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Structural Variation: The “Key” to Brassica oleracea Evolution

Diverse Morphotypes of Brassica oleracea

Brassica oleracea is widely cultivated worldwide and is one of the most important categories of vegetable crops. It is a species that encompasses a wide range of cultivated vegetables including cabbage, broccoli, cauliflower, kale, Brussels sprouts, and kohlrabi, etc. These vegetables, though are all belong to Brassica oleracea, appear very differently. The diverse morphotypes have been developed through selective breeding over centuries, resulting in distinct variations in morphology, taste, and nutritional content. For example, cabbage has a leafy head wrapped in multiple layers of leaves; cauliflower and broccoli develop enlarged inflorescences; Brussels sprouts form small leaf balls from axillary bud differentiation; kohlrabi develops swollen tuberous stems; kale has scattered leaves (Figure 1).

Abundant Nutrients in Brassica oleracea

Brassica oleracea, besides being morphologically diverse, also exhibits a rich variety of nutritional and flavor-related traits. One of the significant characteristics of Brassica oleracea is the high content of glucosinolates. The most important hydrolysis product of glucosinolates is sulforaphane, which is one of the best natural active substances with anti-cancer effects in vegetables. In Brassica oleracea, the content and ratio of different glucosinolates vary. Since glucosinolates can produce compounds with pungent or bitter tastes when Brassica oleracea is chewed or heated, different Brassica oleracea may have distinct flavors. These compounds not only bring unique flavors to Brassica oleracea but also possess abundant nutritional value and potential health benefits.

Furthermore, Brassica oleracea is rich in vitamins and dietary fiber, which benefits human digestive system. For example, vitamin U protects the gastric mucosa and regulates gastric acid secretion; Vitamin C helps promote a healthy immune system; Vitamin K helps maintain bone health and promote the coagulation process; Vitamin B12 plays a crucial role in DNA synthesis and maintaining the health of blood cells, nerve cells. They also contain abundant minerals such as potassium, calcium, magnesium, etc., which aid in maintaining nerve and muscle function and electrolyte balance. 

Despite Brassica Oleracea’s rich variety, their domestication history is relatively short, spanning only about 2500 years. Compared to other crops, Brassica Oleracea exhibits characteristics of rapid and diverse morphological domestication. The mechanism behind the exceptionally abundant phenotypic variation during the short domestication process of Brassica Oleracea is still under study. Therefore, elucidating the driving force behind the rapid domestication and the genetic mechanisms regulating the differentiation of Brassica Oleracea variants are urgent scientific questions for studying plant development, evolution, and diversification.

Genomic Changes Underlie Brassica oleracea Morphotypes

Recently, researchers from Wageningen University and Research and Chinese Academy of Agricultural Sciences have constructed a phylogenetic tree using resequencing data from over 700 wild Brassica oleracea species and all variant types. The results revealed that Brassica oleracea variants mainly originated from two independent domestication events, one leading to the diversification of leaf morphology/leaf ball forms, and the other resulting in morphological variations centered around enlarged stems and flowers. (Figure 1) Based on this, they de novo assembled genomes of 22 selected representative wild type Brassica oleracea or its variant accessions, constructed a pan-genome and a graph-based genome using these 22 plus five reported genomes and determined genomic variations in a Brassica oleracea population of 704 accessions. 

By comparing homologous genes among Brassica oleracea variants, they revealed that structural variations (SVs) introduced large-scale gene expression alterations, affecting gene expression bidirectionally by either suppressing or promoting specific gene expression. And these genes were enriched in particular metabolic pathways. For instance, in cauliflower, these genes were associated with sulfate transport and sulfatase activity involved metabolic pathways. While in kohlrabi, they were related to α-glucose and vitamin B6 synthesis. The study results suggest that genes specifically suppressed or promoted during domestication are related to the differences in nutrients and flavors among Brassica oleracea variants.

Further comparison of sequence differences among the genomes of 27 Brassica oleracea variants revealed a large number of structural variations (SVs) between different Brassica oleracea variant genomes, with the majority (73%) located in the upstream and downstream regions of genes, which does not affect the functionality of the genes themselves. Most interestingly, the study showed that about 70% of gene expression changes were related to structural variations (SVs). Structural variations (SVs) can both promote gene expression containing significantly more transcription factor binding sites or suppress gene expression with significantly high level of DNA methylation modifications. As we know, transposable elements (TEs) are always highly methylated and suppress the expression of adjacent genes. Researchers found that most structural variations (SVs) overlap with transposable elements (TEs) and are likely introduced by transposable elements (TEs). The transposable element (TE) methylation may be the main factor for the suppressive effects of structural variation (SV) genes. Meanwhile, transcription factors (TFs)-binding sites were found to be enriched in the promotion SVs, which may cause the increased transcription of corresponding structural variation (SV) genes. (Figure 2)

Conclusion and Future Perspectives

The changes in gene expression levels produced a series of morphological diversities, which, through domestication selection, promoted the diversification of Brassica oleracea variants. This study reveals a new pattern of domestication selection driven by changes in gene expression levels to shape vegetable diversity morphotypes. It also highlights the important role of structural variations (SVs) as regulators of gene expression levels in crop domestication and phenotypic diversification. In the future study, more molecular biology techniques will be utilized to analyze the functions of key genes, develop novel molecular markers, and apply the structural variations (SVs) and functional genes in the field of breeding Brassica oleracea and other crops. It will lead to the creation of more crops meeting the demand for high-quality and diversified vegetables. 

References

Structural variations fine-tune gene expression to steer Brassica oleracea diversification. Nat Genet. 2024 Feb 19;

Guo N, Wang S, Gao L, Liu Y, Wang X, Lai E, et al. Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification. BMC Biol. 2021 May 5;19(1):93.

Li X, Wang Y, Cai C, Ji J, Han F, Zhang L, et al. Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea. Nat Genet. 2024 Feb 13;

Note: Images in this post have been created with BioRender and Tome.