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Open Access Research article

Genome survey sequencing provides clues into glucosinolate biosynthesis and flowering pathway evolution in allotetrapolyploid Brassica juncea

Jinghua Yang12, Ning Song12, Xuan Zhao12, Xiaohua Qi3, Zhongyuan Hu12 and Mingfang Zhang12*

Author Affiliations

1 Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, P. R. China

2 Key laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, P. R. China

3 College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, P. R. China

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BMC Genomics 2014, 15:107  doi:10.1186/1471-2164-15-107

Published: 6 February 2014

Abstract

Background

Brassica juncea is an economically important vegetable crop in China, oil crop in India, condiment crop in Europe and selected for canola quality recently in Canada and Australia. B. juncea (2n = 36, AABB) is an allotetraploid derived from interspecific hybridization between B. rapa (2n = 20, AA) and B. nigra (2n = 16, BB), followed by spontaneous chromosome doubling.

Results

Comparative genome analysis by genome survey sequence (GSS) of allopolyploid B. juncea with B. rapa was carried out based on high-throughput sequencing approaches. Over 28.35 Gb of GSS data were used for comparative analysis of B. juncea and B. rapa, producing 45.93% reads mapping to the B. rapa genome with a high ratio of single-end reads. Mapping data suggested more structure variation (SV) in the B. juncea genome than in B. rapa. We detected 2,921,310 single nucleotide polymorphisms (SNPs) with high heterozygosity and 113,368 SVs, including 1-3 bp Indels, between B. juncea and B. rapa. Non-synonymous polymorphisms in glucosinolate biosynthesis genes may account for differences in glucosinolate biosynthesis and glucosinolate components between B. juncea and B. rapa. Furthermore, we identified distinctive vernalization-dependent and photoperiod-dependent flowering pathways coexisting in allopolyploid B. juncea, suggesting contribution of these pathways to adaptation for survival during polyploidization.

Conclusions

Taken together, we proposed that polyploidization has allowed for accelerated evolution of the glucosinolate biosynthesis and flowering pathways in B. juncea that likely permit the phenotypic variation observed in the crop.

Keywords:
Brassica juncea; Comparative genome analysis; Flowering pathway; Genome survey sequencing; Glucosinolate biosynthesis