Uncovering genetic determinants of rice root anatomy using genome wide analysis

Abstract

Root anatomy plays a critical role in water and nutrients acquisition and influences plant adaptation to abiotic stresses. A better understanding of the genetic control of anatomical traits is important to improve rice production, a staple crop for half of the worlds population. In this study, we measured eleven root anatomical traits in a collection of 185 Vietnamese rice landraces, and conducted genome-wide association studies to uncover the genetic architecture underlying these traits. A total of 24 significant small nucleotide polymorphisms were identified, corresponding to 19 quantitative trait loci for traits such as root cross section area, cortex area, metaxylem area or theoretical axial conductance. Interestingly, several root anatomical traits correlated with previously characterized root architectural traits measured within the same Vietnamese rice collection, and some genetic regions associated with anatomical traits and drought-tolerance-related traits colocalized. Candidate genes potentially involved in root development and cell wall patterning were identified within these QTLs regions. In particular, the significant SNP in qRA10.1 associated with metaxylem area induces an amino-acid change in the kinase domain of a wall associated kinase (WAK) receptor-like protein kinase (OsWAK111) with an extracellular epidermal growth factor (EGT)-containing domain that bind pectin, which presumably sense perturbations in this component to influence cell elongation during plant development. This study reveal key determinants of the genetic control of root anatomy in rice, which could be exploited to enhance tolerance to abiotic stresses such as drought.