Lack Of Genetic Correlation Research Articles

Breeding options for nematode resistance in Lacaune dairy sheep

Due to progressing anthelmintic resistance of gastrointestinal nematodes (GIN), supportive measures are needed to control these parasites. In sheep, it has been shown that selection towards an increased nematode resistance is feasible and that faecal egg count (FEC) is the generally acknowledged trait for selection. However, a selection based on FEC would come with certain costs, therefore auxiliary, cheaper resistance traits would be most welcome. FAMACHA©, a colour classification of the eyelid, usually used to determine the manifestation of an infection with Haemonchus contortus, could serve as such. Therefore, we collected FAMACHA©, packed cell volume (PVC) and FEC phenotypes of approx. 1150 naturally infected Lacaune ewes on 15 commercial farms in Switzerland. The Haemonchus-proportion was determined on farm level. Phenotypic correlations of FEC and FAMACHA© as well as FAMACHA© and PCV were 0.25 (SE 0.03) and −0.35 (SE 0.08), respectively, and correspond well with the results of other studies. A multi-trait animal model was applied to estimate genetic parameters with FEC, FAMACHA©, PVC and milk yield as dependent variables. The heritabilities of FEC, FAMACHA©, PCV and milk yield were estimated to be moderate with values of 0.33 (SE 0.08), 0.30 (SE 0.08), 0.36 (SE 0.08) and 0.34 (SE 0.08), respectively. The genetic correlations between FEC and FAMACHA© and between FEC and PCV were estimated to be close to zero with values of 0.03 (SE 0.22) and 0.01 (SE 0.21), respectively. The average Haemonchus-proportion compared to other GIN was found to be 43%. The FAMACHA© classification of the Lacaune ewes seems to indicate a rather high worm challenge, with 38, 14 and 2% of observations classified to scores 3, 4 and 5, respectively. However, the worm challenge according to FEC was moderate. It has been suggested that the genetic correlation between FAMACHA© and FEC is more pronounced when FEC was high. It could therefore be that the lack of genetic correlation was due to an insufficient worm challenge, even though the Lacaune were grazing at least 70 days before phenotyping. The genetic correlation between FEC and milk yield was estimated to be 0.07 (SE 0.22, slightly unfavourable). We conclude that if FEC is used as trait, the Lacaune could be selected for lower susceptibility towards nematode infection. The use of FAMACHA© as an auxiliary trait for FEC is not feasible, due to an inexistent genetic correlation between these two traits.

Quantitative analysis of black blotching in a crossbred red tilapia and its effects on performance traits via a path analysis methodology.

Red tilapia is a phenotype with potential value to the tilapia industry due to its attractive skin coloration. However, the presence of black blotches scattered on the body makes these fish less valuable than blemish-free red fish. The correlation between the degree of blotching and other economic traits is important for selective breeding programs including high-performance red fish without black blotches. Therefore, this study aimed to assess the magnitude and direct and indirect effects of blotching in crossbred red tilapia on the growth rate and body measure traits using path analysis methodology. Six genetic groups were evaluated in terms of body measurements, body weight rate, and proportion of black blotching over 250days of growth: Chitralada and Red-Stirling; crossbred F1-♀ Red-Stirling × ♂ Chitralada and ♀ Chitralada × ♂ Red-Stirling, and the introgressive crossbreeding-♀ CR × ♂ Chitralada and ♀ Chitralada × ♂ CR (C × CR). All variables showed high and positive linear correlations. Individuals with black blotches had lower coefficients of correlation with other variables (body weight and measurements); the direct and indirect effects are near zero. The path analysis indicated a lack of genetic correlation between the degree of black blotches and the economic traits of red tilapia. This facilitates the development of high growth performance red fish with blotched-free reddish skin.

Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification.

Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA.

An alternative covariance estimator to investigate genetic heterogeneity in populations.

BackgroundFor genomic prediction and genome-wide association studies (GWAS) using mixed models, covariance between individuals is estimated using molecular markers. Based on the properties of mixed models, using available molecular data for prediction is optimal if this covariance is known. Under this assumption, adding individuals to the analysis should never be detrimental. However, some empirical studies showed that increasing training population size decreased prediction accuracy. Recently, results from theoretical models indicated that even if marker density is high and the genetic architecture of traits is controlled by many loci with small additive effects, the covariance between individuals, which depends on relationships at causal loci, is not always well estimated by the whole-genome kinship.ResultsWe propose an alternative covariance estimator named K-kernel, to account for potential genetic heterogeneity between populations that is characterized by a lack of genetic correlation, and to limit the information flow between a priori unknown populations in a trait-specific manner. This is similar to a multi-trait model and parameters are estimated by REML and, in extreme cases, it can allow for an independent genetic architecture between populations. As such, K-kernel is useful to study the problem of the design of training populations. K-kernel was compared to other covariance estimators or kernels to examine its fit to the data, cross-validated accuracy and suitability for GWAS on several datasets. It provides a significantly better fit to the data than the genomic best linear unbiased prediction model and, in some cases it performs better than other kernels such as the Gaussian kernel, as shown by an empirical null distribution. In GWAS simulations, alternative kernels control type I errors as well as or better than the classical whole-genome kinship and increase statistical power. No or small gains were observed in cross-validated prediction accuracy.ConclusionsThis alternative covariance estimator can be used to gain insight into trait-specific genetic heterogeneity by identifying relevant sub-populations that lack genetic correlation between them. Genetic correlation can be 0 between identified sub-populations by performing automatic selection of relevant sets of individuals to be included in the training population. It may also increase statistical power in GWAS.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0171-z) contains supplementary material, which is available to authorized users.

Genetic correlations between spiral grain and growth and quality traits in Picea abies

In Norway spruce ( Picea abies (L.) Karst), spiral grain is a major cause of twist development in sawn timber; this problem could be addressed by breeding for reduced grain angles. This study presents estimates of genetic correlations between grain angle under bark and height and diameter growth; branch number, angle, and thickness; stem straightness; ramicorn occurrence; and pilodyn penetration using data from three progeny trials. The genetic relationship between grain angle development and radial growth was also investigated by measuring multiple annual rings (3–15) in stem sections from two clonal trials. Grain angles under the bark exhibited substantial heritability but near-zero genetic correlations with all the other traits studied. The genetic correlations between multiple ring grain angle and radial growth were also close to zero among all rings. However, radial growth exhibited positive genetic correlations with grain angles at specific distances from the pith and with radial grain angle trends, suggesting that the higher grain angles in juvenile wood extend further from the pith as a result of increased radial growth. Therefore, from a sawtimber perspective, the genetic relationship with radial growth may be unfavourable, despite the lack of genetic correlations between grain angle and radial growth at any particular annual ring.

THE QUANTITATIVE GENETICS AND COEVOLUTION OF MALE AND FEMALE REPRODUCTIVE TRAITS

Studies of experimental sexual selection have tested the effect of variation in the intensity of sexual selection on male investment in reproduction, particularly sperm. However, in several species, including Drosophila pseudoobscura, no sperm response to experimental evolution has occurred. Here, we take a quantitative genetics approach to examine whether genetic constraints explain the limited evolutionary response. We quantified direct and indirect genetic variation, and genetic correlations within and between the sexes, in experimental populations of D. pseudoobscura. We found that sperm number may be limited by low heritability and evolvability whereas sperm quality (length) has moderate V(A) and CV(A) but does not evolve. Likewise, the female reproductive tract, suggested to drive the evolution of sperm, did not respond to experimental sexual selection even though there was sufficient genetic variation. The lack of genetic correlations between the sexes supports the opportunity for sexual conflict over investment in sperm by males and their storage by females. Our results suggest no absolute constraint arising from a lack of direct or indirect genetic variation or patterns of genetic covariation. These patterns show why responses to experimental evolution are hard to predict, and why research on genetic variation underlying interacting reproductive traits is needed.

Genetic variation of inbreeding depression among floral and fitness traits in Silene nutans

The magnitude and variation of inbreeding depression (ID) within populations is important for the evolution and maintenance of mixed mating systems. We studied ID and its genetic variation in a range of floral and fitness traits in a small and large population of the perennial herb Silene nutans, using controlled pollinations in a fully factorial North Carolina II design. Floral traits and early fitness traits, that is seed mass and germination rate, were not much affected by inbreeding (delta<0.2). In contrast, 'late' fitness traits and multiplicative fitness suffered severely from inbreeding (delta>0.4). Lack of genetic correlations indicated that ID in floral, early and late traits is genetically decoupled. There was a trend that the smaller population was less affected by ID than the large one, although the differences were not significant for most traits. Hence, evidence for purging of deleterious alleles remains inconclusive in this study. Genetic variation in ID among paternal families was statistically significant in most floral and all seed traits, but not in late fitness traits. However, some paternal families had delta<0.5, even in the multiplicative fitness measure that suffered most from ID (delta=0.74), suggesting that the mixed mating system of S. nutans might be evolutionary stable.

Growth Rate of Ascites-Resistant Versus Ascites-Susceptible Broilers in Commercial and Experimental Lines

The high growth rate (GR) of contemporary broilers is driven by high rate of feed intake and metabolism. Because of the consequent high oxygen demand, especially when coupled with exposure to high altitude or low temperatures, some broilers fail to regulate oxygen supply and develop the ascites syndrome (AS), which leads to mortality and economic losses. Because of the association between high GR, oxygen demand, and AS, it has been suggested that AS is induced by high GR. If true, further GR enhancement should be avoided because it will increase the proportion of AS-susceptible individuals in contemporary stocks. An alternative hypothesis claims that AS is associated with high actual GR only because the latter increases oxygen demand and that there are genetically AS-resistant broilers that do not develop AS, even when exhibiting high GR. These hypotheses were tested in trials in the years 2002 and 2006, with broilers differing in potential GR: contemporary fast-growing commercial lines and an experimental line derived from commercial broilers in 1986, and (in 2002 only) divergently selected AS-susceptible and AS-resistant lines. A protocol of high-challenge ascites-inducing conditions (AIC) from d 19 was used to distinguish between AS-susceptible and AS-resistant individuals and to determine their GR up to this age. The difference in AS incidence between the divergent lines (93.9 vs. 9.5%) was not explained by the 5% difference in their GR, thus indicating a lack of genetic correlation. In the broiler lines, AS incidence was 31 and 47% in 2002 and 2006, respectively, and 32% in the 1986 slow-growing line. Most broilers that remained healthy under the high-challenge AIC exhibited the same early GR and BW as those that later developed AS. These results, and the relatively high incidence of AS in the slow-growing line, indicate that there is very little, if any, direct genetic association between AS and genetic differences in potential GR, and suggest that AS-resistant broilers can be selected for higher GR and remain healthy even under AIC.

Genetic parameters of aggressiveness, ferocity and mobility in the fighting bull breed

Genetic parameter estimates for Aggressiveness, Ferocity and Mobility in the fighting bull bovine breed were obtained using the restricted maximum likelihood (REML) methodology applied to a multiple trait animal model. The year of birth and the sex of the animal were the environmental fixed effects considered in the model. Genetic trends were determined from the average predicted breeding value over the year of birth. The behavioural traits considered showed an important additive genetic component which can be used to modulate the phenotype expression by selection. Heritability values around 0.3 (0.286-0.362) for all traits could explain the successful empirical selection carried out on the Aggressiveness trait. Similarly, the lack of genetic correlation (P > 0.05) between all traits explains the absence of a correlated response for the Ferocity and Mobility traits.

Genetics of physical wood properties and early growth in a tropical pine hybrid

Quantitative trait locus (QTL) detection was carried out for physical wood properties and early growth traits in an interspecific hybrid between Pinus elliottii var. elliottii Engelm. and Pinus caribaea var. hondurensis (Sénécl) Barr. et Golf. A pseudo-testcross QTL detection strategy was used to identify genome regions that influenced wood density, secondary growth, and dry wood mass index on each genetic map for the parents of a single F1family (n = 133). Traits were measured for annual ring and earlywood and latewood components and were based on both individual and average ring values from 1996 to 1999. A total of 12 significant putative QTLs were identified that clustered into four genomic regions in the P. elliottii var. elliottii parent and a single region in the P. caribaea var. hondurensis parent. The P. elliottii var. elliottii parent largely contributed putative QTLs for diameter growth and wood density, whereas the P. caribaea var. hondurensis parent contributed a putative QTL for earlywood formed in 1997. Putative QTLs that influenced density and ring width did not colocate, suggesting independent inheritance of these characters. This was consistent with the lack of genetic correlation between wood density and diameter growth observed in quantitative studies in hybrid pines.

Age-age and trait-trait correlations for Eucalyptus grandis Hill ex Maiden and their implications for optimal selection age and design of clonal trials.

Previous results from seven locations of Eucalyptus grandis clonal trials in Colombia supported the a priori contention of sub-dividing them into three different environmental zones for testing and deployment. Within these zones, the determination of age-age genetic correlations for both height and mean annual increment (MAI) showed that strong age-age correlations are present for a rotation age of 6 years starting at 3 years age and, thereafter, suggesting this age as appropriate for selection. This biological selection age coincides with an "economical" age for selection based on discounted selection efficiency in perpetuity, considering a range of interest rates between 10% and 20%. High genetic correlations between wood density at 3 years and 6 years as well as the lack of genetic correlation between this trait and growth traits, also favors selection at age 3 and facilitates breeding strategies that consider the utilization of both traits for improvement. A simulation of optimal clonal test designs indicated that by using six locations and six blocks per location in a single-tree plot design, between 80% and 90% of the maximum selection efficiency could be obtained. This type of design allows testing of a large number of genotypes across a reasonable number of locations in a cost-effective manner.

Quantitative genetics of growth and development in Populus. II. The partitioning of genotype × environment interaction in stem growth

Two interspecific hybrid pedigrees of Populus trichocarpa and P. deltoides, each containing parental, F1 and F2 generations, and planted in two contrasting environments in northern Oregon, served to estimate the interactions of genotypes × environments for stem growth during the first two years of growth. All three generations showed greater mean growth in the warm, high-radiation, and well-watered regime of the interior (Boardman) than in the cooler coastal conditions of Clatskanie. In the two F2 families, all stem traits displayed significant genotype × environment interactions which accounted for ≈10 per cent of the total phenotypic variance. Genetic correlations across environments were larger for basal area and volume growth than for stem height and proportion. Genotype × environment interaction variance was further partitioned into two components attributable to the heterogeneity of genetic variance between environments and the lack of genetic correlation across environments. For radial and volume growth, a large amount of genotype × environment interaction was associated with the heterogeneity of genetic variance across environments. For stem height and proportion, lack of genetic correlation across environments explained more of the genotype × environment interaction. The Spearman rank correlations of phenotypic means between the two environments were moderately high but significantly less than unity in most cases. Much of the growth difference in the two F2 families had a significant genetic component, with broad-sense heritabilities at each location ranging from 0.70–0.90. The implications for breeding and selection of superior poplars for these environments are discussed.

HERITABILITY OF MANGANESE TOLERANCE IN RABBITEYE BLUEBERRY

To determine whether manganese tolerance in rabbiteye blueberry (Vaccinium ashei Reade) is heritable, a 10-parent diallel cross was produced. A 250 ppm Mn solution (200 ml/plant) was applied to a sand culture, of the progeny daily. Visual ratings (1 - dead plant - 13 - no Mn toxicity symptom) were made after 6 weeks. Shoot weight and Mn content of leaves were determined. Narrow-sense heritability estimates (h2) were 0.45±0.28 for Mn content, 0.49±0.27 for visual ratings, and 0.37± 0.21 for shoot weight. The genetic correlation between neither shoot weight nor visual rating and Mn content (0.11 and -0.15, respectively) was very high; however, the correlation between shoot weight and visual ratings (1.00) was extremely high. This suggests that visual ratings provide an estimate of Mn effects on plans equal to objective measurements of shoot weight. Though h2 estimates for Mn content and visual ratings were similar, the lack of genetic correlation between the traits indicates that tolerance to Mn toxicity is independent of Mn content. The high h2 for visual ratings suggests mass selection as the method of choice for improving Mn tolerance in a rabbiteye blueberry population.

Genetic and Maternal Influences on Life History Plasticity in Response to Photoperiod by Milkweed Bugs (Oncopeltus fasciatus)

Using two geographically adjacent, temperate-zone populations of the milkweed bug Oncopeltus fasciatus, we employed a split-family experimental design to estimate genotype-environment interaction (g-e) and across-environment genetic correlations for two female life history characters, age at first reproduction and fecundity over the first 5 days of reproduction. For each of a number of families, some sisters were reared in a short-day environment (LD 11:13, 23$^\circ$C) and others in a long-day environment (LD 14:10, 23$^\circ$C); the environments were chosen to simulate the temporal environmental heterogeneity experienced by lineages of temperate-zone bugs. Bugs normally exhibit a plastic response to such heterogeneity by delaying the onset of reproduction in short days relative to that in long days, the delay providing time for migration to occur. In one population, there is significant variation caused by g-e for the age at first reproduction, indicating the existence of genetic variance for plasticity in this character. This result suggests that there is potential for the evolution of phenotypic plasticity in the timing of reproduction. In each population, however, there is a positive genetic correlation between the timing of reproduction in the long- and short-day environments, implying that the evolution of life history in one environment can influence evolution in the alternative environment. In particular, the potential rate of evolution toward a joint optimum of early reproduction in long days and delayed reproduction in short days will be less than if the across-environment correlation were zero or negative. During the attainment of equilibrium at the joint optimum, selection can prevent optimization of the age at first reproduction and maintain genetic variation for this character within environments. However, a maternal effect that prevents long delays in the onset of reproduction from occurring in two successive generations of bugs provides a means for lessening the influence of selection in the alternative environment. This maternal effect also ensures that a spring generation of bugs does not exhibit an inappropriate diapause. For fecundity, one population has a positive across-environment genetic correlation, indicating that performance generalizes across environments for this fitness component. In the other population, primarily because of the performance of one sibship, a negative across-environment correlation implies that performance is specialized. The populations also differ in life history. The basis for such microgeographic differentiation, the first recorded for migratory temperate-zone populations of this species, may be sampling, differential migration, or adaptation. More work is necessary to distinguish among these hypotheses. Consistent with previous studies, we found high levels of genetic variation for life history characters within populations and, in general, a lack of genetic correlation between the age at first reproduction and fecundity.

Quantitative genetics of skeletal nonmetric traits in the rhesus macaques on Cayo Santiago. II. Phenotypic, genetic, and environmental correlations between traits.

The general lack of phenotypic correlation among skeletal nonmetric traits has been interpreted as indicating a lack of genetic correlation among these traits. Nonmetric traits scored on animals in the skeletal collection of rhesus macaques from Cayo Santiago are used to calculate phenotypic, genetic, and environmental correlations between traits. The results show that even when phenotypic correlations are low, there may be large, significant genetic correlations among these traits. The genetic correlation pattern suggests that genes which affect nonmetric trait variation act primarily at a local level in the cranium, even though there are genes with pleiotropic effects on skeletal nonmetric traits throughout the cranium. Environmental and phenotypic correlations do not show this neighborhood pattern of correlation.