Inheritance of adult field resistance to yellow rust disease among broad-based hexaploid spring wheat germplasm

 Complete F₁ and F₂ diallel crosses were used to investigate the inheritance of yellow rust resistance among eight bread wheat lines, developed by CIMMYT for the East African Highlands, which showed a wide response to this disease. Both diallel sets were grown at a site with a high incidence of yellow rust, although for one season, during which the F₁ diallel was grown, disease incidence was unusually low. Analyses disclosed the presence of additive, dominance and epistatic effects among those genes controlling rust resistance, with the former being the most important. At normal disease levels, excluding two arrays having resistant common parents removed non-allelic interactions from the F₁ diallels. For all F₂ diallels, and the remaining F₁ diallel, omitting two arrays based on susceptible parents removed these interactions. Local selection of material from a broadly based germplasm appears to be a feasible method of developing adapted cultivars resistant to endemic diseases. Received: 1 March 1998 / Accepted: 19 March 1998     

Comparison of methods for calculating the heritability of adult field resistance to yellow rust and grain yield in spring wheat

Several methods are available for estimating heritability in disomic species, including parent-offspring regression, realized heritability, intraclass correlations of recombinant inbred lines, and diallel-cross analysis. Estimates were obtained by these various methods for a set of eight bread wheat (Triticum aestivum) lines adapted to the East African highlands, which had been intercrossed and selfed in a half-diallel arrangement to give F₁, F₂ and F₃ generations, and F₆ recombinant inbred lines. Significant genetic variation existed among parents and crosses for both grain yield and yellow rust resistance in all generations. Based on the heritability calculated from the analysis of F₆ recombinant inbred lines, analysis of the F₂ diallel crosses was recommended for determining the heritability of both characters in early segregating generations. The results also suggest that a form of tandem selection may be effective in developing locally adapted germplasm which combines high grain yield with yellow rust resistance. Received: 15 February 1999 / Accepted: 11 March 1999     

Heritability of and correlations among genotype-by-environment stability statistics for grain yield in bread wheat

Several genotype-by-environment stability measures are in use, but little information exists about their inheritance or genetic inter-relationships. Among those measures in common use are the linear regression coefficient (b), deviations from regression (s_b), coefficient of determination (R²), coefficient of phenotypic variation (CPV) and, more recently, interaction principal components (IPCA) of the additive-main-effect-and-multiplicative-interaction (AMMI) model. Because of the factorial structure of the data, the diallel cross is well suited to study these parameters and their relationship to quantitative traits. For this study a complete diallel cross, derived by mating eight lines from a broad based bread wheat breeding population, was grown for several growing seasons at two Ugandan locations, one of which was prone to yellow rust. Stability parameters and grain yield were measured for each cross. CPV had the highest narrow-sense heritability (h²=0.522) followed by IPCA1 of the AMMI (h²=0.461). Lowest narrow-sense heritabilities were calculated for b and R² (h²=0.150 and 0.100 respectively). There were high additive genetic correlations (r_A) between grain yield and CPV (r_A=−0.933), grain yield and IPCA1 (r_A=0.707), and grain yield and IPCA2 (r_A=0.751). The genetic association between CPV and IPCA1 was also high and negative (r_A= −0.934). These results suggest that it may be possible to select simultaneously for high and stable grain yield in this broad-based bread wheat breeding pool by selecting outyielders that exhibit a low CPV. Received: 25 July 2000 / Accepted: 7 December 2000     

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.     

Assessment of genes controlling Area under Disease Progress Curve (AUDPC) for stripe rust (P. Striiformis F. Sp. Tritici) in two wheat (Triticum Aestivum L.) crosses

Genetic effects on controlling stripe rust resistance were determined in two wheat crosses, Bakhiawar-92 × Frontana (cross 1) and Inqilab-91 × Fakhre Sarhad (cross 2) using Area under Disease Progress Curve (AUDPC) as a measure of stripe rust resistance. The resistant and susceptible genotypes for crosses were identified by initial assessment of 45 wheat accessions for stripe rust resistance. Mixed inheritance model was applied to the data analysis of six basic populations P ₁, F ₁, P ₂, B ₁, B ₂, and F ₂ in the crosses. The results indicated that AUDPC in cross 1 was controlled by two major genes with additive-dominance epistatic effect plus polygenes with additive-dominance epistatic effects (model E). Whereas in case of cross 2, it was under the control of two major genes with additive-dominance epistatic effect plus additive-dominant polygenes (model E-1). Additive effect was predominant then all other types of genetic effects suggesting the delay in selection for resistance till maximum positive genes are accumulated in the individuals of subsequent generations. Occurrence of transgressive segregants for susceptibility and resistance indicated the presence of resistance as well as some negative genes for resistance in the parents. The major gene heritability was higher than the polygene heritability in B ₁, B ₂ and F ₂ for the crosses. The major gene as well as the polygene heritability was ranging from 48.99 to 87.12% and 2.26 and 36.80% for the two crosses respectively. The highest phenotypic variations in AUDPC (2504.10 to 5833.14) for segregating progenies (BC ₁, BC ₂ and F ₂) represent that the character was highly influenced by the environment. The article is published in the original.     

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.     

Prediction of testcross means and variances among F3 progenies of F1 crosses from testcross means and genetic distances of their parents in maize

 Prediction of the means and genetic variances in segregating generations could help to assess the breeding potential of base populations. In this study, we investigated whether the testcross (TC) means and variances of F₃ progenies from F₁ crosses in European maize can be predicted from the TC means of their parents and F₁ crosses and four measures of parental genetic divergence: genetic distance (GD) determined by 194 RFLP or 691 AFLP^{TM 1} markers, mid-parent heterosis (MPH), and absolute difference between the TC means of parents (∣P₁−P₂∣). The experimental materials comprised six sets of crosses; each set consisted of four elite inbreds from the flint or dent germplasm and the six possible F₁ crosses between them, which were evaluated for mid-parent heterosis. Testcross progenies of these materials and 20 random F₃ plants per F₁ cross were produced with a single-cross tester from the opposite heterotic group and evaluated in two environments. The characters studied were plant height, dry matter content and grain yield. The genetic distance between parent lines ranged between 0.17 and 0.70 for RFLPs and between 0.14 and 0.57 for AFLPs in the six sets. Testcross-means of parents, F₁ crosses, and F₃ populations averaged across the six crosses in a particular set generally agreed well for all three traits. Bartlett’s test revealed heterogeneous TC variances among the six crosses in all sets for plant height, in four sets for grain yield and in five sets for dry matter content. Correlations among the TC means of the parents, F₁ crosses, and F₃ populations were highly significant and positive for all traits. Estimates of the TC variance among F₃ progenies for the 36 crosses showed only low correlations with the four measures of parental genetic divergence for all traits. The results demonstrated that for our material, the TC means of the parents or the parental F₁ cross can be used as predictors for the TC means of F₃ populations. However, the prediction of the TC variance remains an unsolved problem. Received: 4 August 1997 / Accepted: 17 November 1997     

Effectiveness of indirect selection for wheat yield in a stress environment

 Effectiveness of indirect selection for grain yield was investigated among eight bread wheat lines, selected in a stress environment in the East African Highlands, where they showed a wide response to yellow rust, the biotic factor causing the stress. The lines were intercrossed to give an 8×8F₁ diallel, which was grown in this same environment for three consecutive growing seasons during 1994 and 1995. Half of the last trial was sprayed with fungicide. From the estimates of narrow-sense heritabilities for yield and yellow rust severity, and the genetic correlation between them, indirect selection for yield in the unsprayed plots, obtained by choosing the most resistant 5% of this material was, on average, 12% higher than selecting for yield itself. In the fungicide-treated plots, indirect selection was only 73% as efficient as direct selection. The implications of these results for selecting for yield in stress environments are discussed. Received: 10 April 1998 / Accepted: 5 August 1998     

Analysis of genetic effects of major genes and polygenes on quantitative traits I. Genetic model for diploid plants and animals

A genetic model was proposed to simultaneously investigate genetic effects of both polygenes and several single genes for quantitative traits of diploid plants and animals. Mixed linear model approaches were employed for statistical analysis. Based on two mating designs, a full diallel cross and a modified diallel cross including F₂, Monte Carlo simulations were conducted to evaluate the unbiasedness and efficiency of the estimation of generalized least squares (GLS) and ordinary least squares (OLS) for fixed effects and of minimum norm quadratic unbiased estimation (MINQUE) and Henderson III for variance components. Estimates of MINQUE (1) were unbiased and efficient in both reduced and full genetic models. Henderson III could have a large bias when used to analyze the full genetic model. Simulation results also showed that GLS and OLS were good methods to estimate fixed effects in the genetic models. Data on Drosophila melanogaster from Gilbert were used as a worked example to demonstrate the parameter estimation. Received: 11 November 2000 / Accepted: 2 May 2001     

Estimation of genetic parameters in barley (Hordeum vulgare L.)

Summary Four different sets of partial diallels were analysed for their relative efficiencies for estimating the genetic parameters in barley: (1) partial diallel with 12 parents, each involved in only 5 crosses; (2) partial diallel with 12 parents, each involved in only 3 crosses; (3) partial diallel with 8 parents, each involved in only 5 crosses; and (4) partial diallel with 8 parents, each involved in only 3 crosses. In partial diallel experiments, the estimates of gca effects were higher than in those of full diallel. Ranking pattern of the parents on the basis of gca effects in partial diallels deviated considerably from the ranking in full diallel. With decreasing s per parent, the deviation in ranking was also more. This clearly suggests the unsuitability of partial diallel analysis for screening high general combiners. Selection of best cross combinations is also not possible because only a sample of crosses (s out of n) is analysed under partial diallel so that there is every possibility of the best cross being excluded from the sample. In general, overdominance was exhibited, indicating that there is ample scope for heterosis breeding in barley.     

Mapping quantitative trait loci controlling silking date in a diallel cross among four lines of maize

 We describe and apply an interval mapping method for quantitative trait locus (QTL) detection using F₃ and testcross progenies derived from F₂ populations obtained from a diallel cross among four elite lines of maize. Linear model-based procedures were used for the test and estimation of putative QTL effects together with genetic interactions including epistasis. We mapped QTL associated with silking date and explored their genetic effects. Ten QTL were detected, and these explained more than 40% of the phenotypic variance. Most of these QTL had consistent and stable effects among genetic backgrounds and did not show significant epistasis. QTL-by-environment interaction was important for four QTL and was essentially due to changes in magnitude of allelic effects. These results show the efficiency of our method in several genetic situations as well as the power of the diallel design in detecting QTL simultaneously over several populations. Received: 2 September 1996 / Accepted: 20 December 1996     

Inheritance of Semidwarfism in Rice, ORYZA SATIVA L

The inheritance of plant height was investigated in a ten-parent diallel cross of diverse rice cultivars. Parents included two tall japonica lines and eight semidwarf lines. Data from parent, F₁, F₂ , and F₃ generations indicated that the majority of height variation among the ten parents could be accounted for by three major genes with additive loci effects. D51, 72/2234–11, and G33 (derived from the known major-gene indica semidwarf Dee-geo-woo-gen) all were found to possess an allelic, partially recessive semidwarfing gene (sd₁). Additional semidwarfing genes were detected in D66 (sd₂, fully recessive) and in CI 9858 (sd₃, partially to fully recessive). Relative magnitudes of additive effects were sd₁ > sd₂ ≥ sd₃. Hokuriki 76, Tedoriwase, and IV 29–4 were found to be dwarfed by a multiple-gene system. Hayman-Jinks diallel cross analysis on parent and F₁ information (1974 and 1975) and on parent and F₂ information demonstrated the presence of significant additive and dominance variation, but epistasis was not detected. A preponderance of dominant alleles with partial dominance for increased plant height was observed. Since diallel statistics reflect properties of genes with larger effects, the genetic model proposed from segregation analysis was in substantial agreement with predictions of the Hayman-Jinks analysis.     

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.     

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

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

Detection of genic interactions by analyzing the F2 generation of diallel crosses

Summary The ability of the Hayman and Jinks method of analysis of diallel crosses to detect genic interactions was studied in peanuts. Six traits, measured in the F₂ generation of a diallel cross of four cultivars, were analyzed. In F₂ analyses of the diallel, least squares estimates of variance components D, H₁ , H₂, F, E, were used as an additional criteria for the adequacy of the diallel model. They were found to be in substantial agreement with the tests based on W_r and V_r values, and probably more reliable. The regression of W_r on V_r was shown to be unsuitable to detect duplicate gene type of interactions; it was detected, however, by the ratio of the mean within-F₂ — family variance and the variance among the parents. Using the different criteria, duplicate genes type of interactions was detected for two traits, complementary genes type was detected for one trait and three traits were found to fit the additive-dominance model without any genic interactions.     

An EST-SSR marker linked with yellow rust resistance in wheat

Expressed sequenced tags containing simple sequence repeats (EST-SSRs) were used to identify molecular markers associated with yellow rust resistance in wheat (Triticum aestivum L.). A cross between yellow rust resistant (PI178383) and susceptible (Harmankaya99) wheat genotypes was performed and respective DNA pools from the resistant and susceptible F₂ seedlings were constructed. 78 EST-SSR primers were used for bulked segregant analysis and one EST-SSR marker (Pk54), identified as 200 bp fragment, was present in the resistant parent and resistant F₂ hybrids but not in the susceptible ones. 108 wheat genotypes differing in yellow rust resistance were screened with Pk54 and 68 % of the wheat genotypes, known to be yellow rust resistant, had the Pk54 marker, further suggesting that the presence of this marker correlates with yellow rust resistance.     

Identification and estimation of a QTL model and its effects

 A joint segregation analysis of a genetic system and the effects of QTLs based on the six populations P₁, F₁, P₂, B₁, B₂ and F₂ is proposed in this paper. The major steps were as follows. Firstly, under the supposition that the segregating population was composed of component distributions controlled by a major gene(s) and modified by both polygenes and environments, four groups and 17 types of genetic models, including a one major-gene model, a two major-gene model, a polygene model, and a mixed one-major gene and polygene model, were set up. Secondly, the joint maximum-likelihood function was constructed from the six generations so as to estimate the parameters of component distributions through an EM algorithm. Thirdly, the best-fitting genetic model was chosen according to Akaike’s information criterion, a likelihood-ratio test, and tests for goodness of fit. Fourthly, the related genetic parameters, including gene effects, as well as the genetic variances of major genes and polygenes, were obtained from the estimates of component distributions. Finally, the individuals in segregating populations were classified into their major-gene genotypes according to their posterior probabilities. An example of the genetic analysis of plant height of a rice cross between Nanjing No. 6 and Guangcong was used to illustrate the above procedure. The method was especially appropriate to those crops with easy to obtain hybrid seeds. Received: 11 February 1998 / Accepted: 28 May 1998     

Genetic analysis and location of gene for resistance to stripe rust in wheat international differential host Strubes Dickkopf

Strubes Dickkopf is the sixth differential in the world set for wheat stripe (yellow) rust. It is very important to clarify its genetic character of resistance to stripe rust and to develop the molecular markers linked to resistance genes. The NIL Taichung 29*6/Strubes Dickkopf, which was obtained by Strubes Dickkopf as the gene donor and Taichung 29 as the genetic background through backcross breeding, was crossed with the recurrent parent Taichung 29, inbred, and backcrossed to obtain the F₁, F₂ and BC₁ population. The genetic analysis of the cross Taichung 29/(Taichung 29*6/Strubes Dickkopf) was assessed by inoculating the rust race CYR26 at seedling stage. Bulked segregant analysis (BSA) and F₂ segregation analysis were used for detecting polymorphic primers to locate the gene. The resistance of the NIL Taichung 29*6/Strubes Dickkopf to CYR26 was controlled by a single dominant gene, named YrSD. The primer pair Xbarc59 on 5B was linked to YrSD and the genetic distance between Xbarc59 and YrSD was 2.4 cM. The molecular marker Xbarc59 closely linked to the gene YrSD could be used in marker-assisted selection for resistance to stripe rust in wheat breeding programmes.     

Evaluation of circulant partial diallel crosses in maize

Summary The present study was conducted in maize (Zea mays L.) on crosses among 20 diverse parents. The materials were evaluated in four different environments for eight characters. Combining ability analysis was carried out following diallel and partial diallel crosses. The number of crosses per parent (s) varied from 3 to 19 and the results were studied to identify the critical value of s that would provide an adequate information with minimum resources. The S₅ partial diallel was as good as the S₁₉ for the detection of differences among general combining ability (GCA) effects. Even the S₃ gave adequate information in the case of characters with high heritability. However, partial diallel analysis was less efficient in detecting the differences due to specific combining ability (SCA) effects. These results varied with environments, and characters with low heritability were more prone to misinterpretation. GCA effects showed fluctuations in partial diallel analysis which were more pronounced in S₅ and S₃, particularly for characters with low heritability. The average standard error of difference between GCA effects increased with a decrease in s, with a steep slope for s < 7. The partial diallel analysis was more efficient for the estimation of the variance component of GCA than for SCA, as the estimate of SCA was biased upwards. Estimates of broad sense heritability obtained from the partial diallels agreed with the full diallel analysis better than the narrow sense estimates. Smaller partial diallels gave erratic estimates of heritability, particularly for the characters with low heritability.     

Orange, yellow and white-cream: inheritance of carotenoid-based colour in sunflower pollen

Inheritance of pollen colour was studied in sunflower (Helianthus annuus L.) using three distinct pollen colour morphs: orange, yellow and white‐cream. Orange is the most common colour of sunflower pollen, while the yellow morph is less frequent. These two types were observed in the inbred lines F11 and EF2L, respectively. White‐cream pollen is a rare phenotype in nature, and was identified in a mutant, named white‐cream pollen, recovered in the R₂ generation of an in vitro regenerated plant. The F11 inbred line was used as starting material for in vitro regeneration. The carotenoid content of these three pollen morphs differed, and was extremely reduced in white‐cream pollen. The phenotype of F₁ populations obtained by reciprocal crosses revealed that the orange trait was dominant over both white‐cream and yellow. Segregation of F₂ populations of both crosses, orange × yellow and orange × white‐cream, approached a 3:1 ratio, indicating the possibility of simple genetic control. By contrast, a complementation cross between the two lines with white‐cream and yellow pollen produced F₁ plants with orange pollen. The F₂ populations of this cross‐segregated as nine orange: four white‐cream: four yellow. A model conforming to the involvement of two unlinked genes, here designated Y and O, can explain these results. Accessions with yellow pollen would have the genotype YYoo, the white‐cream pollen mutant would have yyOO and the accession with orange pollen would have YYOO. Within F₂ populations of the cross white‐cream × yellow a new genotype, yyoo, with white‐cream pollen was scored. The results of the cross yyoo × YYoo produced only F₁ plants with yellow pollen, supporting a recessive epistatic model of inheritance between two loci. In this model, yy is epistatic on O and o. In F₂ populations, the distributions of phenotypic classes suggested that the genetic control of carotenoid content is governed by major genes, with large effects segregating in a background of polygenic variation. These three pollen morphs can provide insight into the sequence in which genes act, as well into the biochemical pathway controlling carotenoid biosynthesis in anthers and the transfer of these different pigments into pollenkitt.