A consensus map of rapeseed (Brassica napusL.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits

BMC Genomics

Research Article

Derek Lydiate¹  Nick Larkan¹  Isobel AP Parkin¹  Andrew G Sharpe²  Frank Detering³  Andrzej Kilian³  Rosy Raman⁴  Harsh Raman⁴  Jinling Meng⁵  Yan Long⁵  Jun Zou⁵  David Edwards⁶  Jacqueline Batley⁶  M Naveed Aslam⁷  Matthew N Nelson⁸  Wallace A Cowling⁹ 

[1] Agriculture and Agri-Food Canada, 107 Science Place, SK S7N 0X2, Saskatoon, Canada;DNA Technologies Laboratory, National Research Council of Canada, 110 Gymnasium Place, SK S7N 0X2, Saskatoon, Canada;Diversity Arrays Technology Pty Ltd, 1 Wilf Crane Crescent, ACT 2600, Yarralumla, Canberra, Australia;EH Graham Centre for Agricultural Innovation (an alliance between NSWDPI and Charles Sturt University), Wagga Wagga Agricultural Institute, 2650, Wagga Wagga, NSW, Australia;National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China;School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia;School of Plant Biology, The University of Western Australia, 35 Stirling Highway, WA 6009, Crawley, Australia;School of Plant Biology, The University of Western Australia, 35 Stirling Highway, WA 6009, Crawley, Australia;The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, 6009, Crawley, WA, Australia;The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, 6009, Crawley, WA, Australia;

关键词: Double Haploid;    Double Haploid Line;    DArT Marker;    Double Haploid Population;    Diversity Array Technology;   

DOI  :  10.1186/1471-2164-14-277

 received in 2012-10-11, accepted in 2013-04-06,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundDense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular breeding, and map-based gene cloning. This report describes the construction of the first B. napus consensus map consisting of a 1,359 anchored array based genotyping platform; Diversity Arrays Technology (DArT), and non-DArT markers from six populations originating from Australia, Canada, China and Europe. We aligned the B. napus DArT sequences with genomic scaffolds from Brassica rapa and Brassica oleracea, and identified DArT loci that showed linkage with qualitative and quantitative loci associated with agronomic traits.ResultsThe integrated consensus map covered a total of 1,987.2 cM and represented all 19 chromosomes of the A and C genomes, with an average map density of one marker per 1.46 cM, corresponding to approximately 0.88 Mbp of the haploid genome. Through in silico physical mapping 2,457 out of 3,072 (80%) DArT clones were assigned to the genomic scaffolds of B. rapa (A genome) and B. oleracea (C genome). These were used to orientate the genetic consensus map with the chromosomal sequences. The DArT markers showed linkage with previously identified non-DArT markers associated with qualitative and quantitative trait loci for plant architecture, phenological components, seed and oil quality attributes, boron efficiency, sucrose transport, male sterility, and race-specific resistance to blackleg disease.ConclusionsThe DArT markers provide increased marker density across the B. napus genome. Most of the DArT markers represented on the current array were sequenced and aligned with the B. rapa and B. oleracea genomes, providing insight into the Brassica A and C genomes. This information can be utilised for comparative genomics and genomic evolution studies. In summary, this consensus map can be used to (i) integrate new generation markers such as SNP arrays and next generation sequencing data; (ii) anchor physical maps to facilitate assembly of B. napus genome sequences; and (iii) identify candidate genes underlying natural genetic variation for traits of interest.

【 授权许可】

CC BY   
© Raman et al.; licensee BioMed Central Ltd. 2013