The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses

Abstract

Roots are fundamental organs for water and nutrient uptake as well as for signal transduction in response to biotic and abiotic stresses. Flax has a shallow tap root system that relies mostly on top soil nutrient and moisture resources. The crop can easily be outcompeted by weeds or other crops in intercropping systems, especially in moisture deficit conditions. However, there is a wide range of variation among genotypes in terms of performance under scarce resources such as moisture limitation. Here we phenotyped 15 root, two shoot traits and shoot to root dry weight ratio on 115 flax accessions grown in a hydroponic pouch system and performed a genome-wide association study (GWAS) based on seven different models to identify quantitative trait loci underlying these traits. Significant variation among genotypes was observed for the two shoot and 12 of the 14 root traits. Shoot dry weight was correlated with root network volume, length, surface area, and root dry weight (r > 0.5, P < 0.001) but not significantly correlated with root depth (r = 0.033, P > 0.05). The seven GWAS models detected a total of 228 quantitative trait nucleotides (QTNs) for 16 traits. Most loci, defined by an interval of 100 kb up and downstream of the QTNs, harbored genes known to play role(s) in root and shoot development, suggesting them as candidates. Examples of candidate genes linked to root network QTNs included genes encoding GRAS transcription factors, mitogen-activated protein kinases, and auxin related lateral organ boundary proteins while QTN loci for shoot dry weight harbored genes involved in photomorphogenesis and plant immunity. These results provide insights into the genetic bases of early shoot and root development traits in flax that could be capitalized upon to improve its root architecture, particularly in view of better withstanding water limiting conditions during the cropping season.

Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean (Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity

“…Genes Phvul.011G000700 and Phvul.011G001300 were examples of this class. These genes are likely to encode pentatricopeptide repeat (PPR) proteins known to be involved in post-transcriptional regulation of gene expression (Kosová et al, 2018) during abiotic stresses like drought and salinity (Xing et al, 2018;Sertse et al, 2019). The finding was supported by the fact that we also found many genes associated with salt and drought tolerance.…”

Genetic Dissection of Seedling Root System Architectural Traits in a Diverse Panel of Hexaploid Wheat through Multi-Locus Genome-Wide Association Mapping for Improving Drought Tolerance

“…Due to the difficulty of high-throughput phenotyping of RSA characteristics in field conditions, their optimization was ignored [10,12,19]. However, seedling level root architecture is associated with adult plant root architecture and is being studied to translate the knowledge for later growth stages [20,21].…”

Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.)

“…Then, the application of designating a potential candidate gene of a QTL depends on many other factors, such as the number of markers used, marker density on chromosomes, the recombination rate of genomic regions, and so on. To date, the most popular and simple approach for predicting candidate genes is to investigate the annotated genes in the vicinity of the QTL, such as a window of a specific physical distance flanking the QTL [ 51 , 52 , 53 ]. Although functional validation is the ultimate goal, candidate gene prediction of QTL/QTNs based on chromosomal location combined with a priori knowledge of gene functions has the potential to significantly narrow down the candidate gene list.…”