Seed Quality Traits Can Be Predicted with High Accuracy in Brassica napus Using Genomic Data

Abstract

Improving seed oil yield and quality are central targets in rapeseed (Brassica napus) breeding. The primary goal of our study was to examine and compare the potential and the limits of marker-assisted selection and genome-wide prediction of six important seed quality traits of B. napus. Our study is based on a bi-parental population comprising 202 doubled haploid lines and a diverse validation set including 117 B. napus inbred lines derived from interspecific crosses between B. rapa and B. carinata. We used phenotypic data for seed oil, protein, erucic acid, linolenic acid, stearic acid, and glucosinolate content. All lines were genotyped with a 60k SNP array. We performed five-fold cross-validations in combination with linkage mapping and four genome-wide prediction approaches in the bi-parental population. Quantitative trait loci (QTL) with large effects were detected for erucic acid, stearic acid, and glucosinolate content, blazing the trail for marker-assisted selection. Despite substantial differences in the complexity of the genetic architecture of the six traits, genome-wide prediction models had only minor impacts on the prediction accuracies. We evaluated the effects of training population size, marker density and phenotyping intensity on the prediction accuracy. The prediction accuracy in the independent and genetically very distinct validation set still amounted to 0.14 for protein content and 0.17 for oil content reflecting the utility of the developed calibration models even in very diverse backgrounds.

Linkage mapping and whole-genome predictions in canola (Brassica napus) subjected to differing temperature treatments

“…The seed-quality traits had high heritability and accuracies ranging from 0.38 to 0.56. These values were lower than reported previously (Jan et al 2016;Zou et al 2016); however, this can be explained by the larger training population sizes utilised in those studies. Würschum et al (2014) reported on prediction accuracies within DH families consisting of few individuals and reported accuracies similar to, or slightly lower than, the results reported here.…”

“…In maize, WGP has been more effective for improving grain yield under drought stress than phenotypic selection alone (Vivek et al 2017). WGP has been applied to B. napus doubled-haploid (DH) populations for yield and quality traits with varying degrees of success, depending on the population structure, number of individuals within the population, marker density and trait heritability (Würschum et al 2014;Zou et al 2016). With respect to heat stress, Bita and Gerats (2013) discuss the difficulty in using low-effect QTLs for improving quantitative traits such as tolerance to increased temperatures and suggest WGP as a promising alternative.…”

Effects of genotype and environment on seed quality traits variability in interspecific cross-derived Brassica lines

“…Generally, in Brassica napus breeding, traits related to commercial success are of highest importance (Friedt and Snowdon 2010). For this reason rapeseed breeding strategies are oriented on developnig new cultivars with high oil, protein as well as low erucic acid, glucosinolate and fiber content (Möllers 2004;Abbadi and Leckband 2011;Zou et al 2016;Körber et al 2016). For this purpose knowledge of genetic diversity is indispensible in the development of commercial cultivars (Ahmad et al 2013;Liu et al 2016).…”

Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed

“…The markers showing the same segregation pattern were classified into the same genetic bins, and one of the markers with the highest quality were choose to construct genetic map using JoinMap 4.0 (Van Ooijen, 2006). Double crosses and recombination frequency were checked by Mapdisto 2.0 (Lorieux, 2012;Zou et al, 2014;Zou et al, 2016).…”