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Background  Rice growth is frequently affected by salinity. When exposed to high salinity, rice seed germination and seedling establishment are significantly inhibited. With the promotion of direct-seeding in Asia, improving rice seed germination under salt stress is crucial for breeding.    Results  In this study, an  indica  landrace Wujiaozhan (WJZ) was identified with high germinability under salt stress. A BC 1 F 2  population derived from the crossing WJZ/Nip ( japonica , Nipponbare)//Nip, was used to quantitative trait loci (QTL) mapping for the seed germination rate (GR) and germination index (GI) under H 2 O and 300 mM NaCl conditions. A total of 13 QTLs were identified, i.e. ten QTLs under H 2 O conditions and nine QTLs under salt conditions. Six QTLs,  qGR6.1 ,  qGR8.1 ,  qGR8.2 ,  qGR10.1 ,  qGR10.2  and  qGI10.1  were simultaneously identified under two conditions. Under salt conditions, three QTLs,  qGR6.2 ,  qGR10.1  and  qGR10.2  for GR were identified at different time points during seed germination, which shared the same chromosomal region with  qGI6.2 ,  qGI10.1  and  qGI10.2  for GI respectively. The  qGR6.2  accounted for more than 20% of phenotypic variation under salt stress, as the major effective QTL. Furthermore,  qGR6.2  was verified via the BC 2 F 2  population and narrowed to a 65.9-kb region with eleven candidate genes predicted. Based on the microarray database, five candidate genes were found with high transcript abundances at the seed germination stage, of which  LOC_Os06g10650  and  LOC_Os06g10710  were differentially expressed after seed imbibition. RT-qPCR results showed the expression of  LOC_Os06g10650  was significantly up-regulated in two parents with higher levels in WJZ than Nip during seed germination under salt conditions. Taken together, it suggests that  LOC_Os06g10650 , encoding tyrosine phosphatase family protein, might be the causal candidate gene for  qGR6.2 .    Conclusions  In this study, we identified 13 QTLs from a landrace WJZ that confer seed germination traits under H 2 O and salt conditions. A major salt-tolerance-specific QTL  qGR6.2  was fine mapped to a 65.9-kb region. Our results provide information on the genetic basis of improving rice seed germination under salt stress by marker-assisted selection (MAS).    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02820-7.

Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress