High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets

Abstract

A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.

QTL analysis for the identification of candidate genes controlling phenolic compound accumulation in broccoli (Brassica oleracea L. var. italica)

“…The parents were VI-158, a calabrese-type double haploid of the F 1 hybrid ''Viking'' by a broccolette neri (black broccoli) accession BNC, PI 462209. Freeze-dried samples of 92 F 2:3 families grown in two field replications in 2009 and 2010 at North Carolina State University as described by Brown et al (2014) were obtained from the Brown laboratory.…”

“…The linkage map used in this analysis was developed by Brown et al (2014), with minor updates. It consists of 553 SNP markers from the Brassica napus (AACC) Illumina 60K iSelect array that are named according to the progenitor genome (''A'' = B. rapa or ''C'' = B. oleracea) followed by the position of the SNP as referenced by the ''Chiifu-401'' or ''TO1000'' genome sequence, respectively.…”

“…This population was recently saturated with single nucleotide polymorphism (SNP) markers from the Illumina 60K iSelect array designed for rapeseed (Brassica napus, N = 19 AACC) and anchored to the TO1000 B. oleracea reference sequence ) by genome-specific markers. This information was used to conduct QTL mapping of carotenoid and glucosinolate profiles and to identify putative candidate genes co-localizing with the QTL (Brown et al 2014(Brown et al , 2015. The present effort extends similar analysis to phenolic compound accumulation in the same population.…”

Genetic analysis of glucosinolate variability in broccoli florets using genome-anchored single nucleotide polymorphisms

“…The construction of the genetic linkage map has been previously described (Brown et al 2014). Briefly, the map was constructed using Brassica napus (AACC) single nucleotide markers (Illumina Brassica Infinium array) and contains 547 markers with an average interval size of 1.7 cM (no intervals exceeding 7.5 cM).…”

“…The map was constructed utilizing genome-specific markers anchored to the TO1000 B. oleracea reference sequence and was most recently used to identify candidate genes associated with three consistent loci impacting the accumulation of carotenoids in the same population (Brown et al 2014). The map was constructed utilizing genome-specific markers anchored to the TO1000 B. oleracea reference sequence and was most recently used to identify candidate genes associated with three consistent loci impacting the accumulation of carotenoids in the same population (Brown et al 2014).…”