Drought response of flax accessions and identification of quantitative trait nucleotides (QTNs) governing agronomic and root traits by genome-wide association analysis
Citation
Soto-Cerda, B.J., Cloutier, S., Gajardo, H.A., Aravena, G., Quian, R., You, F.M. (2020). Drought response of flax accessions and identification of quantitative trait nucleotides (QTNs) governing agronomic and root traits by genome-wide association analysis. Molecular Breeding, [online] 40(1), http://dx.doi.org/10.1007/s11032-019-1096-y
Plain language summary
Drought resistance in plants is a complex trait controlled by many genes. In flax, shortage of water during the growing season negatively impacts the yield and the quality of the seed and the fibre. Here, we evaluated 41 flax lines grown under irrigated and drought conditions for eight traits: yield, height, flowering time, seed weight, total root length, total root volume, mean root diameter and root surface area. The DNA of these 41 lines was also sequenced and 170,000 genetic markers called single nucleotide polymorphisms (SNPs) were identified across all 15 chromosomes of flax. With this data, we conducted a genome-wide association study which is essentially a method to identify chromosomal regions harboring genes or genetic features responsible for the traits or trait indices - the latter takes into consideration the response to the water regimes. The 118 SNP markers associated with one or more of the traits are termed quantitative trait nucleotides (QTNs) and each of them explain a percentage of the traits’ variation. For example, one of these QTNs explained between 45 and 65% of the variation for stress tolerance index (STI) and, as such, is considered to harbor one or many major genetic features responsible for yield under drought. Lines that carried many of the beneficial markers for root traits for example performed significantly better than the other lines. These markers are now available for use by breeder to speed-up improvement for drought resistance through either marker-assisted selection or genomic selection strategies.
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.