BackgroundSalinity is one of the most severe and widespread abiotic stresses that affect rice production. The identification of major-effect quantitative trait loci (QTLs) for traits related to salinity tolerance and understanding of QTL × environment interactions (QEIs) can help in more precise and faster development of salinity-tolerant rice varieties through marker-assisted breeding. Recombinant inbred lines (RILs) derived from IR29/Hasawi (a novel source of salinity) were screened for salinity tolerance in the IRRI phytotron in the Philippines (E1) and in two other diverse environments in Senegal (E2) and Tanzania (E3). QTLs were mapped for traits related to salinity tolerance at the seedling stage.ResultsThe RILs were genotyped using 194 polymorphic SNPs (single nucleotide polymorphisms). After removing segregation distortion markers (SDM), a total of 145 and 135 SNPs were used to construct a genetic linkage map with a length of 1655 and 1662 cM, with an average marker density of 11.4 cM in E1 and 12.3 cM in E2 and E3, respectively. A total of 34 QTLs were identified on 10 chromosomes for five traits using ICIM-ADD and segregation distortion locus (SDL) mapping (IM-ADD) under salinity stress across environments. Eight major genomic regions on chromosome 1 between 170 and 175 cM (qSES1.3, qSES1.4, qSL1.2, qSL1.3, qRL1.1, qRL1.2, qFWsht1.2, qDWsht1.2), chromosome 4 at 32 cM (qSES4.1, qFWsht4.2, qDWsht4.2), chromosome 6 at 115 cM (qFWsht6.1, qDWsht6.1), chromosome 8 at 105 cM (qFWsht8.1, qDWsht8.1), and chromosome 12 at 78 cM (qFWsht12.1, qDWsht12.1) have co-localized QTLs for the multiple traits that might be governing seedling stage salinity tolerance through multiple traits in different phenotyping environments, thus suggesting these as hot spots for tolerance of salinity. Forty-nine and 30 significant pair-wise epistatic interactions were detected between QTL-linked and QTL-unlinked regions using single-environment and multi-environment analyses.ConclusionsThe identification of genomic regions for salinity tolerance in the RILs showed that Hasawi possesses alleles that are novel for salinity tolerance. The common regions for the multiple QTLs across environments as co-localized regions on chromosomes 1, 4, 6, 8, and 12 could be due to linkage or pleiotropic effect, which might be helpful for multiple QTL introgression for marker-assisted breeding programs to improve the salinity tolerance of adaptive and popular but otherwise salinity-sensitive rice varieties.Electronic supplementary materialThe online version of this article (10.1186/s12284-017-0186-x) contains supplementary material, which is available to authorized users.

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Salinity is the second most important abiotic stress after drought that hampers rice production, especially in south and Southeast Asia. Breeding approach supplemented with molecularmarkers-assisted selection is the most promising approach in terms of efficiency to increase the productivity under salt-affected soils. Thirty-day-old rice seedlings of 300 F recombinant-inbred lines derived from a cross between the salt sensitive, IR29 (indica), and a salt tolerant, Hasawi (aus), were used to identify quantitative trait loci (QTLs) linked to salinity tolerance. One hundred and ninety four polymorphic SNP markers were used to construct a genetic linkage map involving 142 selected RILs that covered 1441.96 cM genome with an average distance of 7.88 cMbetween loci. Twenty new QTLs (LOD > 3) were identified on chromosomes 1, 2, 4, 6, 8, 9 and 12 using composite interval mapping with R as high as >20% with LODvalue of 7.21. Many earlier studies reported big qSaltol for seedling stage salinity tolerance in rice is on short arm of chromosome 1 but none of the QTL in our study was on qSaltol or nearby position, therefore, Hasawi conferred salinity tolerance in RILs due to novel QTLs. It is suggested to fine map the novel QTLs so that the level of salinity tolerance could be further enhanced by pyramiding of the different QTLs in one genetic background through marker-assisted selection.

Temperate japonica rice (Oryza sativa) is usually grown in temperate regions. When grown in tropical areas, most temperate japonica rice plants flower prematurely and do not show sufficient vegetative growth. Fourteen japonica rice varieties and lines adapting to tropical environments were developed in the Philippines (tropical Asia) between 2008 and 2014. Their genomes were characterized by genomewide single nucleotide polymorphism genotyping, and their grain yields were examined in the Philippines during the wet and dry seasons and in a high-altitude area of Burundi (tropical Africa). Based on the genotyping, all 14 materials were found to belong to the temperate japonica rice group. Grain yields were more affected by the environment than by the genotypes. Two of the fourteen rice materials showed more stable and higher yields than the check varieties across the three environments, and one of the two has been released as a commercial variety in the Philippines.Together, these results demonstrate that rice plants genetically belonging to the temperate japonica group can be bred to adapt to tropical areas.