Elsevier

Plant Science

Volume 283, June 2019, Pages 157-164
Plant Science

Genome-wide haplotype analysis improves trait predictions in Brassica napus hybrids

https://doi.org/10.1016/j.plantsci.2019.02.007Get rights and content
Under a Creative Commons license
open access

Highlights

  • The GCA of 950 F1 hybrids from 475 spring-type canola pollinator lines crossed with two tester lines.

  • 24,403 single-copy, genome-wide SNP loci were employed using 60 K Brassica SNP Infinium Consortium array.

  • Eight and seven haplotype regions were detected significantly association with the GCA values for DTF and GSL, respectively.

  • Interactions between haplotypes producing low GSL and early flowering time in hybrid crosses were identified.

  • Reconstructed phased F1 hybrid genotypes from the beneficial parental haplotype alleles.

Abstract

Combining ability is crucial for parent selection in crop hybrid breeding. Many studies have attempted to provide reliable and quick methods to identify genome regions in parental lines correlating with improved hybrid performance. The local haplotype patterns surrounding densely spaced DNA markers include a large amount of genetic information, and analysis of the relationships between haplotypes and hybrid performance can provide insight into the underlying genome regions which might contribute to enhancing combining ability. Here, we generated 24,403 single-copy, genome-wide SNP loci and calculated the general combining ability (GCA) of 950 hybrids from a diverse panel of 475 pollinators of spring-type canola inbred lines crossed with two testers for days to flowering (DTF) and seed glucosinolate content (GSL). We performed a genome-wide analysis of the haplotypes and detected eight and seven haplotype regions that were significantly associated with the GCA values for DTF and seed GSL, respectively. Additionally, two haplotype blocks containing orthologs of flowering time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC) on chromosome A02 showed additive epistatic interactions influencing flowering time. Moreover, two homoeologous haplotype regions on chromosomes A02 and C02 corresponded to major quantitative trait loci (QTL) for GSL which showed additive effects related to reduction of seed GSL in F1 hybrids. Our study showed that haplotype analysis has the potential to substantially improve the efficiency of hybrid breeding programs.

Keywords

Canola
GWAS
Haplotype
Flowering time
Glucosinolate
GCA

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These authors contributed equally to this work.