scholarly journals Sex-specific additive genetic variances and correlations for fitness in a song sparrow (Melospiza melodia) population subject to natural immigration and inbreeding

2018 ◽  
Author(s):  
Matthew E. Wolak ◽  
Peter Arcese ◽  
Lukas F. Keller ◽  
Pirmin Nietlisbach ◽  
Jane M. Reid
Keyword(s):  
Reproductive Success ◽  
Inbreeding Depression ◽  
Evolutionary Dynamics ◽  
Additive Genetic Variance ◽  
Genetic Effects ◽  
Melospiza Melodia ◽  
Adult Survival ◽  
Fitness Components ◽  
In The Wild ◽  
Additive Genetic Effects

ABSTRACTQuantifying sex-specific additive genetic variance (VA) in fitness, and the cross-sex genetic correlation (rA), is pre-requisite to predicting evolutionary dynamics and the magnitude of sexual conflict. Quantifying VAand rAin underlying fitness components, and multiple genetic consequences of immigration and resulting gene flow, is required to identify mechanisms that maintain VAin fitness. However, these key parameters have rarely been estimated in wild populations experiencing natural environmental variation and immigration. We used comprehensive pedigree and life-history data from song sparrows (Melospiza melodia) to estimate VAand rAin sex-specific fitness and underlying fitness components, and to estimate additive genetic effects of immigrants as well as inbreeding depression. We found substantial VAin female and male fitness, with a moderate positive cross-sex rA. There was also substantial VAin adult reproductive success in males but not females, and moderate VAin juvenile survival but not adult survival. Immigrants introduced alleles for which additive genetic effects on local fitness were negative, potentially reducing population mean fitness through migration load, yet alleviating expression of inbreeding depression. Substantial VAfor fitness can consequently be maintained in the wild, and be concordant between the sexes despite marked sex-specific VAin reproductive success.

scholarly journals Genomic dissection of maternal, additive and non-additive genetic effects for growth and carcass traits in Nile tilapia

2019 ◽  
Author(s):  
Rajesh Joshi ◽  
John Woolliams ◽  
Theodorus Meuwissen ◽  
Hans Magnus Gjøen
Keyword(s):  
Inbreeding Depression ◽  
Nile Tilapia ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Genomic Data ◽  
Genetic Effects ◽  
Phenotypic Variance ◽  
Breeding Schemes ◽  
Additive Genetic Effects ◽  
The Impact

AbstractBackgroundThe availability of both pedigree and genomic sources of information for animal breeding and genetics has created new challenges in understanding how best they may be utilized and how they may be interpreted. This study computed the variance components obtained using genomic information and compared these to the variances obtained using pedigree in a population generated to estimate non-additive genetic variance. Further, the impact of assumptions concerning Hardy-Weinberg Equilibrium (HWE) on the component estimates was examined. The magnitude of inbreeding depression for important commercial traits in Nile tilapia was estimated for the first time, here using genomic data.ResultsThe non-additive genetic variance in a Nile tilapia population was estimated from fullsib families and, where present, was found to be almost entirely additive by additive epistatic variance, although in pedigree studies this source is commonly assumed to arise from dominance. For body depth (BD) and body weight at harvest (BWH), the estimates of the additive by additive epistatic ratio (P<0.05) were found to be 0.15 and 0.17 in the current breeding population using genomic data. In addition, we found maternal variance (P<0.05) for BD, BWH, body length (BL) and fillet weight (FW), explaining approximately 10% of the observed phenotypic variance, which are comparable to the pedigree-based estimates. This study also disclosed detrimental effects of inbreeding in commercial traits of tilapia, which were estimated to cause 1.1%, 0.9%, 0.4% and 0.3% decrease in the trait value with 1% increase in the individual homozygosity for FW, BWH, BD and BL, respectively. The inbreeding depression and lack of dominance variance was consistent with an infinitesimal dominance modelConclusionsAn eventual utilisation of non-additive genetic effects in breeding schemes is not evident or straightforward from our findings, but inbreeding depression suggests for cross-breeding, although commercially this conclusion will depend on cost structures. However, the creation of maternal lines in Tilapia breeding schemes may be a possibility if this variation is found to be heritable.

scholarly journals SNP-based mate allocation strategies to maximize total genetic value in pigs

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
David González-Diéguez ◽  
Llibertat Tusell ◽  
Céline Carillier-Jacquin ◽  
Alban Bouquet ◽  
Zulma G. Vitezica
Keyword(s):  
Inbreeding Depression ◽  
Genetic Gain ◽  
Variance Components ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Genetic Effects ◽  
Breeding Values ◽  
Genetic Merit ◽  
Additive Genetic Effects ◽  
Allocation Strategies

Abstract Background Mate allocation strategies that account for non-additive genetic effects can be used to maximize the overall genetic merit of future offspring. Accounting for dominance effects in genetic evaluations is easier in a genomic context, than in a classical pedigree-based context because the combinations of alleles at loci are known. The objective of our study was two-fold. First, dominance variance components were estimated for age at 100 kg (AGE), backfat depth (BD) at 140 days, and for average piglet weight at birth within litter (APWL). Second, the efficiency of mate allocation strategies that account for dominance and inbreeding depression to maximize the overall genetic merit of future offspring was explored. Results Genetic variance components were estimated using genomic models that included inbreeding depression with and without non-additive genetic effects (dominance). Models that included dominance effects did not fit the data better than the genomic additive model. Estimates of dominance variances, expressed as a percentage of additive genetic variance, were 20, 11, and 12% for AGE, BD, and APWL, respectively. Estimates of additive and dominance single nucleotide polymorphism effects were retrieved from the genetic variance component estimates and used to predict the outcome of matings in terms of total genetic and breeding values. Maximizing total genetic values instead of breeding values in matings gave the progeny an average advantage of − 0.79 days, − 0.04 mm, and 11.3 g for AGE, BD and APWL, respectively, but slightly reduced the expected additive genetic gain, e.g. by 1.8% for AGE. Conclusions Genomic mate allocation accounting for non-additive genetic effects is a feasible and potential strategy to improve the performance of the offspring without dramatically compromising additive genetic gain.

scholarly journals A multivariate analysis with direct additive and inbreeding depression load effects

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Luis Varona ◽  
Juan Altarriba ◽  
Carlos Moreno ◽  
María Martínez-Castillero ◽  
Joaquim Casellas
Keyword(s):  
Beef Cattle ◽  
Inbreeding Depression ◽  
Negative Correlation ◽  
Simulated Data ◽  
Genetic Effects ◽  
Strong Negative Correlation ◽  
Additive Variance ◽  
Inbreeding Coefficients ◽  
Load Effects ◽  
Additive Genetic Effects

Abstract Background Inbreeding is caused by mating between related individuals and its most common consequence is inbreeding depression. Several studies have detected heterogeneity in inbreeding depression among founder individuals, and recently a procedure for predicting hidden inbreeding depression loads associated with founders and the Mendelian sampling of non-founders has been developed. The objectives of our study were to expand this model to predict the inbreeding loads for all individuals in the pedigree and to estimate the covariance between the inbreeding loads and the additive genetic effects for the trait of interest. We tested the proposed approach with simulated data and with two datasets of records on weaning weight from the Spanish Pirenaica and Rubia Gallega beef cattle breeds. Results The posterior estimates of the variance components with the simulated datasets did not differ significantly from the simulation parameters. In addition, the correlation between the predicted and simulated inbreeding loads were always positive and ranged from 0.27 to 0.82. The beef cattle datasets comprised 35,126 and 75,194 records on weights between 170 and 250 days of age, and pedigrees of 308,836 and 384,434 individual-sire-dam entries for the Pirenaica and Rubia Gallega breeds, respectively. The posterior mean estimates of the variance of inbreeding depression loads were 29,967.8 and 28,222.4 for the Pirenaica and Rubia Gallega breeds, respectively. They were larger than those of the additive variance (695.0 and 439.8 for Pirenaica and Rubia Gallega, respectively), because they should be understood as the variance of the inbreeding depression achieved by a fully inbred (100%) descendant. Therefore, the inbreeding loads have to be rescaled for smaller inbreeding coefficients. In addition, a strong negative correlation (− 0.43 ± 0.10) between additive effects and inbreeding loads was detected in the Pirenaica, but not in the Rubia Gallega breed. Conclusions The results of the simulation study confirmed the ability of the proposed procedure to predict inbreeding depression loads for all individuals in the populations. Furthermore, the results obtained from the two real datasets confirmed the variability in the inbreeding depression loads in both breeds and suggested a negative correlation of the inbreeding loads with the additive genetic effects in the Pirenaica breed.

Additive Genetic Variance, Heritability, and Inbreeding Depression in Male Extra-Pair Reproductive Success

2011 ◽  
Vol 177 (2) ◽  
pp. 177-187 ◽  
Author(s):  
Jane M. Reid ◽  
Peter Arcese ◽  
Rebecca J. Sardell ◽  
Lukas F. Keller
Keyword(s):  
Reproductive Success ◽  
Inbreeding Depression ◽  
Genetic Variance ◽  
Additive Genetic Variance

scholarly journals Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects

2021 ◽  
Author(s):  
Seema Yadav ◽  
Xianming Wei ◽  
Priya Joyce ◽  
Felicity Atkin ◽  
Emily Deomano ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Complex Traits ◽  
Genetic Variance ◽  
Prediction Models ◽  
Additive Genetic Variance ◽  
Genetic Effects ◽  
Additive Effects ◽  
Genetic Progress ◽  
Accurate Identification ◽  
Additive Genetic Effects

AbstractKey messageNon-additive genetic effects seem to play a substantial role in the expression of complex traits in sugarcane. Including non-additive effects in genomic prediction models significantly improves the prediction accuracy of clonal performance.AbstractIn the recent decade, genetic progress has been slow in sugarcane. One reason might be that non-additive genetic effects contribute substantially to complex traits. Dense marker information provides the opportunity to exploit non-additive effects in genomic prediction. In this study, a series of genomic best linear unbiased prediction (GBLUP) models that account for additive and non-additive effects were assessed to improve the accuracy of clonal prediction. The reproducible kernel Hilbert space model, which captures non-additive genetic effects, was also tested. The models were compared using 3,006 genotyped elite clones measured for cane per hectare (TCH), commercial cane sugar (CCS), and Fibre content. Three forward prediction scenarios were considered to investigate the robustness of genomic prediction. By using a pseudo-diploid parameterization, we found significant non-additive effects that accounted for almost two-thirds of the total genetic variance for TCH. Average heterozygosity also had a major impact on TCH, indicating that directional dominance may be an important source of phenotypic variation for this trait. The extended-GBLUP model improved the prediction accuracies by at least 17% for TCH, but no improvement was observed for CCS and Fibre. Our results imply that non-additive genetic variance is important for complex traits in sugarcane, although further work is required to better understand the variance component partitioning in a highly polyploid context. Genomics-based breeding will likely benefit from exploiting non-additive genetic effects, especially in designing crossing schemes. These findings can help to improve clonal prediction, enabling a more accurate identification of variety candidates for the sugarcane industry.

scholarly journals The quantitative genetics of fitness in a wild bird population

2021 ◽  
Author(s):  
Maria Moiron ◽  
Anne Charmantier ◽  
Sandra Bouwhuis
Keyword(s):  
Reproductive Success ◽  
Genetic Variance ◽  
Evolutionary Ecology ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Common Tern ◽  
Adult Survival ◽  
Lifetime Fitness ◽  
Mean Fitness ◽  
Change In Mean

Additive genetic variance in fitness equals the change in mean fitness due to selection. It is a prerequisite for adaptation, as a trait must be genetically correlated with fitness in order to evolve. Despite its relevance, additive genetic variance in fitness has not often been estimated in wild populations. Here, we investigate additive genetic variance in lifetime fitness, as well as its underlying components, in common terns (Sterna hirundo). Using a series of animal models applied to 28 years of data comprising ca. 6000 pedigreed individuals, we find nominally zero additive genetic variance in the Zero-inflated component of lifetime fitness, and low but unreliable variance in the Poisson component. We also find low but likely nonzero additive genetic variance in adult annual reproductive success, but not in survival. As such, our study (i) suggests heritable variance in common tern fitness to result mostly from heritable variance in reproductive success, rather than in early-life or adult survival, (ii) shows how studying the genetic architecture of fitness in natural populations remains challenging, and (iii) highlights the importance of maintaining long-term individual-based studies such that a major research aim in evolutionary ecology will come within better reach in the next decade.

Additive genetic variance for stem strength in field pea (Pisum sativum)

2008 ◽  
Vol 59 (1) ◽  
pp. 80 ◽  
Author(s):  
C. P. Beeck ◽  
J. Wroth ◽  
W. A. Cowling
Keyword(s):  
Pisum Sativum ◽  
Recurrent Selection ◽  
Seed Quality ◽  
Additive Genetic Variance ◽  
Genetic Effects ◽  
Field Pea ◽  
Lodging Resistance ◽  
Diverse Range ◽  
Stem Strength ◽  
Additive Genetic Effects

Weak stem strength in field pea (Pisum sativum) is a major restriction to yield, seed quality and ease of harvest. Three aspects of stem strength: load at breaking point, flexion and compressed stem thickness, showed substantial genetic variation among a diverse range of six parents including modern cultivars, landrace accessions, and interspecific progeny. Diallel analysis of parents and F1 progeny was conducted using a simple additive-dominance model, which was adequate for load and compressed stem thickness. There were significant additive genetic effects for load and compressed stem thickness with no evidence of dominance or maternal effects, and also significant additive genetic effects for flexion which was subject to more complex genetic control. Valuable alleles for these stem strength traits were present in commercial cultivars and landrace types of field pea. Efficient and practical breeding for improved stem strength will involve several recurrent selection cycles with moderate selection pressure for compressed stem thickness in early generations, followed by verification of improvements in lodging resistance in subsequent field trials. Compressed stem thickness is relatively easy to measure on individual plants in the field and is closely associated with load.

scholarly journals Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)

2020 ◽  
Author(s):  
Louise Arathoon ◽  
Parvathy Surendranadh ◽  
Nicholas Barton ◽  
David L. Field ◽  
Melinda Pickup ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Spatial Scales ◽  
Pollen Dispersal ◽  
Antirrhinum Majus ◽  
Fitness Components ◽  
Term Study ◽  
Long Term Study ◽  
In The Wild ◽  
Long Term Studies

AbstractInbreeding depression can be estimated by correlating heterozygosity with fitness components, but such heterozygosity-fitness correlations are typically weak. For over ten years, we studied a population of the self-incompatible plant, Antirrhinum majus, measuring heterozygosity and fitness proxies from 22,353 plants. Using a panel of 91 SNPs, we find that relatedness declines rapidly over short spatial scales. Individual heterozygosity varies more between individuals than expected, reflecting identity disequilibrium (g2) due to variation in inbreeding – a prerequisite for detecting inbreeding depression. We use two types of simulations to ask whether the heterozygosity distribution is consistent with spatially structured mating. First, we simulate offspring from matings with fathers at different distances and find that the distribution of heterozygosity in the field data is consistent with the measured pollen dispersal kernel. Second, we simulate a 1000-generation pedigree using the known spatial distribution, and find that identity disequilibrium, though highly variable between simulations, is consistent with that observed. Finally, we estimate inbreeding depression through the relationships between heterozygosity and six fitness proxies. Only the number of flowering stems is predicted by heterozygosity. Our approach provides a novel example of how long-term studies can elucidate population structure and fitness variation in the wild.

Combining Ability of Plant Height and Yield components in Indian Mustard (Brassica junceaL.Czern & Coss.) under Salt affected Soil using Line×Tester Analysis

2016 ◽  
Vol 3 (2) ◽  
Author(s):  
SHAILESH CHAND GAUTAM ◽  
MP Chauhan
Keyword(s):  
Plant Height ◽  
Seed Yield ◽  
Combining Ability ◽  
Yield Components ◽  
Indian Mustard ◽  
Heritability Estimate ◽  
Genetic Effects ◽  
Narrow Sense ◽  
Narrow Sense Heritability ◽  
Additive Genetic Effects

Line × tester analysis of twenty lines and three testers of Indian mustard (Brassica juncea L. Czern & Coss.) cultivars were used to estimate general combining ability (GCA), specific combining ability (SCA) effects, high parent heterosis and narrow-sense heritability estimate for plant height, yield components and seed yield. Significant variance of line x tester for the traits like pods per plant and seed yield indicating non additive genetic effects have important role for controlling these traits. Significant mean squares of parents v/s crosses which are indicating significant average heterosis were also significant for all the traits except seeds per pod. High narrow-sense heritability estimates for all the traits except seeds per pod exhibited the prime importance of additive genetic effects for these traits except seeds per pod. Most of the crosses with negative SCA effect for plant height had at least one parent with significant negative or negative GCA effect for this trait. For most of the traits except pods per plant, the efficiency of high parent heterosis effect was more than SCA effect for determining superior cross combinations.

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