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Journal of Integrative Agriculture  2019, Vol. 18 Issue (7): 1541-1546    DOI: 10.1016/S2095-3119(19)62635-3
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Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines
HUO Dong-ao*, ZHU Bin*, TIAN Gui-fu, DU Xu-ye, GUO Juan, CAI Meng-xian
School of Life Sciences, Buckwheat Research Center, Guizhou Normal University, Guiyang 550025, P.R.China
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The economically valuable oil crop Brassica napus (AACC, 2n=38), which arose from interspecific hybridization between the diploid ancestors Brassica rapa (AA, 2n=20) and Brassica oleracea (CC, 2n=18), has a complex genome.  More than 10% of the assembled sequences, most of which belong to the C subgenome, have not been anchored to the corresponding chromosome.  Previously, a complete set of monosomic alien addition lines (MAALs, C1–C9) with each of the nine C-subgenome chromosomes added to the extracted A subgenome was obtained from the allotetraploid B. napus donor Oro, after the ancestral B. rapa (RBR Oro) genome was restored.  These MAALs effectively reduced the complexity of the B. napus genome.  Here, we determined the expression values of genes on unanchored scaffolds in the MAALs and RBR Oro.  Then, multiple comparisons of these gene expression values were used to determine the affiliations of the non-anchored scaffolds on which the genes were located.  In total, 54.68% (44.11 Mb) of the 80.67 Mb of non-anchored scaffolds belonging to the C subgenome were assigned to corresponding C chromosomes.  This work highlights the potential value of these MAALs in improving the genome quality of B. napus.
Keywords:  Brassica napus        genome sequence        RNA-seq        monosomic alien addition lines        scaffolds  
Received: 21 September 2018   Online: 23 January 2019   Accepted: 01 July 2019
Fund: This work was supported by the National Natural Science Foundation of China (31801391), the Doctoral Foundation of Guizhou Normal University, China (11904-0517061 and 11904-0517054), the Project for Young Growth of Education Department of Guizhou Province, China (GPED, qianjiaoheKYzi[2017]127), and the Collaborative Fund of Guizhou Science and Technology, China (QKHLHZ[2017]7356 and [2012]21).
Corresponding Authors:  Correspondence CAI Meng-xian, Tel: +86-851-83227351, E-mail:   
About author:  * These authors contributed equally to this study.

Cite this article: 

HUO Dong-ao, ZHU Bin, TIAN Gui-fu, DU Xu-ye, GUO Juan, CAI Meng-xian. 2019. Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines. Journal of Integrative Agriculture, 18(7): 1541-1546.

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