Universität zu Köln

van Rengs, Willem M. J. (2025). Genome structure and meiotic recombination in cultivated tomatoes, wild relatives and derived hybrids. PhD thesis, Universität zu Köln.

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Abstract

Evolution, or the adaptation of organisms to survive their ever-changing environments, is facilitated by genetic variation and selection upon it. Genetic information is recombined during meiosis, facilitating the generation of genetic variation. Meiosis is a key feature of sexual reproduction and is a specialized cell division which leads to the production of genetically unique and ploidy-reduced gametes. Meiosis research in plants is often linked with crop improvement as recombination is an important substrate for crop breeders to generate elite genotypes. Increasing recombination rates, e.g. through mutation of anti-CO genes such as RECQ4, and altering recombination distribution has been shown to be possible in the model plant Arabidopsis and has the potential to increase genetic gain in a reduced number of breeding cycles in crops. However, only a limited number of species and genetic contexts have been tested for the discovered approaches. Current advances in DNA sequencing and bioinformatic tools are revolutionizing comparative plant genomics and make it possible to rapidly generate near-complete genome sequences of any plant material of interest where high molecular weight DNA can be extracted. Here, we aim to increase our understanding of meiosis in tomato species through generation of fundamental genetic and genomic resources that facilitate comparative genomics and have direct potential usage in plant breeding. First, we generated a gap-free de novo chromosome scale assembly of our model tomato species S. lycopersicum cv. Moneyberg-TMV by combining PacBio HiFi and ONT sequencing approaches alone. Our assembly was validated through orthogonal approaches and showed improved statistics compared to gold standard reference genomes. This assembly provided the complete sequence and structure of a 64.1 Mbp introgression from S. peruvianum on chromosome 9 that harbours the Tm-22 TMV resistance gene, which was previously unknown. We suggest the location of the resistance gene on the periphery of pericentromeric heterochromatin together with complex structural variation contributes to the extensive introgression size which has not been reduced despite 60 years of breeding (Chapter II). Second, we selected three more tomato species, including S. lycopersicum cv. Micro-Tom, S. cheesmaniae LA1039 and S. pennellii LA0716, that represent different levels of genetic divergence from Moneyberg-TMV. By generating reference quality chromosome scale de novo genomes we could identify genomic variation including large megabase scale structural variants. Genomic comparison of our S. pennellii and the previous S. pennellii genome shows long-read sequencing technologies greatly improve assembly quality. We performed hybridization of each of these lines with our Moneyberg-TMV model. F1 hybrids were cultivated and used to generate male and female backcross populations. We used parental single nucleotide polymorphisms (SNPs) to identify COs in each of the six backcross populations and found 1) female crossovers recombine at higher rates than male crossovers, and 2) recombination cold-spots directly correlate to large genomic variations (including inversions and regions of high genetic diversity) between the species (Chapter III). Finally, we generated RECQ4 mutants in two previously mentioned interspecific hybrids to increase CO rates. We observed reduced fertility in recq4 mutants and even complete sterility within the S. lycopersicum x S. pennellii F1 background, showing detrimental defects during meiosis. Fertility was restored by whole genome doubling, resulting in viable mutant allotetraploid offspring. Our results suggest RECQ4 is necessary for meiotic progression in divergent hybrids and thereby has different functions compared to Arabidopsis (Chapter IV). By assembling high quality genomes including S. cheesmaniae and S. pennellii genomes, we now have next-generation genomic resources available of the complete tomato clade, allowing for maximal utilization in breeding and research. Combined, our results will further facilitate meiosis research in tomato species and complement that in Arabidopsis to provide a better understanding of how recombination is controlled in plant species alongside direct possible applications in hybrid tomato breeding.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code van Rengs, Willem M. J. wmj.vanrengs@gmail.com UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-789074
Date:	2025
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Außeruniversitäre Forschungseinrichtungen > MPI for Plant Breeding Research
Subjects:	Life sciences Technology (Applied sciences) Agriculture
Uncontrolled Keywords:	Keywords Language Meiosis, Crossovers, Recombination, Breeding, Tomatoes, Solanum, Genomes, Structural variants, RECQ4 English
Date of oral exam:	20 November 2023
Referee:	Name Academic Title Thomma, Bart Prof. Dr. Rose, Laura Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/78907