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Drought response of flax accessions and identification of quantitative trait nucleotides (QTNs) governing agronomic and root traits by genome-wide association analysis

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Abstract

Flaxʼs fiber yield and quality can be severely impaired due to water deprivation. Herein, 41 diverse flax accessions were evaluated for four agronomic and four root traits under drought stress (DS) and irrigated (IR) conditions. In order to identify quantitative trait nucleotides (QTNs) positively influencing the stability of these traits under DS, the stress tolerance index (STI) and trait stability index were calculated, which were analyzed using two single-locus and three multi-locus genome-wide association (GWA) methods with 170,534 single-nucleotide polymorphisms (SNPs). Significant genotype and treatment effects (p < 0.001) were observed for the traits assessed. A total of 118 QTNs were identified by multiple GWA methods. Fifteen QTNs were commonly detected by two or more methods. One QTN for STI was consistently identified by four methods and explained between 45 and 65% of the phenotypic variation (R2). A maximum of 12 out of 15 favorable QTNs were observed in flax accessions. Genotypes F_UNK_C_CN33393 and F_NLD_C_CN18987 showed superior plant height and root trait stability under DS, each one harboring 12 and 10 favorable QTNs, respectively. QTNs were further validated in an independent set of accessions under DS and IR conditions. Most of accessions performed as expected based on their corresponding haplotypes, confirming the robustness of the QTNs indentified by multiple GWA methods. Candidate genes involved in drought-responsive pathways and root and vascular tissue development were identified nearby QTNs. Collectively, our results should facilitate marker-assisted breeding toward the goal of improving flax production under water scarcity.

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Acknowledgments

CGNA acknowledges the collaboration of Agriculture and Agri-Food Canada (AAFC) and the Total Utilization Flax GENomics (TUFGEN) project formerly funded by Genome Canada and other stakeholders of the Canadian flax industry. Dr. Bradley Till is also gratefully acknowledged for his helpful suggestions in preparing this manuscript.

Funding information

This work was funded by Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) project N°1161133 and supported by the Agriaquaculture Nutritional Genomic Center (CGNA), the Programa Regional de Investigación Científica y Tecnológica and the Gobierno Regional de La Araucania, Chile.

Author information

BJSC designed the research experiments, analyzed the data, interpreted the results, and wrote the manuscript. SC amplified the SSRs and performed the resequencing of the flax association panel and co-wrote and edited the manuscript. HAG planted the flax panel and performed the root traits analysis. GA planted the flax panel and analyzed the agronomic data. RQ planted the flax panel and performed root traits experiments. FMY generated the genome-wide SNP data. All the authors read and approved the final manuscript.

Correspondence to Braulio J. Soto-Cerda.

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Soto-Cerda, B.J., Cloutier, S., Gajardo, H.A. et al. Drought response of flax accessions and identification of quantitative trait nucleotides (QTNs) governing agronomic and root traits by genome-wide association analysis. Mol Breeding 40, 15 (2020). https://doi.org/10.1007/s11032-019-1096-y

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Keywords

  • Linum usitatissimum
  • Flax
  • Drought tolerance
  • Root traits
  • Single-locus GWAS
  • Multi-locus GWAS