Genetic Control of Rice Shoot and Root Growth Under Jasmonate Treatment Conditions by Genome Wide Association Study

Jasmonates (JAs) are phytohormones that play important roles in plants, such as regulating plant growth and development as well as responding to environmental challenges. Many studies reported that endogenous JAs level increase immediately when plant respond to stress such as wounding, herbivory and pathogene attacks. The exogenous application of JAs has been widely used to mimic the stresses-induced effects of the plant. In this study, a large scale phenotyping experiment of JA-treated rice varieties was performed in order to discover the quantitative trait loci (QTLs) associated with the sensitivity to JAs which linked to plant growth inhibition. After 7 days exposure to exogenous jasmonic acid, the effect on root length, shoot length, root mass, shoot mass and total mass were evaluated as parameters to analyze the effect of jasmonic acid (5µM) compare to the normal condition (0µM). Association analyses using Mixed Linear Model that take in account both the population structure and kinship matrix were conducted on whole panel having 155 rice accessions with 21632 markers to identify genetic variants. The results obtained showed up to 66 QTLs associated with the sensitivity to JAs linked to interested agronomical traits. A list of 160 promising candidate genes related to the stress responses connected with these traits is also determined. Using GO-slim term, near half of the candidate genes found in this study links to the metabolism, binding, biosynthesis, catalytic, hydrolase and transferase activity, in which metabolism and binding process occupy the most important portion. In conclusion, the identified QTLs associated with the morphology of rice under the treatment with exogenous jasmonic acid provides a valuable information to dissect the underlying molecular mechanism controlling the response to biotic and abiotic stress in rice.