Loci harboring genes with important role in drought and related abiotic stress responses in flax revealed by multiple GW
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ORIGINAL ARTICLE
Loci harboring genes with important role in drought and related abiotic stress responses in flax revealed by multiple GWAS models Demissew Sertse1,2 · Frank M. You2 · Sridhar Ravichandran2 · Braulio J. Soto‑Cerda3 · Scott Duguid4 · Sylvie Cloutier1,2 Received: 8 January 2020 / Accepted: 18 September 2020 © Crown 2020
Abstract Key message QTNs associated with drought tolerance traits and indices were identified in a flax mini-core collection through multiple GWAS models and phenotyping at multiple locations under irrigated and non-irrigated field conditions. Abstract Drought is a critical phenomenon challenging today’s agricultural sector. Crop varieties adapted to moisture deficit are becoming vital. Flax can be greatly affected by limiting moisture conditions, especially during the early development and reproductive stages. Here, a mini-core collection comprising genotypes from more than 20 major growing countries was evaluated for 11 drought-related traits in irrigated and non-irrigated fields for 3 years. Heritability of the traits ranged from 44.7 to 86%. Six of the 11 traits showed significant phenotypic difference between irrigated and non-irrigated conditions. A genome-wide association study (GWAS) was performed for these six traits and their corresponding stress indices based on 106 genotypes and 12,316 single nucleotide polymorphisms (SNPs) using six multi-locus and one single-locus models. The SNPs were then assigned to 8050 linkage disequilibrium (LD) blocks to which a restricted two-stage multi-locus multiallele GWAS was applied. A total of 144 quantitative trait nucleotides (QTNs) and 13 LD blocks were associated with at least one trait or stress index. Of these, 16 explained more than 15% of the genetic variance. Most large-effect QTN loci harbored gene(s) previously predicted to play role(s) in the associated traits. Genes mediating responses to abiotic stresses resided at loci associated with stress indices. Flax genes Lus10009480 and Lus10030150 that are predicted to encode WAX INDUCER1 and STRESS-ASSOCIATED PROTEIN (SAP), respectively, are among the important candidates detected. Accessions with multiple favorable alleles outperformed others for grain yield, thousand seed weight and fiber/biomass in non-irrigated conditions, suggesting their potential usefulness in breeding and genomic selection.
Communicated by Peter Langridge. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03691-0) contains supplementary material, which is available to authorized users. * Sylvie Cloutier [email protected] 1
Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada
2
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
3
Agriaquaculture Nutritional Genomic Centre (CGNA), Las Heras 350, 4781158 Temuco, Chile
4
Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, Canada
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