The Brassica napus mRNA-Seq platform

19 Jan 2021

Brassica RNA-Seq platform

Brassica napus is one of the major oil crops in the world. It bears a tetraploid AACC genome and, similarly to its parent species B. rapa and B. oleracea, displays high phenotypical variability. Three subspecies are recognized within B. napus, which are represented by three distinct morphotypes: oilseed rape, leafy kales, and turnip-like swede (or rutabaga); economically, oilseed rape is the most important. The intensive breeding of oilseed rape in the past century focused mainly on the development of varieties of high-quality seed with low erucic acid and low glucosinolate levels, where two key cultivars served as parents of many subsequent crosses (Liho and Bronowski, respectively). This resulted in a relatively narrow gene pool of modern oilseed rape cultivars, posing a challenge for breeding plants with enough resistance to pests and tolerance to abiotic stresses, especially in the light of climate shifts and extreme conditions.

The Brassica napus mRNA-Seq platform

The Brassica napus mRNA-Seq platform in GENEVESTIGATOR® comprises 35 experiments with 1’110 samples from > 250 cultivars and covers the wide diversity of B. napus specimen with > 470 samples of winter oilseed rape, > 300 samples of spring oilseed rape, > 30 samples of kale, and > 35 samples of swede.

post thumb Figure 1: The research areas covered by published Brassica napus experiments include pathogens, abiotic stress, tissues, development, nutrients, genotypes, and other topics as heterosis, male sterility, and specific phenotype traits. Besides the genotype diversity and genetic variability within the Brassica napus species, the two major topics of experiments represented in GENEVESTIGATOR® are abiotic and biotic stress (pathogens). There are now 7 experiments with 117 samples covering different abiotic stresses, including salt, drought and simulated drought, cold or freezing. To explore biotic interactions, we have annotated studies on three major pathogens of B. napus: Leptosphaeria maculans and L. biglobosa causing the blackleg disease, Sclerotinia sclerotiorum causing the sclerotinia stem rot and the causal agent of clubroot disease, Plasmodiophora brassicae (fungus-like protist, Rhizaria).

Dissecting the complexity of Brassica napus

Example from experiment BN-00040 (data of An et al., 2019, Nat. Commun.) shows clustering of leafy kales and root tuber-forming swede, the spring oilseed rape characterized by no need of vernalization, the winter oilseed rape or a group of South-Asian cultivars sometimes recognized as semi-winter oilseed rape. The Dimension Reduction tool in GENEVESTIGATOR® allows customization with color labels for any annotated parameter, such as crop type (as shown here) or e.g. seed quality.

post thumb Figure 2: The Anatomy tool under GENE SEARCH allows finding genes expressed in a selected Sorghum anatomy. The list of tissue-specific genes can be stored and further analysed with other GENEVESTIGATOR® tools to better characterize how they are regulated. In this example, 131 inflorescence samples, most of them are panicles, are aggregated from 10 mRNA-Seq experiments.

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