Prediction of the performance of inbred lines derived from a population cross in autumn-sown onions (Allium cepa L.)

Summary A design and model are presented to allow the prediction, in early generations, of the mean and distribution of recombinant inbred lines derived from a cross between two parental populations or partially inbred lines. The procedure has been tested in autumn-sown onions (in the UK) using a wide cross between the openpollinated Japanese cultivar, Senshyu, and a partially inbred line derived from the European cultivar, Rawska. The early generations used for prediction included the first self-pollinated generation of the two parental populations and the F₃ generation produced from the hybrid population. The predictions were tested by reference to the field performance of a random array of inbred lines, which were produced by single-seed descent (SSD) and had been selfed for three generations. The early generations, used for prediction, and a sample of SSD lines were raised alongside each other in each of two seasons. Within each season, good agreement was found between the predicted and observed performance of the recombinant inbred lines for three characters — yield, quality and maturity. This is used as evidence of the validity of the genetical model and the assumptions made. The effects of genotype x environment interactions prevented predictions made in one season being reliably applied to those made in the other and, therefore, reduce the attraction of this type of prediction study to the plant breeder.     

Heterosis for biomass-related traits in Arabidopsis investigated by quantitative trait loci analysis of the triple testcross design with recombinant inbred lines

Arabidopsis thaliana has emerged as a leading model species in plant genetics and functional genomics including research on the genetic causes of heterosis. We applied a triple testcross (TTC) design and a novel biometrical approach to identify and characterize quantitative trait loci (QTL) for heterosis of five biomass-related traits by (i) estimating the number, genomic positions, and genetic effects of heterotic QTL, (ii) characterizing their mode of gene action, and (iii) testing for presence of epistatic effects by a genomewide scan and marker x marker interactions. In total, 234 recombinant inbred lines (RILs) of Arabidopsis hybrid C24 x Col-0 were crossed to both parental lines and their F1 and analyzed with 110 single-nucleotide polymorphism (SNP) markers. QTL analyses were conducted using linear transformations Z1, Z2, and Z3 calculated from the adjusted entry means of TTC progenies. With Z1, we detected 12 QTL displaying augmented additive effects. With Z2, we mapped six QTL for augmented dominance effects. A one-dimensional genome scan with Z3 revealed two genomic regions with significantly negative dominance x additive epistatic effects. Two-way analyses of variance between marker pairs revealed nine digenic epistatic interactions: six reflecting dominance x dominance effects with variable sign and three reflecting additive x additive effects with positive sign. We conclude that heterosis for biomass-related traits in Arabidopsis has a polygenic basis with overdominance and/or epistasis being presumably the main types of gene action.     

The role of epistasis in the manifestation of heterosis: a systems-oriented approach

Heterosis is widely used in breeding, but the genetic basis of this biological phenomenon has not been elucidated. We postulate that additive and dominance genetic effects as well as two-locus interactions estimated in classical QTL analyses are not sufficient for quantifying the contributions of QTL to heterosis. A general theoretical framework for determining the contributions of different types of genetic effects to heterosis was developed. Additive x additive epistatic interactions of individual loci with the entire genetic background were identified as a major component of midparent heterosis. On the basis of these findings we defined a new type of heterotic effect denoted as augmented dominance effect di* that comprises the dominance effect at each QTL minus half the sum of additive x additive interactions with all other QTL. We demonstrate that genotypic expectations of QTL effects obtained from analyses with the design III using testcrosses of recombinant inbred lines and composite-interval mapping precisely equal genotypic expectations of midparent heterosis, thus identifying genomic regions relevant for expression of heterosis. The theory for QTL mapping of multiple traits is extended to the simultaneous mapping of newly defined genetic effects to improve the power of QTL detection and distinguish between dominance and overdominance.     

Genetic basis of heterosis for growth-related traits in Arabidopsis investigated by testcross progenies of near-isogenic lines reveals a significant role of epistasis

Epistasis seems to play a significant role in the manifestation of heterosis. However, the power of detecting epistatic interactions among quantitative trait loci (QTL) in segregating populations is low. We studied heterosis in Arabidopsis thaliana hybrid C24 x Col-0 by testing near-isogenic lines (NILs) and their triple testcross (TTC) progenies. Our objectives were to (i) provide the theoretical basis for estimating different types of genetic effects with this experimental design, (ii) determine the extent of heterosis for seven growth-related traits, (iii) map the underlying QTL, and (iv) determine their gene action. Two substitution libraries, each consisting of 28 NILs and covering approximately 61 and 39% of the Arabidopsis genome, were assayed by 110 single-nucleotide polymorphism (SNP) markers. With our novel generation means approach 38 QTL were detected, many of which confirmed heterotic QTL detected previously in the same cross with TTC progenies of recombinant inbred lines. Furthermore, many of the QTL were common for different traits and in common with the 58 QTL detected by a method that compares triplets consisting of a NIL, its recurrent parent, and their F(1) cross. While the latter approach revealed mostly (75%) overdominant QTL, the former approach allowed separation of dominance and epistasis by analyzing all materials simultaneously and yielded substantial positive additive x additive effects besides directional dominance. Positive epistatic effects reduced heterosis for growth-related traits in our materials.     

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.     

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.     

Measurement and Selection of Parasitoid Quality for Mass-Reared Trichogramma minutum Riley Used in Inundative Release

Parasitoid quality, subject to both genetic and environmental influences, is critical to the success of any biological control program, however, its measurement and improvement is poorly understood. In this study, a classic genetic approach is taken to develop two indices, namely a character index and a fitness index, for the measurement and selection of high quality parasitoids used in inundative release. Six life-history traits and corresponding fitness components in 33 inbred strains of Trichogramma minutum were used to generate both genotypic and phenotypic variance-covariance matrices that then allowed for the construction of the indices. Most traits and their fitness components were positively correlated, both phenotypically and genotypically, with lifetime fecundity and the number of female offspring appearing to have an important influence. Selection of the top three strains showed that parasitoid quality could be improved by 36% using the character index and possibly up to 150% using the fitness index. The two indices were linearly correlated suggesting that either could be used to measure quality. The character index is recommended because it requires information on only three life-history traits (fecundity, number of female offspring, and number of male offspring) and has highly correlated responses of fitness components. Our work demonstrates that the best quality T. minutum will be obtained by using the character index to select for inbred strains which have high fecundity and number of female offspring.     

Analysis of genetic control of mating behavior in screwworm (Diptera: Calliphoridae) males through diallel crosses and artificial selection

Summary The mode of genetic control of male screw-worm (Diptera: Calliphoridae) mating behavior was examined using diallel cross and artificial selection. Diallel crosses showed strong dominance effects, with hybrids being uniformly more successful in copulation than their more inbred parental strains. Weaker additive and reciprocal effects were also noted. Environmental (replicate) effects were highly significant. Regression of array variances and covariances indicated that epistatic interactions or unequal allele distribution during gametogenesis may have occurred and that high courtship propensity polygenes show dominance over low propensity genes. Artificial selection on males from outbred strains from Guatemala and Belize resulted in a decreased number of mating attempts for lines selected for reduced activity, but mating attempts in lines selected for high mating activity did not increase. A combination of inbreeding during the selection cycles as well as selection for recessive traits would explain this response. The two types of experiments were in general agreement, indicating significant dominance and environmental influence on male mating behavior with weaker additive and possible maternal effects.     

Quantitative trait loci for life span in Drosophila melanogaster: interactions with genetic background and larval density

The genetic architecture of variation in adult life span was examined for a population of recombinant inbred lines, each of which had been crossed to both inbred parental strains from which the lines were derived, after emergence from both high and low larval density. QTL affecting life span were mapped within each sex and larval density treatment by linkage to highly polymorphic roo-transposable element markers, using a composite interval mapping method. We detected a total of six QTL affecting life span; the additive effects and degrees of dominance for all were highly sex- and larval environment-specific. There were significant epistatic interactions between five of the life span QTL, the effects of which also differed according to genetic background, sex, and larval density. Five additional QTL were identified that contributed to differences among lines in their sensitivity to variation in larval density. Further fine-scale mapping is necessary to determine whether candidate genes within the regions to which the QTL map are actually responsible for the observed variation in life span.     

The response of recombinant inbred strains of mice to bacterial lipopolysaccharides.

Fourteen recombinant inbred strains of mice have been produced by the inbreeding of the F2 generation of a cross between C57BL/6J and C3H/HeJ progenitor mice. The responses of these BXH strains to bacterial lipopolysaccharides (LPS) have been characterized. Four BXH strains are high LPS responders and nine strains are low LPS responders. One BXH strain shows intermediate responsiveness which may reflect residual heterozygosity. F1 hybrid mice from low x high responder strains were intermediate in their response to LPS suggesting additive genetic control. The LPS responses in backcross mice from the F1 x low LPS responders showed segregation consistent with LPS responsiveness being determined by a single gene. In 13/14 BXH strains, there was concordant inheritance of LPS responsiveness and the major urinary protein locus Mup-1b. The association of the expression of the Mup-1 alleles with LPS responsiveness in the BXH strains suggests that the defective LPS response gene in C3H/HeJ mice is located on chromosome 4.     

The evolution of age-specific mortality rates in Drosophila melanogaster: genetic divergence among unselected lines.

Age-specific effects of spontaneous mutations on mortality rates in Drosophila are inferred from three large demographic experiments. Data were collected from inbred lines that were allowed to accumulate spontaneous mutations for 10, 19, and 47 generations. Estimates of age-specific mutational variance for mortality were based on data from all three experiments, totalling approximately 225,000 flies, using a model developed for genetic analysis of age-dependent traits (the character process model). Both within- and among-generation analyses suggest that the input of genetic variance is greater for early life mortality rates than for mortality at older ages. In females, age-specific mutational variances ranged over an order of magnitude from 5.96 x 10(-3) at 2 wk posteclosion to 0.02 x 10(-3) at 7 wk. The male data show a similar pattern. Age-specific genetic variances were substantially less at generation 47 than at generation 19-an unexplained observation that is likely due to block effects. Mutational correlations among mortality rates at different ages tend to increase with the accumulation of new mutations. Comparison of the mutation-accumulation lines at generations 19 and 47 with their respective control lines suggests little age-specific mutational bias.     

The evolution of genetic architecture. I. Diversification of genetic backgrounds by genetic drift

The genetic architecture of a phenotype plays a critical role in determining phenotypic evolution through its effects on patterns of genetic variation. Genetic architecture is often considered to be constant in evolutionary quantitative genetic models. However, genetic architecture may be variable and itself evolve when there are dominance and epistatic interactions among alleles at the same and different loci, respectively. The evolution of genetic architecture by genetic drift is examined here by testing the breeding value of four standard inbred mouse strains mated across a set of 26 related recombinant quasi-inbred (RqI) lines generated from the intercross of the Large (LG/J) and Small (SM/J) inbred mouse strains. Phenotypes of interest include age-specific body weights, growth, and adult body composition. If the genetic architecture of these traits has differentiated by genetic drift during the production of the RqI strains, we should observe interactions between tester strain and RqI strain. The breeding values of the tester strains will change relative to one another depending on which RqI strain they are crossed to. The study included an average of 15.1 offspring per cross, over a total of 100 different crosses. Multivariate and univariate analyses of variance indicate that there is strongly significant interaction for all traits. Interaction is more pronounced in males than in females and accounted for an average of about 40% of the explained variation in males and 30% in females. These results indicate that the genetic architecture of these traits has differentiated by genetic drift in the RqI strains since their isolation from a common founder population. Further analysis indicates that this differentiation results in changes in the order of tester strain effects so that common patterns of selection in these differentiated populations could result in the fixation of different alleles.     

Factors Influencing Fitness in Chromosomal Strains in DROSOPHILA SUBOBSCURA

Chromosomal polymorphism can be maintained by means of genic dominance, genic overdominance, recombination effects and karyotype selection. Experiments were carried out which allow us to distinguish among these factors as they effect egg hatch and larva-to-adult survival in D. subobscura. A strong karotype selection was observed. A small but highly significant recombination effect was also observed despite the fact that the material used in the experiment consisted of inbred, related strains and was therefore less likely to show such an effect than strains randomly chosen from a population. On the other hand, these strains, being inbred, were more likely to show genic dominance or genic overdominance than randomly picked samples. However neither genic dominance nor genic overdominance was detected.     

Genetic differences in the frequency of acetazolamide-induced ectrodactyly in the mouse exhibit directional dominance of relative embryonic resistance

Eleven of the common inbred strains of the mouse were surveyed for their teratogenic response to acetazolamide that was administered three times per os at 1,000 mg/kg (9 A.M. and 4 P.M. on day 9 and 9 A.M. on day 10). The products of conception were examined for gross malformations on day 15. One strain, SJL/J, exhibited maternal toxicity to the dosage regime and was excluded from the survey. Five strains exhibited significantly increased resorption rates after treatment. All strains responded with the expected malformation of postaxial forelimb ectrodactyly with a right-sided predominance. Nine of the strains could be assigned to one of four mutually exclusive classes of frequency of ectrodactyly and the tenth strain (BALB/cByJ) showed overlap between the two intermediate classes. The data suggest major genes determine the difference in sensitivity to ectrodactyly rather than a polygenic mode of inheritance. Induced cleft lip was found in four strains and one of these strains, SWR/J, exhibited a significantly higher frequency. The strain differences in sensitivity to induced resorption, forelimb ectrodactyly, and cleft lip were genetically independent. A reciprocal cross study was conducted with five of the strains from the four classes of frequency of ectrodactyly response in order to determine gene action. A significant maternal effect on the ectrodactyly response was found only with one of the strain pairs in the ten sets of reciprocal crosses with the five strains. When there was a significant difference between two strains, the F1 embryos exhibited dominance of relative resistance to ectrodactyly. The directional dominance of relative resistance to acetazolamide-induced ectrodactyly suggests that regulatory genes control the embryonic differences in frequency of ectrodactyly response to acetazolamide. By analogy with other metric traits of development that exhibit directional dominance, the genetic variation in ectrodactyly response that has been observed so far in the mouse embryo may not be involved with the primary target of acetazolamide teratogenesis.     

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.     

Quantitative trait loci for body weight, blood pressure, blood glucose, and serum lipids: linkage analysis with wild rats (Rattus norvegicus).

To study polygenetically inherited human diseases like hypertension, inbred rat strains are usually the preferred models. Because many inbred generations under optimized environmental conditions may have led to the survival of "silent" disease genes, we used a cross between one wild rat and genetically hypertensive SHR rats to analyze quantitative trait loci (QTLs) of blood pressure and related traits. The (Wild x SHR)F1 hybrids were transferred into a pathogen-free environment by wet-hysterectomy and were backcrossed onto SHR to generate first backcross hybrids (BC1). Progeny from one F1 female (n = 72) were phenotypically and genetically characterized to map QTLs. Significant, subsignificant, and suggestive evidence was found for more sex-specific than common linkage of blood pressure and most blood-pressure-related traits. Male- and female-specific regions were determined on different chromosomes for blood pressures (Chrs. 2 and 7 vs 5 and 11), body weight (Chrs. 10 vs 18), and blood glucose (Chr. 17 vs 20). A linkage in both males and females was shown for serum triglycerides on chromosomes 6 and 17, respectively, and blood glucose on chromosome 15. For serum total cholesterol, a significant linkage was found on chromosome 14 only in males. Our findings not only indicate the complex character of quantitative traits per se but also show impressively their dependence on sex, age, and strains in cosegregation analysis.     

Genetic analysis of susceptibility to isoniazid-induced seizures in mice

Four sets of recombinant inbred lines of mice have been used to analyze genetic differences in acute toxicity of the drug, isonicotinic acid hydrazide. Standard inbred strains, their F₁ hybrids and recombinant inbred strains were all challenged with a single dose of the drug. The percent mortality of the different groups was analyzed to estimate heritability and the number of genes affecting resistance. The data indicated that resistance factors were dominant, heritability was moderate (.25-.37), and more than one gene was involved in each of four different sets of recombinant inbred lines. Possible approaches for identifying and mapping individual genes affecting resistance are discussed.     

Quantitative trait loci determining weight reduction of testes and pituitary by diethylstilbesterol in LEXF and FXLE recombinant inbred strain rats.

Increasing exposure to environmental endocrine disruptor, xeno-estrogen, is a serious hazard to male reproductive activity. To explore possible genetic control in susceptibility to xeno-estrogen, the weight reduction of testes induced by the continuous administration of a synthetic estrogen, diethylstilbesterol, were investigated by quantitative trait analysis in LEXF and FXLE recombinant inbred strain rats, consisting of 21 independent strains, 9 of their substrains, parental F344/Stm and LE/Stm strains, and (F344 x LE)F1. For the weight of testes, one highly significant quantitative trait locus (QTL) and one significant QTL were mapped on chromosomes 7 and 1, respectively. The QTL on chromosome 7 is closely associated with c-myc. Pituitary weight and serum prolactin were also variable among recombinant inbred strains, but no QTL was detected for them in this study.     

The decline in fitness with inbreeding: evidence for negative dominance‐by‐dominance epistasis in Drosophila melanogaster

Genetic interactions can play an important role in the evolution of reproductive strategies. In particular, negative dominance‐by‐dominance epistasis for fitness can theoretically favour sex and recombination. This form of epistasis can be detected statistically because it generates nonlinearity in the relationship between fitness and inbreeding coefficient. Measures of fitness in progressively inbred lines tend to show limited evidence for epistasis. However, tests of this kind can be biased against detecting an accelerating decline due to line losses at higher inbreeding levels. We tested for dominance‐by‐dominance epistasis in Drosophila melanogaster by examining viability at five inbreeding levels that were generated simultaneously, avoiding the bias against detecting nonlinearity that has affected previous studies. We find an accelerating rate of fitness decline with inbreeding, indicating that dominance‐by‐dominance epistasis is negative on average, which should favour sex and recombination.