Genetics of leaf blight resistance in wheat

Summary Studies on the genetics of leaf blight caused byAlternaria triticina using generation mean analysis revealed that additive components played a major role, but that dominance components also contributed significantly in controlling the variability for leaf blight resistance in wheat crosses. Furthermore, the additive x additive type of epistasis was predominant in the first three crosses, whereas in the fourth cross additive x dominance (j) and dominance x dominance (1) components of epistasis were most significant. Because of this it may be desirable to follow a simple recurrent selection scheme for higher tolerance, to isolate resistant plants from the segregating populations derived from crosses of parents of diverse origin following the pedigree method of breeding. CPAN-1887 was very tolerant to leaf blight in the present study and should be utilized in hybridization programs to develop leaf-blight-resistant varieties.     

Genetic analyses for certain plant and ear characters in pearl millet top-crosses

Summary Combining ability and the genetics of tiller number, days taken to flower and ear thickness were studied in top-cross progenies of pearl millet. General combining ability seemed to be more important for all the characters. The prevalence of epistatic variation, presumably of the type additive x additive, additive x dominance and dominance x dominance gene effects, with a non-significant contribution of additive and dominance components of genetic variance, was observed for tiller number. For days taken to flower, the importance of additive genetic variance was greater than that of the dominance component with directional dominance towards the recessive allele. However, for ear thickness, the existence of additive genetic variability together with the additive x additive type of genic interaction was suggested.An appreciable effect of epistasis on and ₁ components was observed for tiller number, whereas this effect was not so marked for other characters.The author is grateful to Dr. D. S. Athwal, formerly Professor and Head (now Assistant Director, The International Rice Research Institute, Los Banõs, Laguna, Philippines), Department of Plant Breeding, Punjab Agricultural University, Ludhiana, for providing the facilities.     

Inheritance of partial resistance to powdery mildew in spring wheat

Summary Four spring wheat (Triticum aestivum L.) cultivars exhibiting partial resistance to powdery mildew induced by Erysiphe graminis f.sp. tritici were crossed to a common susceptible cultivar to study the inheritance of resistance. The genetic parameters contributing to resistance were estimated by generation means analyses. Additive gene action was the most important genetic component of variation among generation means in all four crosses. Additive by additive effects were significant in one cross and both additive by additive and additive by dominance effects were significant in another. Dominance effects were not significant. The F2/F3 correlations in three crosses ranged from 0.27 to 0.43. Three additional crosses among resistant cultivars were employed to study the effectiveness of selection in improving resistance. By selecting the most resistant plants from the F2 and evaluating the progenies in the F4, increases in resistance ranging from 21% to 31% were obtained. In all crosses, there was transgressive segregation in both directions indicating that the genes conferring resistance to these cultivars differ and exhibit additive effects.     

Local Adaptation and Genetics of Acid-Stress Tolerance in the Moor Frog, Rana arvalis

As potential to adapt to environmental stress can be essential for population persistence, knowledge on the genetic architecture of local adaptation is important for conservation genetics. We investigated the relative importance of additive genetic, dominance and maternal effects contributions to acid stress tolerance in two moor frog (Rana arvalis) populations originating from low and neutral pH habitats. Experiments with crosses obtained from artificial matings revealed that embryos from the acid origin population were more tolerant to low pH than embryos from the neutral origin population in embryonic survival rates, but not in terms of developmental stability, developmental and growth rates. Strong maternal effect and small additive genetic contributions to variation were detected in all traits in both populations. In general, dominance contributions to variance in different traits were of similar magnitude to the additive genetic effects, but dominance effects outweighed the additive genetic and maternal effects contributions to early growth in both populations. Furthermore, the expression of additive genetic variance was independent of pH treatment, suggesting little additive genetic variation in acid stress tolerance. The results suggest that although local genetic adaptation to acid stress has taken place, the current variation in acid stress tolerance in acidified populations may owe largely to non-genetic effects. However, low but significant heritabilities (h ² 0.07–0.22) in all traits – including viability itself – under a wide range of pH conditions suggests that environmental stress created by low pH is unlikely to lower moor frog populations' ability to respond to selection in the traits studied. Nevertheless, acid conditions could lower populations' ability to respond to selection in the long run through reduction in effective population size.     

Genetic Analysis of the Latent Period of Stripe Rust in Wheat Seedlings

Genetics of slow‐rusting resistance to yellow rust (Puccinia striiformis f.sp. tritici) was studied by a half‐diallel design using six wheat varieties, Tiritea (susceptible), Tancred, Kotare, Otane, Karamu, and Briscard. The parents and 15 F₁ progenies were evaluated in the greenhouse by three pathotypes 7E18A^?, 38E0A⁺, and 134E134A⁺. The latent period was measured as the number of days from inoculation to the appearance of the first pustule. For each pathotype a randomized complete block design was used and data were analysed by methods of Griffing and Hayman. The range of average degree of dominance was from complete dominance to over‐dominance. Positive and negative degrees of dominance were observed for each pathotype that showed the reversal of dominance. Analysis of variance showed the importance of both additive and dominance effects in controlling the latent period. Broad‐sense heritabilities were 0.99 and narrow‐sense heritabilities ranged from 0.85 to 0.94. Briscard and Karamu for the pathotypes 38E0A⁺ and 134E134A⁺, Kotare for the pathotype 7E18A^? and Tancred for the pathotype 38E0A⁺ had significant and positive general combining ability (GCA) (more resistance) for latent period. The crosses of Kotare with Tancred, Briscard and Karamu indicated the highest and positive specific combining ability (SCA) for the pathotype 7E18A^?. Significant additive genetic component and moderate narrow‐sense heritability indicate the possibility of improving for longer latent period of stripe rust in breeding programmes.     

Inheritance of resistance to wheat yellow rust at adult plant stage

In order to investigate on inheritance and gene action for resistance to yellow rust, the resistant line C.B227 was crossed with the susceptible variety Avocet. Parents (P1 and P2) and the resulting F1, F2 and F3 generations were planted in a randomised complete block design with two replications in the field. The plants were inoculated with 70E0A⁺ pathotype of yellow rust in the research station of Gharakhil, Iran, and evaluated for resistance at adult plant stage. Disease severity and infection type of flag leaf were recorded for each single plant and final coefficient of infection was calculated. The results of weighted ANOVA indicated that the difference among the generations was significant (p?<?0.01) for the trait final infection type. Generation mean analysis showed that dominant effect was more important than additive one. The degree of dominance indicated the presence of complete dominance. Additive, dominance and epistasic additive?×?additive [i] effects were important in genetic control of resistance. The results of generation variance analysis were consistent with generation mean analysis.     

Inheritance of photoperiod-induced flowering in three photoperiodic lines of Aeschynomene americana L.

Summary Induction of flowering by photoperiod was studied in the parental, F₁, F₂, and reciprocal backcross generations of crosses between three photoperiod-responsive Aeschynomene americana L. lines. Generation means appeared additive. Analysis with Mather and Jinks' scaling tests showed little or no epistasis and indicated that an additive-dominance model was adequate. Partitioning components of variation revealed that nearly all variation was additive genetic with dominance and environmental variation negligible. An additive genetic model with two loci, each with two alleles and all alleles having equal net effect, was tested using Power's partitioning method. Results demonstrated that the model fit the data and that there is a major additive genetic system controlling flowering in these crosses, with minor genetic and environmental influences present. Selection for flowering at a desired day length should be feasible.Accepted by A.R. HallauerFlorida Agricultural Experiment Station, Journal Series No. 9251     

Genetic studies in an exotic population of corn (Zea mays L.) grown under two plant densities

Summary Progenies of a Design II [Comstock and Robinson (1948)] using random S ₁ lines from an exotic population of corn (Zea mays L.) were evaluated in a randomized incomplete block design with two replications at two plant-population densities (1 7,222 plants/ha and 68,888 plants/ha) in 1970 and 1971, at Lincoln, Nebraska. Five traits were studied i.e. grain weight, number of ears, days to flower, plant height and ear height.Under both densities the estimates of additive genetic variance were much larger than those of dominance genetic variance for all traits. The ratio of dominance to additive genetic variance estimates was less than 0.5 suggesting that for the majority of loci controlling the traits, partial to complete dominance is likely.The estimates of additive genetic x year interaction variance were high and significantly different from zero under both densities, indicating that estimates of additive genetic variance in this population obtained from experiments conducted in only one year may be seriously biased. The estimates of dominance genetic x year interaction variance were not significant and most of them were negative.Under both densities high genetic inter-relationships were indicated between grain weight and number of ears, days to flower and plant height, days to flower and ear height, and plant height and ear height.Even though there was a large difference between the two densities used in the study, the differences between the estimates of genetic parameters were not significant in all cases.The sample size of S ₁ plants representing each S₀ parent in the crossing nursery used in the present study (11.75) caused a small upward bias in the estimates of additive genetic variance, but it caused an upward bias in the estimates of dominance genetic variance of 6–7% of the total genetic variance.It is suggested that a trait such as grain weight should be expressed on a unit area basis when genetic parameters (except for correlation and the ratio between two values) obtained from experiments with different plant-population densities are to be compared.Published as Paper Number 3542, Journal Series, Nebraska Agricultural Experimental Station. Part of a thesis submitted by the senior author in partial fulfillment of the requirements for the Ph. D. degree.A. I. D. Participant.The work was supported in part by a grant from the Rockefeller Foundation.     

On the Probabilities of Obtaining Negative Estimates of Genetic Variance Components

This paper derives the probabilities of obtaining negative estimates of additive and dominance genetic variances when one uses the traditional weighted least square method for estimating genetic variances as given in MATHER and JINKS (1971). The model considered involves P₁, P₂, F₂, B₁ (Backcross to P₁) and B₂ (Backcross to P₂). The results are derived under the ordinary assumptions as made in the genetic literatures. It is shown that unless the genetic effects are very large and environmental effects small, the probabilities of obtaining negative estimates of additive and dominance variances are in general quite large.     

Analysis of cytoplasmic and maternal effects. II. Genetic models for triploid endosperms

Genetic models for quantitative traits of triploid endosperms are proposed for the analysis of direct gene effects, cytoplasmic effects, and maternal gene effects. The maternal effect is partitioned into maternal additive and dominance components. In the full genetic model, the direct effect is partitioned into direct additive and dominance components and high-order dominance component, which are the cumulative effects of three-allele interactions. If the high-order dominance effects are of no importance, a reduced genetic model can be used. Monte Carlo simulations were conducted in this study for demonstrating unbiasedness of estimated variance and covariance components from the MINQUE (0/1) procedure, which is a minimum norm quadratic unbiased estimation (MINQUE) method setting 0 for all the prior covariances and 1 for all the prior variances. Robustness of estimating variance and covariance components for the genetic models was tested by simulations. Both full and reduced genetic models are shown to be robust for estimating variance and covariance components under several situations of no specific effects. Efficiency of predicting random genetic effects for the genetic models by the MINQUE (0/1) procedure was compared with the best linear unbiased prediction (BLUP). A worked example is given to illustrate the use of the reduced genetic model for kernel growth characteristics in corn (Zea mays L.).     

Gene actions at loci underlying several quantitative traits in two elite rice hybrids

To understand the gene activities controlling nine important agronomic quantitative traits in rice, we applied a North Carolina design 3 (NC III design) analysis to recombinant inbred lines (RILs) in highly heterotic inter- (IJ) and intra-subspecific (II) hybrids by performing the following tasks: (1) investigating the relative contribution of additive, dominant, and epistatic effects for performance traits by generation means analysis and variance component estimates; (2) detecting the number, genomic positions, and genetic effects of QTL for phenotypic traits; and (3) characterizing their mode of gene action. Under an F∞-metric, generation means analysis and variance components estimates revealed that epistatic effects prevailed for the majority of traits in the two hybrids. QTL analysis identified 48 and 66 main-effect QTL (M-QTL) for nine traits in IJ and II hybrids, respectively. In IJ hybrids, 20 QTL (41.7%) showed an additive effect of gene actions, 20 (41.7%) showed partial-to-complete dominance, and 8 (16.7%) showed overdominance. In II hybrids, 34 QTL (51.5%) exhibited additive effects, 14 (21.2%) partial-to-complete dominance, and 18 (27.3%) overdominance. There were 153 digenic interactions (E-QTL) in the IJ hybrid and 252 in the II hybrid. These results suggest that additive effects, dominance, overdominance, and particularly epistasis attribute to the genetic basis of the expression of traits in the two hybrids. Additionally, we determined that the genetic causes of phenotypic traits and their heterosis are different. In the plants we studied, the phenotypic traits investigated and their heterosis were conditioned by different M-QTL and E-QTL, respectively, and were mainly due to non-allelic interactions (epistasis).     

Genetic investigation of contributions of embryo and endosperm genes to malt Kolbach index, alpha-amylase activity and wort nitrogen content in barley

 A genetic model is proposed for the analysis of embryo and endosperm effects as well as GE interaction effects. An investigation of three malting quality traits in grains of seven parents and their F₂s was undertaken in a half-diallel cross of barley (Hordeum distichum L.) over 2 years. The results indicated that the malt Kolbach index (KI), alpha-amylase activity (αAA) and wort soluble nitrogen (Wort-N) are controlled by both embryo genetic effects and endosperm genetic effects. Variance of the endosperm additive effects was obviously larger than that of the embryo additive effects. In the contribution of the embryo genetic effects to variation in malt αAA and Wort-N, the dominance effects were considerably larger than the additive effects. The endosperm dominance effects constituted a major part of the total genetic effect on the KI. Significant endosperm GE interactions were also detected in the malt traits concerned. Endosperm general heritability (h ² _e ) tended to be larger than interaction heritability (h ² _oE or h ² _eE ) for all the traits. Endosperm heterosis was observed to be significantly positive for αAA but negative for Wort-N in the F₂ seed generation. Prediction of main gene effects for seven parents showed that ‘Ganmu 2’ and ‘Supi1’ were suitable parental varieties for malt αAA and Wort-N improvement. Our genetic model for malting quality traits and its application in breeding are discussed. Received: 5 August 1997 / Accepted: 11 September 1997     

Genomic analysis of dominance effects on milk production and conformation traits in Fleckvieh cattle

Background

Estimates of dominance variance in dairy cattle based on pedigree data vary considerably across traits and amount to up to 50% of the total genetic variance for conformation traits and up to 43% for milk production traits. Using bovine SNP (single nucleotide polymorphism) genotypes, dominance variance can be estimated both at the marker level and at the animal level using genomic dominance effect relationship matrices. Yield deviations of high-density genotyped Fleckvieh cows were used to assess cross-validation accuracy of genomic predictions with additive and dominance models. The potential use of dominance variance in planned matings was also investigated.

Results

Variance components of nine milk production and conformation traits were estimated with additive and dominance models using yield deviations of 1996 Fleckvieh cows and ranged from 3.3% to 50.5% of the total genetic variance. REML and Gibbs sampling estimates showed good concordance. Although standard errors of estimates of dominance variance were rather large, estimates of dominance variance for milk, fat and protein yields, somatic cell score and milkability were significantly different from 0. Cross-validation accuracy of predicted breeding values was higher with genomic models than with the pedigree model. Inclusion of dominance effects did not increase the accuracy of the predicted breeding and total genetic values. Additive and dominance SNP effects for milk yield and protein yield were estimated with a BLUP (best linear unbiased prediction) model and used to calculate expectations of breeding values and total genetic values for putative offspring. Selection on total genetic value instead of breeding value would result in a larger expected total genetic superiority in progeny, i.e. 14.8% for milk yield and 27.8% for protein yield and reduce the expected additive genetic gain only by 4.5% for milk yield and 2.6% for protein yield.

Conclusions

Estimated dominance variance was substantial for most of the analyzed traits. Due to small dominance effect relationships between cows, predictions of individual dominance deviations were very inaccurate and including dominance in the model did not improve prediction accuracy in the cross-validation study. Exploitation of dominance variance in assortative matings was promising and did not appear to severely compromise additive genetic gain.     

Non-additive genetic effects for fertility traits in Canadian Holstein cattle (Open Access publication )

The effects of additive, dominance, additive by dominance, additive by additive and dominance by dominance genetic effects on age at first service, non-return rates and interval from calving to first service were estimated. Practical considerations of computing additive and dominance relationships using the genomic relationship matrix are discussed. The final strategy utilized several groups of 1000 animals (heifers or cows) in which all animals had a non-zero dominance relationship with at least one other animal in the group. Direct inversion of relationship matrices was possible within the 1000 animal subsets. Estimates of variances were obtained using Bayesian methodology via Gibbs sampling. Estimated non-additive genetic variances were generally as large as or larger than the additive genetic variance in most cases, except for non-return rates and interval from calving to first service for cows. Non-additive genetic effects appear to be of sizeable magnitude for fertility traits and should be included in models intended for estimating additive genetic merit. However, computing additive and dominance relationships for all possible pairs of individuals is very time consuming in populations of more than 200 000 animals.     

DIURNAL PREFERENCE AND SLEEP QUALITY: SAME GENES? A STUDY OF YOUNG ADULT TWINS

The aims of this study were to examine the genetic and environmental influences on diurnal preference and sleep quality, the association between these phenotypes, the genetic and environmental influences on this association, and the magnitude of overlap between these influences. Using a twin design, data on diurnal preference (measured by the Morningness-Eveningness Questionnaire) and sleep quality (measured by the Pittsburgh Sleep Quality Index) were collected from 420 monozygotic twins, 773 dizygotic twins, and 329 siblings (mode age?=?20 yrs, range?=?18–27 yrs) from a population-based twin registry across the UK. Univariate analyses indicated that dominance genetic influence accounted for 52% and non-shared environment 48% of variance in diurnal preference. For sleep quality, additive genetic influence explained 43% and non-shared environment 57% of the variance. The bivariate analysis indicated a significant association between greater eveningness preference and poorer sleep quality (r?=?.27). There was substantial overlap in the additive genetic influences on both phenotypes (rA?=?.57), and overlap in the dominance genetic influences common to both phenotypes was almost absolute (rD = .99). Overlap in non-shared environment was much smaller (rE?=?.02). Additive genetic influence accounted for 2% of the association, dominance genetic influence accounted for 94%, and non-shared environmental influences accounted for the remaining 4%. The substantial overlap in genetic influence between these phenotypes indicates that similar genes are important for diurnal preference and sleep quality. Therefore, those genes already known to influence one phenotype may be possible candidates to explore with regards to the other phenotype. (Author correspondence: ps701nh@gold.ac.uk)     

Epistasis causes outbreeding depression in eucalypt hybrids

The genetic architecture underlying species differentiation is essential for understanding the mechanisms of speciation and post-zygotic reproductive barriers which exist between species. We undertook line-cross analysis of multiple hybrid (F₁, F₂ and backcrosses) and pure-species populations of two diploid eucalypt species from different subseries, Eucalyptus globulus and Eucalyptus nitens, to unravel the genetic architecture of their differentiation. The populations were replicated on two sites and monitored for growth and survival over a 14-year period. The hybrids exhibited severe outbreeding depression which increased with age. Of the composite additive, dominance and epistatic effects estimated, the additive × additive epistatic component was the most important in determining population divergence in both growth and survival. Significant dominance × dominance epistasis was also detected for survival at several ages. While favourable dominance and, in the case of survival, dominance × dominance epistasis could produce novel gene combinations which enhance hybrid fitness, at the population level, these effects were clearly overridden by adverse additive × additive epistasis which appears to be a major driver of overall outbreeding depression in the hybrid populations. The lack of model fit at older ages suggested that even high-order epistatic interactions may potentially have a significant contribution to outbreeding depression in survival. The estimated composite genetic parameters were generally stable across sites. Our results argue that the development of favourable epistasis is a key mechanism underlying the genetic divergence of eucalypt species, and epistasis is an important mechanism underlying the evolution of post-zygotic reproductive barriers.     

Cross prediction studies on spring barley

Summary Additive genetic, dominance genetic and environmental correlations between pairs of agronomically important characters in five spring barley crosses were calculated from estimates of the components of variance and covariance, obtained by Triple Test Cross analysis. Phenotypic correlations were calculated from the Triple Test Cross family means and compared to the additive genetic correlations. Phenotypic correlations were generally lower than the additive genetic correlations and, occasionally, of different sign. The highest phenotypic correlations between single plant yield and its components were found with number of tillers whereas these were the lowest additive genetic correlations, thousand grain weight giving the highest. High dominance genetic correlations were found between single plant yield and both grain number and thousand grain weight thus indirect early generation selection for single plant yield using these two characters would be ineffective. Additive and dominance genetic correlations confirm association of the erectoides dwarfing gene with low thousand grain weight and plant yield.     

Single tester triple test cross analysis in spring wheat

Summary Two experiments, each including the same 30 homozygous varieties of spring wheat plus one separate tester variety, were conducted in order to detect epistasis and to test and estimate the additive and dominance components of genetic variation for five quantitative traits: final plant height, spike length, number of spikelets per spike, 100-kernel weight and grain yield per plant. Epistasis played a significant role in the control of 100-kernel weight and yield per plant. There was a gratifyingly good agreement between the two independent methods (2¯B₁i — ¯f_1i — ¯P_i and 2¯B_ci — ¯F_1i) used to test the presence of epistasis. In both experiments, there was a remarkably uniform high dominance ratio for most of the traits studied indicating that this test cross design is equally sensitive to both additive and dominance genetic variation.     

Power of tests for QTL detection using replicated progenies derived from a diallel cross

In crop species, most QTL (quantitative trait loci) mapping strategies use segregating populations derived from an initial cross between two lines. However, schemes including more than two parents could also be used. We propose an approach using a high-density restriction fragment length polymorphism (RFLP) map established on six F ₂ populations derived from diallel crosses among four inbred lines and the phenotypic performances of two types of replicated progenies (F ₃ and topcross). The QTL is supposed to be on the marker locus considered. Three linear model tests for the detection of QTL effects (T ₁, T ₂ and T ₃) are described and their power studied for the two types of progeny. T ₁ tests the global genetic effects of the QTL (additivity and dominance) and T ₂ tests only additive effects assuming dominance is absent when it could exist. The models of these two tests assume that the main effects of QTL alleles are constant in different genetic backgrounds. The additive model of test T ₃ considers the six F ₂ populations independently, and T ₃ is the equivalent of the classical mean comparison test if we neglect dominance; it uses only contrasts between the homozygote marker classes. The results show that T ₂ is much more powerful than T ₃. The power of T ₁ and T ₂ depends on the relative sizes of the additive and dominance effects, and their comparison is not easy to establish. Nevertheless, T ₂ seems to be the more powerful in most situations, indicating that it is often more interesting to ignore dominance when testing for a QTL effect. For a given size of genetic effects, the power is affected by the total number of individuals genotyped in F ₂ and the recombination rate between the marker locus and the putative QTL. The approach presented in this paper has some drawbacks but could be easily generalized to other sizes of diallels and different progeny types.