Abstract
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.
Highlights
Dense 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
These linkage maps have been based on a range of marker systems such as restriction fragment length polymorphisms (RFLPs), randomly amplified polymorphic DNAs (RAPD), amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), sequence- tagged sites (STSs), sequence-related amplified polymorphisms (SRAPs) and single nucleotide polymorphisms (SNPs) [5,6,7,8,9,10,11,12,13,14]
Map construction from individual mapping populations Individual component maps were constructed from six populations that were genotyped with Diversity Arrays Technology (DArT), along with a selection of SSR markers (Table 1, Additional file 1)
Summary
Dense 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. Several linkage maps have been constructed from recombination data in B. napus mapping populations, which depict the distances between loci, as well as their order on a chromosome These linkage maps have been based on a range of marker systems such as restriction fragment length polymorphisms (RFLPs), randomly amplified polymorphic DNAs (RAPD), amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), sequence- tagged sites (STSs), sequence-related amplified polymorphisms (SRAPs) and single nucleotide polymorphisms (SNPs) [5,6,7,8,9,10,11,12,13,14]. The number of marker loci in these genetic linkage maps varied from 219 to 13,551, where the marker density was dependent upon the level of polymorphism between the parental lines of mapping populations and type of marker system used for detecting polymorphisms
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