Technology-driven approaches for meiosis research in tomato and wild relatives

Abstract

Meiosis is a specialized cell division during reproduction where one round of chromosomal replication is followed by genetic recombination and two rounds of segregation to generate recombined, ploidy-reduced spores. Meiosis is crucial to the generation of new allelic combinations in natural populations and artificial breeding programs. Several plant species are used in meiosis research including the cultivated tomato (Solanum lycopersicum) which is a globally important crop species. Here we outline the unique combination of attributes that make tomato a powerful model system for meiosis research. These include the well-characterized behavior of chromosomes during tomato meiosis, readily available genomics resources, capacity for genome editing, clonal propagation techniques, lack of recent polyploidy and the possibility to generate hybrids with twelve related wild species. We propose that further exploitation of genome bioinformatics, genome editing and artificial intelligence in tomato will help advance the field of plant meiosis research. Ultimately this will help address emerging themes including the evolution of meiosis, how recombination landscapes are determined, and the effect of temperature on meiosis.

Keywords: Crossover; Genome editing; Genomics; Meiosis; Plant hybrids; Tomato.

Fig. 1

Pollen nuclei sequencing to profile meiotic recombination in tomato hybrids. From top to bottom, a cultivated tomato (Parent 1) is pollinated by a wild tomato (Parent 2). The hybrid progeny is grown and pollen harvested from open flowers. A photo of a S. lycopersicum x S. cheesmaniae flower is shown as an example. Germination of pollen grains is carried out in vitro to allow for the extraction of pollen nuclei. High molecular weight DNA can be extracted from pollen nuclei and used for the generation of DNA sequencing libraries. DNA sequence reads, from both parents and recombinant pollen, are mapped against a reference genome sequence and used for SNP calling. The mapped reads can be used to call phase shifts, estimate crossover (CO) positions at high precision, and subsequently to generate chromosomal CO distributions. This figure was created with BioRender.com

Fig. 2

Genome editing and cultivation methods that make tomato an ideal meiotic model. From top to bottom, a cultivated tomato is pollinated by a wild tomato, and hybrid seeds can be germinated in vitro. Non-expanded, cut, leaves from 4–5-week-old plants are used as explants for infection with Agrobacterium strains harboring CRISPR/Cas9 constructs targeting meiotic genes of interest. Selection by antibiotic resistance allows for isolation of putative transgenic shoots which are used to generate rooted plantlets. Rooted, PCR-validated, transgenic plants can be transferred to soil. Flowering plants can be checked for fertility traits (including pollen viability, fruit setting and seed production) and meiotic recombination can be analyzed through cytological analysis of meiotic chromosome spreads by microscopy or through sequencing of recombinant gametes/offspring (see also Fig. 1). Clonal propagation through cuttings allows specific tomato genotypes to be maintained indefinitely and to be continuously flowering. Tomato genotypes can also be re-introduced into tissue culture by sterilizing early lateral shoots and propagation on rooting media. This figure was created with BioRender.com