Open AccessEffective Genomic Selection in a Narrow‐Genepool Crop with Low‐Density Markers: Asian Rapeseed as an Example
Author(s) -
Werner Christian R.,
VossFels Kai P.,
Miller Charlotte N.,
Qian Wei,
Hua Wei,
Guan ChunYun,
Snowdon Rod J.,
Qian Lunwen
Publication year - 2018
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2017.09.0084
Subject(s) - biology , linkage disequilibrium , quantitative trait locus , plant breeding , genetics , single nucleotide polymorphism , genotyping , genomic selection , trait , snp genotyping , genetic marker , genome wide association study , rapeseed , genetic gain , selection (genetic algorithm) , association mapping , genotype , genetic variation , agronomy , gene , artificial intelligence , computer science , programming language
Genomic selection (GS) has revolutionized breeding for quantitative traits in plants, offering potential to optimize resource allocation in breeding programs and increase genetic gain per unit of time. Modern high‐density single nucleotide polymorphism (SNP) arrays comprising up to several hundred thousand markers provide a user‐friendly technology to characterize the genetic constitution of whole populations and for implementing GS in breeding programs. However, GS does not build upon detailed genotype profiling facilitated by maximum marker density. With extensive genome‐wide linkage disequilibrium (LD) being a common characteristic of breeding pools, fewer representative markers from available high‐density genotyping platforms could be sufficient to capture the association between a genomic region and a phenotypic trait. To examine the effects of reduced marker density on genomic prediction accuracy, we collected data on three traits across 2 yr in a panel of 203 homozygous Chinese semiwinter rapeseed ( Brassica napus L.) inbred lines, broadly encompassing allelic variability in the Asian B. napus genepool. We investigated two approaches to selecting subsets of markers: a trait‐dependent strategy based on genome‐wide association study (GWAS) significance thresholds and a trait‐independent method to detect representative tag SNPs. Prediction accuracies were evaluated using cross‐validation with ridge‐regression best linear unbiased predictions (rrBLUP). With semiwinter rapeseed as a model species, we demonstrate that low‐density marker sets comprising a few hundred to a few thousand markers enable high prediction accuracies in breeding populations with strong LD comparable to those achieved with high‐density arrays. Our results are valuable for facilitating routine application of cost‐efficient GS in breeding programs.