Diallel and generation means analyses for the components of resistance to Cercospora arachidicola in peanut

Summary The inheritance of the components of partial resistance to Cercospora arachidicola Hori in peanut (Arachis hypogaea L.) was examined in two five-parent diallels and in the six generations of two single crosses in greenhouse tests. The Griffing (1956) analysis indicated general combining ability (GCA) to be of most importance, yet large ratios of SCA/GCA sum of squares suggested nonadditive genetic variance as well. Reciprocal effects were found for lesion area and lesion number/10 cm² leaf area. The importance of nonadditive genetic variance was substantiated by the lack of fit for the additive-dominance model in the Hayman's analysis (1954 a, b). Further evidence from the Hayman's analysis indicated that epistasis may be important in determining the inheritance of some of the components of resistance. Additive gene effects alone accounted for the genetic variability observed among the generation means from two single crosses for all components of resistance except latent period. There was evidence that epistasis was an important mode of gene action for the inheritance of latent period.Paper No. 10172 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC 27601, USA     

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.     

Evaluation of inheritance to leaf rust in wheat using area under disease progress curve

Six varieties, Kundan (K), Galvez-87 (G), Trap (T), Chris (C), Mango (M) and PBW-348 (P) along with fast ruster, Agra Local (AL), were screened for seedling reaction and adult pant response to leaf rust. Seedlings of all six varieties were susceptible while adult plants showed lower susceptability response than Agra Local. The F1s among the varieties, and also with Agra Local, showed the values lesser than the respective mid parental values for AUDPC suggesting a polygenic mode of inheritance. ANOVA for combining ability effects indicated variation due to the GCA and SCA effects, which indicated that both additive as well as non-additive type of genetic variances, govern AUDPC. The higher values for the GCA variance over the SCA variance indicated the predominance of an additive component over the dominance component for AUDPC. Significant values for GCA effects indicated that Kundan, Galvez-87 and Trap can be used as good general combiners for AUDPC. The crosses, KxAL, GxAL and TxAL showed significant sca effects for AUDPC, which indicated the predominance of non-additive gene effects in these crosses. Additive x additive and dominance x dominance components of the 5- parameter model were highly significant and contributed maximum extent compared to the additive and dominance components in the cross KxG, while dominance and dominance x dominance components contributed maximum in the remaining crosses. Under such a situation, improvement in the character may be expected through standard selection procedure, which may first exploit the additive gene effects and simultaneously care should be taken to see that the dominance effects are not dissipated, but rather they should be concentrated.     

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.     

Inheritance of emergence time at low temperatures in segregating generations of maize

Summary North Carolina Design III and generation means analyses were used to study the inheritance of seedling emergence time and a related seedling growth parameter in crosses between 5–154, a line from CIMMYT Pool 5 with rapid seedling emergence under cool conditions, and two Corn Belt Dent lines of maize (Zea mays L.). The crosses were evaluated at low temperatures in controlled environment rooms. Additive genetic variances were larger than dominance variances in both crosses and estimates of the average levels of dominance were in the partial dominance range. Dominance was in the direction of rapid seedling emergence and rapid utilization of seed reserve. Estimates of minimum numbers of effective factors provided evidence for polygenic inheritance.     

Epistasis in maize (Zea mays L.)

Summary Three flint and three dent maize (Zea mays L.) inbred lines, their possible F₁ crosses, F₂ and backcross progenies, and all possible three-way crosses were evaluated in a three-year experiment for yield, ear moisture, and plant height. The purpose was to estimate genetic parameters in European breeding materials from (i) generation means analysis, (ii) diallel analysis of generation means, and (iii) analysis of F₁ and three-way cross hybrids. Method (i) was based on the F-metric model and methods (ii) and (iii) on the Eberhart-Gardner (1966) genetic model; both models extended for heterotic maternal effects.Differences among generation means for yield and plant height were mainly attributable to dominance effects. Epistatic effects were significantly different from zero in a few crosses and considerably reduced heterosis in both traits. Additive x additive and domiance x dominance effects for yield were consistently positive and negative, respectively. Significant maternal effects were established to the advantage of generations with a heterozygous seed parent. In the diallel analysis, mean squares for dominance effects were greater than for additive effects for yield and plant height but smaller for ear moisture. Though significant for yield and plant height, epistatic variation was small compared to additive and dominance variation. Estimates of additive x additive epistasis for yield were significantly negative in 11 of 15 crosses, suggesting that advantageous gene combinations in the lines had been disrupted by recombination in the segregating generations. The analysis of hybrids supported the above findings regarding the analysis of variance. However, the estimates of additive x additive epistasis for yield were considerably smaller and only minimally correlated with those from the diallel analysis. Use of noninbred materials as opposed to materials with different levels of inbreeding is considered the main reason for the discrepancies in the results.     

THE EVOLUTIONARY GENETICS OF MALE LIFE-HISTORY CHARACTERS IN DROSOPHILA MELANOGASTER

Alternative models of the maintenance of genetic variability, theories of life-history evolution, and theories of sexual selection and mate choice can be tested by measuring additive and nonadditive genetic variances of components of fitness. A quantitative genetic breeding design was used to produce estimates of genetic variances for male life-history traits in Drosophila melanogaster. Additive genetic covariances and correlations between traits were also estimated. Flies from a large, outbred, laboratory population were assayed for age-specific competitive mating ability, age-specific survivorship, body mass, and fertility. Variance-component analysis then allowed the decomposition of phenotypic variation into components associated with additive genetic, nonadditive genetic, and environmental variability. A comparison of dominance and additive components of genetic variation provides little support for an important role for balancing selection in maintaining genetic variance in this suite of traits. The results provide support for the mutation-accumulation theory, but not the antagonistic-pleiotropy theory of senescence. No evidence is found for the positive genetic correlations between mating success and offspring quality or quantity that are predicted by “good genes” models of sexual selection. Additive genetic coefficients of variation for life-history characters are larger than those for body weight. Finally, this set of male life-history characters exhibits a very low correspondence between estimates of genetic and phenotypic correlations.     

AN ANALYSIS OF SELECTIONAL RESPONSE IN RELATION TO A POPULATION BOTTLENECK

Selection for increased morphometric shape (ratio of wing length to thorax width) was compared between control (nonbottlenecked) populations and bottlenecked populations founded with two male–female pairs of flies. Contrary to neutral expectation, selectional response was not reduced in bottlenecked populations, and the mean realized heritabilities and additive genetic variances were higher for the bottlenecked lines than for the nonbottlenecked lines. Additive genetic variances based on these realized heritabilities were consistent with independent estimates of genetic variances based on parent–offspring covariances. Joint scaling tests applied to the crosses between selected lines and their controls revealed significant nonadditive components of genetic variance in the ancestor, which were not detected in the crosses involving bottlenecked lines. The nonbottlenecked lines responded principally by changes in one trait or the other (wing length or thorax width) but not in both, and regardless of which trait responded, larger trait size was dominant and epistatic to smaller size. Stabilizing selection for morphometric shape in the ancestor likely molded the genetic architecture to include nonadditive genetic effects.     

Maternal effects and generation mean analysis of seed-oil content in cotton (Gossypium hirsutum L.)

Summary The nature of gene action and of maternal influence governing cottonseed oil attributes were determined with four lines, two each with high and low seed-oil percentage. For this purpose, P1, P2, F0, F1, F2 and alternative sets of BC1 and BC2 generations were analysed in six cross-combinations and their reciprocals. Marginal extents of heterosis for seed-oil percentage were noticeable in F1, with inbreeding depression in F2. Data from reciprocal backcrosses provided evidence in favour of maternal rather than cytoplasmic effects of seed-oil development. Relatively higher extents of heterosis, sizeable inbreeding depression and reciprocally unequal F2 averages were characteristic of the seed index trait, which often showed a reversal of effects from F1 to F2. Reverse reciprocal backcrosses exhibited some differences, including greater resemblance between the types, (A/B)A and (B/A)A, in addition to variable dose effects in seed index. Thus, the differences between F1 seed index values were not due to cytoplasmic influence. Positive heterotic effects for seed-oil index, especially among the backcrosses, ranged between 16.08% and 47.29% over midparent averages. Genetic component estimates from analysis of similar sets of crosses differing only in reciprocal backcrosses, and also from sets of reciprocal crosses between any two parental combinations, were inconsistent. Scaling tests detected presence of epistasis within and between a majority of cross-combinations. Despite reciprocal differences, additive gene effects for seed-oil percentage were significant in 7 out of 24 crosses, representing high x low, low x high and low x low seed-oil parents. Those were, however, accompanied by significant dominance effects of higher order. In crosses involving low seed-oil percentage parents SA1060 and SA229, all six components were detected significant, with opposite effects of dominance and dominance x dominance epistatic components. Significant additive components were also detected for seed index and seed-oil index in 7 and 5 out of 24 crosses, respectively. In the inheritance of seed index and seed-oil index, dominance effects were more important. Epistatic components of additive x additive, and to a lesser extent, those of dominant x dominant were found significant.     

Gene action for cold tolerance in chickpea

Summary Six crosses were investigated using combining ability and generation mean analyses for reaction to cold tolerance in chickpea (Cicer arietinum L.). The combining ability variances revealed the significance of both additive and nonadditive gene effects, with preponderance of additive gene effects. The generation mean analysis revealed the presence of genie interactions in addition to additive and dominance gene effects. Among the interactions, additive×additive and dominance×dominance with duplicate epistasis were present. Cold tolerance was dominant over susceptibility to cold. Selection for cold tolerance would be more effective if dominance and epistatic effects were reduced after a few generations of selfing.Joint contribution from ICARDA and ICRISAT (International Crops Research Institute for the Semi-Arid Tropics), Patancheru P.O., A.P. 502 324, India. ICRISAT JA No. 1239.     

Estimation of components of genetic variance and heritability for flowering time and yield in gerbera using Derivative-Free Restricted Maximum Likelihood (DFRML)

Summary Additive genetic components of variance and narrow-sense heritabilities were estimated for flowering time (FT) and cut-flower yield (Y) for six generations of the Davis Population of gerbera using Derivative-Free Restricted Maximum Likelihood (DFRML). Additive genetic variance accounted for 54% of the total variability for FT and 30% of the total variability for Y. The heritability of FT (0.54) agreed with previous ANOVA-based estimates. However, the heritability of Y (0.30) was substantially lower than estimates using ANOVA. The advantages of DFRML and its applications in the estimation of components of genetic variance and heritabilities of plant populations are discussed.     

Unraveling Additive from Nonadditive Effects Using Genomic Relationship Matrices

The application of quantitative genetics in plant and animal breeding has largely focused on additive models, which may also capture dominance and epistatic effects. Partitioning genetic variance into its additive and nonadditive components using pedigree-based models (P-genomic best linear unbiased predictor) (P-BLUP) is difficult with most commonly available family structures. However, the availability of dense panels of molecular markers makes possible the use of additive- and dominance-realized genomic relationships for the estimation of variance components and the prediction of genetic values (G-BLUP). We evaluated height data from a multifamily population of the tree species Pinus taeda with a systematic series of models accounting for additive, dominance, and first-order epistatic interactions (additive by additive, dominance by dominance, and additive by dominance), using either pedigree- or marker-based information. We show that, compared with the pedigree, use of realized genomic relationships in marker-based models yields a substantially more precise separation of additive and nonadditive components of genetic variance. We conclude that the marker-based relationship matrices in a model including additive and nonadditive effects performed better, improving breeding value prediction. Moreover, our results suggest that, for tree height in this population, the additive and nonadditive components of genetic variance are similar in magnitude. This novel result improves our current understanding of the genetic control and architecture of a quantitative trait and should be considered when developing breeding strategies.     

Phenotypic plasticity for life-history traits in Drosophila melanogaster. III. Effect of the environment on genetic parameters.

We estimated genetic and environmental variance components for developmental time and dry weight at eclosion in Drosophila melanogaster raised in ten different environments (all combinations of 22, 25 and 28 degrees C and 0.5, 1 and 4% yeast concentration, and 0.25% yeast at 25 degrees C). We used six homozygous lines derived from a natural population for complete diallel crosses in each environment. Additive genetic variances were consistently low for both traits (h2 around 10%). The additive genetic variance of developmental time was larger at lower yeast concentrations, but the heritability did not increase because other components were also larger. The additive genetic effects of the six parental lines changed ranks across environments, suggesting a mechanism for the maintenance of genetic variation in heterogenous environments. The variance due to non-directional dominance was small in most environments. However, there was directional dominance in the form of inbreeding depression for both traits. It was pronounced at high yeast levels and temperatures but disappeared when yeast or temperature were decreased. This meant that the heterozygous flies were more sensitive to environmental differences than homozygous flies. Because dominance effects are not heritable, this suggests that the evolution of plasticity can be constrained when dominance effects are important as a mechanism for plasticity.     

Gene action for adult-plant resistance to powdery mildew in wheat.

Gene action for adult-plant resistance to powdery mildew was studied using generation mean analyses of parents and of F1, F2, and backcross populations derived from a diallel cross of one susceptible and three adult-plant resistant wheat cultivars. Joint scaling tests showed that an additive-dominance model was sufficient to explain the variability in the expression of adult-plant resistance in one cross, while digenic epistasis was involved in the other five crosses. Additive gene effects were predominant; however, dominance was significant in four crosses, additive x additive interaction was significant in three crosses, additive x dominance interaction was significant in three crosses, and dominance x dominance interaction was significant in one cross. Therefore, selection for adult-plant resistance would likely be most effective in advanced generations derived from crosses among the adult-plant resistant cultivars Redcoat, Houser, and Massey.     

Estimates of genetic variance in an F2 maize population

Maize (Zea mays L.) breeders have used several genetic-statistical models to study the inheritance of quantitative traits. These models provide information on the importance of additive, dominance, and epistatic genetic variance for a quantitative trait. Estimates of genetic variances are useful in understanding heterosis and determining the response to selection. The objectives of this study were to estimate additive and dominance genetic variances and the average level of dominance for an F2 population derived from the B73 x Mo17 hybrid and use weighted least squares to determine the importance of digenic epistatic variances relative to additive and dominance variances. Genetic variances were estimated using Design III and weighted least squares analyses. Both analyses determined that dominance variance was more important than additive variance for grain yield. For other traits, additive genetic variance was more important than dominance variance. The average level of dominance suggests either overdominant gene effects were present for grain yield or pseudo-overdominance because of linkage disequilibrium in the F2 population. Epistatic variances generally were not significantly different from zero and therefore were relatively less important than additive and dominance variances. For several traits estimates of additive by additive epistatic variance decreased estimates of additive genetic variance, but generally the decrease in additive genetic variance was not significant.     

Misspecification in Mixed-Model-Based Association Analysis

Additive genetic variance in natural populations is commonly estimated using mixed models, in which the covariance of the genetic effects is modeled by a genetic similarity matrix derived from a dense set of markers. An important but usually implicit assumption is that the presence of any nonadditive genetic effect increases only the residual variance and does not affect estimates of additive genetic variance. Here we show that this is true only for panels of unrelated individuals. In the case that there is genetic relatedness, the combination of population structure and epistatic interactions can lead to inflated estimates of additive genetic variance.     

Improvement of Prediction Ability for Genomic Selection of Dairy Cattle by Including Dominance Effects

Dominance may be an important source of non-additive genetic variance for many traits of dairy cattle. However, nearly all prediction models for dairy cattle have included only additive effects because of the limited number of cows with both genotypes and phenotypes. The role of dominance in the Holstein and Jersey breeds was investigated for eight traits: milk, fat, and protein yields; productive life; daughter pregnancy rate; somatic cell score; fat percent and protein percent. Additive and dominance variance components were estimated and then used to estimate additive and dominance effects of single nucleotide polymorphisms (SNPs). The predictive abilities of three models with both additive and dominance effects and a model with additive effects only were assessed using ten-fold cross-validation. One procedure estimated dominance values, and another estimated dominance deviations; calculation of the dominance relationship matrix was different for the two methods. The third approach enlarged the dataset by including cows with genotype probabilities derived using genotyped ancestors. For yield traits, dominance variance accounted for 5 and 7% of total variance for Holsteins and Jerseys, respectively; using dominance deviations resulted in smaller dominance and larger additive variance estimates. For non-yield traits, dominance variances were very small for both breeds. For yield traits, including additive and dominance effects fit the data better than including only additive effects; average correlations between estimated genetic effects and phenotypes showed that prediction accuracy increased when both effects rather than just additive effects were included. No corresponding gains in prediction ability were found for non-yield traits. Including cows with derived genotype probabilities from genotyped ancestors did not improve prediction accuracy. The largest additive effects were located on chromosome 14 near DGAT1 for yield traits for both breeds; those SNPs also showed the largest dominance effects for fat yield (both breeds) as well as for Holstein milk yield.     

Genetic analysis of crossfostering data with sire and dam records

A method is presented for the analysis of data from crossfostering experiments in which parts of litters are reciprocally interchanged at birth. Observed variances and covariances of differently related individuals are expressed as functions of theoretical causal components of phenotypic variance (additive direct, dominance direct, additive maternal, dominance maternal, direct-maternal covariance, and environmental). Causal components are estimated by weighted least squares analysis of this system of equations, including a ridge-regression procedure to examine consequences of correlation between observed components. Ridge regression suggests that dominance direct genetic variance is generally underestimated, but that narrow-sense heritability estimates are reliable.     

Epistasis and genotype-by-environment interaction of grain protein content in durum wheat

Parental, F(1) , F (2) , BC (1) and BC (2) generations of four crosses involving four cultivars of durum wheat (Triticum durum Desf.) were evaluated at two sites in Tunisia. A three-parameter model was found inadequate for all cases except crosses Chili x Cocorit 71 at site Sidi Thabet and Inrat 69 x Karim at both sites. In most cases a digenic epistatic model was sufficient to explain variation in generation means. Dominance effects (h) and additive x additive epistasis (i) (when significant) were more important than additive (d) effects and other epistatic components. Considering the genotype-by-environment interaction, the non-interactive model (m, d, h, e) was found adequate. Additive variance was higher than environmental variance in three crosses at both sites. The estimated values of narrow-sense heritability were dependent upon the cross and the sites and were 0%-85%. The results indicate that appropriate choice of environment and selection in later generations would increase grain protein content in durum wheat.     

Generation means analysis for productivity in two diverse peanut crosses

Summary Utilization of exotic germplasm resources for population improvement in peanut (Arachis hypogaea L.) has increased as the need to increase genetic diversity among peanut cultivars was recognized. Progeny of crosses of two unadapted germplasm lines (GP-NC 343 and FESR-11-P11-32) with an adapted cultivar (NCV11) of peanut were evaluated for the genetic factors influencing the inheritance of yield and fruit characters in crosses among diverse lines. Objectives were to (1) estimate the relative importance of additive and nonadditive genetic effects in the inheritance of yield and fruit characters in two diverse peanut crosses; (2) determine the proportion of exotic germplasm that gave the optimum combination of mean productivity and genetic variability for each of the crosses; (3) relate the results to theories regarding the transfer of desirable alleles from exotic germplasm into adapted breeding populations. Crosses and backcrosses were made to generate germplasm lines (ten generations) ranging from 0 to 100% exotic germplasm for each cross. The populations were evaluated in replicated field trials. Yield and six fruit characters were measured, and a weighted analysis of variance was conducted to determine if significant differences existed among generations. Generation means analyses were performed for each trait measured in each of the crosses using both three- and six-parameter models, which were tested for goodness-of-fit with a joint-scaling test. Significant differences were detected among generations for most traits measured in both crosses. Estimates of additive genetic effects were significant for pod weight and seed weight in cross 1 (NC-V11 x GP-NC 343) and for all traits in cross 2 (NC-V11 x FESR-11-P11-32) except seedpod ratio. Significant estimates of dominance effects were found for pod length, pod width, and pod weight in cross 1 and for pod length in cross 2. No significant estimates of digenic effects were observed in cross 1, whereas in cross 2 estimates of additive x dominance epistatic effects were significant for yield and pod length, while estimates of additive x additive effects were significant for seed number. Regression of trait means on generations showed a curvilinear response for all traits in cross 1 except seed weight, which gave a linear response. For all traits in cross 2, the relationship between productivity and proportion of unadapted germplasm was effectively linear. Based on generation means and variances, progeny from the first or second backcross generation to the recurrent parent should be expected to give an optimum combination of mean productivity and relative variability in the population.The research reported in this publication was funded in part by the North Carolina Agricultural Research Service