GENOME-WIDE ANALYSIS OF JAPONICA RICE PERFORMANCES UNDER ALTERNATE WETTING AND DRYING AND PERMANENT FLOODING CONDITIONS.

A rice GWAS panel of 281 accessions of japonica rice was phenotypically characterized for traits related to phenology, plant and seed morphology, physiology, yield and grain ionome for two years in field conditions under permanent flooding (PF) or AWD. A genome-wide analysis approach uncovered a total of 360 significant marker-trait associations (MTAs), of which 105 were AWD-specific, 178 were PF-specific and 77 were in common between the two water management systems. AWD-specific associations were identified for several agronomic traits including days to maturation, days from flowering to maturation, leaf traits, plant height, panicle and seed traits, hundred grain weight, yield, tillering, mineral nutrient and toxic trace elements level in grains. Significant MTAs were detected across all the 12 rice chromosomes. The analysis of genes annotated in the Nipponbare reference sequence and included in the regions associated to the analyzed traits allowed the identification of several loci known to affect the respective traits. The high number of MTAs identified open new perspectives for the development of functional genomic and breeding strategies.