title: 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.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zou
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
authors.forename: Yusheng
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Peifa
authors.initials: P
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Shi
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Jinling
authors.initials: J
authors.lastname: Meng
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
authors.forename: Jochen Christoph
authors.initials: JC
authors.lastname: Reif
mesh_terms: D029688:Brassica napus / Q000235:genetics*; D004883:Erucic Acids / Q000032:analysis; D018745:Genome, Plant; D005838:Genotype; D005961:Glucosinolates / Q000032:analysis; D015810:Linkage Disequilibrium; D008042:Linolenic Acids / Q000032:analysis; D010641:Phenotype; D010938:Plant Oils / Q000737:chemistry; D010940:Plant Proteins / Q000032:analysis; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012639:Seeds / Q000235:genetics
chemical_list: D004883:Erucic Acids; D005961:Glucosinolates; D008042:Linolenic Acids; D010938:Plant Oils; D010940:Plant Proteins; C049811:erucic acid