Haploid-aware genome reconstruction and genetic mapping for tetraploid Leek

Haploid-aware genome reconstruction and genetic mapping for tetraploid Leek






Landbouw, Water, Voedsel>Sleuteltechnologieën LWV>Biotechnologie en Veredeling






This proposed precompetitive project contributes to the development of new plant varieties, new breeding technologies, and strengthening the knowledge infrastructure in genome bioinformatics, breeding, and genetics. The Leek Genome Project fits well into the TKI ambition to build a knowledge infrastructure that facilitates the application of genomics and genetic information for the creation of crops with improved performance and quality. The implication of the technology developed in this project is that large complex polyploid crop genomes like Allium ampeloprasum (Leek) can be sequenced and reconstructed. Furthermore, we will deliver a high-density genetic map and the SNP data on which it is based.
Our approach will be based on strategies that we have successfully used in previous genome projects like for example the 150 tomato genome, ILGC, and Rose. In addition to this we will apply technological innovations that have recently come to the market to further advance on polyploid genome reconstruction, phasing, genetic map construction, and profiling a mapping population.
Taking advantage of the latest developments and insights (further described in Annex 3) and the experience we have gained from previous genome sequencing projects, the reconstruction of polyploid genomes becomes attainable. Technical improvements, such as PacBio ‘Sequel’ and Oxford Nanopore technology, render large insert sequencing (>20kb) for large polyploids genomes such as Leek (~16Gb) economically feasible. In addition, whole transcriptome profiling with Illumina NovaSeq has proven successful. In addition, building a genetic linkage map, dosage scoring, and IBD probability scoring are now well supported by latest developments in array technology, scoring of high quality SNPs in polyploids, and new or improved software tools such as fitPoly, TetraOrigin, ClusterCall, TetraploidSNPmap, and polymapR.
The reconstructed genome, transcriptome, and the genetic map for Leek will serve as a new standard to assess complex polyploidy genomes. The knowledge gained in the Leek Genome project will allow breeders to; (i) have insight in genetic and genome structure diversity to advance on precision breeding; (ii) reduce their R&D costs; (iii) and better respond to economic, environmental, social and health issues inherent to agricultural crop production.

Doel van het project

The Leek Genome Project is a key technology project falling under category ‘Smart technologies in Agri-Horti-Water-Food’ and by its range of applications transects and is linked to missions Circular Agriculture (mission A), Climate neutral agriculture and food production (mission B), and Appreciated, heathy and safe food (mission D) set out in the Knowledge and Innovation Agenda. It answers to economic, environmental, social and health issues inherent to agricultural crop production. The project uses genomics, bioinformatics, and breeding to explore and benefit from the potential of genetically diverse germplasm panels, and test progeny from different parental combinations. This key technology aims to genetically map the tetraploid Leek genome. It guides and anticipates on optimal breeding material and puts breeding at a precision level (MMIP S2, sub programmes 1-genome technology, 2-bioinformatics, and 5-guiding breeding technologies) and response level enabling the accelerated development of robust and innovative crops (MMIP A2) that are more in line with economic societal demands. Our key technology will speed up precision breeding e.g. for biotic and abiotic stress tolerance, disease resistance, drought tolerance, longer shelf-life, more safe healthy crops and ‘precision designed food crops’ thereby contributing to MMIP D2 and D3. Here we aim to (1) construct genetic map with unprecedented resolution and accuracy. It thus has great potential guiding Leek breeding and thereby contributes to the realization of MJP Breeding 2.0.

Relatie met missie (Motivatie)

The world population is growing each year and is expected to keep growing to reach 9 billion by 2050. The demand for water, energy, minerals and arable lands will increase and is reaching the capacity limits of Earth’s ecosystems, while at the same time the environmental footprints of today’s agricultural production systems are far from sustainable. These drivers demand for more efficient agricultural production systems and advanced crops that are more in line with environmental, economic and social needs. During past decades breeding focused on higher productivity and adaption to different growing systems. According to the FAO worldwide fresh Leek production in 2016 (http://faostat3.fao.org) was 353.093 tons and this massive production reflects the success of modern leek breeding in the Netherlands. Nevertheless, production is threatened by lack of disease resistance and (a)biotic stress tolerance traits (http://www.nunhems.com/www/NunhemsInternet.nsf/id/CW_EN_AUS/$file/AUS_LEL_Diseases.pdf) and lack of genomics resources (Genetic Improvement of Vegetable Crops, 1993). Furthermore, consumer preferences, need for increased shelf live and improved crop quality are becoming increasingly important. These needs push breeding efforts towards better biotic and abiotic stress tolerance, higher productivity and increased sensory and nutritional value.
However, genome reconstruction and genetic linkage mapping of complex medium to large-sized polyploid genomes as a basis for advanced breeding such as for leek, is a bioinformatics and genetics challenge and often problematic. Furthermore, the lack of a phased Leek reference genome complicates sequence based breeding efforts and assessment of genetic diversity. This situation urgently calls for the use of innovative genomics technologies such as Next generation Sequencing to realize genome and transcriptome assembly of complex polyploids. The methodology itself will be general and can be applied to other complex crops as well.

Geplande acties

In the last decade the breeding sector has shown worldwide expansion even though in recent years we have been in a recessive economy. Because of the excellent agri-business and knowledge infrastructure, breeding companies have consolidated their unique and competitive position in the Dutch high-tech horticulture and breeding industry. In order to maintain a leading position in horticulture and commercial breeding, innovation is of utmost importance. The Leek Genomics Project targets a unique combination of Leek genome complexity reduction, high-throughput screening, bioinformatics and genetics technology will provide new insights, permitting the development of breeding tools that will drive innovation for the consortium partners and plant breeding and horticulture of polyploid crops. This applied research project contributes to meeting the challenge of ensuring Food Security through developing advanced precision breeding methods for the vegetable and field crops subsector in the plant breeding and propagation industry. The novelty of the project lies in its multidisciplinary and overarching character, tackling Leek genomics from different, yet complementary angles involving state-of-the-art genomics and genetics technology and expertise. The project addresses the interplay between genome bioinformatics and linkage analysis of the leek gene space, and molecular (precision) breeding. The generated knowledge in the project will help to; (i) explain breeding problems for cultivated Leek; (ii) analyse sequence features and gene content; (iii) develop a genetic linkage map for Leek. The insight will enable plant breeders to optimize their breeding strategy permitting them to; (1) reduce their ‘time-to-market’ introduction for new crop varieties; (2) realize R&D cost savings and alternative usage of R&D resources; (3) respond more flexibly to new consumer requests and market trends; and (4) develop advanced breeding parents with complex traits such as pathogen resistance and improved (a)biotic stress tolerance. Furthermore, the concept potentially can be used not only for Leek but for a number of other economically important polyploid crops as well. The deliverables that are anticipated within the project run time of 36 months are; (1) all raw sequence data; ; (3) all read alignments, contig assemblies and scaffold sequences; (5) all SNP calls and gene phased data; (6) a phased as well as an integrated genetic linkage map of leek; (7) knowledge infrastructure that combines genetic and genomic phasing of complex polyploid crops.