. Selection against RFI showed a direct response of -1.01 to -2.23 kg/d RFI and correlated responses of -0.031 to -0.056 kg/kg for FCR, 0.104 to 0.160 kg/kg for FCE, and -0.316 to -1.057 kg/d for DMI in different weeks of lactation. Selection against RFI had no significant effect on production traits but selection for ratio traits reduced BW and BCS. Posterior means of genetic correlation between DMI and ratio traits were low. In conclusion, the Bayesian procedure allowed us to estimate genetic RFI without the need for separate multiple regression analysis and considered the non-normal posterior distribution of ratio traits. Selection against genetic RFI might be an effective means to improve feed efficiency compared with ratio traits for feed efficiency in dairy cattle

An extended anchored linkage map and virtual mapping for the american mink genome based on homology to human and dog

AbstractIn this report we present an extended linkage map of the American mink (Neovison vison) consisting of 157 microsatellite markers and comprising at least one linkage group for each of the autosomes. Each linkage group has been assigned to a chromosome and oriented by fluorescence in situ hybridization (FISH) and/or by means of human/dog/mink comparative homology. The average interval between markers is 8.5 cM and the linkage groups collectively span 1340 cM. In addition, 217 and 275 mink microsatellites have been placed on human and dog genomes, respectively. In conjunction with the existing comparative human/dog/mink data, these assignments represent useful virtual maps for the American mink genome. Comparison of the current human/dog assembled sequential map with the existing Zoo-FISH-based human/dog/mink maps helped to refine the human/dog/mink comparative map. Furthermore, comparison of the human and dog genome assemblies revealed a number of large synteny blocks, some of which are corroborated by data from the mink linkage map

Refined localization of the Escherichia coliF4ab/F4ac receptor locus on pig chromosome 13

Diarrhoea in newborn and weaned pigs caused by enterotoxigenic Escherichia coli (ETEC) expressing F4 fimbriae leads to considerable losses in pig production. In this study, we refined the mapping of the receptor locus for ETEC F4ab/F4ac adhesion (F4bcR) by joint analysis of Nordic and Swiss data. A total of 236 pigs from a Nordic experimental herd, 331 pigs from a Swiss experimental herd and 143 pigs from the Swiss performing station were used for linkage analysis. Genotyping data of six known microsatellite markers, two newly developed markers (MUC4gt and HSA125gt) and an intronic SNP in MUC4 (MUC4-8227) were used to create the linkage map. The region for F4bcR was refined to the interval SW207–S0075 on pig chromosome 13. The most probable position of F4bcR was in the SW207–MUC4 region. The order of six markers was supported by physical mapping on the BAC fingerprint contig from the Wellcome Trust Sanger Institute. Thus, the region for F4bcR could be reduced from 26 to 14 Mb. Keywords chromosome 13, enterotoxigenic Escherichia coli, Escherichia coli, F4ab/F4ac receptor, linkage mapping, pig

Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace I: carcass traits

We report the identification of quantitative trait loci (QTL) affecting carcass composition, carcass length, fat deposition and lean meat content using a genome scan across 462 animals from a combined intercross and backcross between Hampshire and Landrace pigs. Data were analysed using multiple linear regression fitting additive and dominance effects. This model was compared with a model including a parent-of-origin effect to spot evidence of imprinting. Several precisely defined muscle phenotypes were measured in order to dissect body composition in more detail. Three significant QTL were detected in the study at the 1% genome-wide level, and twelve significant QTL were detected at the 5% genome-wide level. These QTL comprise loci affecting fat deposition and lean meat content on SSC1, 4, 9, 10, 13 and 16, a locus on SSC2 affecting the ratio between weight of meat and bone in back and weight of meat and bone in ham and two loci affecting carcass length on SSC12 and 17. The well-defined phenotypes in this study enabled us to detect QTL for sizes of individual muscles and to obtain information of relevance for the description of the complexity underlying other carcass traits