Validation of associations between plant traits and thrips damage in cabbage

When cabbage is cultivated for storage in the Netherlands, it is usually harvested around mid-October. This type of cabbage crop may be severely damaged by thrips (Thrips tabaci). The thrips population on the plants and the more severe symptoms develop mostly during September and October. Also during cold storage symptoms continue to develop. The damage caused by thrips is due to the symptoms that develop after feeding, which are small callus-like growths that will turn brownish after some time and which may cover substantial amounts of leaf area. Large differences exist between cabbage varieties in their susceptibility to thrips damage. Based on several years of field trials with more than 40 commercial varieties and gene bank accessions it was established that a large proportion of the variation for thrips damage could be explained by a few plant traits: the amount of leaf surface wax, earliness and Brix (Voorrips et al, 2008). Using an F3-line population derived from a cross between a high-damage, low-wax, high-Brix, earlier heading and a low-damage, high-wax, low-Brix, later heading accession we determine whether the relations between plant traits and thrips damage can be confirme

Analysis of a database of DNA profiles of 734 hybrid tea rose varieties

Over 10,000 Hybrid Tea rose varieties have been described. The large number of varieties and the size of the reference collections may cause problems in DUS (Distinctiveness, Uniformity, and Stability) testing. Molecular markers may help to solve these problems by providing high power to identify and recognise seedling-derived varieties based on unique genotypes, while grouping mutants into groups with identical marker scores. Here we describe the use of a set of 11 rose microsatellite markers to generate a database of molecular profiles of Hybrid Tea varieties. The data were analysed with respect to reproducibility, discriminative power, genetic (sub) structure, and correlation between molecular and DUS characteristics. The use of the markers in the DUS context is discussed with respect to the options 2 and 3 as they were formulated by the UPOV-BMT working group. It is concluded that an option 3 approach (granting of PBR based on distinctness observed with molecular markers) is feasible for ros

Plant traits associated with resistance to Thrips tabaci in cabbage (Brassica oleracea var capitata)

Thrips tabaci is a major problem in the cultivation of cabbage for storage, as this pest causes symptoms that necessitate the removal of affected leaves from the product. Between cabbage varieties large differences in susceptibility occur. This study aimed to identify plant traits associated with these differences, in field experiments with natural infestation in 2005 and 2006. One factor affecting the amount of thrips damage was the timing of the development of the head. In an experiment with different planting dates especially the early maturing, more susceptible varieties were shown to benefit from later planting. In comparisons of multiple varieties in both years, regression studies showed that more advanced plant development in August and early September increased thrips damage at the final harvest. However, no single plant trait explained more than 25% (2005, Brix) or 48% (2006, compactness) of the variation in thrips damage. Optimal regression models, explaining up to 75% of the variation in thrips damage included Brix and leaf surface wax late in the season, as well as an indicator of plant development earlier in the season, and in 2005 also leaf thickness. The possible role of these plant traits in relation to thrips is discusse

Earliness, leaf surface wax and sugar content predict varietal differences for thrips damage in cabbage

When cabbage is cultivated for storage in the Netherlands, it is usually harvested around mid-October. This type of cabbage crop may be severely damaged by thrips (Thrips tabaci). The thrips population on the plants and the more severe symptoms develop mostly during September and October. Also during cold storage symptoms continue to develop. The damage caused by thrips is due to the symptoms that develop after feeding, which are small callus-like growths that will turn brownish after some time and which may cover substantial amounts of leaf area. Large differences exist between cabbage varieties in their susceptibility to thrips damage. It is not clear whether these differences are due to resistance (affecting the thrips population in the plant) or to tolerance (affecting the development of symptoms upon thrips feeding). Further, not much is known about plant traits affecting the resistance or tolerance to thrips. In order to guide selection and breeding for resistance to thrips, this study aimed to identify plant traits causing these differences. In the years 2005, 2006 and 2007 we performed field experiments with collections of varieties differing in a number of plant traits, with earliness varying from moderately late to very late. In the field experiments we relied upon natural infestation by thrips. Several times during the period August-October plants were harvested and assessed for the amount of thrips damage and the number of thrips, as well as for several morphological and physiological traits, including head circumference, leaf thickness, developmental stage, head compactness, leaf surface wax, and Brix value as an indication of the content of soluble sugars. One factor affecting the amount of thrips damage was the timing of the development of the head. Regression studies showed that more advanced plant development at the end of August increased thrips damage at the final harvest. Other plant traits affecting thrips damage were Brix and the amount of leaf surface wax. However no single plant trait explained more than 45% of the variation in thrips damage at the final harvest. Optimal regression models, explaining up to 75% of the variation in thrips damage included Brix and leaf surface wax late in the season, as well as an indicator of plant development earlier in the season, and in 2005 also leaf thickness. The possible role of these plant traits in relation to thrips is discussed

Meer kennis over ziekten en plagen in kool helpt aanpak

Trips, zwartnervigheid, bladvlekkenziekte en valse meeldauw: het zijn een paar van de ziekten en plagen die de teelt van kwalitatief goede kool en goed zaaizaad belemmeren. Kennis over de plaag of de schimmel levert aanwijzingen voor bestrijding

Exploratory QTL analyses of some pepper physiological traits in two environments

behind phenotypic differences and led to selection of genotypes having favourable traits. Continuous monitoring of environmental conditions has also become an accessible option. Rather than single trait evaluation, we would prefer smarter approaches capable of evaluating multiple, often correlated and time dependent traits simultaneously as a function of genes (QTLs) and environmental inputs, where we would The use of molecular breeding techniques has increased insight into the genetics like to include intermediate genomic information as well. In this paper, an exploratory QTL analysis over two environments was undertaken using available genetic and phenotypic data from segregating recombinant inbred lines (RIL) of pepper (Capsicum annuum). We focused on vegetative traits, e.g. stem length, speed of stem development, number of internodes etc. We seek to improve the estimation of allelic values of these traits under the two environments and determine possible QTL x E interaction. Almost identical QTLs are detected for each trait under the two environments but with varying LOD scores. No clear evidence was found for presence of QTL by environment interactions, despite differences in phenotypes and in magnitude of QTLs expression. Within the EU project SPICY (Voorrips et al., 2010 this issue), a larger number of environments will be studied and more advanced statistical analysis tools will be considered. The correlation between the traits will also be modelled. The identification of markers for the important QTL (Nicolaï et al., 2010 this issue) will improve the speed and accuracy of genomic prediction of these complex phenotype

Crop growth models for the -omics era: the EU-SPICY project

The prediction of phenotypic responses from genetic and environmental information is an area of active research in genetics, physiology and statistics. Rapidly increasing amounts of phenotypic information become available as a consequence of high throughput phenotyping techniques, while more and cheaper genotypic data follow from the development of new genotyping platforms. , A wide array of -omics data can be generated linking genotype and phenotype. Continuous monitoring of environmental conditions has become an accessible option. This wealth of data requires a drastic rethinking of the traditional quantitative genetic approach to modeling phenotypic variation in terms of genetic and environmental differences. Where in the past a single phenotypic trait was partitioned in a genetic and environmental component by analysis of variance techniques, nowadays we desire to model multiple, interrelated and often time dependent, phenotypic traits as a function of genes (QTLs) and environmental inputs, while we would like to include transcription information as well. The EU project 'Smart tools for Prediction and Improvement of Crop Yield' (KBBE-2008-211347), or SPICY, aims at the development of genotype-to-phenotype models that fully integrate genetic, genomic, physiological and environmental information to achieve accurate phenotypic predictions across a wide variety of genetic and environmental configurations. Pepper (Capsicum annuum) is chosen as the model crop, because of the availability of genetically characterized populations and of generic models for continuous crop growth and greenhouse production. In the presentation the objectives and structure of SPICY as well as its philosophy will be discussed

Pedigree genotyping: a new pedigree-based approach of QTL identification and allele mining

To date, molecular markers are available for many economically important traits. Unfortunately, lack of knowledge of the allelic variation of the related genes hampers their full exploitation in commercial breeding programs. These markers have usually been identified in one single cross. Consequently, only one or two favourable alleles of the related QTL are identified and exploitable for marker-assisted breeding (MAB), whereas a breeding program may include several alleles. Selection for just these alleles means that many favourable genotypes are ignored, which decreases efficiency and leads to genetic erosion. A new approach, called Pedigree Genotyping, allows the identification and exploitation of most alleles present in an ongoing breeding program. This is achieved by including breeding material itself in QTL detection, thus covering multiple generations and linking many crosses through their common ancestors in the pedigree. The principle of Identity by Descent (IBD) is utilised to express the identity of an allele of a modern selection in terms of alleles of founding cultivars. These founder alleles are used as factors in statistical analyses. Co-dominant markers like SSR (microsatellite) markers are essential in this approach since they are able to connect cultivars, breeding selections and progenies at the molecular marker level by monitoring specific chromosomal segments along family trees. Additional advantages of the use of breeding genetic material are (1) a major reduction in experimental costs since plant material is already available and phenotyped by default (2) continuity over generations within breeding programs with regard to marker research (3) the testing of QTL-alleles against a wide range of genetic backgrounds, making results generally applicable, (4) intra- as well as inter-QTL interactions can be explored. Fruit firmness in apple will be used as an example to illustrate the principles of this powerful approach to detect QTLs and estimate their allelic variatio

Pedigree genotyping: a new pedigree-based approach of QTL identification and allele mining by exploiting breeding material

To date, molecular markers have been made available for many economically important traits. Unfortunately, lack of knowledge of their allelic variation hampers their full exploitation in commercial breeding programs. These markers have usually been identified in one single cross. Consequently, only one or two favourable alleles of the related QTL are identified and may be exploited for marker-assisted breeding (MAB), while a breeding program may include several alleles. Selection for only these alleles means that many favourable genotypes are ignored, which decreases efficiency and leads to genetic erosion. A new approach, called pedigree genotyping, allows the identification and exploitation of the majority of alleles present in an ongoing breeding program. This is achieved by including breeding material itself in QTL detection, so covering multiple generations and linking many crosses through their common ancestors in the pedigree. The principle of Identity by Descent (IBD) is utilised to express the identity of an allele of a modern selection in terms of alleles of founding cultivars. These founder alleles are used as factors in statistical analysis. Co-dominant markers, like SSR (= microsatellite) markers, are essential in this approach since they are able to connect cultivars, breeding selections and progenies at the molecular marker level by monitoring specific chromosomal segments along family trees. Additional advantages of the use of breeding genetic material are (1) a major reduction in experimental costs since plant material is already available and phenotyped by default (2) continuity over generations within breeding programs with regard to marker research (3) the testing of QTL-alleles against a wide range of genetic backgrounds, making results generally applicable (4) possibility to explore intra- as well as inter-QTL interactions. Fruit firmness in apple is used as an example to illustrate the principles of this powerful approach to detect QTLs and estimate their allelic variation. Prospects for strawberry are also indicate