A genome-wide association study (GWAS) identifies multiple loci linked with the natural variation for Al3+ resistance in Brassica napus
Hanmei Du A B , Harsh Raman C , Akitomo Kawasaki A D , Geetha Perera A , Simon Diffey E , Rod Snowdon F , Rosy Raman C and Peter R. Ryan
A *
+ Author Affiliations
- Author Affiliations
A CSIRO Agriculture and Food, Canberra, ACT 2601, Australia.
B Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, China.
C NSW Department of Primary Industries, Wagga Wagga, NSW 2650, Australia.
D NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Advanced Gene Technology Centre, Menangle, NSW 2568, Australia.
E Apex Biometry, Fremantle, WA, Australia.
F Justus Liebig University, Department of Plant Breeding Institute, Giessen 35391, Germany.
Functional Plant Biology 49(10) 845-860 https://doi.org/10.1071/FP22073
Submitted: 5 April 2022 Accepted: 28 May 2022 Published: 27 June 2022
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)
Abstract
Acid soils limit yields of many important crops including canola (Brassica napus), Australia’s third largest crop. Aluminium (Al3+) stress is the main cause of this limitation primarily because the toxic Al3+ present inhibits root growth. Breeding programmes do not target acid-soil tolerance in B. napus because genetic variation and convincing quantitative trait loci have not been reported. We conducted a genome-wide association study (GWAS) using the BnASSYST diversity panel of B. napus genotyped with 35 729 high-quality DArTseq markers. We screened 352 B. napus accessions in hydroponics with and without a toxic concentration of AlCl3 (12 μM, pH 4.3) for 12 days and measured shoot biomass, root biomass, and root length. By accounting for both population structure and kinship matrices, five significant quantitative trait loci for different measures of resistance were identified using incremental Al3+ resistance indices. Within these quantitative trait locus regions of B. napus, 40 Arabidopsis thaliana gene orthologues were identified, including some previously linked with Al3+ resistance. GWAS analysis indicated that multiple genes are responsible for the natural variation in Al3+ resistance in B. napus. The results provide new genetic resources and markers to enhance that Al3+ resistance of B. napus germplasm via genomic and marker-assisted selection.
Keywords: acidity, aluminium, candidate genes, canola, genetic variation, genome-wide association analysis, pH, QTL, soil, tolerance, toxicity.
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