Beyond genomic variation - comparison and functional annotation of three Brassica rapagenomes: a turnip, a rapid cycling and a Chinese cabbage

Abstract

BackgroundBrassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops.ResultsTo investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two B. rapa subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resulting genomes together with the Chinese cabbage Chiifu reference genome to obtain an impression of the B. rapa pan-genome. The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of Arabidopsis thaliana, which can be explained by the smaller effective population size of B. rapa due to its domestication. Based on orthology to a number of non-brassica species, we estimated the date of divergence among the three B. rapa morphotypes at approximately 250,000 YA, far predating Brassica domestication (5,000-10,000 YA).ConclusionsBy analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation. The estimated date of divergence among three B. rapa morphotypes implies that prior to domestication there was already considerably divergence among B. rapa genotypes. Our study thus provides two new B. rapa reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in B. rapa.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-250) contains supplementary material, which is available to authorized users.

The pangenome of an agronomically important crop plant Brassica oleracea

“…7). A similar observation was made in Brassica rapa , where a rapid cycler was also missing several flowering time-related genes24, suggesting that PAV may be a contributing factor of flowering time regulation. The genes identified include orthologues of genes encoding: MAF5 , SEP2 , ARP4 , GID1B , FPF1 -like, FHY1 , GA2 , GA3 and CO .…”

“…Genes associated with flowering time listed in ref. 24 were downloaded. All the genes belonging to the pathways of interest and the flowering time genes were compared with the orthologous gene clusters.…”

SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete?

“…This has led to a series of similar studies in other micro-organisms [4,5,6,7] as well as higher organisms including maize [8,9], soybean [10,11], rice [12,13], and Brassicas [14,15]. The pangenome can be thought of as the full complement of genes in a given species.…”

ECOLOGICAL AND GENETIC EVALUATION OF MORPHOLOGICAL AND BIOCHEMICAL CHARACTERS OF QUALITY IN Brassica rapa L. ACCESSIONS FROM VIR COLLECTION

“…In the past decade, the character of basic metabolite accumulation, including biologically active substances, in previously poorly studied East Asian B. rapa wild cabbage plants and varieties have been reported [6,7]. The explanation for the widest variability of morphological features in B. rapa is suggested by K. Lin et al [8], who found unique genes in three morphotypes of B. rapa, the root turnip and short-stage form, whose genomes were sequenced and compared with the genome of the headed napa cabbage.…”