Cultivated spinach ( Spinacia oleracea L . ) has two different types of wild species, S. turkestanica and S. tetrandra . Wild materials often possess strong adaptability and stress resistance, making them important resources for crop genetic improvement. However, the genomic information of the two wild types of spinach is unclear, hindering further utilization of spinach wild species. Therefore, deciphering the genome sequences of spinach wild species and identifying important genes related to domestication traits lay the foundation for breeding high-quality spinach varieties.

Recently, the Spinach Genetic Breeding Research Team led by Wei Qian from the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF-CAAS), published a research paper titled 'Insights into spinach domestication from genomes sequences of two wild spinach progenitors, Spinacia turkestanica and Spinacia tetrandra ' in the internationally renowned journal New Phytologist. The study assembled the genomes of two wild spinach progenitors and elucidated their important domestication traits.

The research assembled two high-quality reference genomes of wild spinach (Figure 1). Based on single-copy genes, it was confirmed that Spinacia turkestanica is the direct ancestor of cultivated spinach, with an estimated divergence time of approximately 0.8 million years ago, while Spinacia tetrandra diverged even earlier, approximately 6.3 million years ago.

Figure 1 Morphology of individuals and inflorescences of the two wild spinach species, illustrating the differences between them, and the species’ genome features.

The team led by Wei Qian previously assembled a high-quality reference genome of cultivated spinach (She et al., 2023, Plant Physiology ) and combined it with genetic linkage maps to discover that the telomeric regions of each autosomal end and the central region of the sex chromosome (chromosome 4) are enriched with abundant repetitive sequences and exhibit lower recombination rates. This phenomenon is also observed in the genomes of the two wild species, where these regions may serve as pericentromeric regions. Within these regions, nucleotide polymorphism decreases, linkage disequilibrium (LD) values increase, the rate of LD decay decreases, and recombination rates decrease (Figure 2).

Figure 2 Distribution of nucleotide diversity (p), recombination rate, and linkage disequilibrium (LD) values.

Based on the high-quality reference genome of spinach and 94 accessions, we identified 982,999 high-quality SNPs and 71,115 structural variations (SVs). Then, we identified six introgression regions in the genome, of which the spinach downy mildew resistance loci RPF1 – RPF3 and RPF12 are located in one of the regions, indicating that the resistance of cultivated spinach to downy mildew is derived from introgression from wild species. Additionally, we identified numerous domestication-related genes, mainly related to photoperiod and disease resistance (Figure 3). For example, a 620-bp sequence insertion was found downstream of SpCUC3 , which is under selection pressure in cultivated spinach. This gene may account for the different leaf margin between cultivated (smooth) and wild (serrated) spinach.

Figure 3 Phylogeny, introgression, and domestication in cultivated spinach and its wild relative specie

In summary, these findings provide theoretical guidance for further utilization of wild spinach resources and breeding high-quality spinach varieties.

Assistant Professor Hongbing She and Professor Zhiyuan Liu from the IVF-CAAS, are the co-first authors of this paper; Professor Wei Qian and Professor Feng Cheng from the IVF-CAAS, as well as Professor Deborah Charlesworth from the University of Edinburgh, United Kingdom, are the co-corresponding authors.

This research was supported by the Chinese Academy of Agricultural Sciences Innovation Project (CAAS-ASTIP-IVFCAAS, CAAS-ZDRW202103) and the China Agricultural Research System (CARS-23-A-17).

More information can be found through the link: https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.19799

By Hongbing She (shehongbing@caas.cn)