Meiotic recombination profiling by multi-locus genotyping and recombination bin mapping of nuclei from F1 pollen

Projecttitel: Meiotic recombination profiling by multi-locus genotyping and recombination bin mapping of nuclei from F1 pollen
Projectnummer: LWV19283
Missie: Sleuteltechnologieën
MMIP: ST2 - Biotechnologie en veredeling
Looptijd: 2020 – 2023
Projectleider: Gert-Jan de Boer

Meiotic recombination is a key fundamental biological process that ensures the reshuffling of parental alleles into new combinations. In molecular breeding the rearrangement of alleles via recombination in offspring is assessed to seek out preferred allele combinations for crop innovation. Molecular marker based screenings are routinely used for recombination profiling of segregating populations, though which is a time-consuming and costly process.
Given the recent developments in key technologies (genomics technology, ICT, bioinformatics), high throughput recombination bin mapping has become a feasible approach for efficient recombination profiling with unprecedented resolution, without being dependent on marker based approaches and the construction of large mapping populations. 
The project addresses the technological innovation that is needed to realize precision breeding for advanced crops. The novelty of the project lies in its multidisciplinary character, tackling genomics from different but yet complementary angles involving state-of-the-art genomics technology and genome bioinformatics. 
The new technology developed in this project serves as a key technology supporting fundamental and applied research purposes, varying from genome reconstruction and genome evolution related studies, to structural variation analysis, genetic map construction, QTL analysis, and genetic diversity analysis. 
Here we will focus on sequence based identification of crossover recombination, aiding the identification of compatible trait - plant parent combinations for introgression breeding. We will analyse crossover recombination in pollen gametes from F1 plants obtained from crosses between S. lycopersicum Heinz 1706 and its related wild species (pimpinellifolium, cheesmanii, arcanum, habrochaites, pennellii, etc) as well as crosses preferred by private partners including other species (e.g. pepper, melon, lettuce, tulip, papaya, maize (corn), spinach, onion, sugar beet, etc). 
The project targets a unique combination of linked read sequencing, bioinformatics and genetics technology which provides new insights and permits the development of breeding tools that will drive innovation for the consortium partners and plant breeding and horticulture in general. The generated knowledge in the project will help to; (i) explain crossover recombination and resolve linkage drag problems for cultivated crops; (ii) analyse sequence features and gene content of recombined segments and CO junctions; and (iii) determine the synteny and structural homology of parental breeding lines. 
The insight will enable plant breeders to optimize their introgression breeding strategy permitting them to; 
(1) reduce their ‘time-to-market’ introduction for new crops varieties; 
(2) realize R&D cost savings and alternative usage of R&D resources; 
(3) respond more flexible to new consumer requests and market trends; and 
(4) develop advanced breeding lines with complex traits such as pathogen resistance and improved (a)biotic stress tolerance. 

Furthermore, the concept potentially can be used for a wide range of economically important crops as well. 
This applied research project answers to the food security and sustainable production challenges by developing advanced precision breeding methods for the vegetable and field crops subsector in the plant breeding and propagation industry, and strengthening the unique and competitive position of high-tech horticulture and breeding industry.