scholarly journals Incomplete Dominance of Deleterious Alleles Contributes Substantially to Trait Variation and Heterosis in Maize

2016 ◽  
Author(s):  
Jinliang Yang ◽  
Sofiane Mezmouk ◽  
Andy Baumgarten ◽  
Edward S. Buckler ◽  
Katherine E. Guill ◽  
...  
Keyword(s):  
Grain Yield ◽  
Genomic Selection ◽  
Phenotypic Variation ◽  
Crop Improvement ◽  
Empirical Support ◽  
Sequence Conservation ◽  
Hybrid Vigor ◽  
Deleterious Mutations ◽  
Incomplete Dominance ◽  
Deleterious Alleles

AbstractDeleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring by crossing two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.Author SummaryA key long-term goal of biology is understanding the genetic basis of phenotypic variation. Although most new mutations are likely disadvantageous, their prevalence and importance in explaining patterns of phenotypic variation is controversial and not well understood. In this study we combine whole genome-sequencing and field evaluation of a maize mapping population to investigate the contribution of deleterious mutations to phenotype. We show that a priori prediction of deleterious alleles correlates well with effect sizes for grain yield and that variants predicted to be more damaging are on average more recessive. We develop a simple model allowing for variation in the heterozygous effects of deleterious mutations and demonstrate its improved ability to predict both phenotypes and hybrid vigor. Our results help reconcile alternative explanations for hybrid vigor and highlight the use of leveraging evolutionary history to facilitate breeding for crop improvement.

High-throughput phenotyping platforms enhance genomic selection for wheat grain yield across populations and cycles in early stage

2019 ◽  
Vol 132 (6) ◽  
pp. 1705-1720 ◽  
Author(s):  
Jin Sun ◽  
Jesse A. Poland ◽  
Suchismita Mondal ◽  
José Crossa ◽  
Philomin Juliana ◽  
...  
Keyword(s):  
Grain Yield ◽  
Genomic Selection ◽  
High Throughput ◽  
Early Stage ◽  
Wheat Grain ◽  
High Throughput Phenotyping ◽  
Selection For

scholarly journals Temporal covariance structure of multi-spectral phenotypes and their predictive ability for end-of-season traits in maize

2020 ◽  
Vol 133 (10) ◽  
pp. 2853-2868
Author(s):  
Mahlet T. Anche ◽  
Nicholas S. Kaczmar ◽  
Nicolas Morales ◽  
James W. Clohessy ◽  
Daniel C. Ilut ◽  
...  
Keyword(s):  
Grain Yield ◽  
Vegetation Index ◽  
Near Infrared ◽  
Normalized Difference Vegetation Index ◽  
Crop Improvement ◽  
Genetic Correlations ◽  
Random Regression ◽  
Multiple Time ◽  
Heritable Variation ◽  
Using Data

Abstract Key message Heritable variation in phenotypes extracted from multi-spectral images (MSIs) and strong genetic correlations with end-of-season traits indicates the value of MSIs for crop improvement and modeling of plant growth curve. Abstract Vegetation indices (VIs) derived from multi-spectral imaging (MSI) platforms can be used to study properties of crop canopy, providing non-destructive phenotypes that could be used to better understand growth curves throughout the growing season. To investigate the amount of variation present in several VIs and their relationship with important end-of-season traits, genetic and residual (co)variances for VIs, grain yield and moisture were estimated using data collected from maize hybrid trials. The VIs considered were Normalized Difference Vegetation Index (NDVI), Green NDVI, Red Edge NDVI, Soil-Adjusted Vegetation Index, Enhanced Vegetation Index and simple Ratio of Near Infrared to Red (Red) reflectance. Genetic correlations of VIs with grain yield and moisture were used to fit multi-trait models for prediction of end-of-season traits and evaluated using within site/year cross-validation. To explore alternatives to fitting multiple phenotypes from MSI, random regression models with linear splines were fit using data collected in 2016 and 2017. Heritability estimates ranging from (0.10 to 0.82) were observed, indicating that there exists considerable amount of genetic variation in these VIs. Furthermore, strong genetic and residual correlations of the VIs, NDVI and NDRE, with grain yield and moisture were found. Considerable increases in prediction accuracy were observed from the multi-trait model when using NDVI and NDRE as a secondary trait. Finally, random regression with a linear spline function shows potential to be used as an alternative to mixed models to fit VIs from multiple time points.

scholarly journals Genetic Gains in Grain Yield Through Genomic Selection in Eight Bi-parental Maize Populations under Drought Stress

Crop Science ◽  
2015 ◽  
Vol 55 (1) ◽  
pp. 154-163 ◽  
Author(s):  
Yoseph Beyene ◽  
Kassa Semagn ◽  
Stephen Mugo ◽  
Amsal Tarekegne ◽  
Raman Babu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Grain Yield ◽  
Genomic Selection ◽  
Genetic Gains ◽  
Maize Populations

Genetic variation and path analysis for yield and other agronomic traits in Nigella sativa L. germplasm

2019 ◽  
Vol 48 (3) ◽  
pp. 521-527
Author(s):  
Muhammad Sajjad Iqbal ◽  
Abdul Ghafoor ◽  
Muhammad Akbar ◽  
Shamim Akhtar ◽  
Sammer Fatima ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Grain Yield ◽  
Root Length ◽  
Agronomic Traits ◽  
Nigella Sativa ◽  
Crop Improvement ◽  
Path Coefficient ◽  
Root Weight ◽  
Days To Maturity ◽  
Improvement Programs

Thirty two genotypes of Nigella sativa L. were evaluated for three consecutive years which showed significant differences for all the traits indicating high level of genetic variation. Heritability in broad sense ranged from 0.28 to 0.98 and the highest heritability was calculated for days to maturity and days to flowers. Grain yield was positively associated with plant height, capsule weight, capsule length, root length, whereas negatively with capsule width and 1000-seed weight that required the use of novel breeding techniques to break this undesired linkage to improve grain yield in N. sativa. Path coefficient indicated that direct effects of all the traits were positive except days to first flower, days to 50% flowers, flowering duration, number of capsules, root weight and harvest index. The characters exhibiting correlation along with direct effect towards grain yield viz., days to maturity, capsule weight, capsule length and root length should be given more preference while selecting high yielding N. sativa genotypes for future crop improvement programs.

scholarly journals The effect of background selection against deleterious mutations on weakly selected, linked variants

1994 ◽  
Vol 63 (3) ◽  
pp. 213-227 ◽  
Author(s):  
Brian Charlesworth
Keyword(s):  
Genetic Diversity ◽  
Molecular Evolution ◽  
Effective Size ◽  
Background Selection ◽  
Deleterious Mutations ◽  
Deleterious Alleles ◽  
Rates Of Evolution ◽  
Selection Approach ◽  
Slightly Deleterious Mutations ◽  
Neutral Case

SummaryThis paper analyses the effects of selection against deleterious alleles maintained by mutation (‘ background selection’) on rates of evolution and levels of genetic diversity at weakly selected, completely linked, loci. General formulae are derived for the expected rates of gene substitution and genetic diversity, relative to the neutral case, as a function of selection and dominance coefficients at the loci in question, and of the frequency of gametes that are free of deleterious mutations with respect to the loci responsible for background selection. As in the neutral case, most effects of background selection can be predicted by considering the effective size of the population to be multiplied by the frequency of mutation-free gametes. Levels of genetic diversity can be sharply reduced by background selection, with the result that values for sites under selection approach those for neutral variants subject to the same regime of background selection. Rates of fixation of slightly deleterious mutations are increased by background selection, and rates of fixation of advantageous mutations are reduced. The properties of sex-linked and autosomal asexual and self-fertilizing populations are considered. The implications of these results for the interpretation of studies of molecular evolution and variation are discussed.

scholarly journals Deleterious mutation accumulation in Arabidopsis thaliana pollen genes: a role for a recent relaxation of selection

2015 ◽  
Author(s):  
MC Harrison ◽  
EB Mallon ◽  
D Twell ◽  
RL Hammond
Keyword(s):  
Arabidopsis Thaliana ◽  
Life History ◽  
Deleterious Mutation ◽  
Rapid Evolution ◽  
Relative Strength ◽  
Pollen Competition ◽  
Deleterious Mutations ◽  
Deleterious Alleles ◽  
Polymorphism Data ◽  
Plant Pollen

AbstractIn many studies sex related genes have been found to evolve rapidly. We therefore expect plant pollen genes to evolve faster than sporophytic genes. In addition, pollen genes are expressed as haploids which can itself facilitate rapid evolution because recessive advantageous and deleterious alleles are not masked by dominant alleles. However, this mechanism is less straightforward to apply in the model plant species Arabidopsis thaliana. For 1 million years A.thaliana has been self-compatible, a life history switch that has caused: a reduction in pollen competition, increased homozygosity and a dilution of masking in diploid expressed, sporophytic genes. In this study we have investigated the relative strength of selection on pollen genes compared to sporophytic genes in A. thaliana. We present two major findings: 1) before becoming self-compatible positive selection was stronger on pollen genes than sporophytic genes for A. thaliana; 2) current polymorphism data indicate selection is weaker on pollen genes compared to sporophytic genes. These results indicate that since A. thaliana has become self-compatible, selection on pollen genes has become more relaxed. This has led to higher polymorphism levels and a higher build-up of deleterious mutations in pollen genes compared to sporophytic genes.

scholarly journals Sex differences in deleterious genetic variants in a haplodiploid social insect

2021 ◽  
Author(s):  
Sara E. Miller ◽  
Michael J. Sheehan
Keyword(s):  
Genetic Load ◽  
Low Frequency ◽  
Paper Wasp ◽  
Deleterious Mutations ◽  
Wild Populations ◽  
Nonsense Mutations ◽  
Low Frequencies ◽  
Complete Dominance ◽  
Deleterious Alleles ◽  
Population Allele Frequency

AbstractDeleterious variants are selected against but can linger in populations at low frequencies for long periods of time, decreasing fitness and contributing to disease burden in humans and other species. Deleterious variants occur at low frequency but distinguishing deleterious variants from low frequency neutral variation is challenging based on population genetics data. As a result, we have little sense of the number and identity of deleterious variants in wild populations. For haplodiploid species, it has been hypothesized that deleterious alleles will be directly exposed to selection in haploid males, but selection can be masked in diploid females due to partial or complete dominance, resulting in more efficient purging of deleterious mutations in males. Therefore, comparisons of the differences between haploid and diploid genomes from the same population may be a useful method for inferring rare deleterious variants. This study provides the first formal test of this hypothesis. Using wild populations of Northern paper wasps (Polistes fuscatus), we find that males have fewer overall variants, and specifically fewer missense and nonsense variants, than females from the same population. Allele frequency differences are especially pronounced for rare missense and nonsense mutations and these differences lead to a lower genetic load in males than females. Based on these data we estimate that a large number of highly deleterious mutations are segregating in the paper wasp population. Stronger selection against deleterious alleles in haploid males may have implications for adaptation in other haplodiploid insects and provides evidence that wild populations harbor abundant deleterious variants.

scholarly journals Deleterious mutations, apparent stabilizing selection and the maintenance of quantitative variation.

Genetics ◽  
1992 ◽  
Vol 132 (2) ◽  
pp. 603-618 ◽  
Author(s):  
A S Kondrashov ◽  
M Turelli
Keyword(s):  
Quantitative Trait ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Pleiotropic Effects ◽  
Direct Selection ◽  
Selection Function ◽  
Stabilizing Selection ◽  
Deleterious Mutations ◽  
Additive Variance ◽  
Deleterious Alleles

Abstract Apparent stabilizing selection on a quantitative trait that is not causally connected to fitness can result from the pleiotropic effects of unconditionally deleterious mutations, because as N. Barton noted, "...individuals with extreme values of the trait will tend to carry more deleterious alleles...." We use a simple model to investigate the dependence of this apparent selection on the genomic deleterious mutation rate, U; the equilibrium distribution of K, the number of deleterious mutations per genome; and the parameters describing directional selection against deleterious mutations. Unlike previous analyses, we allow for epistatic selection against deleterious alleles. For various selection functions and realistic parameter values, the distribution of K, the distribution of breeding values for a pleiotropically affected trait, and the apparent stabilizing selection function are all nearly Gaussian. The additive genetic variance for the quantitative trait is kQa2, where k is the average number of deleterious mutations per genome, Q is the proportion of deleterious mutations that affect the trait, and a2 is the variance of pleiotropic effects for individual mutations that do affect the trait. In contrast, when the trait is measured in units of its additive standard deviation, the apparent fitness function is essentially independent of Q and a2; and beta, the intensity of selection, measured as the ratio of additive genetic variance to the "variance" of the fitness curve, is very close to s = U/k, the selection coefficient against individual deleterious mutations at equilibrium. Therefore, this model predicts appreciable apparent stabilizing selection if s exceeds about 0.03, which is consistent with various data. However, the model also predicts that beta must equal Vm/VG, the ratio of new additive variance for the trait introduced each generation by mutation to the standing additive variance. Most, although not all, estimates of this ratio imply apparent stabilizing selection weaker than generally observed. A qualitative argument suggests that even when direct selection is responsible for most of the selection observed on a character, it may be essentially irrelevant to the maintenance of variation for the character by mutation-selection balance. Simple experiments can indicate the fraction of observed stabilizing selection attributable to the pleiotropic effects of deleterious mutations.

scholarly journals Sexual selection and inbreeding: two efficient ways to limit the accumulation of deleterious mutations

2018 ◽  
Author(s):  
E. Noël ◽  
E. Fruitet ◽  
D. Lelaurin ◽  
N. Bonel ◽  
A. Ségard ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Experimental Evolution ◽  
Genetic Load ◽  
Deleterious Mutations ◽  
Mutation Load ◽  
Male Function ◽  
Female Function ◽  
Deleterious Alleles ◽  
Self Fertilization ◽  
Male Specific

AbstractTheory and empirical data showed that two processes can boost selection against deleterious mutations, thus facilitating the purging of the mutation load: inbreeding, by exposing recessive deleterious alleles to selection in homozygous form, and sexual selection, by enhancing the relative reproductive success of males with small mutation loads. These processes tend to be mutually exclusive because sexual selection is reduced under mating systems that promote inbreeding, such as self-fertilization in hermaphrodites. We estimated the relative efficiency of inbreeding and sexual selection at purging the genetic load, using 50 generations of experimental evolution, in a hermaphroditic snail (Physa acuta). To this end, we generated lines that were exposed to various intensities of inbreeding, sexual selection (on the male function) and nonsexual selection (on the female function). We measured how these regimes affected the mutation load, quantified through the survival of outcrossed and selfed juveniles. We found that juvenile survival strongly decreased in outbred lines with reduced male selection, but not when female selection was relaxed, showing that male-specific sexual selection does purge deleterious mutations. However, in lines exposed to inbreeding, where sexual selection was also relaxed, survival did not decrease, and even increased for self-fertilized juveniles, showing that purging through inbreeding can compensate for the absence of sexual selection. Our results point to the further question of whether a mixed strategy combining the advantages of both mechanisms of genetic purging could be evolutionary stable.

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