Genome-wide Association Mapping for the Identification of SNPs Controlling Lateral Root Plasticity in Selected Rice Germplasms of the Philippines

Abstract

Lateral root plasticity is a key adaptive mechanism for drought and fluctuating moisture-induced stresses in rice. Thus, understanding the genetic control of lateral root plasticity is important to enhance the climate-resilience and productivity of rice in abiotic stressed-prone environments. Genome-wide association analysis was conducted on a selected panel of traditional rice varieties (TRVs) to find single nucleotide polymorphisms (SNPs) associated with root plasticity traits under different gradients of soil moisture stress. A total of 17 SNPs, which were significantly correlated to root plasticity traits under soil moisture stress conditions, were located in six chromosomes (2, 5, 7, 9, 10, and 12). Additionally, the accessions that showed high plasticity in total lateral root length (TLRL) under severe drought were identified from among the TRVs and assumed to possess the lone SNP associated with the trait found in Chromosome 2. Specifically, the Baksalan Kawalwal accession showed an increase in L-type lateral root length under fluctuating soil moistures (SMF) (+10.31 m) and progressive drought (PDR) (+0.90 m), relative to their continuously waterlogged (CWL) counterparts under rootbox pinboard system. This may suggest the performance of the SNP in controlling the promotion of lateral roots. Furthermore, a possible candidate gene found near the SNP in Chromosome 2 is a member of PYR/PYL/RCAR-like protein family of abscisic acid (ABA) receptors, likely suggesting that plasticity in lateral root development in rice under severe drought could be regulated by ABA. Taken together, these novel root plasticity SNPs and the respective candidate genes on Chromosome 2 have potential use in developing climate-smart rice varieties.