Identification and fine mapping of a novel qGR6.2 locus controlling rice salt tolerance during seed germination

Abstract Background Rice growth is frequently affected by salinity. When rice plants are exposed to high salinity, seed germination and seedling establishment are significantly inhibited. In particular, with the promotion of rice direct-seeding in Asia, improving rice salt tolerance during seed germination is of strong importance for rice breeding. Results In this study, we found that the indica rice landrace Wujiaozhan (WJZ) showed a high capability of seed germination under both water (H 2 O) and salt (NaCl) conditions, particularly under high salt stress. The BC 1 F 2 population produced by crossing WJZ with japonica Nipponbare (Nip) was used to evaluate the germination traits under water (H 2 O) and salt (300 mM NaCl) conditions using germination rate (GR) and germination index (GI). A total of 13 quantitative trait loci (QTLs) were identified, including eight QTLs of GR, two QTLs of GI under H 2 O conditions, six QTLs of GR, and three QTLs of GI under 300 mM NaCl conditions. Six QTLs ( qGR6.1 , qGR8.1 , qGR8.2 , qGR10.1 , qGR10.2 and qGI10.1 ) contributed to GR under both H 2 O and 300 mM NaCl conditions. Three QTLs ( qGR6.2 , qGR10.1 and qGR10.2 ) under 300 mM NaCl conditions were identified at different time points of seed germination and shared the same region with qGI6 , qGI10.1 and qGI10.2 for GI. These QTLs could be used to improve seed germination ability via marker-assisted selection (MAS). One major effective salt-tolerance-specific QTL, qGR6.2, on chromosome 6 was further confirmed via the BC 2 F 2 population, which explained more than 20% of the phenotypic variation. Fine mapping results showed that qGR6.2 was narrowed to a 65.9-kb region between the Z654 and Z619 molecular markers, with eleven candidate genes being predicted. Based on the microarray database, there were high transcript abundances of six genes ( LOC_Os06g10650 , LOC_Os06g10660 , LOC_Os06g10690 , LOC_Os06g10710 , LOC_Os06g10730 and LOC_Os06g10750 ) at all developmental stages, and only LOC_Os06g10750 was differentially expressed after salt incubation. RT-qPCR showed that two genes ( LOC_Os06g10650 and LOC_Os06g10750 ) were significantly differentially expressed at 300 mM NaCl during seed germination. This result suggested that LOC_Os06g10650 and LOC_Os06g10750 might be the causal candidate genes for the major effective salt-tolerance-specific QTL qGR6.2 identified in WJZ, which may facilitate map-based cloning and help to elucidate the molecular mechanism underlying salt tolerance during seed germination. Conclusions In our study, we identified 13 QTLs from indica landrace WJZ that confer seed germination traits under water and salt conditions. A major salt-tolerance-specific QTL qGR6.2 was confirmed and fine mapped to a 65.9-kb region flanked by the Z654 and Z619 markers. Our results provide information on the genetic basis of improving salt tolerance during seed germination by MAS.