Quantitative aspects of Plant Breeding
The group focuses on research aimed at understanding the interaction between genotype, environment and management by using all kinds of different techniques and databases. Therefore database development, maintenance and use is an important area of attention. Furthermore statistical aspects of using large datasets especially in the field of transcriptomics and metabolomics is a major focus area.
Crops: potato, brassica, tomato and other crops of importance.
- Construction of linkage maps and QTL analysis
- Linkage Disequillibrium mapping and association mapping
- Epistatis mapping
- Genetical genomics
- Genomic prediction and selection
- Estimation of Genotype x Environment interaction
- Relating henotype data to microarray, metabolomics or proteomics data
- Methods and software for genetic analysis in polyploid species
Data Management & Data Integration
Plant breeding has a strong link with quantitative genetics, statistics and bioinformatics, for example in identifying regions on crop genomes that are associated with observed variation in phenotypic traits, and in identifying candidate genes for these genomic regions.
Research within Plant breeding is multi-disciplinary and is dealing with a lot of different types of data, obtained from field-trials but also from high-throughput analysis of molecular markers, RNA transcripts (microarrays), proteins and secondary metabolites.
An efficient database will help in elucidating the genetics of economically important traits, in identifying molecular markers associated with agronomic traits, in allele mining and choosing interesting accessions fur further breeding with improved traits important for consumers, processors and producers.
One goal within plant breeding is to find the causal gene(s) explaining a given phenotype. Semantic web technology brings opportunities to integration data and information across spread data sources. For example, Annotex and Marker2sequence are two applications developed by Plant Breeding, which rely on this semantic web technology to integration genes, proteins, metabolites, pathways, and literature.
Contact: Richard Finkers
Current activities include combined data analysis of molecular markers, gene expression and metabolomics data and phenotype (e.g. disease resistance or product quality) scored on segregating populations of crosses. Methods being used are procedures such as random forest for classification or multiple regression in cases where the number of predictor variables (e.g. molecular markers, genes, metabolites) is much larger than the number of samples in which they have been measured (plants, tissues). Other areas of interest are modelling genotype x environment interaction, mapping and QTL analysis in single segregating populations, multiple populations or collections of germplasm. A specific focus area is also the development of a genetic analysis pipeline for polyploid crops.
Contact: Chris Maliepaard
Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruitPlant Biotechnology Journal 21 (2023)2. - ISSN 1467-7644 - p. 369 - 380.
Marker imputation and linkage map construction using a skim sequenced diploid potato population
Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata).: Wageningen University & Research
PolyHaplotyper : haplotyping in polyploids based on bi-allelic marker dosage dataBMC Bioinformatics 23 (2022)1. - ISSN 1471-2105
Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata)Theoretical and Applied Genetics 135 (2022)10. - ISSN 0040-5752 - p. 3611 - 3628.
4s2b: Insect problems in a changing world: reduce pesticide use by breeding for insect resistant plants under salinity stressIn: Circular@WUR 2022. - : Wageningen University & Research - ISBN 9789464471625
Multiallelic models for QTL mapping in diverse polyploid populationsBMC Bioinformatics 23 (2022)1. - ISSN 1471-2105
Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlRBioinformatics 37 (2021)21. - ISSN 1367-4803 - p. 3822 - 3829.
Genomics-based discrimination of 2n gamete formation mechanisms in polyploids : A case study in nonaploid Diospyros kaki ‘Akiou’G3 : Genes Genomes Genetics 11 (2021)8. - ISSN 2160-1836
Using probabilistic genotypes in linkage analysis of polyploidsTheoretical and Applied Genetics 134 (2021). - ISSN 0040-5752 - p. 2443 - 2457.
- Micaela Colley
- Alejandro Therese Navarro
- Hongbo Li
- Ran Wang
- Yanlin Liao