Seedling development traits in Brassicanapus examined by gene expression analysis and association mapping

BMC Plant Biology

Research Article

Isobel Alison Papworth Parkin¹  Erin Eileen Higgins¹  Rod John Snowdon²  Bertha Salazar-Colqui²  Ian Bancroft³  Benjamin Stich⁴  Jinquan Li⁴  Anja Bus⁵  Niklas Körber⁵  Janet Higgins⁶ 

[1] Agriculture and Agri-Food Canada, 107 Science Place, SK S7N OX2, Saskatoon, Canada;Department of Plant Breeding, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany;John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK;Department of Biology, Wentworth Way, University of York, Heslington, YO41 5DD, York, UK;Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany;Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany;Institute of Crop Science and Resource Conservation, Plant Breeding and Biotechnology, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany;The Genome Analysis Centre, Norwich Research Park, NR4 7UH, Norwich, UK;

关键词: Brassica napus;    Seedling development;    RT-qPCR;    Candidate genes;    Genome-wide association mapping;    Digital gene expression analysis (DGE-seq);    Weighted gene co-expression network analysis (WGCNA);    Plant breeding;    Ribulose 1;    5-bisphosphate carboxylase/oxygenase small subunit;    Fructose-1;    6-bisphosphatase;    Linkage disequilibrium (LD);   

DOI  :  10.1186/s12870-015-0496-3

 received in 2014-10-20, accepted in 2015-04-20,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundAn optimal seedling development of Brassica napus plants leads to a higher yield stability even under suboptimal growing conditions and has therefore a high importance for plant breeders. The objectives of our study were to (i) examine the expression levels of candidate genes in seedling leaves of B. napus and correlate these with seedling development as well as (ii) detect genome regions associated with gene expression levels and seedling development traits in B. napus by genome-wide association mapping.ResultsThe expression levels of the 15 candidate genes examined in the 509 B. napus inbreds showed an averaged standard deviation of 5.6 across all inbreds and ranged from 3.2 to 8.8. The gene expression differences between the 509 B. napus inbreds were more than adequate for the correlation with phenotypic variation of seedling development. The average of the absolute value correlations of the correlation coefficients of 0.11 were observed with a range from 0.00 to 0.39. The candidate genes GER1, AILP1, PECT, and FBP were strongly correlated with the seedling development traits. In a genome-wide association study, we detected a total of 63 associations between single nucleotide polymorphisms (SNPs) and the seedling development traits and 31 SNP-gene associations for the candidate genes with a P-value < 0.0001. For the projected leaf area traits we identified five different association hot spots on the chromosomes A2, A7, C3, C6, and C7.ConclusionA total of 99.4% of the adjacent SNPs on the A genome and 93.0% of the adjacent SNPs on the C genome had a distance smaller than the average range of linkage disequilibrium. Therefore, this genome-wide association study is expected to result on average in 14.7% of the possible power. Compared to previous studies in B. napus, the SNP marker density of our study is expected to provide a higher power to detect SNP-trait/-gene associations in the B. napus diversity set. The large number of associations detected for the examined 14 seedling development traits indicated that these are genetically complex inherited. The results of our analyses suggested that the studied genes ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit (RBC) on the chromosomes A4 and C4 and fructose-1,6-bisphosphatase precursor (FBP) on the chromosomes A9 and C8 are cis-regulated.

【 授权许可】

Unknown   
© Körber et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License(http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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