Integrating multi-locus genome-wide association studies with transcriptomic data to identify genetic loci underlying adult root trait responses to drought stress in flax (Linum usitatissimum L.)

Water stress is a major constraint on crop production and, root systems are one of the key features of plants determining drought tolerance and yield. In this study, five root morphological traits and their stability indices were evaluated at the reproductive stage on an association panel consisting of 120 diverse Linum usitatissimum accessions grown under well-watered and water-limiting conditions. To identify quantitative trait loci (QTL) and candidate genes positively influencing root traits under drought, combined multi-locus genome-wide association studies (ML-GWAS) and transcriptomic data analysis were carried out. A total of 112 QTL were identified accounting for 0.45–24.28 % of the phenotypic variation for root-related traits. Fifty QTL were detected by at least two ML-GWAS models, and 26 were co-located with previously reported QTL associated with yield-related traits under drought and early root and shoot development. Phenotypic differences between two contrasting subsets of accessions for the traits assessed were attributable to the accumulation of positive QTL alleles (PQTL), where the subset with the largest number of PQTL registered 154 % and 69 % greater total root length and yield under drought stress, respectively, than the subset with the fewest PQTL. Transcriptomic data analysis identified 766 differentially expressed genes (DEGs) responsive to drought stress in 108 QTL. Annotation of the 766 DEGs yielded functional genes involved in root development, stomatal closure, ROS (reactive oxygen species) scavenging, and hormone responses, among others. Taken together, the combined use of GWAS and transcriptomic data analyses provide the foundation for our enhanced understanding of root trait morphological changes in response to drought stress, and to achieve superior yield resilience/stability under water shortages in flax through enhanced molecular breeding. All data supporting the findings of this study are available within the paper and within its Supplementary data