Genome-Wide Analysis of japonica Rice Performance under Limited Water and Permanent Flooding Conditions

Abstract

A rice GWAS panel of 281 accessions of japonica rice was phenotypically characterized for 26 traits related to phenology, plant and seed morphology, physiology and yield for 2 years in field conditions under permanent flooding (PF) and limited water (LW). A genome-wide analysis uncovered a total of 160 significant marker-trait associations (MTAs), of which 32 were LW-specific, 59 were PF-specific, and 69 were in common between the two water management systems. LW-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 and tillering. Significant MTAs were detected across all the 12 rice chromosomes, while clusters of effects influencing different traits under LW or in both watering conditions were, respectively, observed on chromosomes 4, 8, and 12 and on chromosomes 1, 3, 4, 5, and 8. The analysis of genes annotated in the Nipponbare reference sequence and included in the regions associated to traits related to plant morphology, grain yield, and physiological parameters allowed the identification of genes that were demonstrated to affect the respective traits. Among these, three (OsOFP2, Dlf1, OsMADS56) and seven (SUI1, Sd1, OsCOL4, Nal1, OsphyB, GW5, Ehd1) candidate genes were, respectively, identified to co-localize with LW-specific associations and associations in common between the two water treatments. For several LW-specific MTAs, or in common among the two treatments, positional co-localizations with previously identified QTLs for rice adaptation to water shortages were observed, a result that further supports the role of the loci identified in this work in conferring adaptation to LW. The most robust associations identified here could represent suitable targets for genomic selection approaches to improve yield-related traits under LW.

Dissection of coleoptile elongation in japonica rice under submergence through integrated genome‐wide association mapping and transcriptional analyses

“…The panel was genotyped by sequencing (GBS) following a pipeline described by Biscarini et al (2016) and Volante et al (2017), which resulted in 246,084 SNPs mapped to the Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecule assembly. The genetic structure of the population and the chromosome-wide extension of linkage disequilibrium have been previously described (Volante et al, 2017).…”

“…Globally, rain‐fed lowlands and deep‐water rice account for about one third of the total rice‐growing area (Singh et al, ). In Europe, cultivation is now focused on aerobic rice, which restricts the use of water in order to increase sustainability and reduce costs (Volante et al, ). In Asia, due to the increasing costs and scarcity of labour together with water shortages, farmers are opting for direct seeding in both rain‐fed and irrigated systems (Miro & Ismail, ).…”

“…and reduce costs (Volante et al, 2017). In Asia, due to the increasing costs and scarcity of labour together with water shortages, farmers are opting for direct seeding in both rain-fed and irrigated systems (Miro & Ismail, 2013).…”

QTL Mapping of Wheat Stripe Rust Resistance in Relation to Epidermal Flavonoids Measured Using a Leaf‐Clip, Optical Sensor

“…However, estimates of broad‐sense heritability were relatively low, varying from 0.16 to 0.47, which indicates strong environmental variation relative to genotypic variation for measures of epidermal flavonoids assessed using the Dualex, optical sensor. A recent genome‐wide mapping of japonica rice ( Oryza sativa L.) showed higher heritability estimates of 0.49 to 0.65 (Volante et al, 2017).…”

“…They are thought to function as molecular chaperones, assisting in the recovery from stress, either by repairing damaged proteins (protein refolding) or by degrading them, thus restoring protein homeostasis and promoting cell survival (Jolly and Morimoto, 2000). Volante et al (2017) recently identified genetic loci for epidermal flavonoids measured using the Dualex sensor on rice chromosome 3, and it would be interesting to further research the extent of collinearity between the rice and wheat QTL.…”