Loci harboring genes with important role in drought and related abiotic stress responses in flax revealed by multiple GWAS models
Citation
Sertse, D., You, F.M., Ravichandran, S., Soto-Cerda, B.J., Duguid, S., Cloutier, S. (2021). Loci harboring genes with important role in drought and related abiotic stress responses in flax revealed by multiple GWAS models. Theoretical and Applied Genetics (TAG), [online] 134(1), 191-212. http://dx.doi.org/10.1007/s00122-020-03691-0
Plain language summary
Drought is a critical phenomenon challenging today’s agricultural sector; a phenomenon that has been put at the forefront with the current and anticipated climate change situation. As such, the development of varieties adapted to moisture deficit is becoming an important breeding objective for many crops including flax which is particularly affected by limiting moisture conditions. In this research, we studied the drought resistance in the field of more than 100 flax lines originating from more than 20 major growing countries. The collection was grown at two locations for three years in irrigated and non-irrigated fields and, we evaluated each line for 11 drought-related traits. Of these, six showed significant differences between irrigated and non-irrigated conditions. Sequencing of the DNA of all lines was performed and we identified 12,316 markers that differentiate the various lines. Statistical analyses, falling under the general term “genome-wide association study”, were performed to identify the genetic markers linked to the drought-resistance traits. A total of 144 DNA markers were significantly associated with at least one of the traits. Of these, 16 explained more than 15% of the trait variation which is considered high for a trait as complex as drought resistance. Because the flax genome has been sequenced previously, we could investigate the genes linked to the drought-resistance markers. For example, we identified a WAX INDUCER1 and STRESS-ASSOCIATED PROTEIN (SAP) as potential candidate genes with important roles in drought resistance. Finally, lines with multiple positive markers were found to outperform others for grain yield, thousand seed weight and fiber and biomass production when grown in non-irrigated conditions, suggesting their potential usefulness in breeding for drought tolerance.
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 multi-allele 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.