Search

This study was carried out to investigate variance components, direct heritability, maternal genetic parameters, estimated breeding values and factors affecting pre-weaning growth criteria of Romney sheep. Data were collected over the period from 2006 to 2012 with records of 4989 lambs descended from 76 rams and 2190 ewes of Romney sheep maintained at S. Island of New Zealand via Gene Marker Lab., Faculty of Agric. and Life Sci., Lincoln Univ., New Zealand. Results proved that genetic and non-genetic factors affecting studied criteria had significant effects (P2a±SE); 0.59±0.219, 0.41±0.023 and 0.08±0.002 for maternal heritability (h2m±SE); 0.11684, 2.6378 and 0.27565 for additive variances (σ2a), 0.34596, 7.1179 and 0.14532 for maternal variances (σ2m); and 0.002395, 10.1262 and 0.509339 for permanent environmental variances (σ2e), respectively. EBV’s of LBW, LWW and KR ranged from -0.555: 0.502, -1.554: 3.006 and -0.633: 0.242 direct, -0.863: 0.954, -4.942: 2.554 and -0.469: 0.179 maternal for rams, respectively; and -0.664: 0.830, -2.996: 4.586 and -1.651: 0.677 direct, 1.429: 1.142, -7.541: 4.920 and -1.223: 0.492 maternal for ewes, respectively. Results suggest the importance of considering the non-genetic factors in pre-weaning growth performance of lambs. Moderate heritability and positive coefficients of phenotypic and genetic correlation for studied criteria indicate to the possibility of improving them using traditional selection.

In the mountainous areas of Europe with a humid climate, dairy cattle production is a major agricultural activity, and the milk is often processed into cheese according to protected designation of origin (PDO) specifications. We analyzed the extent to which PDO specifications and/or a mountain environment influence the spatial distribution of estimated breeding values (EBVs) of cows and the herd–year effects (HYEs) for milk yield (kg/lactation) and protein and fat contents (g/kg), as well as lactation ranks and calving months. The study focused on the northern French Alps. A total of 37 023 lactations, recorded in 2006, in 1153 herds were analyzed. The cows belonged to the Montbéliarde (21 516 lactations), Abondance (10 346 lactations) and Tarentaise (5161 lactations) breeds. The two factors of variation considered were the status of the commune where the farm was located in relation to PDO (three categories: area with no PDO, area with a PDO with no milk yield limit, area with a PDO with a milk yield limit) and ‘mountain’ environment (four categories based on the European regulation: plain, piedmont, mountain and high mountain). In the Abondance breed, the average lactation rank increased with an increase in production constraints due to the PDO or to a mountain environment. In the Abondance and Tarentaise breeds, grouping of calving in winter was most marked in the ‘PDO with a milk yield limit’ and ‘high-mountain’ categories. In the Tarentaise breed, no significant effect on any trait and any variable was found in the ‘PDO’ or ‘mountain’ categories. In the other two breeds, the average EBV for milk yield decreased with an increase in the constraints due to PDO, with differences of 226 and 93 kg between extreme values in the Abondance and Montbéliarde breeds, respectively. The average HYE for milk yield was higher in the Abondance breed in the ‘PDO with no milk yield limit’ category than in the other categories (+740 and +1110 kg, respectively); HYE was not affected by the ‘PDO’ factor in the Montbéliarde breed or by the ‘mountain’ factor in either breed. Concerning the protein and fat contents, the effect of the ‘PDO’ and ‘mountain’ factors depended on the trait, the variable and the breed. The proportion of individual decisions (the farmer makes the decision) v. collective decisions (breed management) concerning herd dynamics in the face of existing constraints is discussed.

Data on 305-d milk yield from the Dutch dairy evaluation were used to obtain breeding value estimates from an animal model for 1984 to 1992. Changes in sire evaluations were investigated for bias and realized accuracy. Evaluations based on progeny records were generally lower than their expectation based on parent average. The average decrease was 157kg for Black and White bulls and 73kg for Red and White bulls. Evaluations based on test daughters changed about –50kg when second and third lactations became available, but estimates for breeding value changed insignificantly when records on daughters from the breeding period of the bull were used. The standard deviation of changes from evaluations for first to second batch was about 14% larger than expected from population parameters. Breeding values of imported bulls, based on Dutch data, decreased 75kg when more information became available in subsequent evaluations. Heterogeneity of variance was estimated by a quasi-likelihood approach with a model that accounted for sampling variance on estimates of variances within herd. The coefficient of variation of the variances within herd-year was 31%. A simple method for standardization of variances within herd-year decreased bias of parent averages by about 20%, and fluctuations of breeding values were within the expected range. A correction for heterogeneity of variance within herd may not remove all bias of parent averages, but a general improvement of bias and accuracy of breeding values can be expected.

International audience

The genome sequence of apple (Malus×domestica Borkh.) was published more than a year ago, which helped develop an 8K SNP chip to assist in implementing genomic selection (GS). In apple breeding programmes, GS can be used to obtain genomic breeding values (GEBV) for choosing next-generation parents or selections for further testing as potential commercial cultivars at a very early stage. Thus GS has the potential to accelerate breeding efficiency significantly because of decreased generation interval or increased selection intensity. We evaluated the accuracy of GS in a population of 1120 seedlings generated from a factorial mating design of four females and two male parents. All seedlings were genotyped using an Illumina Infinium chip comprising 8,000 single nucleotide polymorphisms (SNPs), and were phenotyped for various fruit quality traits. Random-regression best liner unbiased prediction (RR-BLUP) and the Bayesian LASSO method were used to obtain GEBV, and compared using a cross-validation approach for their accuracy to predict unobserved BLUP-BV. Accuracies were very similar for both methods, varying from 0.70 to 0.90 for various fruit quality traits. The selection response per unit time using GS compared with the traditional BLUP-based selection were very high (>100%) especially for low-heritability traits. Genome-wide average estimated linkage disequilibrium (LD) between adjacent SNPs was 0.32, with a relatively slow decay of LD in the long range (r(2) = 0.33 and 0.19 at 100 kb and 1,000 kb respectively), contributing to the higher accuracy of GS. Distribution of estimated SNP effects revealed involvement of large effect genes with likely pleiotropic effects. These results demonstrated that genomic selection is a credible alternative to conventional selection for fruit quality traits.

Returns from the utilization of genetic markers in breeding programs have been computed in two ways. In the first approach, returns accrue from additionally improved milk yield that was due to marker utilization in selection. In the second approach, changes in returns from semen sales for a breeding organization operating in a competitive market are determined. The genetic effect of markers is taken to result from preselection of young bulls. Based on the literature, the increase in mean breeding value of young bulls as a result of marker-based preselection was taken to range from .15 to .45 additive genetic standard deviation. When additive genetic standard deviation is assumed at $67 with an interest rate of 5% and a time horizon of 25 yr, cumulative discounted returns from 1 yr of marker utilization ranged from $7 to $21 per cow for progeny testing and from $20 to $60 for an open nucleus. Additional discounted financial returns from increased semen sales range from $5.0 million to $16.2 million for a situation in which an AI firm utilizes markers during 20 yr and competitors do not follow. Lower costs are expected as technology improves, and improved statistical analysis should reduce the number of typings required. Thus, utilization of markers is expected to become financially justified.