Salinity is a common and increasing problem in many coastal rice producing areas around the world. Salinity tolerance at the reproductive stage in rice is crucial as it determines grain yield. An F2 mapping population was developed from two modern rice cultivars contrasting in tolerance: NSIC Rc222 (a high-yielding salt-sensitive variety released in the Philippines) and BRRI dhan 47 (a salt-tolerant variety released in Bangaldesh). The performance of the F2 population showed transgressive segregation in the yield components under salinity stress of EC 10 dS/m under salinized field conditions. Ninety-six single nucleotide polymorphism (SNP) markers using 96-plex FluidigmTM genotyping were used to construct a linkage map of 1306.2 cM (Kosambi), with an average interval size of 13.6 cM. Seven putative quantitative trait loci (QTLs) for reproductive stage salinity tolerance traits having LOD values ranging from 2.9 to 4.1 were identified on chromosomes 1, 2, 5 and 11, explaining 13.4 to 18.4% of the phenotypic variation. Results of this mapping study identified a genomic region on chromosome 2 that confers salinity tolerance at the reproductive stage as measured by the number of filled spikelets, percent filled spikelets and yield. This study reports the molecular mapping of QTLs controlling reproductive-stage salinity tolerance-related traits, which will be useful in marker-assisted selection and breeding population development in rice.
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