Exploration of Candidate Genes Derived from SNPs Associated with Phenotypic Root Plasticity Using Philippine Rice Germplasm for Drought Adaptation

Abstract

Phenotypic root plasticity is a crucial trait for stable growth, adaptability, and productivity under abiotic-stressed growing environments. However, the genetic determinants and mechanisms controlling the trait are largely unknown, thus limiting its breeding application. We previously found 17 single nucleotide polymorphism (SNPs) significantly associated with phenotypic root plasticity traits – particularly, total root length (TRL), total nodal root length (TNRL), and total lateral root length (TLRL) – under moderate and severe drought using selected Philippine rice germplasm by employing the genome-wide association studies (GWAS) approach. Here, we present around 92 candidate genes using these SNP data. The genes were derived from various functional categories and drought intensity dependent. These were further narrowed via Gene Ontology and gene expression profile at root apical regions using databases to those whose putative functions were likely to be associated with root development in response to drought stress. Sixteen (16) more interesting known or novel genes were selected and discussed. When these genes are validated, they can help improve rice adaptation to water-limited environments.