Assessing the genetic variation of tolerance to red needle cast in a <Emphasis Type="Italic">Pinus radiata</Emphasis> breeding population

Breeding for disease resistance or tolerance is a viable option for disease management programmes and is important for the continued success and resilience of planted forests. Red needle cast (RNC) is a disease that affects radiata pine (Pinus radiata) and is caused by Phytophthora pluvialis. Knowledge is still very limited regarding the potential for genetic tolerance to this pathogen. The application of controlled screening techniques is clearly required. Using a detached needle assay, we screened 392 clonally replicated individuals (clones) from an elite P. radiata population for quantitative tolerance to RNC. Data was highly skewed and required logarithmic data transformation and Poisson distributions for the estimation of best linear unbiased predictions. These estimates revealed a broad range in susceptibility/tolerance to RNC, and enabled the identification of clones that were clearly susceptible and clones that were clearly tolerant. There was a high correlation between the number and length of lesions that developed in response to inoculation with P. pluvialis. Broad-sense heritability estimates were low to moderate, indicating that there is potential for improving tolerance through breeding. These results provide evidence that breeding for tolerance to P. pluvialis is possible, although continued work into understanding and minimising causes for variance are required.     

Partial resistance to leaf rust (Hemileia vastatrix) in coffee (Coffea arabica L.): genetic analysis and molecular characterization of putative candidate genes

One of the major production limiting diseases in coffee is the orange leaf rust caused by the fungus Hemileia vastatrix (Berkeley and Broome). Little is known about the inheritance and genetic determinism of partial resistance in coffee (C. arabica L.) to H. vastatrix. This information would be useful to breed durable resistant cultivars efficiently. In this report, a genetic analysis of partial resistance to leaf rust in Coffea arabica was performed using nine segregating progenies from a cross between the susceptible variety Caturra and the resistant introgressed line DI200. Evolution of partial resistance was evaluated under field conditions by measuring rust incidence (RI) and defoliation (DEF) in two separate regions of productive branches per tree and during four successive years (2003–2006). Genetic components of rust resistance were estimated using the Means and Variance Generation Method, under an additive-dominant model. The most important genetic effect was the additive one, while resistance heritability estimates ranged from 73 to 53% for broad and narrow sense heritabilities, respectively. Genetic estimates for the number of segregating genes showed that at least five independent genes or genetic regions are implicated in the partial resistance to rust. We further analyzed the presence of resistance (RGC) and defense (DGC) gene candidates in the resistant and susceptible parents by using a degenerated-primer PCR approach. A total of 40 different genomic coffee sequences were isolated exhibiting strong similarity to known RGC or DGC homologous. Phylogenetic analysis clustered these sequences into nine families. One family exhibited the TIR protein element, representing the first TIR class proteins identified in coffee. While genetic analysis suggest a predictable success in the processes to improve the selection of resistant lines for future varieties with durable resistance, the molecular characterization of candidate genes represent a primary approach towards the identification of mechanisms involved in partial resistance to coffee leaf rust.     

Genetic parameter estimates in a clonally replicated progeny test of teak (Tectona grandis Linn. f.)

Teak (Tectona grandis Linn. f.) has been planted extensively in the tropics for its highly valued timber. We analysed data from a 3.5-year-old teak progeny test with clonal replication located in northern Australia. Additive and non-additive genetic variances were estimated for commercially important traits. Trees originating from seedlings were on average 2% taller and 4% straighter than those of the same genotype originating from cuttings. Non-additive genetic variance represented 35–50% of total genetic variance for growth traits and 63% of total genetic variance for incidence of flowering. Narrow-sense heritability was 0.22 for diameter, 0.18 for height and volume, 0.07 for stem straightness, 0.05 for insect defoliation, 0.03 for epicormic sprouts and 0.30 for incidence of flowering (estimated on an assumed underlying continuous scale). Broad-sense heritability was 0.37 for diameter, 0.28 for height, 0.35 for volume, 0.12 for stem straightness, 0.06 for insect defoliation, 0.12 for epicormic sprouts and 0.71 for incidence of flowering. Positive correlations were found between tree volume and flowering and between tree volume and stem straightness. The presence of sizeable non-additive variance supports the selection and deployment of clones to capture the full extent of genetic variation in commercially important traits.     

Inheritance of Resistance to Pratylenchus penetrans in Alfalfa

Fifty-two alfalfa (Medicago sativa L.) clones, randomly selected from the cultivar Baker and the experimental line MNGRN-4, were evaluated for resistance (based on nematode reproduction) to Pratylenchus penetrans in growth chamber tests (25 C). Twenty-five clones, representing the range of nematodes and eggs per plant, were selected and retested. Four moderately resistant and two susceptible alfalfa clones were identified. Inheritance of resistance to P. penetrans was studied in these six clones using a diallel mating design. The S₁, Fl, and reciprocal progenies differed for numbers of nematodes and eggs per g dry root and for shoot and root weights (P < 0.05). Resistance, measured as numbers of nematodes in roots, was correlated between parental clones and their S₁ families (r = 0.94), parental clones and their half-sib families (r = 0.81), and S₁ and half-sib families (r = 0.88). General combining ability (GCA) effects were significant for nematode resistance traits. Both GCA and specific combining ability (SCA) effects were significant for plant size traits, but SCA was more important than GCA in predicting progeny plant size. Reciprocal effects were significant for both nematode resistance and plant size traits, which may slow selection progress in long-term selection programs. However, the GCA effects are large enough that breeding procedures that capitalize on additive effects should be effective in developing alfalfa cultivars with resistance to P. penetrans.     

Patterns and drivers of fungal disease communities on Arabica coffee along a management gradient

Plants, including those managed by humans, are often attacked by multiple diseases. Yet, most studies focus on single diseases, even if the disease dynamics of multiple species is more interesting from a farmers’ perspective. Moreover, most studies are from single management systems, although it is valuable to understand how diseases are distributed across broad management gradients, especially in cases where less intensive management also provides biodiversity values in the landscape. To understand the spatial dynamics and drivers of diseases across such a broad management gradient, we assessed four major fungal diseases on Arabica coffee (Coffea arabica) at 60 sites in southwestern Ethiopia along a gradient from only little managed wild coffee in the forest understory to intensively managed coffee plantations. We found that environmental and management factors related to disease incidence and severity differed strongly among the four fungal diseases. Coffee leaf rust (Hemileia vastatrix) and Armillaria root rot (Armillaria mellea) were more severe in intensively managed sites, whereas coffee berry disease (Colletotrichum kahawae) and wilt disease (Gibberella xylarioides) were more severe in less managed sites. Among sites, incidence and severity of the four fungal diseases poorly correlated with each other. Within sites, however, shrubs that were severely attacked by coffee leaf rust also had high levels of berry disease symptoms. A better understanding of disease dynamics is important for providing management recommendations that benefit smallholder farmers, but also to evaluate possibilities for maintaining biodiversity values in the landscape related to shade cover complexity and wild coffee genetic variation.     

Diallel analysis of the latent period of stripe rust in wheat

A half diallel was made amongst five wheat (Triticum aestivum L.) genotypes of which one was susceptible, while the others had adult-plant resistance, to stripe rust (Puccinia striiformis West.). The five parent and ten F₁ progeny were grown in the glasshouse and were inoculated with three rust pathotypes at the seedling stage. The latent period was measured on the first leaf. Two procedures were used to analyze the half diallel. Both methods showed that the average effects of alleles were of much greater importance than was dominance in conditioning resistance in response to two of the pathotypes, while for the third pathotype dominance was important. Resistance was conditioned by partial dominance for two pathotypes whereas for the third it was determined by full dominance. Broad-sense heritabilities range from 60–73% and the number of genes involved was different (from 1 to 4), depending on the pathotype.     

Genetic variability of mineral concentrations in Festuca arundinacea Schreb.

Summary Nine randomly chosen clones of tall fescue (Festuca arundinacea Schreb.) were mated in all possible combinations to determine the nature of genetic variation for Mg, Ca, K, and P concentrations in a broad genetic base population. General combining ability mean squares were significant for most variables, whereas specific combining ability mean squares were not significant in most instances indicating that additive genetic variance was more important. Genotype x year interactions were significant for most variables, suggesting that selection should be evaluated over many environments. Broad-sense heritability estimates based on parental and progeny variance components were generally high for P, K, Ca, and Mg but low for the ratio K/(Ca + Mg). Narrow-sense heritabilities for these minerals were close to the broad sense values since the additive genetic variance was the largest component of the total genetic variation. Correlations between mineral concentrations and herbage dry matter yield were low. It was concluded that adequate genetic variation exists to improve mineral concentration without altering herbage dry matter yields.Journal Series no. 5886     

Comparison of variation in adaptive traits between wild-type and transgenic silver birch (Betula pendula) in a field trial

The use of genetic modification (GM) in tree breeding would require that GM trees are superior to currently used seed orchard seedlings in the target trait and equal in other traits. We compare the variation of silver birch (Betula pendula Roth) lines carrying a sugar beet chitinase IV gene (chiIV) with the objective to improve fungal disease resistance to the variation of wild-type genotypes in disease resistance and other adaptive traits. The genetic variation in disease resistance was at the same level in transgenic (CV_g 0.9?C19.0%) and wild-type trees (CV_g 0?C19.7%), but the resistance characteristics of the most resistant wild-type genotype were usually equal or better than those of the best transgenic line. The broad-sense heritabilities varied from very low to moderate in disease resistance in both types. Broad-sense heritabilities in growth and leaf phenology-related traits were moderate and generally higher among the transgenic than the wild-type trees. The introduction of the sugar beet chiIV gene is likely to have fitness consequences in the form of lowered growth and quality characteristics of the transgenic lines without significant improvement in disease resistance compared with the natural variation of the same traits.     

Confidence intervals for heritability for two-factor mating design single environment linear models

Summary Precision measurement is an essential part of heritability estimate interpretation. Approximate standard errors are commonly used as measures of precision for heritability on a progeny mean basis (H). Their derivation, however, is not inferred from the distribution theory for H. F-distribution based exact confidence intervals have been derived for some onefactor mating design H estimators. Extension of the confidence interval results from one-factor to twofactor mating designs is reported in this paper. Functions of heritability on a full-sib or half-sib progeny mean basis from nested or factorial mating design parameters were distributed according to the F-distribution. Exact confidence intervals were derived for heritability on a full-sib progeny mean basis. Exact confidence intervals for heritability on a half-sib progeny basis were adapted from previous results. Maize (Zea mays L.) data were used to estimate confidence intervals. Complete equations were given for interpolation in F-tables.Oregon Agricultural Experiment Station Technical Paper No. 7659     

Diallel analysis for mineral element absorption in tropical adapted soybeans [Glycine max (L.) Merrill]

The Brazilian tropical adapted soybeans contains, in addition to superior morphological characters, genetic factors for tolerance to cultivation in acidic, mineral-stressed soils. However, the selection process for these hindrances has been empirical, and information on the genetics of mineral element uptake by the plant is necessary. The objective of this investigation was to identify the mode of inheritance for the absorption of phosphorus, potassium, calcium, magnesium, iron, aluminium, manganese, zinc and copper in a 9 × 9 diallel cross. General combining ability (GCA) was higher than specific combining ability (SCA), with the exception of copper, manganese and zinc, indicating predominantly additive effects. The ratios of GCA/SCA varied between 3.4 (calcium) and 8.5 (magnesium). The regression of covariance (W_r) on variance (V_r) showed that the additive-dominance model explained the genetic differences in this germ plasm. However, the detection of overdominance could be related to possible heterozygosity in the parental varieties for mineral absorption. Broad-sense heritability values were higher than narrow sense heritability values for aluminium, iron, potassium, calcium and magnesium, being in the range of 67.9–86.9% and 42.0–56.6%, respectively. This is an indication that soybeans can be further improved to efficient utilisation of nutrients and to tolerate toxic factors in the soil.     

Heritability estimates of citral content in East Indian lemongrass

Summary Citral content in oil obtained from 80 representative clones, chosen randomly from a population raised from open-pollinated seeds of clonally propagated East Indian lemongrass variety SD-68 and their half-sib progenies was estimated by gas chromatography. Heritability estimates were determined by variance component and parent-offspring regression analyses. Broad-sense heritability was 0.49 while narrow sense heritabilities by variance and regression analyses were 0.37 and 0.24, respectively. Phenotypic and genotypic correlations between citral content in oil and oil content were very low both among the parental clones (-0.01 and -0.01, respectively) and among their progenies (0.13 and 0.08, respectively) indicating that selection for either of these traits would not have much effect on the other.     

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.     

PATERNAL EFFECTS IN INHERITANCE OF A PATHOGEN RESISTANCE TRAIT IN IPOMOEA PURPUREA

For continuously variable, polygenic characters, the response to selection depends upon the proportion of phenotypic variance that is caused by additive genetic variance, or narrow-sense heritability. Thus, a major goal of quantitative genetics is to partition phenotypic variance for a trait in a way that isolates additive genetic variance from other causes. The variance among paternal half-sib families, which is frequently used to estimate additive variance, is commonly recognized to include additive epistatic effects. However, this variance component can also include non-Mendelian paternal effects. We report here the results from a diallel crossing design used to isolate nonnuclear effects from the paternal nuclear contribution to disease resistance in the common morning glory, Ipomoea purpurea. In particular, we found that genetic variance for resistance to anthracnose, a disease caused by the fungal pathogen Colletotrichum dematium, was determined largely by a nonnuclear, additive paternal effect. We discuss potential mechanisms for this effect as well as some of their evolutionary implications.     

BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution

Coffee is one of the world’s most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome.     

Stabilizing Selection for Pupa Weight in TRIBOLIUM CASTANEUM

Ninety-five generations of stabilizing selection for pupa weight in Tribolium castaneum resulted in a significant decrease in phenotypic variance, moderate reductions in additive genetic variance, but only slight changes in heritability for the trait. Sterility was significantly lower and the average number of live progeny per fertile mating was significantly higher in populations where stabilizing selection was practiced as compared with random selected populations. The results indicate that more genetic variability is being maintained than would be expected unless a fraction of the genes have a heterozygote advantage on the fitness scale. The reduction in phenotypic variance indicated that the populations with stablizing selection became somewhat more buffered against environmental sources of variation over the course of the experiment.     

The genetic basis for variation in the concentration of phenolic glycosides in Salix sericea: an analysis of heritability

Willows and many other members of the Salicaceae often produce phenolic glycosides, and the concentrations of these are known to vary among plants. We used progeny from a factorial half-sib quantitative genetics experiment with Salix sericea to determine whether the concentration of two phenolic glycosides, salicortin and 2′-cinnamoylsalicortin, show additive heritability. We found that the concentration of salicortin was much higher than 2′-cinnamoylsalicortin, and that both compounds showed additive genetic variation. However, the heritability of these two chemicals differed dramatically. We obtained heritability values of 0.20 for salicortin and 0.59 for 2′-cinnamoylsalicortin. Plant growth parameters were not strongly correlated with the concentrations of these phenolic glycosides.     

Clonal variation for tolerance to polyethylene glycol-induced water stress in cultured tomato cells

Cell clones were isolated from a population of cultured tomato (Lycopersicon esculentum Mill cv VFNT-cherry) cells and their tolerance to polyethylene glycol (PEG)-induced water stress was measured. Considerable variation for tolerance among the clones was found. Tolerance differences between clones appeared to be spontaneous and were different from tolerance differences between adapted and unadapted cells. Unlike adapted (selected by exposure to PEG) cells, cell clones retained their relative tolerance for many generations in the absence of selection pressure, and tolerance of both relatively tolerant and intolerant clones was very dependent on growth cycle stage and inoculum density. Analysis of subclones isolated from relatively tolerant and intolerant parent clones revealed that each parent clone gives rise to progeny with tolerances near the mean tolerance of both parents. However, progeny populations of both tolerant and intolerant parents are enriched with individuals with phenotypes nearer the mean response of their respective parent populations. When exposed to PEG, relatively tolerant and intolerant clones alike become adapted to the level of PEG to which they are exposed, and have the same phenotypic level of tolerance. Thus, selection by exposure to stress is unable to discriminate (on the basis of growth) between the innately tolerant and intolerant cell types within the population. This is indicated also by the fact that clones isolated from a population of cells adjusted to growth on 25% PEG do not show an enriched frequency of tolerant phenotypes when grown in the absence of PEG compared to the nonselected normal cell population which has never been adjusted to growth on PEG.     

Inheritance of deeper root length and grain yield in half-diallel durum wheat (Triticum durum) crosses

Inheritance, heterosis and combining ability of deeper root length (DRL) and grain yield (GY) were investigated in durum wheat populations obtained from half‐diallel crossings among five parental lines differing in their DRL and GY. The study was conducted with the final objective of identifying parent lines to be used in a breeding programme to develop drought‐tolerant wheat varieties. General combining ability and specific combining ability effects were significant for both traits; however, additive gene effects were predominant over non‐additive effects. Partial dominance was ambidirectional for DRL and unidirectional for GY. Lines INRAT69 and Omrabia conferred DRL whereas Omrabia and Khiar transmitted high GY to their respective progenies. In the studied material, both characters were controlled mainly by dominant alleles, but they could also be attributed to recessive alleles although less frequently. Both broad‐sense and strict‐sense heritabilities were high for DRL, confirming the importance of additive gene effects, whereas strict‐sense heritability for GY was average, indicating the importance of interaction effects as compared with the additive effects; this could mean reduced selection efficiency for the latter trait. Thus, the expected genetic progress per cycle of selection will be lower for GY compared with DRL. Omrabia should be included in the breeding programme as a parent so that while maintaining high GY, resulting progeny should be better able to resist drought through DRL.     

An estimation of the heritability of phototaxis in Daphnia magna Straus

Summary The phototactic responses of four clones of Daphnia magna were experimentally analysed. Broad-sense heritability of this behavioural character was estimated through an analysis of variance, and it was very high under the standardised experimental conditions of this study.