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

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.

Genome-Wide Association Study of Genetic Control of Seed Fatty Acid Biosynthesis in Brassica napus

“…The peak of significantly associated SNPs for oleic and linoleic fatty acid content in seeds was identified on chromosome A05, which corresponds with previous quantitative genetic studies reporting major QTL for those fatty acids on linkage group A05 (Smooker et al, 2011; Raman et al, 2013; Wang et al, 2015; Hu et al, 2006). Recently, integration of QTL and transcript abundance (eQTL) analysis in B. rapa also identified a QTL hotspot for polyunsaturated FAs on chromosome A05 (Basnet et al, 2016).…”

Construction of a genetic linkage map and QTL analysis in bambara groundnut

“…This may indicate the presence of gene-rich regions, potentially as a reflection of hypomethylated regions of the restriction enzyme sites, which is consistent with the observations found in the genetic maps of other species such as chickpea and rapeseed (Raman et al 2013;Thudi et al 2011). Mapping of DArT array markers to the Eucalyptus reference genomes using the unique sequence tag of each marker has suggested that PstI-based DArT markers are predominant at the low copy gene-rich regions (Petroli et al 2012).…”

SNP markers‐based map construction and genome‐wide linkage analysis in Brassica napus

“…We used the sequence of the 50‐mer probes provided by Illumina to compare colinearity between the linkage (SNP marker) map of the SASDH population based on meiotic recombinations and the physical maps. In previous studies, we already compared colinearity between non‐SNP markers and the coordinates of A and C genomes (Raman et al ., ,b). Using the outlined approach, most of the markers were aligned only with a single reference scaffold.…”