Abstract
BackgroundStagnant flooding, where water of 25–50 cm remains until harvest time, is a major problem in rainfed lowland areas. Most of the Sub1 varieties, which can withstand around 2 weeks of complete submergence, perform poorly in these conditions. Hence, varieties tolerant of stagnant flooding are essential.ResultsThis paper presents the first study to map QTLs associated with tolerance to stagnant flooding, along with a parallel study under normal irrigation, using an F7 mapping population consisting of 148 RILs derived from a cross of Ciherang-Sub1 and the stagnant-flooding tolerant line IR10F365. Phenotypic data was collected for 15 key traits under both environments. Additionally, survival rate was measured under stress conditions. Genotyping was performed using the Illumina Infinium genotyping platform with a 6 K SNP chip, resulting in 469 polymorphic SNPs. Under stress and irrigated conditions, 38 and 46 QTLs were identified, respectively. Clusters of QTLs were detected in both stress and normal conditions, especially on chromosomes 3 and 5.ConclusionsUnique and common QTLs were identified and their physiological consequences are discussed. These beneficial QTLs can be used as targets for molecular breeding and can be further investigated to understand the underlying molecular mechanisms involved in stagnant flooding tolerance in rice.
Highlights
Stagnant flooding, where water of 25–50 cm remains until harvest time, is a major problem in rainfed lowland areas
The susceptibility of Sub1 lines was worse with varieties having short stature, as in the case of Swarna-Sub1—which was used as a susceptible check in our stagnant flooding stress phenotyping, showing very low survival by the end of the experiment
There is no significant difference of survival rates among Ciherang-Sub1 (69%), IRRI154 (62%), and IR10F365 (56%) (Table 1)
Summary
Stagnant flooding, where water of 25–50 cm remains until harvest time, is a major problem in rainfed lowland areas. Most of rainfed lowlands and some irrigated areas in South and Southeast Asia are prone to flooding which causes huge crop losses worldwide. This situation may worsen under future climate change scenarios (Redfern et al 2012). Floods are largely caused by incessant rainfall during the monsoon season from mid-June to early October, often causing complete submergence followed by stagnant flooding in areas with poor drainage, resulting in huge financial losses (Singh et al 2011). A number of Sub varieties have been developed and released as remedies for this type of flooding, as the Sub gene enables the submerged plants to become dormant and conserve resources for a rapid recovery after the floods recede. While the second generation of Sub lines developed by IRRI were Ciherang-Sub and PSB Rc18-Sub in which IR64-Sub was used as the donor for the SUB1 gene (Iftekharuddaula et al 2011; Singh et al Rice (2017) 10:15
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