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


Sertse, D., You, F.M., Ravichandran, S., Cloutier, S. (2019). The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses. Frontiers in Plant Science, [online] 10

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Roots are fundamental organs for water and nutrient uptake, and, as such, they play a key role in drought response. Flax is sensitive to drought because it has a shallow tap root system. It can be easily outcompeted by weeds during water deficit times. However, some flax lines are more resistant to water limiting conditions. To understand the diversity in the root system of flax, we grew 115 lines in a semi-hydroponic system and measured 15 root traits, two shoot traits and the shoot to root dry weight ratios. We observed significant variations among the lines from the majority of the traits including root network volume, root length, root dry weight and so on. The DNA of the115 lines was also sequenced and DNA variations in the form of single nucleotide polymorphism were identified for each lines. Computational analyses were conducted to determine if variations at the DNA level could explain the variations observed in the traits. Indeed, 228 DNA sites explained the variation in 16 of the traits. Further bioinformatics analyses of the DNA sequences surrounding these sites pointed to genes that may be responsible for the variations in these traits. Such genes include transcription factors that affect the expression of other genes, kinases that can modify proteins and so on. With these new insights into the root architecture of flax and the gene regions controlling them, breeders can endeavour to use molecular markers to screen for these difficult to evaluate traits.


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.

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