A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly

Yan Wang,Yongcui Liao,Jian Wu,Bo Liu,Hui Wang,Xiaowu Wang,Feng Cheng,Jie Deng,Qian Wang,Silong Sun

doi:10.1186/1471-2164-12-239

Yan Wang, Yongcui Liao + Show 8 more

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https://doi.org/10.1186/1471-2164-12-239

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Abstract

BackgroundBrassica rapa is an economically important crop and a model plant for studies concerning polyploidization and the evolution of extreme morphology. The multinational B. rapa Genome Sequencing Project (BrGSP) was launched in 2003. In 2008, next generation sequencing technology was used to sequence the B. rapa genome. Several maps concerning B. rapa pseudochromosome assembly have been published but their coverage of the genome is incomplete, anchoring approximately 73.6% of the scaffolds on to chromosomes. Therefore, a new genetic map to aid pseudochromosome assembly is required.ResultsThis study concerns the construction of a reference genetic linkage map for Brassica rapa, forming the backbone for anchoring sequence scaffolds of the B. rapa genome resulting from recent sequencing efforts. One hundred and nineteen doubled haploid (DH) lines derived from microspore cultures of an F1 cross between a Chinese cabbage (B. rapa ssp. pekinensis) DH line (Z16) and a rapid cycling inbred line (L144) were used to construct the linkage map. PCR-based insertion/deletion (InDel) markers were developed by re-sequencing the two parental lines. The map comprises a total of 507 markers including 415 InDels and 92 SSRs. Alignment and orientation using SSR markers in common with existing B. rapa linkage maps allowed ten linkage groups to be identified, designated A01-A10. The total length of the linkage map was 1234.2 cM, with an average distance of 2.43 cM between adjacent marker loci. The lengths of linkage groups ranged from 71.5 cM to 188.5 cM for A08 and A09, respectively. Using the developed linkage map, 152 scaffolds were anchored on to the chromosomes, encompassing more than 82.9% of the B. rapa genome. Taken together with the previously available linkage maps, 183 scaffolds were anchored on to the chromosomes and the total coverage of the genome was 88.9%.ConclusionsThe development of this linkage map is vital for the integration of genome sequences and genetic information, and provides a useful resource for the international Brassica research community.

Highlights

Brassica rapa is an economically important crop and a model plant for studies concerning polyploidization and the evolution of extreme morphology
A range of annealing temperatures from 55°C to 63°C for 16 primer pairs were tested, and the results demonstrated that annealing at 57°C produced favourable results for all primer pairs
The size of amplified DNA fragments was within the range of 80-200 bp and 4-10 bp insertion/deletions were used as markers

Summary

Introduction

Brassica rapa is an economically important crop and a model plant for studies concerning polyploidization and the evolution of extreme morphology. Several maps concerning B. rapa pseudochromosome assembly have been published but their coverage of the genome is incomplete, anchoring approximately 73.6% of the scaffolds on to chromosomes. The multi-national B. rapa Genome Sequencing Project (BrGSP) was launched in 2003 owing to the economical and biological importance of B. rapa, and the A3 chromosome was sequenced using traditional Sanger technology [5]. Several maps concerning B. rapa have been published to be used as reference genetic maps for pseudochromosome assembly (http://www.brassica-rapa.org) [6,7,8] despite their coverage only allowing in total 73.6% of the scaffolds being anchored on to chromosomes [The Brassica rapa Genome Sequencing Project Consortium: The genome of the mesohexaploid crop species Brassica rapa, submitted]

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