The consequences of using inadequate testers in the simplified triple test-cross.

The genetical consequences of common alleles in the L1 and L2 testers of a simplified version of the triple test-cross which is applicable to populations of inbred lines are examined. The test for epistasis under these circumstances becomes ambiguous and can spuriously detect non-allelic interactions when they may not exist although it still provides a test for epistasis and the adequacy of the testers simultaneously. The tests of significance and the estimates of additive variation are biased to an extent related to the dominance and dominance x additive effects of the common loci while the significance and estimates of dominance variation are deflated because they reflect the dominance effects at the non-common loci only. The covariance of sums and differences is also underestimated for the same reasons. These expectations are illustrated by analysing the 190 simplified triple test-crosses that could be extracted from a 20 x 20 diallel set of crosses between pure-breeding lines of Nicotiana rustica.     

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.     

The genetical basis of hybrid vigour in a highly heterotic cross of Nicotiana tabacum

The genetical control of F₁ heterosis, observed in a cross of desirable Nicotiana tabacum varieties, was investigated by analysing the data of the basic generations, triple test cross-families and random samples of doubled haploids (DH) and single-seed descent (SSD) lines. Analyses of the first-degree statistics revealed a complex control underlying the genetic variation, including the presence of epistasis, linkage, maternal effects and their interactions, in addition to the additive and dominance effects of the genes segregating in the cross. These analyses identified gene dispersion, directional dominance, and duplicate epistasis, as the main causes of heterosis. The triple test-cross analysis also confirmed the presence of non-allelic interactions and indicated that the dominance ratio, although inflated by epistasis, is consistently partial for all the traits. The extent of transgression in the recombinant inbred lines finally established unequivocally that, as in numerous other crosses, gene dispersion and unidirectional, but partial, dominance are the true causes of heterosis in this cross too.     

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.     

Epistasis between calpain 1 and its inhibitor calpastatin within breeds of cattle

The calpain gene family and its inhibitors have diverse effects, many related to protein turnover, which appear to affect a range of phenotypes such as diabetes, exercise-induced muscle injury, and pathological events associated with degenerative neural diseases in humans, fertility, longevity, and postmortem effects on meat tenderness in livestock species. The calpains are inhibited by calpastatin, which binds directly to calpain. Here we report the direct measurement of epistatic interactions of causative mutations for quantitative trait loci (QTL) at calpain 1 (CAPN1), located on chromosome 29, with causative mutations for QTL variation at calpastatin (CAST), located on chromosome 7, in cattle. First we identified potential causative mutations at CAST and then genotyped these along with putative causative mutations at CAPN1 in >1500 cattle of seven breeds. The maximum allele substitution effect on the phenotype of the CAPN1:c.947G>C single nucleotide polymorphism (SNP) was 0.14 sigma(p) (P = 0.0003) and of the CAST:c.155C>T SNP was also 0.14 sigma(p) (P = 0.0011) when measured across breeds. We found significant epistasis between SNPs at CAPN1 and CAST in both taurine and zebu derived breeds. There were more additive x dominance components of epistasis than additive x additive and dominance x dominance components combined. A minority of breed comparisons did not show epistasis, suggesting that genetic variation at other genes may influence the degree of epistasis found in this system.     

The genetic architecture of male colour differences between a sympatric Lake Malawi cichlid species pair

The genetic basis of traits involved in reproductive isolation is a key parameter in models of sympatric speciation by sexual selection, a potential mechanism driving the explosive radiation of East African cichlids. Analysis of hybrid crosses between two sympatric Lake Malawi cichlid species, representing the extremes of the extant colour distribution, generated Castle-Wright estimates of four to seven loci controlling colour differences. Segregation patterns deviated from a purely additive model with a significant contribution from dominance, and possibly also epistasis. Evidence was found for a strong influence of autosomal loci. As departures from simple additive variation could effect the operation of models of sympatric speciation, dominance and epistasis should not be neglected.     

Nature and type of gene action governing resistance to Helminthosporium turcicum leaf blight in maize (Zea mays L.)

Six generations, consisting of three resistant parents, three susceptible parents, their 15 possible F₁ crosses, 15 F₂'s, 15 BC₁'s (F₁ x resistant female parent) and 15 BC₂'s (F₁ x susceptible male parent) were analysed following Hayman (Heredity 12: 371–390, 1958) to evaluate the nature and type of gene action governing resistance to H. turcicum. The results showed that all types of gene effects, viz., additive, dominance and epistasis (i.e., additive x additive, additive x dominance and dominance x dominance) were operating in one cross or the other in controlling resistance. However, it was additive gene action and dominance x dominance type of epistasis with duplicate nature that were important in controlling resistance in most crosses. Depending upon the final objectives, one of the breeding methods, viz., recurrent selection, heterosis breeding, back-cross method or full-sib selection (bi-parental mating) may be followed.     

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     

Self-fertilization and the evolution of recombination

In this article, we study the effect of self-fertilization on the evolution of a modifier allele that alters the recombination rate between two selected loci. We consider two different life cycles: under gametophytic selfing, a given proportion of fertilizations involves gametes produced by the same haploid individual, while under sporophytic selfing, a proportion of fertilizations involves gametes produced by the same diploid individual. Under both life cycles, we derive approximations for the change in frequency of the recombination modifier when selection is weak relative to recombination, so that the population reaches a state of quasi-linkage equilibrium. We find that gametophytic selfing increases the range of epistasis under which increased recombination is favored; however, this effect is substantial only for high selfing rates. Moreover, gametophytic selfing affects the relative influence of different components of epistasis (additive x additive, additive x dominance, dominance x dominance) on the evolution of the modifier. Sporophytic selfing has much stronger effects: even a small selfing rate greatly increases the parameter range under which recombination is favored, when there is negative dominance x dominance epistasis. This effect is due to the fact that selfing generates a correlation in homozygosity at linked loci, which is reduced by recombination.     

THE GENETIC ARCHITECTURE OF WING SIZE DIVERGENCE AT VARYING SPATIAL SCALES ALONG A BODY SIZE CLINE IN DROSOPHILA MELANOGASTER

Latitudinal clines in quantitative traits are common, but surprisingly little is known about the genetic bases of these divergences and how they vary within and between clines. Here, we use line‐cross analysis to investigate the genetic architecture of wing size divergences at varying spatial scales along a body size cline in Drosophila melanogaster. Our results revealed that divergences in wing size along the cline were due to strong additive effects. Significant nonadditive genetic effects, including epistasis and maternal effects, were also detected, but they were relatively minor in comparison to the additive effects and none were common to all crosses. There was no evidence of increased epistasis in crosses between more geographically distant populations and, unlike in previous studies, we found no significant dominance effects on wing size in any cross. Our results suggest there is little variation in the genetic control of wing size along the length of the Australian cline. They also highlight marked inconsistencies in the magnitude of dominance effects across studies, which may reflect different opportunities for mutation accumulation while lines are in laboratory culture.     

The change in quantitative genetic variation with inbreeding

Inbreeding is known to reduce heterozygosity of neutral genetic markers, but its impact on quantitative genetic variation is debated. Theory predicts a linear decline in additive genetic variance (V(A)) with increasing inbreeding coefficient (F) when loci underlying the trait act additively, but a nonlinear hump-shaped relationship when dominance and epistasis are important. Predictions for heritability (h2) are similar, although the exact shape depends on the value of h2 in the absence of inbreeding. We located 22 published studies in which the level of genetic variation in experimentally inbred populations (measured by V(A) or h2) was compared with that in outbred control populations. For life-history traits, the data strongly supported a nonlinear change in genetic variation with increasing F. V(A) and h2 were, respectively, 244% and 50% higher at F = 0.4 than in outbred populations, and dominance plus epistatic variance together exceeded additive variance by a factor of four. For nonfitness traits the decline was linear and estimates of nonadditive variance were small. These results confirm that population bottlenecks frequently increase V(A) in some traits, and imply that life-history traits are underlain by substantial dominance or epistasis. However, the importance of drift-induced genetic variation in conservation or evolutionary biology is questionable, in part because inbreeding depression usually accompanies inbreeding.     

Genetic basis of variation of yield, and yield components in mungbean (Vigna radiata (L.) Wilczek)

Additive, dominance, and epistasis genetic basis of seed yield per plant, number of pods per plant, number of seeds per pod, and 1000 seed weight in mungbean (Vigna radiata (L.) Wilczek) have been examined, using Triple Test Cross (TTC) analysis. The material for TTC test was evaluated in two seasons i.e., kharif (July-October) and spring/summer (March-June), at the research station of the Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan. Epistasis was present significantly for number of pods per plant and number of seeds per pod when grown in the spring/summer season (March to June). Partition of epistasis showed that additive x additive ('i' type) interaction was an important component of number of pods per plant, and number of seeds per pod was found to be of both types 'i' type, and additive x dominance, and dominance x dominance ('j' and 'l' type) interactions. This indicated that epistasis might be a non-trivial factor in the inheritance of pods per plant, and seeds per pod in mungbean. The expression of epistasis was influenced differentially by particular genotypes, indicating that a limited number of genotypes may not be sufficient to detect non-allelic interactions for a trait in mungbean. Additive and dominance genetic components were significant for all four traits in kharif season (July to October) but only for seed yield and 1000 seed weight in spring/summer season. This suggests that the genes controlling seed yield per plant, and 1000 seed weight are equally sensitive to the environment. The predominance additive gene action in those traits is not significantly influenced by epistasis, suggesting that improvement of the traits can be achieved through standard selection procedures.     

云南香型软米水稻资源农艺性状遗传效应研究

选取5份云南地方香型软米水稻种质资源和6份自育香型软米保持系按5×6不完全双列杂交设计(NCⅡ)配制成30个组合,采用加性-显性-上位性遗传模型,分析云南香型软米11个农艺性状的遗传效应。结果表明,云南香型软米多数农艺性状的遗传主要受加×加上位性效应、加性×环境效应、显性×环境效应的影响,还存在不同程度的加性效应和显性效应,单株产量受基因加性效应、显性效应、加×加上位性效应、加性×环境效应、显性×环境效应的影响;株高、有效穗的遗传率以普通狭义遗传率为主,其他性状的普通狭义遗传率和互作狭义遗传率均达极显著水平;产量构成性状之间存在不同类型和不同程度的遗传相关,多数性状之间以加×加上位性、加性×环境和显性×环境互作效应显著。     

A general approach for the study of a population of testcross progenies and consequences for recurrent selection

Summary A model to study genetic effects at the level of a population of testcross progenies is presented. As there is no dominance for the testcross value, with the restriction of epistasis to pairs of loci, only additive x additive epistasis can contribute to the variance among progenies. To estimate the variance among progenies due to epistasis, it is necessary to have the population structured in families of full sibs, half sibs or S₁, with only a few plants per family tested in combination with the tester. Using a two-way mating design to produce the families, it is possible to estimate the variance due to additive x additive epistasis. The consequence of the presence of epistasis is studied at the level of recurrent selection for combining ability with the tester. It seems that epistasis itself does not change the efficiency of the breeding methods considered. However, when the population from intercrossing is structured in families, it could be efficient to use a combined selection when the heritability is very low. In this case it would be efficient to produce full-sib families (by single-pair matings) at the level of intercrossing. The best procedure is to produce such families at the same time as crossing with the tester. In comparison to the classical scheme of selection for combining ability with a tester, such a modification increases the efficiency of selection 41.1% if an off-season generation can be used.     

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.     

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.     

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.     

Epistasis and the temporal change in the additive variance-covariance matrix induced by drift

The effect of population bottlenecks on the components of the genetic covariance generated by two neutral independent epistatic loci has been studied theoretically (additive, covA; dominance, covD; additive-by-additive, covAA; additive-by-dominance, covAD; and dominance-by-dominance, covDD). The additive-by-additive model and a more general model covering all possible types of marginal gene action at the single-locus level (additive/dominance epistatic model) were considered. The covariance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium over replicates randomly derived from the base population, after t consecutive bottlenecks of equal size N (derived components). Formulae were obtained in terms of the allele frequencies and effects at each locus, the corresponding epistatic effects and the inbreeding coefficient Ft. These expressions show that the contribution of nonadditive loci to the derived additive covariance (covAt) does not linearly decrease with inbreeding, as in the pure additive case, and may initially increase or even change sign in specific situations. Numerical examples were also analyzed, restricted for simplicity to the case of all covariance components being positive. For additive-by-additive epistasis, the condition covAt > covA only holds for high frequencies of the allele decreasing the metric traits at each locus (negative allele) if epistasis is weak, or for intermediate allele frequencies if it is strong. For the additive/dominance epistatic model, however, covAt > covA applies for low frequencies of the negative alleles at one or both loci and mild epistasis, but this result can be progressively extended to intermediate frequencies as epistasis becomes stronger. Without epistasis the same qualitative results were found, indicating that marginal dominance induced by epistasis can be considered as the primary cause of an increase of the additive covariance after bottlenecks. For all models, the magnitude of the ratio covAt/covA was inversely related to N and t.     

Genomic prediction of hybrid crops allows disentangling dominance and epistasis

We revisited, in a genomic context, the theory of hybrid genetic evaluation models of hybrid crosses of pure lines, as the current practice is largely based on infinitesimal model assumptions. Expressions for covariances between hybrids due to additive substitution effects and dominance and epistatic deviations were analytically derived. Using dense markers in a GBLUP analysis, it is possible to split specific combining ability into dominance and across-groups epistatic deviations, and to split general combining ability (GCA) into within-line additive effects and within-line additive by additive (and higher order) epistatic deviations. We analyzed a publicly available maize data set of Dent × Flint hybrids using our new model (called GCA-model) up to additive by additive epistasis. To model higher order interactions within GCAs, we also fitted “residual genetic” line effects. Our new GCA-model was compared with another genomic model which assumes a uniquely defined effect of genes across origins. Most variation in hybrids is accounted by GCA. Variances due to dominance and epistasis have similar magnitudes. Models based on defining effects either differently or identically across heterotic groups resulted in similar predictive abilities for hybrids. The currently used model inflates the estimated additive genetic variance. This is not important for hybrid predictions but has consequences for the breeding scheme—e.g. overestimation of the genetic gain within heterotic group. Therefore, we recommend using GCA-model, which is appropriate for genomic prediction and variance component estimation in hybrid crops using genomic data, and whose results can be practically interpreted and used for breeding purposes.     

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.