A rapid real-time PCR assay for detecting columnar growth in apples (Malus × domestica)

Columnar growth in apples can have considerable positive consequences for orchard maintenance, but the lack of columnar cultivars producing fruits with desired market quality prevents their broader utilization in orchards. New crossings focused on their breeding are therefore conducted throughout the world every year. Unfortunately, the reliable discrimination between columnar growth and normal phenotype is difficult until seedlings are 2–3 years of age. However, molecular marker–assisted selection (MAS) can be used in seedlings several weeks old providing immense help in breeding programmes focused on columnar apple production. Here, we describe a rapid and reliable method for the detection of both wild-type (WT) and columnar (Co) alleles originating from ‘McIntosh Wijcik’ in a single reaction using a real-time PCR allelic discrimination approach. Our assay was tested in 130 genotypes (80 normal and 50 columnar habit) from various crossings and their parents, and in all cases, genotype corresponded to phenotype. The assay is thus suitable for laboratories interested in high-throughput MAS for columnar tree habit breeding.     

Assessment of tissue culture-derived ‘Gala’ and ‘Royal Gala’ apples (Malus × domestica Borkh.) for somaclonal variation

To assess somaclonal variation, ‘Gala’ and ‘Royal Gala’ trees obtained via axillary and adventitious bud formation were compared ex vitro to conventionally grafted trees. In general, tissue culture-derived trees were relatively erect in comparison to grafted trees. Their branch angles were narrower than those of grafted trees. All trees that flowered had pink blossoms. There were no obvious differences in flowering time or in floral morphology. Most of the seven-year-old grafted control trees produced more fruits than either axillary or regenerated trees. Although there were differences in the range of fruit color between ‘Royal Gala’ and ‘Gala’ apples in both the control and tissue culture-derived plants (the fruits of ‘Royal Gala’ were darker red and more striped than those of ‘Gala’) and also in the degree of pigmentation from tree-to-tree, none of the variation exceeded that observed among apples harvested from an individual ‘Royal Gala’ or ‘Gala’ control tree for either the plants derived from axillary buds or adventitiously. Since both ‘Gala’ and ‘Royal Gala’ axillary buds showed very little somaclonal variation for the morphological and reproductive traits we studied, it appears that tissue culture may be a useful way to propagate these cultivars. This revised version was published online in August 2006 with corrections to the Cover Date.     

Do floral resources influence pollination rates and subsequent fruit set in pear (Pyrus communis L.) and apple (Malus x domestica Borkh) cultivars?

Pear and apple are among the main fruit crops worldwide. These species can be planted in mixed orchards, and they both depend on insect pollination for fruit set. As pollinating insects are attracted by the floral resources, we investigated nectar and pollen production and chemical composition in four pear (‘Concorde’, ‘Conférence’, ‘Doyenné du Comice’, ‘Triomphe de Vienne’) and five apple (‘Braeburn’, ‘Golden Reinders’, ‘Jonagored’, ‘Pinova’, ‘Wellant’) cultivars commonly grown in Belgium. We also investigated whether insect flower visitation rate and pollination efficiency are linked to floral resource quantity and quality. The pear cultivars flowered one week before the apple cultivars in early spring, and their flowers were about six times less visited by insects. The visitors foraged more on the pollen of the pear trees and the nectar of the apple trees. Pear flowers produced higher volumes of nectar than apple flowers (1.3–3.2 μl vs. 0.4-0.6 μl), but with lower sugar concentration (9.6%-10.8% vs. 28.3%-36.4%). Pear flowers also produced fewer pollen grains per anther than apple flowers (2425–4937 vs. 3284–7919), but these had higher polypeptide (346–362 μg/mg vs. 216–303 μg/mg), amino-acid (40–77 μg/mg vs. 12–18 μg/mg) and phytosterol (21–47 μg/mg vs. 15–43 μg/mg) concentrations. The foraging behavior of the insects is thus better explained by nectar and pollen quality rather than quantity. Despite the differences in flower visitation rates, pollination of both species resulted in valuable fruit production.     

QTL examination of a bi-parental mapping population segregating for “short-stature” in hop (<Emphasis Type="Italic">Humulus lupulus</Emphasis> L.)

Increased labor costs and reduced labor pools for hop production necessitate the development of strategies that improve efficiency and automation of hop production. One solution for reducing labor inputs is the use of “short-trellis” hop varieties. Unfortunately, little information exists on the genetic control of this trait in hop, and there are no known molecular markers available for selection. This preliminary study was enacted to identify QTLs associated with expression of short-stature growth phenotype using SNPs identified within genome-assembled scaffolds. A bi-parental mapping population of 87 offspring was obtained from the cross, “Pioneer × 25/95/15”. Genotyping-by-sequencing was performed on parents and offspring. SNPs were identified using TASSEL v3.0 with either ‘Teamaker’ reference genome or ‘Shinsuwase’ genome. The genetic map derived from ‘Teamaker’ SNPs was far superior and was used for all further analysis. QTL analysis identified eight QTLs linked to short stature with five showing strong statistical association based upon three different statistical analyses. All eight QTLs were found on linkage group one. Evaluation of scaffolds containing SNP markers located at or surrounding QTL regions (±1 cM) identified 67 putative genes—several of which are known structural genes. A genome-wide scan of SNP markers identified an additional marker found on a scaffold containing a putative gene (Aspartyl protease family protein) known to induce dwarf characteristics in other species. Further validation of significantly associated markers on different populations is necessary prior to implementation in marker-assisted selection.     

Degreening behavior in ‘Fallglo’ and ‘Lee × Orlando’ is correlated with differential expression of ethylene signaling and biosynthesis genes

Two citrus types (‘Fallglo’ and ‘Lee × Orlando’) exhibiting differential fruit degreening response when treated with ethylene were selected. Fruit were harvested at commercial maturity but at different developmental periods (Harvest I, II and III). Rate of color change was greater in ‘Fallglo’ than in ‘Lee × Orlando’ when fruit were treated with 5 μL L⁻¹ of ethylene for 24 h. After 24 h of transfer of fruit to ethylene-free storage, rate of change decreased in ‘Fallgo’ and exhibited varied response in ‘Lee × Orlando’ depending on harvest date. ‘Fallglo’ fruit from Harvests I and II were completely degreened at the end of storage for 7 d; however ‘Lee × Orlando’ were not and were green in color. No difference in seedling triple response was observed between ‘Fallglo’ and ‘Lee × Orlando’ and sequences of the four ethylene receptors were identical between them. Expression of genes involved in ethylene biosynthesis and signaling pathways were studied in flavedo to test if differences in these pathways were correlated with differential ethylene sensitivity of the citrus types. Basal levels of ACS2 and ACO expressions declined as maturity progressed, and ethylene-induced expression of ACS1 and ACO were influenced by fruit maturity. At Harvests I and II, ethylene-induced increase in ACS1 and ACO expressions and ACC levels were greater in ‘Fallglo’ than in ‘Lee × Orlando’. Ethylene treatment influenced MACC content only during Harvest I in ‘Lee × Orlando’. MACC levels were generally higher in ‘Lee × Orlando’ than in ‘Fallglo’. Expressions of ETR1 and ETR2 were ethylene responsive in ‘Fallglo’ and only ETR1 expression was ethylene responsive in ‘Lee × Orlando’. Ethylene had more impact on ETR1 expression in ‘Fallglo’ than in ‘Lee × Orlando’. Ethylene had a negative effect on ETR3 expression which was more pronounced in ‘Lee × Orlando’ than in ‘Fallglo’. Expressions of ERS1, CTR1, EIN2, EIL1 and EIL2 were not affected by ethylene in both citrus types. Expression of chlorophyllase gene and rate of total chlorophyll degradation were higher in ‘Fallglo’ than in ‘Lee × Orlando’ during ethylene treatment. Differential degreening behavior of ‘Fallglo’ and ‘Lee × Orlando’ correlated with peel maturity, and factor(s) downstream of ethylene signaling but upstream of ethylene biosynthesis play a role in the differential sensitivity.     

Management targets for continuously stocked mixed oat × annual ryegrass pasture in a no-till integrated crop–livestock system

Feeding livestock with cover crops can improve the efficiency and sustainability of integrated crop–livestock systems under no-till. However, no-till systems are based on permanent soil cover by organic material, so grazing livestock can compete for soil cover. Hence, managing stocking rates during the grazing period of the cultivated forage species is a key factor to assure enough herbage mass for maintaining long-term sustainable no-till systems. In this context, the objective of this study was to determine sward management targets for a continuously stocked mixed oat (Avena strigosa) × annual ryegrass (Lolium multiflorum) pasture in rotation with soybean in a no-till integrated crop–livestock system to determine the optimum balance between animal production and herbage mass for soil cover. The effects of sward height management on animal performance and herbage mass covers were evaluated. Treatments corresponded to four sward heights: 10, 20, 30 and 40 cm, maintained throughout the experimental period through continuous stocking and variable stocking rate, plus a no-grazing control area. Treatments were arranged in a randomized complete block design with three replications. Herbage mass and animal performance increased linearly with sward height, but weight gain per hectare decreased. Grazing efficiency fitted to a quadratic regression and conversion efficiency a logarithmic model. Equilibrium between grazing and conversion efficiencies was reached on swards managed at 20 cm, indicating that this sward height provided enough herbage mass to allow both animal performance and no-till crop demand for soil cover.     

Plant age and in vitro or in vivo propagation considerably affect cold tolerance of Miscanthus × giganteus

The aims of the study were to determine why young Miscanthus × giganteus plants are more frost sensitive during the first winter than older plants, to compare cold tolerance of plants propagated in in vivo and in vitro conditions, and to select plants with higher cold tolerance. The study was performed in three experiments in which plants were prehardened at 12 °C for 2 weeks, hardened at 5 °C for 3 weeks and next chilled at 0 °C or ?3 °C for 3 or 14 days. Afterwards shoot regrowth from rhizomes was evaluated. In Experiment 1 frost tolerance of young plants obtained from a horticultural farm and plants that had already survived the first winter in the field was compared on the basis of LT₅₀ coefficient. In Experiment 2 frost tolerance of plants obtained in vivo and in vitro was compared. Experiment 3 was performed on four groups of plants: in vivo and in vitro obtained plants which were twice selected in cold, as well as in vivo and in vitro obtained plants which were cold treated once. Plants of all these groups were analysed with respect to their frost tolerance. They were prehardened, hardened and subjected to a temperature of 0 °C or ?3 °C for 14 days. The changes in processes accompanying cold acclimation occurring in the rhizomes or leaves of these plants were investigated. The content of abscisic acid, low-molecular antioxidants and phenolics, as well as catalase and non-specific peroxidase activities were analysed.Young commercially obtained plants were more frost sensitive than plants which had survived the first winter in the field. This effect could be caused by a small amount of storage compounds accumulated in finely divided rhizomes produced in a horticultural farm. Prehardening temperature of 12 °C caused more considerable changes in cold acclimation processes in Miscanthus rhizomes than hardening temperature of 5 °C. Plants propagated by in vitro culture were more cold tolerant but only in the first vegetative season compared to plants obtained in vivo. Plants chilled twice demonstrated a higher low-molecular antioxidant level, as well as a greater capability of phenolic accumulation compared to plants which were once cold stressed. Regardless of the recurrence of cold acclimation, ABA level was significantly increased in leaves by prehardening and in rhizomes by hardening. Each repetition of cold acclimation increased cold tolerance and shoot regeneration ability of M. × giganteus rhizomes.     

Screening for grain dormancy in segregating generations of dormant × non-dormant crosses in white-grained wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Pre-harvest sprouting (PHS) in wheat (Triticum aestivum L.) is a significant problem. Introgression of genes controlling grain dormancy into white-grained bread wheat is one means of improving resistance to PHS. In this study seven dormant (containing the SW95-50213 and AUS1408 sources) × non-dormant crosses were produced to investigate the effectiveness of selection for grain dormancy in early segregating generations. Each generation (F₁–F₄) was grown in a temperature controlled glasshouse with an extended photoperiod (i.e. continuous light). F₂ and F₃ generations were subject to selection. Five hundred harvest-ripe grains were tested for germination over a 14 day period, and the 100 most dormant grains were retained and grown-on to produce the next generation within each cross. The response to selection was assessed through analysis of the time to 50% germination (G₅₀) in the F₂, F₃ and F₄ generations. In addition, changes in marker class frequencies for two SSR markers (barc170 and gpw2279) flanking a known quantitative trait locus (QTL) for grain dormancy on chromosome 4A were assessed in DNA from F₂ plants selected from early germinating (non-dormant) and late germinating (dormant) phenotypic extremes within each cross. Selection for grain dormancy in the F₂ and F₃ generations effectively recovered the dormant phenotype in all seven crosses, i.e. the F₄ generation was not significantly different from the dormant parent. Further, selection based on individual F₂ grains changed marker class frequencies for the 4A dormancy QTL; in most cases eliminating the marker class homozygous for the non-dormant alleles. Application of this screening method will enable breeders to better select for grain dormancy and may lead to development of new cultivars offering effective resistance to PHS in the near future.     

Assessing the importance of genotype × environment interaction for root traits in rice using a mapping population III: QTL analysis by mixed models

The phenotypic analysis of field experiments includes information about the experimental design, the randomization structure and a number of putative dependencies of environment and design factors on the trait investigated. In QTL studies, the genetic correlation across environments, which arises when the same set of lines is tested in multiple environments, plays an important role. This paper investigates the effect of model choice on the set and magnitude of detected root QTL in rice. Published studies on QTLs for root traits indicate that different results are obtained if varying genetic populations are used and also if different environmental conditions are included. An experiment was conducted with 168 RILs of the Bala × Azucena mapping population plus parents as checks under four environmental conditions (low light, low nitrogen, drought and a control environment). We propose a model that incorporates all relevant experimental information into a composite interval mapping approach based on a mixed model, which especially considers the correlation of genotypes in different environments. An extensive sequential model selection procedure was applied based on the phenotypic model, using the AIC to determine an appropriate random structure and Type 3 Wald F-tests for selection of fixed effects. In a first step we checked whether any of the fixed effects and random (nested) design effects could be dropped. Secondly, an appropriate covariance structure was chosen for genotype × environment interaction. In a third step Box-Cox transformations were applied based on residual analysis. We compared profiles of composite interval mapping scans with and without the inclusion of genotype × environment interaction and the experimental design information. Some distinct differences in profiles indicate that insufficient modeling of the non-QTL part can lead to an overly optimistic interpretation of QTL main effects in interval mapping. It is concluded that mixed model QTL mapping offers a reasonable way to separate environmental and genetic influences in the evaluation of quantitative genes and especially enables a more realistic assessment of QTL and QTL × environment effects than standard approaches by including all relevant effects.     

Variation for bioactive compounds in ají (Capsicum baccatum L.) and rocoto (C. pubescens R. & P.) and implications for breeding

Ají (Capsicum baccatum L.) and rocoto (C. pubescens R. & P.) are two Capsicum pepper species native to the Andean region that have not been subjected to intensive breeding. However, the increase in its demand in European markets has sparked the development of breeding programmes for adaptation to Mediterranean climates, which include breeding for higher levels of bioactive compounds. We have studied the composition of red and yellow carotenoids (C _R and C _Y, respectively), ascorbic acid (AA), and total phenolics (TP) in 34 accessions of Capsicum, including 23 of C. baccatum, eight of C. pubescens, and 3 controls of C. annuum, which were grown in Spain both under greenhouse (GH) and open field (OF) conditions. The results show that in both growing conditions C. baccatum presents a considerable variation for most of the traits studied, with several accessions having similar or higher levels than C. annuum for the compounds studied. This indicates that C. baccatum is an important source of antioxidant compounds with nutritional value. On the contrary, C. pubescens had a poor performance, with low levels for all the compounds studied, and a poor adaptation to the conditions of Mediterranean climates. When considering the GH or OF growing cycles separately, heritability values were high (>0.75) for C _R, C _Y and AA, and moderate (0.42 for GH and 0.62 for OF) for TP. The existence of an important genotype × environment interaction resulted in lower levels for heritability when considering both growing cycles together, although the values were still high for C _R and AA (>0.6). Positive significant genotypic correlations among all the traits studied were found, except for TP with C _R and AA in the OF cycle. This information indicates that there are good prospects for developing C. baccatum varieties with higher levels of bioactive compounds.     

Advanced-backcross QTL analysis in spring barley: IV. Localization of QTL × nitrogen interaction effects for yield-related traits

The advanced backcross quantitative trait locus (AB-QTL) analysis has proven its usefulness to identify and localize favourable alleles from exotic germplasm and to transfer those alleles into elite varieties. In a balanced design with up to six environments and two nitrogen fertilization (N treatment) levels, a 4-factorial mixed model analysis of variance (ANOVA) was used to identify QTL main effects, QTL × environment interaction effects and QTL × N treatment interaction effects in the spring barley BC₂DH population S42. The yield-related traits studied were number of ears per m², days until heading, plant height, thousand grain weight (TGW) and grain yield. In total, 82 QTLs were detected for all traits. This finding was compared to a previous QTL study of the same population S42, where the current field data was reduced to one half through restriction of the analysis to the standard N treatment level (von Korff et al., Theor Appl Genet 112: 1221–1231, 2006). These authors located 54 QTLs for the same traits by applying a 3-factorial mixed model similar to the current model but excluding the factor N treatment. We found that QTL × environment interaction, alone or in combination, accounted for 24 of the newly uncovered QTLs, whereas QTL × N treatment interaction was of lesser importance with six new cases in total. A valuable QTL interacting with N treatment has been identified on chromosome 7H where lines carrying the wild barley allele were superior in number of ears per m² in either N treatment. We conclude that in population S42 the extension of the phenotype data set and the inclusion of N treatment into the mixed model increased the power of QTL detection by providing an additional replication rather than by revealing specific N treatment QTLs.     

Genotype × environment interactions for seed yield in rainfed winter safflower (Carthamus tinctorius L.) multi-environment trials in Iran

Evaluation of genotype × environment interaction (GEI) is an important component of the variety selection process in multi-environment trials. The objectives of this study were first to analyze GEI on seed yield of 18 spine safflower genotypes grown for three consecutive seasons (2008–2011) at three locations, representative of rainfed winter safflower growing areas of Iran, by the additive main effects and multiplicative interaction (AMMI) model, and second to compare AMMI-derived stability statistics with several stability different methods, and two stability analysis approaches the yield-stability (Ysi) and the GGE (genotype + genotype × environment) biplot that are widely used to identify high-yielding and stable genotypes. The results of the AMMI analysis showed that main effects due to genotype, environment, and GEI as well as first six interaction principle component axes (IPCA1 to 6) were significant (P < 0.01). According to most stability statistics of AMMI analyses, genotypes G5 and G14 were the most stable genotypes across environments. According to the adjusted stability variance (s²), the high-yielding genotype, G2, was unstable due to the heterogeneity caused by environmental index. Based on the definition of stable genotypes by regression method (b = 1, S _d ²  = 0), genotypes G11, G9, G14, G3, G12 and G13 had average stability for seed yield. Stability parameters of Tai indicated that genotype G5 had specific adaptability to unfavorable environments. The GGE biplot and the Ysi statistic gave similar results in identifying genotype G2 (PI-209295) as the best one to release for rainfed conditions of Iran. The factor analysis was used for grouping all stability parameters. The first factor separated static and dynamic concepts of stability, in which the Ysi and GGED (i.e., the distance from the markers of individual genotypes to the ideal genotype) parameters had a dynamic concept of stability, and the other remaining parameters had static concept of stability.     

Perennial growth and salinity tolerance in wheat × wheatgrass amphiploids varying in the ratio of wheat to wheatgrass genomes

Since wheat and other annual cereal crops are often harvested for forage instead of grain in California, replacing them with perennial crops could save energy and reduce the release of heat-trapping gases. To assess the potential for perennial crops based on wheat, biomass yield and stand persistence were studied for nine wheat×wheatgrass amphiploids (8x to 14x) and five wheatgrass species (2x to 10x) over three seasons in the Central Valley, California. The 8x and 10x amphiploids died after one biomass harvest and a single summer period. In contrast, the 14x amphiploids, which were sterile, continued producing biomass over the entire period of the trial. They were also highly salt-stress tolerant with little decline in biomass production in response to an increase in salinity from 100 and 250 mM NaCl in a solution-culture study. The development of a salt-stress-tolerant perennial crop based on wheat for the California-type climate will require either a substantial improvement in perennial growth of low-ploidy (8x) amphiploids or the development of technology for efficient vegetative propagation of the sterile high-ploidy (14x) amphiploids.     

Complex segregation analysis of day-neutrality in domestic strawberry (<Emphasis Type="Italic">Fragaria ×ananassa</Emphasis> Duch.)

Thirty bi-parental progenies were generated using 45 genotypes from the University of California (UC) strawberry breeding population as parents. Both parent genotypes and their offspring were classified for photoperiod insensitivity, or day-neutrality, for flowering using a late-season flowering score and the number of inflorescences per plant recorded during late summer. Complex Segregation Analysis of these traits indicated that their distributions were best explained by a genetic model that postulates a single major locus with partial dominance for day-neutrality in combination with a background of polygenic and environmental variation. The frequency of the allele conferring day-neutrality was estimated as p = 0.59–0.62 in this experimental population. Genotypic values for the inferred major locus were estimated as a = 1.12 and d = −0.81 for the flowering score, and a = 4.93 and d = 2.41 for inflorescence number. Further resolution of inheritance patterns were obtained by comparing the phenotypic variance for each trait with estimates obtained by insertion of these genotypic class values and allele frequencies into standard quantitative genetic models, and by the comparing variance components estimated using a mixed model analysis with and without inferred genotypic classes as a fixed effect. These comparisons suggest that the major gene determines 80.5% and 73.9% of the additive genetic variance for flowering score and inflorescence number respectively. One complicating feature of the results obtained here is that a non-Mendelian model of segregation fit statistically better than a fixed Mendelian model. The genetic parameters estimated using this non-Mendelian model were essentially identical to those obtained with fixed segregation; hybrid and octoploid ancestry, selection affecting flowering response, and limited number of generations in the analysis are discussed as possible explanations of this result.     

Genetic analysis and genotype × environment (G × E) for grey leaf spot disease resistance in elite African maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) germplasm

Maize grey leaf spot (GLS) disease remains an important foliar disease in sub-Saharan Africa accounting for more than 25% yield losses in maize. Information on inheritance of GLS resistance of germplasm adapted to African environments is required in new sources being identified. Therefore, hybrids generated from a 10 × 10 half-diallel mating of tropical advanced maize inbred lines were evaluated in six environments to determine combining ability, genotype × environment interaction (G × E) and the impact of GLS disease on grain yield. General combining ability effects were highly significant and accounted for 72 and 68% of the variation for GLS resistance and grain yield, respectively. Significant specific combining ability effects associated with reduced disease levels were observed in some hybrids when one parent was resistant, and these may be exploited in developing single cross maize hybrids. Regression analysis showed a 260–320 kg ha^?1 decrease in maize grain yield per each increase in GLS disease severity score, and significant associations (r = ?0.31 to ?0.60) were observed between grain yield and GLS severity scores. This showed the potential of GLS disease to reduce yield in susceptible varieties grown under favourable disease conditions, without control measures. Genotype and genotype × environment biplots and correlation analysis indicated that the significant G × E observed was not due to changes in hybrid ranking, implying absence of a significant crossover interaction. Therefore, predominance of additive gene effects imply that breeding progress for GLS disease resistance would be made through selection and this could be achieved at a few hot-spot sites, such as Baynesfield and Cedara locations in South Africa, and still deploy the resistant germplasm to other environments in which they are adapted.