Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

Background

Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency.

Methodology/Principal findings

Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (<0.05 Mb) genes that regulate insulin release and leptin functions. The Bayesian approach identified associations of genomic regions containing insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI, of regions with energy homeostasis (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG, and of fat metabolism genes (e.g., ACOXL, AEBP1) with BF. Specifically, a very highly significantly associated QTL for LMA on SSC7 with skeletal myogenesis genes (e.g., KLHL31) was identified for subsequent fine mapping.

Conclusions/significance

Important genomic regions associated with RFI related traits were identified for future validation studies prior to their incorporation in marker-assisted selection programs.     

Phenotypic and genetic relationships between growth and feed intake curves and feed efficiency and amino acid requirements in the growing pig

Improvement of feed efficiency in pigs has been achieved essentially by increasing lean growth rate, which resulted in lower feed intake (FI). The objective was to evaluate the impact of strategies for improving feed efficiency on the dynamics of FI and growth in growing pigs to revisit nutrient recommendations and strategies for feed efficiency improvement. In 2010, three BWs, at 35±2, 63±9 and 107±7 kg, and daily FI during this period were recorded in three French test stations on 379 Large White and 327 French Landrace from maternal pig populations and 215 Large White from a sire population. Individual growth and FI model parameters were obtained with the InraPorc^R software and individual nutrient requirements were computed. The model parameters were explored according to feed efficiency as measured by residual feed intake (RFI) or feed conversion ratio (FCR). Animals were separated in groups of better feed efficiency (RFI⁻ or FCR⁻), medium feed efficiency and poor feed efficiency. Second, genetic relationships between feed efficiency and model parameters were estimated. Despite similar average daily gains (ADG) during the test for all RFI groups, RFI⁻ pigs had a lower initial growth rate and a higher final growth rate compared with other pigs. The same initial growth rate was found for all FCR groups, but FCR⁻ pigs had significantly higher final growth rates than other pigs, resulting in significantly different ADG. Dynamic of FI also differed between RFI or FCR groups. The calculated digestible lysine requirements, expressed in g/MJ net energy (NE), showed the same trends for RFI or FCR groups: the average requirements for the 25% most efficient animals were 13% higher than that of the 25% least efficient animals during the whole test, reaching 0.90 to 0.95 g/MJ NE at the beginning of the test, which is slightly greater than usual feed recommendations for growing pigs. Model parameters were moderately heritable (0.30±0.13 to 0.56±0.13), except for the precocity of growth (0.06±0.08). The parameter representing the quantity of feed at 50 kg BW showed a relatively high genetic correlation with RFI (0.49±0.14), and average protein deposition between 35 and 110 kg had the highest correlation with FCR (−0.76±0.08). Thus, growth and FI dynamics may be envisaged as breeding tools to improve feed efficiency. Furthermore, improvement of feed efficiency should be envisaged jointly with new feeding strategies.     

Quantifying the genetic parameters of feed efficiency in juvenile Nile tilapia <Emphasis Type="Italic">Oreochromis niloticus</Emphasis>

Background

Improving feed efficiency in fish is crucial at the economic, social and environmental levels with respect to developing a more sustainable aquaculture. The important contribution of genetic improvement to achieve this goal has been hampered by the lack of accurate basic information on the genetic parameters of feed efficiency in fish. We used video assessment of feed intake on individual fish reared in groups to estimate the genetic parameters of six growth traits, feed intake, feed conversion ratio (FCR) and residual feed intake in 40 pedigreed families of the GIFT strain of Nile tilapia, Oreochromis niloticus. Feed intake and growth were measured on juvenile fish (22.4 g mean body weight) during 13 consecutive meals, representing 7 days of measurements. We used these data to estimate the FCR response to different selection criteria to assess the potential of genetics as a means of increasing FCR in tilapia.

Results

Our results demonstrate genetic control for FCR in tilapia, with a heritability estimate of 0.32?±?0.11. Response to selection estimates showed FCR could be efficiently improved by selective breeding. Due to low genetic correlations, selection for growth traits would not improve FCR. However, weight loss at fasting has a high genetic correlation with FCR (0.80?±?0.25) and a moderate heritability (0.23), and could be an easy to measure and efficient criterion to improve FCR by selective breeding in tilapia.

Conclusion

At this age, FCR is genetically determined in Nile tilapia. A selective breeding program could be possible and could help enabling the development of a more sustainable aquaculture production.

     

Combined analysis of group recorded feed intake and individually recorded body weight and litter size in mink

In the mink industry, feed costs are the largest variable expense and breeding for feed efficient animals is warranted. Implementation of selection for feed efficiency must consider the relationships between feed efficiency and the current selection traits BW and litter size. Often, feed intake (FI) is recorded on a cage with a male and a female and there is sexual dimorphism that needs to be accounted for. Study aims were to (1) model group recorded FI accounting for sexual dimorphism, (2) derive genetic residual feed intake (RFI) as a measure of feed efficiency, (3) examine the relationship between feed efficiency and BW in males (BWM) and females (BWF) and litter size at day 21 after whelping (LS21) in Danish brown mink and (4) investigate direct and correlated response to selection on each trait of interest. Feed intake records from 9574 cages, BW records on 16 782 males and 16 875 females and LS21 records on 6446 yearling females were used for analysis. Genetic parameters for FI, BWM, BWF and LS21 were obtained using a multivariate animal model, yielding sex-specific additive genetic variances for FI and BW to account for sexual dimorphism. The analysis was performed in a Bayesian setting using Gibbs sampling, and genetic RFI was obtained from the conditional distribution of FI given BW using genetic regression coefficients. Responses to single trait selection were defined as the posterior distribution of genetic superiority of the top 10% of animals after conditioning on the genetic trends. The heritabilities ranged from 0.13 for RFI in females and LS21 to 0.59 for BWF. Genetic correlations between BW in both sexes and LS21 and FI in both sexes were unfavorable, and single trait selection on BW in either sex showed increased FI in both sexes and reduced litter size. Due to the definition of RFI and high genetic correlation between BWM and BWF, selection on RFI did not significantly alter BW. In addition, selection on RFI in either sex did not affect LS21. Genetic correlation between sexes for FI and BW was high but significantly lower than unity. The high correlations across sex allowed for selection on standardized averages of animals’ breeding values (BVs) for RFI, FI and BW, which yielded selection responses approximately equal to the responses obtained using the sex-specific BVs. The results illustrate the possibility of selecting against RFI in mink with no negative effects on BW and litter size.     

Associations of polymorphisms in GHRL,GHSR, and IGF1R genes with feed efficiency in chickens

The ghrelin (GHRL), ghrelin receptor (GHSR), and insulin-like growth factor 1 receptor (IGF1R) genes have crucial effects on body weight (BW), body weight gain (BWG), feed intake (FI), and feed conversion ratio (FCR) in many species. However, few studies on associations of GHRL, GHSR, and IGF1R with BWG, FI, and FCR have been reported in chickens. In this study, 16 SNPs in GHRL, GHSR, and IGF1R genes were genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The objective of this study was to examine the associations of GHRL, GHSR, and IGF1R genes polymorphisms with BW at 49 days (BW49) and 70 days (BW70) of age, BWG, FI, and FCR in the interval in two yellow meat-type populations with a total of 724 birds. The results showed that rs15675067 of GHRL was significantly associated with BW70, BWG, and FCR (P < 0.05). For GHSR, rs16675844 had significant effects on FI and FCR (P < 0.01), and that rs14678932 showed significant association with BWG and FI (P < 0.05). Rs14011780 of IGF1R was strongly associated with BW49, BW70, and FCR (P < 0.05). Furthermore, haplotypes based on three SNPs of rs14986828, rs15675067, and rs15675065 in GHRL were significantly associated with BW70 and FCR (P < 0.05). Meanwhile, a three-SNP haplotype comprising rs14011783, rs14011780, and rs14011776 in IGF1R showed significant effects on BW49, BW70, and FCR (P < 0.05). Therefore, it was concluded that the identified SNPs and analyzed haplotypes in this study might be useful for broiler breeding programs.     

Unravelling the Relationship between Animal Growth and Immune Response during Micro-Parasitic Infections

Background

Both host genetic potentials for growth and disease resistance, as well as nutrition are known to affect responses of individuals challenged with micro-parasites, but their interactive effects are difficult to predict from experimental studies alone.

Methodology/Principal Findings

Here, a mathematical model is proposed to explore the hypothesis that a host''s response to pathogen challenge largely depends on the interaction between a host''s genetic capacities for growth or disease resistance and the nutritional environment. As might be expected, the model predicts that if nutritional availability is high, hosts with higher growth capacities will also grow faster under micro-parasitic challenge, and more resistant animals will exhibit a more effective immune response. Growth capacity has little effect on immune response and resistance capacity has little effect on achieved growth. However, the influence of host genetics on phenotypic performance changes drastically if nutrient availability is scarce. In this case achieved growth and immune response depend simultaneously on both capacities for growth and disease resistance. A higher growth capacity (achieved e.g. through genetic selection) would be detrimental for the animal''s ability to cope with pathogens and greater resistance may reduce growth in the short-term.

Significance

Our model can thus explain contradicting outcomes of genetic selection observed in experimental studies and provides the necessary biological background for understanding the influence of selection and/or changes in the nutritional environment on phenotypic growth and immune response.     

Genetic parameters for feed efficiency in Romane rams and responses to single-generation selection

Feeding costs represent one of the highest expenditures in animal production systems. Breeding efficient animals that express their growth potential while eating less is therefore a major objective for breeders. We estimated the genetic parameters for feed intake, feed efficiency traits (residual feed intake (RFI) and feed conversion ratio (FCR)), growth and body composition traits in the Romane meat sheep breed. In these traits, selection responses to single-generation divergent selection on RFI were evaluated. From 2009 to 2016, a total of 951 male lambs were tested for 8 weeks starting from 3 months of age. They were weighed at the beginning and at the end of the testing period. Backfat thickness and muscle depth were recorded at the end of the testing period through ultrasound measurements. Feed intake was continuously recorded over the testing period using the automatic concentrate feeders. The heritability of RFI was estimated at 0.45 ± 0.08, which was higher than the heritability of FCR (0.30 ± 0.08). No significant genetic correlations were observed between RFI and growth traits. A favourable low negative genetic correlation was estimated between RFI and muscle depth (−0.30 ± 0.15), though additional data are needed to confirm these results. The selection of low RFI sires based on their breeding values led to the production of lambs eating significantly less concentrate (3% decrease in the average daily feed intake), but with the same growth as lambs from sires selected based on high RFI breeding values. We concluded that in meat sheep, RFI is a heritable trait that is genetically independent of post-weaning growth and body composition traits. A one-generation divergent selection based on RFI breeding values highlighted that substantial gains in feeding costs can be expected in selection schemes for meat sheep breeds.     

Dietary metabolizable energy,digestible lysine,available phosphorus levels and exogenous enzymes affect broiler chicken performance

The nutritional composition of diets and the provision of exogenous enzymes play important roles in animal performance. Here, we evaluated the individual and combined impact of nutrients (metabolizable energy (ME), digestible lysine (dLys), available phosphorus and calcium (avP–Ca)) and exogenous multicarbohydrase and phytase complex (MCPC) enyzmes on the growth performance and feed efficiency of broiler chickens from 10 to 42 days (d) of age. Experimental diets were formulated in a Box-Behnken design to contain various levels of ME (11.89, 12.21, 12.54 or 13.06 MJ/kg), dLys (0.91%, 0.93%, 0.96% or 1.00%) and avP/Ca (0.12/0.47%, 0.21/0.58% or 0.33/0.68%). The effect of MCPC was expressed in terms of the extra nutrients released. The diets were formulated to have consistent substrate contents (i.e., arabinoxylan and phytate). Feed intake (FI), BW gain (BWG) and feed conversion ratio (FCR) were described via polynomial equations (R² = 0.99, 0.98 and 0.81, respectively), with interconnections between variables (ME, dLys and avP–Ca). Available P–Ca was the most important factor affecting FI (quadratically), and BWG and FCR (linearly). Reducing the avP content from 0.33% to 0.12% in diets lacking MCPC resulted in 25% and 33% decreases in FI and BWG, respectively, and a 12% increase in FCR. The ME and dLys contents also linearly affected these performance parameters to a lesser degree; FI decreased by 400 g when the ME was reduced by 1.17 MJ/kg, and by 300 g following a 0.09% reduction of dLys, while the same reductions in ME and dLys decreased BWG by 120 g and 150 g, respectively. The inclusion of MCPC alleviated the reduction of FI, BWG and FCR by decreasing the avP–Ca. Thus, ME and dLys were the most important factors affecting BWG and FCR in broilers fed diets containing MCPC. When MCPC was added, ME negatively affected FI (r = −0.89, P < 0.001), whereas the dLys content was correlated with BWG (r = 0.74, P < 0.001). Both ME and dLys affected FCR (r = −0.83 and −0.85, respectively). Supplementing MCPC allowed the reduction of ME, dLys and avP–Ca in the diet without affecting performance. Indeed, MCPC’s effect promoted with the release of the following nutrients: 0.56 MJ ME/kg, 0.06% dLys, and 0.15% and 0.13% avP and Ca, respectively. The results indicate nutrient effect and interaction on performance and feed additive potential for nutrient release.     

Assessment of residual body weight gain and residual intake and body weight gain as feed efficiency traits in the turkey (Meleagris gallopavo)

Background

Since feed represents 70% of the total cost in poultry production systems, an animal’s ability to convert feed is an important trait. In this study, residual feed intake (RFI) and residual body weight gain (RG), and their linear combination into residual feed intake and body weight gain (RIG) were studied to estimate their genetic parameters and analyze the potential differences in feed intake between the top ranked birds based on the criteria for each trait.

Methods

Phenotypic and genetic analyses were completed on 8340 growing tom turkeys that were measured for feed intake and body weight gain over a four-week period from 16 to 20 weeks of age.

Results

The heritabilities of RG and RIG were 0.19 ± 0.03 and 0.23 ± 0.03, respectively. Residual body weight gain had moderate genetic correlations with feed intake (−0.41) and body weight gain (0.43). All three linear combinations to form the RIG traits had genetic correlations ranging from −0.62 to −0.52 with feed intake, and slightly weaker, 0.22 to 0.34, with body weight gain. Sorted into three equal groups (low, medium, high) based on RG, the most efficient group (high) gained 0.62 and 1.70 kg more (P < 0.001) body weight than that of the medium and low groups, yet the feed intake for the high group was less (P < 0.05) than that of the medium group (19.52 vs. 19.75 kg). When separated into similar partitions, the high RIG group (most efficient) had both the lowest (P < 0.001) feed intake (18.86 vs. 19.57 and 20.41 kg) and the highest (P < 0.001) body weight gain (7.41 vs. 7.03 and 6.43 kg) relative to the medium and low groups, respectively.

Conclusions

The difference in feed intake between the top ranked birds based on different residual feed efficiency traits may be small when looking at the average individual, however, when extrapolated to the production level, the lower feed intake values could lead to significant savings in feed costs over time.     

Genetic and environmental influences on infant growth: prospective analysis of the Gemini twin birth cohort

Objective

Infancy is a critical period during which rapid growth potentially programs future disease risk. Identifying the modifiable determinants of growth is therefore important. To capture the complexity of infant growth, we modeled growth trajectories from birth to six months in order to compare the genetic and environmental influences on growth trajectory parameters with single time-point measures at birth, three and six months of age.

Methods

Data were from Gemini, a population sample of 2402 UK families with twins. An average 10 weight measurements per child made by health professionals were available over the first six months. Weights at birth, three and six months were identified. Longitudinal growth trajectories were modeled using SITAR utilizing all available weight measures for each child. SITAR generates three parameters: size (characterizing mean weight throughout infancy), tempo (indicating age at peak weight velocity (PWV)), and velocity (reflecting the size of PWV). Genetic and environmental influences were estimated using quantitative genetic analysis.

Results

In line with previous studies, heritability of weight at birth and three months was low (38%), but it was higher at six months (62%). Heritability of the growth trajectory parameters was high for size (69%) and velocity (57%), but low (35%) for tempo. Common environmental influences predominated for tempo (42%).

Conclusion

Modeled growth parameters using SITAR indicated that size and velocity were primarily under genetic influence but tempo was predominantly environmentally determined. These results emphasize the importance of identifying specific modifiable environmental determinants of the timing of peak infant growth.     

Genetic architecture is more complex for resistance to Septoria tritici blotch than to Fusarium head blight in Central European winter wheat

Background

Fusarium head blight (FHB) and Septoria tritici blotch (STB) severely impair wheat production. With the aim to further elucidate the genetic architecture underlying FHB and STB resistance, we phenotyped 1604 European wheat hybrids and their 135 parental lines for FHB and STB disease severities and determined genotypes at 17,372 single-nucleotide polymorphic loci.

Results

Cross-validated association mapping revealed the absence of large effect QTL for both traits. Genomic selection showed a three times higher prediction accuracy for FHB than STB disease severity for test sets largely unrelated to the training sets.

Conclusions

Our findings suggest that the genetic architecture is less complex and, hence, can be more properly tackled to perform accurate prediction for FHB than STB disease severity. Consequently, FHB disease severity is an interesting model trait to fine-tune genomic selection models exploiting beyond relatedness also knowledge of the genetic architecture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1628-8) contains supplementary material, which is available to authorized users.     

Interaction and imbalance between indispensable amino acids in young piglets

Lowering protein level in diets for piglets urge to have knowledge on the piglet’s requirements for essential amino acids (AA) and their interactions. The present studies aimed to determine the interaction between the dietary level of valine (Val) and tryptophan (Trp) and the effect of AA imbalance at two levels of dietary Val on the growth performance of post-weaning piglets. In Experiment 1 (duration 4 weeks), the effects of supplementation of free l-Val (1.0 g/kg) and/or l-Trp (0.5 g/kg) in a low-CP diet (CP 17.7%), marginal in Trp and Val, was studied in a 2×2 factorial design and using an additional reference treatment (CP 19.5%). In Experiment 2 (duration 5 weeks), the influence of a stepwise increase in excess supply of isoleucine (Ile), histidine (His) and leucine (Leu), up to 10, 10% and 30% relative to their requirement values respectively, was evaluated at 60% or 70% standardized ileal digestible (SID) Val relative to SID lysine, using a 3×2 factorial design. In Experiment 1, over the whole experimental period, feed intake (FI) was affected by dietary Trp level (P<0.05) and feed conversion ratio (FCR) by both the level of Trp and Val in the diet (both P<0.05). Increasing Trp level increased FI and decreased FCR while increasing dietary Val level reduced FI and increased FCR. For BW gain (BWG), there was an interaction between dietary level of Trp and Val (P<0.05). Valine supplementation decreased BWG using a diet marginal in Trp, whereas it increased BWG when using a Trp sufficient diet. Piglets fed the low-CP diet with adequate levels of Val and Trp showed at least same performance compared to piglets fed the high CP reference diet. In Experiment 2, increasing dietary Val improved FI and BWG (P<0.001) and tended to improve FCR. Dietary AA excess for Ile, His and Leu reduced FI and BWG (P<0.05) and only affected FCR (P<0.01) in the 1^st week of the study. Dietary level of Val and AA excess did not show interactive effects, except for FCR over the final 2 weeks of the study (P<0.05). In conclusion, an interaction exists between dietary supply of Val and Trp on the zootechnical performance of post-weaning piglets and dietary AA excess for Ile, Leu and His, reduces growth performance of piglets in low-protein diets, independent of the dietary level of Val.     

The genetic parameters of feed efficiency and its component traits in the turkey (Meleagris gallopavo)

Residual feed intake (RFI) and feed conversion ratio (FCR) can be incorporated into a breeding program as traits to select for feed efficiency. Alternatively, the direct measures used to calculate RFI and FCR can be analyzed to determine the underlying variation in the traits that impact overall efficiency. These constituent traits can then be appropriately weighted in an index to achieve genetic gain. To investigate feed efficiency in the turkey, feed intake and weight gain were measured on male primary breeder line turkeys housed in individual feeding cages from 15 to 19 weeks of age. The FCR and RFI showed moderate heritability values of 0.16 and 0.21, respectively. Feed intake, body weight, and weight gain were also moderately heritable (0.25, 0.35, and 0.18, respectively). Weight gain was negatively correlated to feed conversion ratio and was not genetically correlated to RFI. Body weight had a small and positive genetic correlation to RFI (0.09) and FCR (0.12). Feed intake was positively genetically correlated to RFI (0.62); however, there was no genetic correlation between feed intake and FCR. These estimates of heritability and the genetic correlations can be used in the development of an index to improve feed efficiency and reduce the cost of production.     

Deregressed EBV as the response variable yield more reliable genomic predictions than traditional EBV in pure-bred pigs

Background

Genomic selection can be implemented by a multi-step procedure, which requires a response variable and a statistical method. For pure-bred pigs, it was hypothesised that deregressed estimated breeding values (EBV) with the parent average removed as the response variable generate higher reliabilities of genomic breeding values than EBV, and that the normal, thick-tailed and mixture-distribution models yield similar reliabilities.

Methods

Reliabilities of genomic breeding values were estimated with EBV and deregressed EBV as response variables and under the three statistical methods, genomic BLUP, Bayesian Lasso and MIXTURE. The methods were examined by splitting data into a reference data set of 1375 genotyped animals that were performance tested before October 2008, and 536 genotyped validation animals that were performance tested after October 2008. The traits examined were daily gain and feed conversion ratio.

Results

Using deregressed EBV as the response variable yielded 18 to 39% higher reliabilities of the genomic breeding values than using EBV as the response variable. For daily gain, the increase in reliability due to deregression was significant and approximately 35%, whereas for feed conversion ratio it ranged between 18 and 39% and was significant only when MIXTURE was used. Genomic BLUP, Bayesian Lasso and MIXTURE had similar reliabilities.

Conclusions

Deregressed EBV is the preferred response variable, whereas the choice of statistical method is less critical for pure-bred pigs. The increase of 18 to 39% in reliability is worthwhile, since the reliabilities of the genomic breeding values directly affect the returns from genomic selection.     

Impact of the exopolysaccharide layer on biofilms,adhesion and resistance to stress in Lactobacillus johnsonii FI9785

Background

The bacterial cell surface is a crucial factor in cell-cell and cell-host interactions. Lactobacillus johnsonii FI9785 produces an exopolysaccharide (EPS) layer whose quantity and composition is altered in mutants that harbour genetic changes in their eps gene clusters. We have assessed the effect of changes in EPS production on cell surface characteristics that may affect the ability of L. johnsonii to colonise the poultry host and exclude pathogens.

Results

Analysis of physicochemical cell surface characteristics reflected by Zeta potential and adhesion to hexadecane showed that an increase in EPS gave a less negative, more hydrophilic surface and reduced autoaggregation. Autoaggregation was significantly higher in mutants that have reduced EPS, indicating that EPS can mask surface structures responsible for cell-cell interactions. EPS also affected biofilm formation, but here the quantity of EPS produced was not the only determinant. A reduction in EPS production increased bacterial adhesion to chicken gut explants, but made the bacteria less able to survive some stresses.

Conclusions

This study showed that manipulation of EPS production in L. johnsonii FI9785 can affect properties which may improve its performance as a competitive exclusion agent, but that positive changes in adhesion may be compromised by a reduction in the ability to survive stress.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0347-2) contains supplementary material, which is available to authorized users.     

Reliability of pedigree-based and genomic evaluations in selected populations

Background

Reliability is an important parameter in breeding. It measures the precision of estimated breeding values (EBV) and, thus, potential response to selection on those EBV. The precision of EBV is commonly measured by relating the prediction error variance (PEV) of EBV to the base population additive genetic variance (base PEV reliability), while the potential for response to selection is commonly measured by the squared correlation between the EBV and breeding values (BV) on selection candidates (reliability of selection). While these two measures are equivalent for unselected populations, they are not equivalent for selected populations. The aim of this study was to quantify the effect of selection on these two measures of reliability and to show how this affects comparison of breeding programs using pedigree-based or genomic evaluations.

Methods

Two scenarios with random and best linear unbiased prediction (BLUP) selection were simulated, where the EBV of selection candidates were estimated using only pedigree, pedigree and phenotype, genome-wide marker genotypes and phenotype, or only genome-wide marker genotypes. The base PEV reliabilities of these EBV were compared to the corresponding reliabilities of selection. Realized genetic selection intensity was evaluated to quantify the potential of selection on the different types of EBV and, thus, to validate differences in reliabilities. Finally, the contribution of different underlying processes to changes in additive genetic variance and reliabilities was quantified.

Results

The simulations showed that, for selected populations, the base PEV reliability substantially overestimates the reliability of selection of EBV that are mainly based on old information from the parental generation, as is the case with pedigree-based prediction. Selection on such EBV gave very low realized genetic selection intensities, confirming the overestimation and importance of genotyping both male and female selection candidates. The two measures of reliability matched when the reductions in additive genetic variance due to the Bulmer effect, selection, and inbreeding were taken into account.

Conclusions

For populations under selection, EBV based on genome-wide information are more valuable than suggested by the comparison of the base PEV reliabilities between the different types of EBV. This implies that genome-wide marker information is undervalued for selected populations and that genotyping un-phenotyped female selection candidates should be reconsidered.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0145-1) contains supplementary material, which is available to authorized users.     

Impact of the use of cryobank samples in a selected cattle breed: a simulation study

Background

High selection pressure on domestic cattle has led to an undesirable increase in inbreeding, as well as to the deterioration of some functional traits which are indirectly selected. Semen stored in a cryobank may be a useful way to redirect selection or limit the loss of genetic diversity in a selected breed. The purpose of this study was to analyse the efficiency of current cryobank sampling methods, by investigating the benefits of using cryopreserved semen in a selection scheme several generations after the semen was collected.

Methods

The theoretical impact of using cryopreserved semen in a selection scheme of a dairy cattle breed was investigated by simulating various scenarios involving two negatively correlated traits and a change in genetic variability of the breed.

Results

Our results indicate that using cryopreserved semen to redirect selection will have an impact on negatively selected traits only if it is combined with major changes in selection objectives or practices. If the purpose is to increase genetic diversity in the breed, it can be a viable option.

Conclusions

Using cryopreserved semen to redirect selection or to improve genetic diversity should be carried out with caution, by considering the pros and cons of prospective changes in genetic diversity and the value of the selected traits. However, the use of genomic information should lead to more interesting perspectives to choose which animals to store in a cryobank and to increase the value of cryobank collections for selected breeds.     

Allele frequency changes due to hitch-hiking in genomic selection programs

Background

Genomic selection makes it possible to reduce pedigree-based inbreeding over best linear unbiased prediction (BLUP) by increasing emphasis on own rather than family information. However, pedigree inbreeding might not accurately reflect loss of genetic variation and the true level of inbreeding due to changes in allele frequencies and hitch-hiking. This study aimed at understanding the impact of using long-term genomic selection on changes in allele frequencies, genetic variation and level of inbreeding.

Methods

Selection was performed in simulated scenarios with a population of 400 animals for 25 consecutive generations. Six genetic models were considered with different heritabilities and numbers of QTL (quantitative trait loci) affecting the trait. Four selection criteria were used, including selection on own phenotype and on estimated breeding values (EBV) derived using phenotype-BLUP, genomic BLUP and Bayesian Lasso. Changes in allele frequencies at QTL, markers and linked neutral loci were investigated for the different selection criteria and different scenarios, along with the loss of favourable alleles and the rate of inbreeding measured by pedigree and runs of homozygosity.

Results

For each selection criterion, hitch-hiking in the vicinity of the QTL appeared more extensive when accuracy of selection was higher and the number of QTL was lower. When inbreeding was measured by pedigree information, selection on genomic BLUP EBV resulted in lower levels of inbreeding than selection on phenotype BLUP EBV, but this did not always apply when inbreeding was measured by runs of homozygosity. Compared to genomic BLUP, selection on EBV from Bayesian Lasso led to less genetic drift, reduced loss of favourable alleles and more effectively controlled the rate of both pedigree and genomic inbreeding in all simulated scenarios. In addition, selection on EBV from Bayesian Lasso showed a higher selection differential for mendelian sampling terms than selection on genomic BLUP EBV.

Conclusions

Neutral variation can be shaped to a great extent by the hitch-hiking effects associated with selection, rather than just by genetic drift. When implementing long-term genomic selection, strategies for genomic control of inbreeding are essential, due to a considerable hitch-hiking effect, regardless of the method that is used for prediction of EBV.     

Divergent selection in trailing- versus leading-edge populations of Biscutella laevigata

Background and Aims

Knowledge on how climate-induced range shifts might affect natural selection is crucial to understand the evolution of species ranges.

Methods

Using historical demographic perspectives gathered from regional-scale phylogeography on the alpine herb Biscutella laevigata, indirect inferences on gene flow and signature of selection based on AFLP genotyping were compared between local populations persisting at the trailing edge and expanding at the leading edge.

Key Results

Spatial autocorrelation revealed that gene flow was two times more restricted at the trailing edge and genome scans indicated divergent selection in this persisting population. In contrast, no pattern of selection emerged in the expanding population at the leading edge.

Conclusions

Historical effects may determine different architecture of genetic variation and selective patterns within local populations, what is arguably important to understand evolutionary processes acting across the species ranges.