LWV24009 The Next Frontier in informed Crop Breeding: single cell genomics (TS-02-227-041)

The construction of a mapping population followed by marker-based profiling to create a genetic linkage map is considered a traditional method in genetics and plant breeding. This approach has been foundational in understanding the genetic basis of traits and has been used for many decades. This traditional breeding strategy, is time-consuming and costly though. We propose a new approach to streamline some aspects of this process, making it faster and more efficient, in particular by using long-read and linked-read sequencing of single nuclei from gametes (pollen, ovules). The sequence data from single nuclei will provide valuable information on recombination frequencies in parental genomes, allowing for genetic linkage map construction without the need to construct mapping populations and subsequent marker-based screening. The project will use two approaches; (i) a split-pool barcode-based long-read sequencing of single nuclei and (ii) sequencing of a picoPLEX®-based whole genome amplified gDNA from sorted nuclei. The main expected results and deliverables include (1) a method to obtain intact nuclei from gametes suitable for sequencing, (2) an algorithm to detect crossovers from recombinant long-reads, (3) the construction of genetic maps using recombination profiles from F1 pollen gametes and subsequent validation of these maps by comparing them to traditional genetic maps. Additional benefits of this approach may include (4) precise detection of introgressed segments, and (5) identification of (in)compatible breeding lines. The project aims to accelerate informed crop breeding, reduce costs and improve resource efficiency and providing insight into linkage of genes helping breeders to determine optimal stacking and pyramiding of traits, thereby empowering plant breeders to efficiently streamline their introgression breeding programs.