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

Lin K, Zhang N, Severing EI, Nijveen H, Cheng F, Visser RG, Wang X, de Ridder D, Bonnema G - BMC Genomics (2014)

Bottom Line: 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.By 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.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands. guusje.bonnema@wur.nl.

ABSTRACT

Background: Brassica 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.

Results: To 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).

Conclusions: By 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.

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ThreeBrassica rapaplants. Left: the Chinese cabbage cultivar, Chiifu; middle: an oil-like rapid cycling line (RC-144); right: Japanese vegetable turnip (VT-117).
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Fig1: ThreeBrassica rapaplants. Left: the Chinese cabbage cultivar, Chiifu; middle: an oil-like rapid cycling line (RC-144); right: Japanese vegetable turnip (VT-117).

Mentions: Our main research goal is to understand the genetic drivers underlying the enormous morphological variation between B. rapa subspecies. In this study, we therefore consider two B. rapa genomes – those of a vegetable turnip double haploid line (DH-VT117) and a rapid cycling inbred line (RC-144) – as representatives of the very distinct morphotypes turnip and annual oil (Figure 1). The vegetable turnip has an enlarged hypocotyl/root, whereas the rapid cycling line is developed in Wisconsin by intercrossing mainly annual oils and pakchois/caixins and selecting for earliness in flowering [5]. As recent studies suggested that the genome-wide density of variants is much higher between accessions of one plant species than between lines in one mammalian species, in this study we not only resequenced the turnip and rapid cycling line genomes, but also assembled and re-annotated them, resulting in two new reference genomes [6–11].Figure 1


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

Lin K, Zhang N, Severing EI, Nijveen H, Cheng F, Visser RG, Wang X, de Ridder D, Bonnema G - BMC Genomics (2014)

ThreeBrassica rapaplants. Left: the Chinese cabbage cultivar, Chiifu; middle: an oil-like rapid cycling line (RC-144); right: Japanese vegetable turnip (VT-117).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230417&req=5

Fig1: ThreeBrassica rapaplants. Left: the Chinese cabbage cultivar, Chiifu; middle: an oil-like rapid cycling line (RC-144); right: Japanese vegetable turnip (VT-117).
Mentions: Our main research goal is to understand the genetic drivers underlying the enormous morphological variation between B. rapa subspecies. In this study, we therefore consider two B. rapa genomes – those of a vegetable turnip double haploid line (DH-VT117) and a rapid cycling inbred line (RC-144) – as representatives of the very distinct morphotypes turnip and annual oil (Figure 1). The vegetable turnip has an enlarged hypocotyl/root, whereas the rapid cycling line is developed in Wisconsin by intercrossing mainly annual oils and pakchois/caixins and selecting for earliness in flowering [5]. As recent studies suggested that the genome-wide density of variants is much higher between accessions of one plant species than between lines in one mammalian species, in this study we not only resequenced the turnip and rapid cycling line genomes, but also assembled and re-annotated them, resulting in two new reference genomes [6–11].Figure 1

Bottom Line: 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.By 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.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands. guusje.bonnema@wur.nl.

ABSTRACT

Background: Brassica 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.

Results: To 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).

Conclusions: By 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.

Show MeSH