Project properties
Title QTL mapping and genomic architecture of biomass-related traits in cardoon
Group Plant Breeding, Laboratory of
Project type thesis
Credits 24-39
Supervisor(s) Dr. Francesco Pancaldi, Prof. Dr. Luisa Trindade
Examiner(s) Prof. Dr. Luisa Trindade
Contact info luisa.trindade@wur.nl, francesco.pancaldi@wur.nl
Begin date 2024/03/01
End date 2026/12/31
Description Cardoon (Cynara cardunculus) is a perennial crop from the Asteraceae family that can grow in adverse environments and has both food and industrial applications. From an industrial point of view, cardoon biomass can be used in biorefineries for the production of biofuels, bioplastics, paper, and other bio-based applications. This is thanks to the high biomass lignocellulosic content and the large biomass yield. However, both these traits are highly variable, and understanding their genetic architecture can enable the development of varieties fitted to specific bio-based applications. Recently, long-read sequencing combined with the generation of Hi-C data have been used to develop a new, high-quality, cardoon genome assembly. In parallel, a new set of molecular markers have also been developed. In this thesis, the genome and markers will be used to map QTLs related to biomass yield and quality in a mapping population created by crossing contrasting cardoon lines for these traits. Moreover, QTL regions will be inspected for their genomic conservation and structural variability across other cardoon genome assemblies and genome assemblies from other angiosperm species. This will enable to both screen for intra-specific genomic diversity at the identified QTLs, and verify the co-localization of the identified QTLs with other known (conserved) QTLs for biomass yield and quality across different plants. The thesis will entail only genetic mapping and bioinformatic analyses. No field, greenhouse, or wet lab work is planned, as all the genetic and phenotypic data for this project are available.
Used skills Used skills (Quantitative) genetics, statistical analysis, bioinformatics, phylogenetics
Requirements Compulsory: PBR-30306 Breeding for Stress Tolerance and Quality or PBR-37306 Advanced Bioresources
Preferred one or more of the following: ABG-30306 Genomics, PBR-31306 Bioresources or PBR-37306 Advanced Bioresources, MAT-20306 Advanced Statistics
Experience with R/Python/Unix are a plus.