Direct multitrait selection realizes the highest genetic response for ratio traits.

For a number of traits the phenotype considered to be the goal trait is a combination of 2 or more traits, like methane (CH) emission (CH/kg of milk). Direct selection on CH4 emission defined as a ratio is problematic, because it is uncertain whether the improvement comes from an improvement in milk yield, a decrease in CH emission or both. The goal was to test different strategies on selecting for 2 antagonistic traits- improving milk yield while decreasing methane emissions. The hypothesis was that to maximize genetic gain for a ratio trait, the best approach is to select directly for the component traits rather than using a ratio trait or a trait where 1 trait is corrected for the other as the selection criteria. Stochastic simulation was used to mimic a dairy cattle population. Three scenarios were tested, which differed in selection criteria but all selecting for increased milk yield: 1) selection based on a multitrait approach using the correlation structure between the 2 traits, 2) the ratio of methane to milk and 3) gross methane phenotypically corrected for milk. Four correlation sets were tested in all scenarios, to access robustness of the results. An average genetic gain of 66 kg of milk per yr was obtained in all scenarios, but scenario 1 had the best response for decreased methane emissions, with a genetic gain of 24.8 l/yr, while scenarios 2 and 3 had genetic gains of 27.1 and 27.3 kg/yr. The results found were persistent across correlation sets. These results confirm the hypothesis that to obtain the highest genetic gain a multitrait selection is a better approach than selecting for the ratio directly. The results are exemplified for a methane and milk scenario but can be generalized to other situations where combined traits need to be improved.

Evolving gene banks: improving diverse populations of crop and exotic germplasm with optimal contribution selection.

We simulated pre-breeding in evolving gene banks - populations of exotic and crop types undergoing optimal contribution selection for long-term genetic gain and management of population genetic diversity. The founder population was based on crosses between elite crop varieties and exotic lines of field pea (Pisum sativum) from the primary genepool, and was subjected to 30 cycles of recurrent selection for an economic index composed of four traits with low heritability: black spot resistance, flowering time and stem strength (measured on single plants), and grain yield (measured on whole plots). We compared a small population with low selection pressure, a large population with high selection pressure, and a large population with moderate selection pressure. Single seed descent was compared with S0-derived recurrent selection. Optimal contribution selection achieved higher index and lower population coancestry than truncation selection, which reached a plateau in index improvement after 40 years in the large population with high selection pressure. With optimal contribution selection, index doubled in 38 years in the small population with low selection pressure and 27-28 years in the large population with moderate selection pressure. Single seed descent increased the rate of improvement in index per cycle but also increased cycle time.

Mating strategies with genomic information reduce rates of inbreeding in animal breeding schemes without compromising genetic gain.

We tested the hypothesis that mating strategies with genomic information realise lower rates of inbreeding (∆F) than with pedigree information without compromising rates of genetic gain (∆G). We used stochastic simulation to compare ∆F and ∆G realised by two mating strategies with pedigree and genomic information in five breeding schemes. The two mating strategies were minimum-coancestry mating (MC) and minimising the covariance between ancestral genetic contributions (MCAC). We also simulated random mating (RAND) as a reference point. Generations were discrete. Animals were truncation-selected for a single trait that was controlled by 2000 quantitative trait loci, and the trait was observed for all selection candidates before selection. The criterion for selection was genomic-breeding values predicted by a ridge-regression model. Our results showed that MC and MCAC with genomic information realised 6% to 22% less ∆F than MC and MCAC with pedigree information without compromising ∆G across breeding schemes. MC and MCAC realised similar ∆F and ∆G. In turn, MC and MCAC with genomic information realised 28% to 44% less ∆F and up to 14% higher ∆G than RAND. These results indicated that MC and MCAC with genomic information are more effective than with pedigree information in controlling rates of inbreeding. This implies that genomic information should be applied to more than just prediction of breeding values in breeding schemes with truncation selection.

Most of the benefits from genomic selection can be realized by genotyping a small proportion of available selection candidates.

We reasoned that marginal returns from genomic selection diminish as the proportion of genotyped selection candidates increases and breeding values (BV) based on a priori information are used to choose candidates that are genotyped. We tested this premise by stochastic simulation of breeding schemes that resembled those used for pigs. We estimated rates of genetic gain and inbreeding realized by genomic selection in breeding schemes where candidates were phenotyped before genotyping and 0 to 100% of the candidates were genotyped based on predicted BV. Genotyping was allocated to male and female candidates at ratios of 100:0, 75:25, 50:50, 25:75, and 0:100. For genotyped candidates, a direct-genomic value (DGV) was sampled with reliabilities 0.10, 0.50, and 0.90. Ten sires and 300 dams with the largest BV after genotyping were selected at each generation. Selection was for a single trait with heritability 0.20. We found that the marginal returns did diminish as genotyping proportion was increased, while the rate at which the returns diminished slowed as DGV became more reliable. With DGV reliability 0.10, genotyping as little as 5% of the selection candidates realized 86% of the additional genetic gain and 67% of the reduction in inbreeding that was realized by genotyping 100% of the candidates. All of the genetic gain and reduction in inbreeding was realized by genotyping 40 and 50% of the candidates. When the reliability was increased to 0.90, genotyping 20% of the candidates was required to realize 76% of the genetic gain and 85% of the reduction in inbreeding. Genotyping 50% of the selection candidates with DGV reliability 0.90 realized 91% of the genetic gain and 94% of the reduction in inbreeding. Regardless of DGV reliability, returns at small genotyping proportions of 0.5 to 10% were maximized when only male candidates were genotyped. At the large genotyping proportions of 20 to 50%, returns were maximized by genotyping both males and females. Our findings indicate that, provided a priori information is available, only 5 to 20% of the selection candidates need to be genotyped to realize most of the benefits from genomic selection. At these genotyping proportions, it is best to target males in schemes when selection intensity for males is greater than females. Our findings should benefit breeders because they suggest that large investments in genotyping are not required to reap most of the benefits from genomic selection.

Consequences of elimination of the Rendement Napole allele from Danish Hampshire.

An elimination programme was carried out to remove the dominant Rendement Napole mutation (RN(-) ) from Danish Hampshire pigs. We reasoned that during and after the elimination of the RN(-) allele, genetic gain of production traits decreased while rate of inbreeding in the population increased compared to the period prior to elimination. The hypothesis was tested by estimating the genetic gain in seven production traits and measuring the rate of inbreeding in the population prior to and during the elimination period. Genetic gain was reduced for quantitative traits daily gain(30-100 kg) and feed conversion ratio, while gain for ultimate-pH, lean meat percentage and slaughter loss were increased slightly. There were no changes in genetic gain for daily gain(birth-30 kg) and conformation. RN polymorphism affected several of the quantitative traits. The RN(-) mutation had a dominant effect on the traits daily gain(birth-30 kg) , daily gain(30-100 kg) , slaughter loss, lean meat percentage and ultimate-pH. It exhibited overdominance for feed conversion ratio and additive effect for conformation. Rate of inbreeding decreased during the elimination of RN(-) . Our findings indicate that the consequences of the elimination programme were not as serious as were feared and that a carefully designed preselection strategy may avoid unacceptable loss of genetic gain and excessive loss of genetic variation.

General and family-specific gene expression responses to viral hemorrhagic septicaemia virus infection in rainbow trout (Oncorhynchus mykiss).

The ability of rainbow trout (Oncorhynchus mykiss) to respond successfully to infection by viral hemorrhagic septicaemia virus (VHSV) is expected to involve a large number of biochemical processes. We hypothesized that this would be reflected at the gene expression level in infected fish, and we tested it by examining gene expression levels in the head kidney of trout at a genome-wide scale with a 16K cDNA microarray for salmonids. Expression levels were recorded during 16 days following bath challenge. The challenge experiment included a relatively low susceptibility (32% survival following challenge) and a relatively high susceptibility (18% survival following challenge) trout family that were both split into a group exposed to virus and a non-exposed control group. In total, 939 genes were differentially expressed between infected and non-infected fish (FDR p=0.05). Five groups of Gene Ontology categories were involved in immune-related processes and over-represented in infected fish: (i) stress and defense response, (ii) NFkappaB signal transduction, (iii) response to non-self, (iv) antigen processing and presentation, and (v) proteasome complexes. The first four categories were also over-represented among the 642 differentially expressed genes in the low-susceptibility trout family but not among the 556 differentially expressed genes in the high-susceptibility trout family. Expression profiles for most immune genes discussed showed increased transcription from day 3 post-challenge. The results suggest that the innate immune system may play an important role in the successful response to VHSV in rainbow trout. In addition, the results indicate that a superior regulation of the transcription of several key innate immune-related genes contribute to the increased survival in resistant fish.

Mating animals by minimising the covariance between ancestral contributions generates less inbreeding without compromising genetic gain in breeding schemes with truncation selection.

We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis by stochastic simulation and compared the mating criteria in hierarchical and factorial breeding schemes, where the animals were selected based on breeding values predicted by animal-model BLUP. Random mating was included as a reference-mating criterion. We found that MCAC mating generated 4% to 8% less inbreeding than minimum-coancestry mating in the hierarchical and factorial breeding schemes without any loss in genetic gain. Moreover, it generated upto 28% less inbreeding and about 3% more genetic gain than random mating. The benefits of MCAC mating over minimum-coancestry mating are worthwhile because they can be achieved without extra costs or practical constraints. MCAC mating merely uses pedigree information to pair the animals more appropriately and is clearly a worthy alternative to minimum-coancestry mating and probably any other mating criterion. We believe, therefore, that MCAC mating should be used in breeding schemes where pedigree information is available.

Polymorphism in the bovine growth hormone gene affects endocrine release in dairy calves.

The objective was to test whether calves with the Leu/Leu genotype release more growth hormone (GH) than calves with Leu/Val and Val/Val genotypes. Danish Holstein (n = 286), Danish Red (n = 68), and Danish Jersey (n = 61) calves were genotyped for the Leu/Val polymorphism in the GH gene and assessed for GH release following inducement by the growth hormone releasing hormone (GHRH). Three GH traits were assessed for each calf: BASELINE, PEAK, and RATE. BASELINE and PEAK are the mean concentration of GH in blood sampled before and after GHRH inducement. RATE is the disappearance rate of GH in blood sampled after GHRH inducement. Danish Jersey calves with Leu/Leu genotype had a higher PEAK and RATE than calves with the Val/Val genotype, whereas the Leu/Val genotype had an intermediate response. The contribution of the Leu/Val polymorphism to the total genetic variation of the BASELINE, PEAK, and RATE traits was 5, 30, and 27%, respectively. By contrast, the amount of GH released by the Danish Holstein and Danish Red calves was not influenced by their GH genotype. Further studies involving calves with all three genotypes are required to further elucidate whether this polymorphism has a functional role or whether it works through a linked-gene effect specific to certain cattle breeds.

Rainbow trout offspring with different resistance to viral haemorrhagic septicaemia.

To study immunological and immunogenetical parameters related to resistance against viral haemorrhagic septicaemia (VHS), attempts to make gynogenetic strains of rainbow trout selected for high and low resistance to VHS were initiated in 1988. The first gynogenetic generation of inbreeding resulted in the more resistant offspring E8 and the low resistance offspring K3; the K3 offspring having the same high mortality as the susceptible reference strain of outbred trout in infection trials. A second gynogenetic generation derived from the E8 strain resulted in some low resistance offspring, and two gynogenetic families in which all, or nearly all, fish survived challenge with VHS virus. In this study, an attempt to associate the distribution of different MHC class II genotypes with low and high resistance gynogenetic offspring was performed. Two different MHC haplotypes could be distinguished, and in both low and high resistance families all three genotypes were found, which could be explained by the fact that the mother fish carried the heterozygous genotype. Although no significant differences in MHC II genotypes were found between the high and low resistance offspring, a significantly different distribution of haplotypes in the low resistance offspring was observed, that could not be explained by a one- or two-locus model.

A new approach to evaluate toxicity of gases on mobile cells in culture.

A novel technique is described that measures the degree of toxicity of short-term exposure to gaseous pollutants or other chemical compounds on cultured cells, in 30 min. This technique, based on the study of the mobility properties of activated macrophages, consists of an image analysis procedure incorporating a specific exposure chamber (EC). The EC, which is developed from commercial culture flasks (50 ml, 25 cm(2) of culture surface), was first used to maintain cells in culture conditions, overnight, prior to the assay. In order to measure toxicity, it was then connected to the gaseous pollutant or chemical source. After exposing the culture medium and cells to the gas stream for 10 min, fMLP, a chemotactic factor, was added and the mobility of the macrophages measured by superimposing sequential analogue images captured by a CCD camera that were digitised and analysed using a software developed for this purpose. For example, the effect of ozone on macrophage-like cell (THP-1) was investigated. After exposure to 0.1 and 0.5 ppm, cells lost, respectively 79% and 90% of their mobility, compared to the control sample.