Analysis of Diallel Table for Experiments in Block Designs

In this paper the analysis of genotypes obtained in diallel crossing system, including parents, one set of F₁s and reciprocal F₁'s, is given. This analysis is presented for data obtained from the experiments laid out in block designs. The analysis of variance, estimator of reciprocal effects, estimators of general and specific combining abilities as well as statistics for testing of hypotheses concerning those parameters are given.     

Analysis of Triangular Diallel Table for Experiments in Block Designs

In this paper the analysis of genotypes obtained in diallel crossing system, including one set of F₁′s and parents, arranged in triangular table is given. This analysis is presented for data obtained from the experiments laid out in block designs. The analysis of variance, estimators of general and specific combining abilities as well as statistics for testing of hypotheses concerning those parameters are given.     

Some Theoretical Aspects of Analysis in Half Diallel

The analysis of F₁ and F₂ half diallel has been discussed as compared to full diallel without reciprocal effects given by MATHER and JINKS (1971). In practice, mostly the half diallel (one-way) crosses are prepared and erroreously analysed using the least square estimates of full diallel without reciprocal effects. The H₁ and H₂, however, appeared to be over estimated when full diallel without reciprocal effects estimates were used in place of those of half diallel. Least square estimates were also obtained assuming heterogeneity of error components between parents and F₁/F₂ families.     

Combining ability for resistance in peanut (Arachis hypogaea) to Peanut bud necrosis tospovirus (PBNV)

The combining abilities of field resistance to peanut bud necrosis disease (PBND) caused by Peanut bud necrosis tospovirus (PBNV) were examined to understand the type of gene action governing resistance to the disease, and to identify peanut lines suitable for use as parents in a PBND‐resistance breeding programme. The Ft and F2 progenies from a six‐parent diallel cross and their parents were evaluated under field conditions. They were assessed for disease incidence at 30, 40, 50 and 60 days after planting (DAP), and reactions of the lines to the disease could be best differentiated at 50 and 60 DAP. Results indicated highly significant general combining ability (GCA) effects for PBND incidence in F₁ and F₂ generations. Specific combining ability (SCA) and reciprocal effects were also found to be significant, but their relative contributions to variation among crosses were much less than those of GCA effects. These results suggested that the type of gene action governing resistance to PBND was mainly additive, and selection for PBND resistance in these populations should be effective. Strong correlation coefficients between parental means and GCA effects for disease incidence were seen in both Ft and F2 generations, suggesting that per se performance of the parental line could be used as a predictor of the capability of the line to transmit its PBND‐resistant attribute to progenies. The reciprocal effects were in favour of using resistant lines as female parents. The peanut lines ICGV 86388, 1C 10 and 1C 34 were found to be suitable for use in a PBND–resistance breeding programme.     

Genetic analysis of plant regeneration in rice (Oryza sativa L.)

Summary A diallel study involving reciprocal crosses of four genotypes (IR8, 36, 54, and 64) was carried out to understand the genetic mechanism of plant regeneration from immature embryo-calli in rice. Regeneration frequency (% of calli that produced plants) varied from a high of 86% for IR54 to a low of 0% for IR36, while regenerated plants per embryo numbered from 0 to 7 when these same IR lines and the F₁ hybrids were compared. Combining ability analysis revealed that both nuclear (with both additive and dominant effects) and cytoplasmic genes are important in controlling regeneration in rice. Parental lines and F1 hybrids with high ability to regenerate were identified.     

Reciprocal effects in anther cultures of wheat hybrids

This study was conducted to determine the reciprocal effects for anther culture response in wheat (Triticum aestivum L.) using a set of 4 × 4 full diallel crosses. Both reciprocal and nuclear genetic effects were highly significant for anther culture response and useful for selection and breeding purposes. General combining ability (GCA) effects were predominant for all investigated anther culture traits. Also, significant differences for specific combining ability (SCA) effects were detected between reciprocal crosses. Although significant reciprocal differences for responding anther, callus number and green plant regeneration were recorded in some reciprocal crosses, there were no significant reciprocal differences for albino plant regeneration. The use of one parent as male or female could lead to change at the production of green plants from the F₁ hybrids and screening of inbred lines for response to anther culture, without reciprocal effects, could decrease the utilization of breeding material.     

The Analysis of Partial Diallel Crosses

The analysis of offsprings from the partial diallel crosses is presented. In considered type of crossing, p parental forms into H separate groups are devided. Single crosses among parental forms, from separate groups only, are performed. The analysis for experiments laid out in efficiency balanced block designs is given.     

REPRODUCTIVE CHARACTERISTICS OF THE FLOWER BREEDING DROSOPHILA HIBISCI BOCK (DROSOPHILIDAE) IN EASTERN AUSTRALIA: GENETIC AND ENVIRONMENTAL DETERMINANTS OF OVARIOLE NUMBER

Quantitative genetic analysis of the ovariole number of the Australian Hibiscus flower-breeding Drosophila hibisci Bock was conducted on populations from two localities along a latitudinal cline in ovariole number previously observed in the species (Starmer et al., in press). Parental strains, F₁, F_1r (reciprocal), F₂, backcross, and backcross reciprocal generations were used in a line-cross (generation means) analysis. This analysis revealed both additive and epistatic effects as important determinants of variation in ovariole number when larvae were reared at 25°C. Maternal effects and maternal-by-progeny genetic interactions were not significant. These results are comparable to previous studies that document epistatic components as genetic determinants of ovariole number in D. melanogaster. Parallel studies on ovariole number in D. hibisci parental and hybrid generations (F₁ and F_1r) reared as larvae at three temperatures (18°, 21.5°, and 25°C) showed environmental effects and genotype-by-environment interactions as significant influences on the phenotype. Maternal effects were present when temperature of larval development was considered and significant, nonlinear environmental effects were detected. Field collections of D. hibisci females showed that field conditions result in significant departure of ovariole number from comparable laboratory reared females. The significant epistatic genetic effects, genotype-by-environment interactions, and maternal effects indicate that the genetic architecture of traits, such as ovariole number, may be more complex than often acknowledged and thus may be compatible with Wright's view of a netlike relationship between the genome and complex characters (Wright 1968).     

Genetic analysis of larval survival and larval growth of two populations of Leptinotarsa decemlineata on tomato

The genetics of adaptation to tomato in Leptinotarsa decemlineata (Say) were investigated in reciprocal F₁, F₂, and backcross populations generated from crosses between beetles from a tomato adapted population and from a population that was poorly adapted to tomato. Larvae from the parent and test populations were reared on tomato for four days, after which survivorship and larval weights were recorded. Most results indicate that differences in larval growth and survival on tomato between the parent populations are largely determined by autosomal, polygenic mechanisms, the inheritance of which involves a significant dominance component. However, results from F₂ crosses are not consistent with this conclusion. A significant difference in larval weights, but not in survival, between reciprocal F₁ populations in an analysis of combined data from four separate experiments suggests that maternal cytoplasmic effects may contribute to differences in larval performance on tomato between the adapted and unadapted populations. The unusual results obtained from F₂ crosses in this study are not atypical of results from previous studies of the genetics of adaptation to host plants by the Colorado potato beetle. Host plant adaptation by Colorado potato beetles may therefore involve unusual genetic mechanisms that are not easily assessed by classical Mendelian analysis.     

Prediction of progeny variation in oat from parental genetic relationships

Summary The ability to predict agronomic performance of progeny from a cross would be a great benefit to plant breeders in selecting parents. The predictive value of parental genetic relationships estimating F₁ progeny means and F₄ family variances of nine argronomic traits was tested in 76 oat crosses, using genetic distance measures based on coefficients-of-parentage, quantitatively inherited morphological characters, and discretely inherited biochemical and morphological characters. Coefficients-of-parentage were better predictors of F₁ performance than similarity measures derived from plant morphology or discretely inherited characters. Combined distance measures were better estimators of F₁ specific combining ability (SCA) effects than any single measure. Among cultivars of similar adaptation and quantitative morphology, crosses between parents with high coefficients-of-parentage gave higher SCA effect values than crosses of distantly related parents for grain yield and total biomass. The opposite was found for crosses among cultivars of different adaptation or quantitative morphology. The best predictor of trait variances among F₄ families was coefficients-of-parentage. Crosses between more distantly related parents produced larger variances among families than crosses between closely related parents for plant biomass. For grain yield, test weight, heading date, grain filling period, and maturity date, crosses between more closely related parents produced larger among-family variances than crosses of distantly related parents. Crosses between more distantly related parents involved at least one parent unadapted to central New York, and resulted in most of the progeny being generally unadapted. This, in part, may account for the low genetic variances for heading date, test weight, and grain yield in crosses of distantly related parents.     

Analysis of heterosis and recombination loss for fitness and productivity traits in different hybrids of mulberry silk moth Bombyx mori

Three different races of lepidopteron silk moth Bombyx mori were used in reciprocal and inter se crosses to determine heterosis effects at F₁ and recombination loss at the F₂ generation for three fitness traits (fecundity, larval duration, survival rate) and four productivity traits (larval weight, cocoon weight, shell weight, filament length). Eleven mating types were represented in the present study, including three pure breeds and a variety of F₁ and F₂ populations arising from regular and reciprocal crosses, respectively. Equations were derived to evaluate heterosis, maternal and overdominance effects for the above traits. Estimates of heterosis and overdominance effects revealed significant heterosis effects for all the traits, but overdominance was only seen for larval duration (favorable effect) and survival rate (unfavorable effect). Maternal effects were significant for the majority of the traits under study. The results revealed significant reduction for all the quantitative traits from F₁ to F₂, except for larval duration. The most obvious explanation for the reduction of fitness parameters and productive traits is the reduction in heterozygosity from F₁ to F₂ (it is expected that one half of the heterozygosity of F₁ is lost in F₂). For larval duration this explanation seems insufficient and breakdown of epistatic gene effects (i.e. recombination loss) has been suggested.     

The use and abuse of genetic marker‐based estimates of relatedness and inbreeding

Genetic marker‐based estimators remain a popular tool for measuring relatedness (r_xy) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of r_xy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker‐based estimators of r_xy and F in a species with very low genetic diversity, New Zealand's little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of r_xy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated r_xy or F is relatively high (Pearson's r = 0.66–0.72 and 0.81–0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker‐based estimates of r_xy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator's performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of r_xy and F debatable.     

The effect of population structure on the relationship between heterosis and heterozygosity at marker loci

The relationship between heterozygosity at neutral marker loci and heterosis of F₁ hybrids is investigated using a theoretical model. Results emphasize that linkage disequilibrium between the markers and the loci implicated in heterosis [quantitative trait loci (QTLs) that exhibit dominance effects] is a necessary condition to finding a correlation ( _mh ) between heterozygosity at marker loci and the heterosis. The effect of population structure, in which the parental inbred lines of the hybrids belong to different heterotic groups, is considered. _mh is investigated for: (1) hybrids between lines that belong to the same heterotic group (within-group hybrids); (2) hybrids between lines that belong to different groups (between-group hybrids); and (3) all hybrids, both within and between-groups. Within a group, significant values of ( _mh ) may arise because of linkage disequilibrium generated by drift. At the between-group level, no correlation is expected since link-age disequilibrium should differ randomly from one group to the other, which is consistent with recent experimental results. Possible ways to achieve prediction of the heterosis in this situation are discussed. When all hybrids are considered simultaneously, divergence of allelic frequencies among groups for the markers and the QTLs produces a correlation between heterosis and heterozygosity at marker loci. This correlation increases with the number of markers that are considered.     

Maternal and Reciprocal Effects on Seedling Characters in ARABIDOPSIS THALIANA (L.) Heynh

Five early growth characters were examined in six races of Arabidopsis thaliana (L.) Heynh, their reciprocal F₁ hybrids (1974) and F₁ by tester hybrids, using a seventh race as a paternal tester. Three of the five characters were also examined at two nutrient levels in reciprocal F₁ hybrids (1972) of all seven races. Analyses of F₁ and F₁ by tester hybrids revealed significant maternal effects in all characters examined in F₁ hybrids (1972) and in root length and plant weight of F₁ (1974) and F₁ by tester hybrids. Significant reciprocal effects were found for plant weight in F₁ by tester hybrids and for seed weight, percentage of germination and root length in F₁ (1974) and F₁ by tester hybrids. The presence of significant maternal and/or reciprocal components in both F₁ (1974) and F₁ by tester diallels suggests that differences in maternal cytoplasm rather than maternal genotype per se were responsible for much of the variation resulting from these non-direct genetic effects.     

Genetics of gel consistency in rice (Oryza sativa L.)

Inheritance of gel consistency in rice was studied in crossés involving highamylose, low-gelatinizalion temperature parents with hard, medium, and soft gel consistency. The results of single-grain analysis of parents, F₁, F₂, B₁F₁, B₂F₂, and their reciprocal crosses from a single-season harvest showed that the differences between hard and soft, hard and medium, and medium and soft gel consistency are under monogenic control and that modifiers affect the expression of the trait. Multiple alleles at the same locus, hereby designated asgec ^a for medium gel consistency andgec ^b for soft gel consistency, were recessive to the wild type allele for hard gel consistency andgec ^a was dominant overgec ^b. The results indicate that selection for desired gel consistency can effectively be done in early segregating generations.     

Genetic control of seed weight in flax (Linum usitatissimum) and possible implications

Summary Mean seed weight data were obtained from the F₁ and F₂ of a six-by-six diallel cross with flax (Linum usita-tissimum L.). Pronounced reciprocal differences appeared in the F₁, but had largely disappeared by the F₂. The genetic control of mean seed weight was examined using two types of analysis of variance. The models underlying both analyses were fitted to the data by matrix methods supplying weighted least-squares estimates of the parameters in the models. Weights, the use of which dealt with the problem of variation in the reliability of means, were the reciprocals of the variances of individual cell (cross/self) means in the diallel data table. Elimination of redundant parameters supplied the minimum adequate models for each analysis type. Dominance was apparently masked by the large transient maternal effects in the F₁, but surfaced in the F₂, where dominance was towards larger mean seed weight. This may be coupled with findings elsewhere of possible advantages for larger seed weights to speculate on a role in preserving infrequent hybrid progeny among inbreeding (flax) species. Maternal effects producing larger seed size, plus dominance with the same result might be valuable, in conjunction with growth and competitive advantages conferred by larger seed, in preventing early elimination of rare hybrids.     

Chromosomal rearrangements directly cause underdominant F1 pollen sterility in Mimulus lewisii–Mimulus cardinalis hybrids

Chromosomal rearrangements can contribute to the evolution of postzygotic reproductive isolation directly, by disrupting meiosis in F₁ hybrids, or indirectly, by suppressing recombination among genic incompatibilities. Because direct effects of rearrangements on fertility imply fitness costs during their spread, understanding the mechanism of F₁ hybrid sterility is integral to reconstructing the role(s) of rearrangements in speciation. In hybrids between monkeyflowers Mimulus cardinalis and Mimulus lewisii, rearrangements contain all quantitative trait loci (QTLs) for both premating barriers and pollen sterility, suggesting that they may have facilitated speciation in this model system. We used artificial chromosome doubling and comparative mapping to test whether heterozygous rearrangements directly cause underdominant male sterility in M. lewisii–M. cardinalis hybrids. Consistent with a direct chromosomal basis for hybrid sterility, synthetic tetraploid F₁s showed highly restored fertility (83.4% pollen fertility) relative to diploids F₁s (36.0%). Additional mapping with Mimulus parishii–M. cardinalis and M. parishii–M. lewisii hybrids demonstrated that underdominant male sterility is caused by one M. lewisii specific and one M. cardinalis specific reciprocal translocation, but that inversions had no direct effects on fertility. We discuss the importance of translocations as causes of reproductive isolation, and consider models for how underdominant rearrangements spread and fix despite intrinsic fitness costs.     

Embryo development in reciprocal crosses of Phaseolus vulgaris L. and P. coccineus Lam.

Summary Embryo development was examined in reciprocal crosses of Phaseolus vulgaris cv. Great Northern and P. coccineus cv. Scarlet Runner. The formation of abnormal (shrunken and underdeveloped) embryos constituted the primary crossing barrier between the two species when P. coccineus was the female parent. Plants of P. coccineus X P. vulgaris were obtained by embryo culture. Although the P. vulgaris X P. coccineus cross resulted in normal seed development, the fertility of the resulting hybrids was much lower (27%) than that of the reciprocal hybrids (81%). Three classes of F₂ embryos, normal, shrunken, and underdeveloped were formed on reciprocal F₁s and the frequencies did not differ between reciprocal populations. Thus, the interactions between embryo and endosperm and/or maternal parent rather than cytoplasmic-nuclear effects seem to be important in the determination of the extent of embryo growth. The examination of pollen fertility of F₂ plants and the development of F₂ and F₃ embryos suggests that the formation of abnormal embryos and reduced male fertility are independent events. The P. vulgaris — P. coccineus crosses may be useful in studying the possible involvement of interspecific differences in hormonal metabolism in the development of hybrid embryos.     

RFLP markers and predicted testcross performance of maize sister inbreds

 Inbreds selfed from the same F₂ or backcross population are referred to as sister inbreds. In some situations, maize (Zea mays L.) sister inbreds may not have testcross data available for best linear unbiased prediction (BLUP) of single-cross performance. This study evaluated the usefulness of BLUP and restriction fragment length polymorphism (RFLP)-based coefficients of coancestry ( f ) in predicting the testcross performance of sister inbreds. Parental contributions (p) were estimated from 70 RFLP loci for 15 inbreds that comprised three sister inbreds selfed from each of five F₂ populations. Estimates of p were subsequently used to calculate RFLP-based f. Grain yield, moisture, and stalk lodging data were obtained for 2265 single crosses tested by Limagrain Genetics in multilocation trials from 1990 to 1995. Performance of the sister inbreds when crossed to several inbred testers was predicted from the performance of the tested single crosses and RFLP-based f. Correlations between predicted and observed performance, obtained with a delete-one cross-validation procedure, were erratic and mostly low for all three traits. Correspondence was poor between ranks for predicted and observed general combining ability of the sister inbreds. The results suggested that the proportion of the genome derived by a sister inbred from a given parental inbred does not solely determine its testcross performance. The failure of BLUP and RFLP-based f to consistently predict testcross performance indicated that actual field testing will continue to be necessary for preliminary evaluation of sister inbreds. Received : 17 March 1997 / Accepted : 18 April 1997     

The empirical Bayes estimators of fine‐scale population structure in high gene flow species

An empirical Bayes (EB) pairwise F_ST estimator was previously introduced and evaluated for its performance by numerical simulation. In this study, we conducted coalescent simulations and generated genetic population structure mechanistically, and compared the performance of the EBF_ST with Nei's G_ST, Nei and Chesser's bias‐corrected G_ST (G_{ST_NC}), Weir and Cockerham's θ (θ_WC) and θ with finite sample correction (θ_{WC_F}). We also introduced EB estimators for Hedrick’ G’_ST and Jost’ D. We applied these estimators to publicly available SNP genotypes of Atlantic herring. We also examined the power to detect the environmental factors causing the population structure. Our coalescent simulations revealed that the finite sample correction of θ_WC is necessary to assess population structure using pairwise F_ST values. For microsatellite markers, EBF_ST performed the best among the present estimators regarding both bias and precision under high gene flow scenarios (). For 300 SNPs, EBF_ST had the highest precision in all cases, but the bias was negative and greater than those for G_{ST_NC} and θ_{WC_F} in all cases. G_{ST_NC} and θ_{WC_F} performed very similarly at all levels of F_ST. As the number of loci increased up to 10 000, the precision of G_{ST_NC} and θ_{WC_F} became slightly better than for EBF_ST for cases with , even though the size of the bias remained constant. The EB estimators described the fine‐scale population structure of the herring and revealed that ~56% of the genetic differentiation was caused by sea surface temperature and salinity. The R package finepop for implementing all estimators used here is available on CRAN.