Genomic Prediction and Genetic Correlation of Agronomic, Blackleg Disease, and Seed Quality Traits in Canola (Brassica napus L.).

Mulusew Fikere,German C Spangenberg,Phillip A Salisbury,Hans D Daetwyler,Denise M Barbulescu,Joe Panozzo,Sally Norton,M Michelle Malmberg,Pankaj Maharjan,Noel O I Cogan,Surya Kant

doi:10.3390/plants9060719

Abstract

Genomic selection accelerates genetic progress in crop breeding through the prediction of future phenotypes of selection candidates based on only their genomic information. Here we report genetic correlations and genomic prediction accuracies in 22 agronomic, disease, and seed quality traits measured across multiple years (2015–2017) in replicated trials under rain-fed and irrigated conditions in Victoria, Australia. Two hundred and two spring canola lines were genotyped for 62,082 Single Nucleotide Polymorphisms (SNPs) using transcriptomic genotype-by-sequencing (GBSt). Traits were evaluated in single trait and bivariate genomic best linear unbiased prediction (GBLUP) models and cross-validation. GBLUP were also expanded to include genotype-by-environment G × E interactions. Genomic heritability varied from 0.31to 0.66. Genetic correlations were highly positive within traits across locations and years. Oil content was positively correlated with most agronomic traits. Strong, not previously documented, negative correlations were observed between average internal infection (a measure of blackleg disease) and arachidic and stearic acids. The genetic correlations between fatty acid traits followed the expected patterns based on oil biosynthesis pathways. Genomic prediction accuracy ranged from 0.29 for emergence count to 0.69 for seed yield. The incorporation of G × E translates into improved prediction accuracy by up to 6%. The genomic prediction accuracies achieved indicate that genomic selection is ready for application in canola breeding.

Highlights

Canola (Brassica napus L., AACC, 2n = 38) is the second most important oilseed worldwide, after soybean [1]
The phenotypic performance (best linear unbiased estimates (BLUEs)), broad-sense heritability shown in (Table S2a–c) and genomic heritability (Figure 1) for 202 canola lines were recorded under rain-fed sites (Wickliffe, Green Lake, Mininera and Horsham rain-fed) and irrigated conditions (Horsham irrigated 2016 and 2017 sites) during the 2015–2017 growing seasons was determined
The greatest phenotypic variation was observed in average internal infection (AvInf) and seed yield per plot (YIELD) across locations and years

Summary

Introduction

Global food production has to double by 2050 to feed the growing human population [2], which underscores the importance of accelerating crop improvement. The development of molecular plant breeding using high throughput genetic markers has enabled breeders to accelerate genetic gain and improved several agronomic and quality traits. High-priority breeding targets are high-yielding cultivars with improved blackleg resistance and improved oil quality. Canola cultivars vary in their FA profiles [5,6] and the presence of such variation allowed breeders to reduce toxic seed components (erucic acid and glucosinolate) to produce double-zero canola oil seed. Several varieties resistant to blackleg disease (caused by Leptosphaeria maculans) were developed and have significantly improved canola yield per unit time and space, which was extensively reviewed by

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