Genetic research in a public-private research consortium: prospects for indirect use of Elige breeding germplasm in academic research

The creation of a public¿private research partnership between plant breeding industry and academia can be beneficial for all parties involved. Academic partners benefit from the material contributions by industry and a practically relevant research focus, while industry benefits from increased insights and methodology tailored to a relevant set of data. However, plant breeding industry is highly competitive and there are obvious limits to the data and material partners are willing and able to share. This will usually include current and historic released cultivated materials, but will very often not include the elite germplasm used in-house to create new cultivars. Especially for crops where hybrid cultivars dominate the market, parental lines of hybrid cultivars are considered core assets that are never provided to outside parties. However, this limitation often does not apply to DNA or genetic fingerprints of these parental lines. We developed a procedure to take advantage of elite breeding materials for the creation of new promising research populations, through indirect selection of parents. The procedure starts with the identification of a number of traits for further study based on the presence of marker-trait associations and a priori knowledge within the participating companies about promising traits for quality improvement. Next, regression-based multi-QTL models are fitted to hybrid cultivar data to identify QTLs. Fingerprint data of parental lines of a limited number of specific hybrids are then used to predict parental phenotypes using the multi-QTL model fitted on hybrid data. The specific hybrids spanned the whole of the sensory space adequately. Finally, a choice of parental lines is made based on the QTL model predictions and new promising line combinations are identified. Breeding industry is then asked to create and provide progeny of these line combinations for further research. This approach will be illustrated with a case study in tomato

Use of molecular markers in plant breeding = [Het gebruik van moleculaire merkers in de plantenveredeling]

Molecular markers provide plant breeding with an important and valuable new source of information. Linkage between molecular markers can be translated to genetic linkage maps, which have become an important tool in plant and animal genetics. Linkage between (quantitative) trait-data and occurrences of marker alleles allow identification of important genetic factors, underlying observable traits. Knowledge that results from such analyses, i.e. the location on the genome of important genetic factors (quantitative trait loci or QTLs), can and should be applied when making selection and breeding decisions.Selection of parents is an important issue in plant breeding. Basing selection on QTL information, i.e. applying marker-assisted selection, can result in an increased selection efficiency. This is especially true for quantitative traits with a low heritability. For efficient application of marker-assisted selection reliable and fairly complete QTL-mapping results are required. When QTLs were mapped for several traits a multiple trait-selection can be devised, through the use of a suitable index. In this case an ideal target genotype, containing favourable alleles for QTLs that affect the traits of interest, can be constructed and crosses can be made between selected parents in such a way that the probability of obtaining the target genotype is maximised. Although this approach looks promising, and simulation results show an improved selection performance, several problems remain which are limiting application in practise. A more reliable and complete mapping of QTLs, including mapping of interaction between QTLs, mapping of QTLs with a higher reliability, for instance resulting from a combined mapping of several traits, and mapping of QTLs in more diverse non-mapping types of populations could greatly contribute to an increased application of marker-assisted selection, and hence a more efficient selection in plant breeding.Although it is common practise to resort to unadapted material when searching for new genetic variation, the undesired characteristics that accompany the genes coding for the target trait of interest, limit the applicability of introducing 'foreign' genes. With the help of marker and QTL-analysis the genome region that harbours genes which are responsible for the desired characteristics can be identified more precisely and thus the size of the fragment that needs to be introgressed can remain restricted. Marker-assisted backcrossing allows a much more controlled method of gene introgression, limiting the amount of 'linkage-drag' and requiring less generations of backcrossing than conventional backcrossing for yielding suitable genotypes.Developments that favour application of marker-assisted selection are still progressing at a high rate. New technical enhancements in the field of molecular biology, new protocols and methods for identification of genetic factors, new versatile software for data analysis and visualisation all contribute to new ways of selection and breeding that take advantage of this newly acquired knowledge and information. These novel methods should be used to continue to create genetic improvement, in a faster or more efficient way than before, and to introduce quality enhancing genetic factors into cultivated crops.<br/

Physiological and genetic aspects of a diploid potato population in the Netherlands and Northern Finland

Tuberization of potatoes exposed to different photoperiod regimes has been earlier investigated in several studies. However, there is still a limited understanding of the entire tuberization process and the factors influencing this process. One of the constraints of the previous studies has been the use of only one or a few genotypes. Furthermore, the experimental designs have not utilised the natural growing conditions with continuous changes in daylength during the growing season. The general aim of the project was to study the developmental dynamics of the broad-based potato (Solanum tuberosum L.) (CxE) population development at different climatical regimes under the very long-day, long-day and short conditions in Finland, the Netherlands and Ecuador/Venezuela, respectively. In this paper we are presenting some of the results achieved in the studies in Finland during the growing season 2004. In addition to population level trait characteristics we also describe here some of the identified QTLs (quantitative trait loci) for stolon related and tuber formation traits. In some cases we also compare the expression of some of the traits both in Finland and Netherlands.The main difference between the CxE population grown in Finland and the Netherlands was that the onset of flowering took place one week later in Finland. The relationship between tuber initiation and onset of flowering differed depending on the day length. In Finland approximately 70 % of the genotypes had swollen stolon tips before the onset of flowering, while in the Netherlands only 30 % of the genotypes had reached this condition. We also found numerous different trait linked QTLs, for example, a QTL associated with tuber formation was identified on chromosome E5, and QTLs associated with stolon characteristics on chromosomes E1, E4, E10 and E12. As a conclusion, the present preliminary results provide a good basis for determining the influence of different environmental conditions on potato development. In addition, the QTLs obtained in this study give a better understanding of the genetics of complex characters, and can be used in improving the potato crop in breeding programs

SolRgene: an online database to explore disease resistance genes in tuber-bearing Solanum species

Background The cultivated potato (Solanum tuberosum L.) is an important food crop, but highly susceptible to many pathogens. The major threat to potato production is the Irish famine pathogen Phytophthora infestans, which causes the devastating late blight disease. Potato breeding makes use of germplasm from wild relatives (wild germplasm) to introduce resistances into cultivated potato. The Solanum section Petota comprises tuber-bearing species that are potential donors of new disease resistance genes. The aim of this study was to explore Solanum section Petota for resistance genes and generate a widely accessible resource that is useful for studying and implementing disease resistance in potato. Description The SolRgene database contains data on resistance to P. infestans and presence of R genes and R gene homologues in Solanum section Petota. We have explored Solanum section Petota for resistance to late blight in high throughput disease tests under various laboratory conditions and in field trials. From resistant wild germplasm, segregating populations were generated and assessed for the presence of resistance genes. All these data have been entered into the SolRgene database. To facilitate genetic and resistance gene evolution studies, phylogenetic data of the entire SolRgene collection are included, as well as a tool for generating phylogenetic trees of selected groups of germplasm. Data from resistance gene allele-mining studies are incorporated, which enables detection of R gene homologs in related germplasm. Using these resources, various resistance genes have been detected and some of these have been cloned, whereas others are in the cloning pipeline. All this information is stored in the online SolRgene database, which allows users to query resistance data, sequences, passport data of the accessions, and phylogenic classifications. Conclusion Solanum section Petota forms the basis of the SolRgene database, which contains a collection of resistance data of an unprecedented size and precision. Complemented with R gene sequence data and phylogenetic tools, SolRgene can be considered the primary resource for information on R genes from potato and wild tuber-bearing relatives

Three QTLs for Botrytis cinerea resistance in tomato

Tomato (Solanum lycopersicum) is susceptible to grey mold (Botrytis cinerea). Partial resistance to this fungus was identified in accessions of wild relatives of tomato such as S. habrochaites LYC4. In order to identify loci involved in quantitative resistance (QTLs) to B. cinerea, a population of 174 F2 plants was made originating from a cross between S. lycopersicum cv. Moneymaker and S. habrochaites LYC4. The population was genotyped and tested for susceptibility to grey mold using a stem bioassay. Rbcq1, a QTL reducing lesion growth (LG) and Rbcq2, a QTL reducing disease incidence (DI) were identified. Rbcq1 is located on Chromosome 1 and explained 12% of the total phenotypic variation while Rbcq2 is located on Chromosome 2 and explained 15% of the total phenotypic variation. Both QTL effects were confirmed by assessing disease resistance in two BC2S1 progenies segregating for either of the two QTLs. One additional QTL, Rbcq4 on Chromosome 4 reducing DI, was identified in one of the BC2S1 progenies. F2 individuals, homozygous for the Rbcq2 and Rbcq4 alleles of S. habrochaites showed a reduction of DI by 48%. QTLs from S. habrochaites LYC4 offer good perspectives for breeding B. cinerea resistant tomato cultivars

Codominant scoring of AFLP in association panels

A study on the codominant scoring of AFLP markers in association panels without prior knowledge on genotype probabilities is described. Bands are scored codominantly by fitting normal mixture models to band intensities, illustrating and optimizing existing methodology, which employs the EM-algorithm. We study features that improve the performance of the algorithm, and the unmixing in general, like parameter initialization, restrictions on parameters, data transformation, and outlier removal. Parameter restrictions include equal component variances, equal or nearly equal distances between component means, and mixing probabilities according to Hardy–Weinberg Equilibrium. Histogram visualization of band intensities with superimposed normal densities, and optional classification scores and other grouping information, assists further in the codominant scoring. We find empirical evidence favoring the square root transformation of the band intensity, as was found in segregating populations. Our approach provides posterior genotype probabilities for marker loci. These probabilities can form the basis for association mapping and are more useful than the standard scoring categories A, H, B, C, D. They can also be used to calculate predictors for additive and dominance effects. Diagnostics for data quality of AFLP markers are described: preference for three-component mixture model, good separation between component means, and lack of singletons for the component with highest mean. Software has been developed in R, containing the models for normal mixtures with facilitating features, and visualizations. The methods are applied to an association panel in tomato, comprising 1,175 polymorphic markers on 94 tomato hybrids, as part of a larger study within the Dutch Centre for BioSystems Genomics

The Potato Ontology: Delimitation of the Domain, Modelling Concepts, and Prospects of Performance.

The ever increasing amount of data gathered by more growers in more years offers possibilities to add value. Therefore a common and controlled vocabulary of the potato domain that describes concepts, attributes, and the relations between them in a formal way using a standardised knowledge representation is being developed: a potato ontology. The advantage is that all possible stakeholders will be able to understand the data expressed by this ontology and that software applications can process them automatically. This paper describes the procedures to establish such an ontology where competency questions formulated by stakeholders and potential users take a central position. The three main classes are those used in crop ecology: Crop, Environment and Management

Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes

Within the Dutch genomics initiative the “Centre for Biosystems Genomics” (CBSG) a major research effort is directed at the identification and unraveling of processes and mechanisms affecting fruit quality in tomato. The basis of this fruit quality program was a diverse set of 94 cultivated tomato cultivars, representing a wide spectrum of phenotypes for quality related traits. This paper describes a diversity study performed on these cultivars, using information of 882 AFLP markers, of which 304 markers had a known map position. The AFLP markers were scored as much as possible in a co-dominant fashion. We investigated genome distribution and coverage for the mapped markers and conclude that it proved difficult to arrive at a dense and uniformly distributed coverage of the genome with markers. Mapped markers and unmapped markers were used to investigate population structure. A clear substructure was observed which seemed to coincide with a grouping based on fruit size. Finally, we studied amount and decay of linkage disequilibrium (LD) along the chromosomes. LD was observed over considerable (genetic) distances. We discuss the feasibility of marker-trait association studies and conclude that the amount of genetic variation in our set of cultivars is limited, but that there exists scope for association studies

Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood

The Composite Link Model is a generalization of the generalized linear model in which expected values of observed counts are constructed as a sum of generalized linear components. When combined with penalized likelihood, it provides a powerful and elegant way to estimate haplotype probabilities from observed genotypes. Uncertain (“fuzzy”) genotypes, like those resulting from AFLP scores, can be handled by adding an extra layer to the model. We describe the model and the estimation algorithm. We apply it to a data set of accurate human single nucleotide polymorphism (SNP) and to a data set of fuzzy tomato AFLP scores

Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation

AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce