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Background  Grain size and weight are important target traits determining grain yield and quality in rice. Wild rice species possess substantial elite genes that can be served as an important resource for genetic improvement of rice. In this study, we identify and validate a novel QTL on chromosome 7 affecting the grain size and weight using introgression lines from cross of  Oryza sativa  and  Oryza minuta .    Results  An introgression line ‘IL188’ has been achieved from a wild species  Oryza minuta  (2n = 48, BBCC, W303) into  O. sativa japonica  Nipponbare. The F 2  and F 2:3  populations derived from a cross between IL188 and Nipponbare were used to map QTLs for five grain size traits, including grain length (GL), grain width (GW), grain length to width ratio (LWR), grain thickness (GT) and thousand grain weight (TGW). A total of 12 QTLs for the five grain traits were identified on chromosomes 1, 2, 3, 6, 7, and 8. The QTL- qGL7  controlling GL on chromosome 7 was detected stably in the F 2  and F 2:3  populations, and explained 15.09–16.30% of the phenotypic variance. To validate the effect of  qGL7 , eight residual heterozygous line (RHL) populations were developed through selfing four F 2:3  and four F 2:4  plants with different heterozygous segments for the target region. By further developing SSR and Indel markers in the target interval,  qGL7  was delimited to a ~ 261 kb region between Indel marker Y7–12 and SSR marker Y7–38, which also showed significant effects on grain width and thousand grain weight. Comparing with the reference genome of Nipponbare, stop or frameshift mutations in the exon of the three putative genes  LOC_Os07g36830 ,  LOC_Os07g36900  and  LOC_Os07g36910  encoding F-box domain-containing proteins may be the candidate genes for  qGL7 . Scanning electron microscopy analysis of the glume’s epidermal cells showed that the cell length and width of NIL- qGL7  IL188  was higher than NIL- qGL7  Nip , indicating that  qGL7  increases grain size and weight by regulating cell expansion.    Conclusions  In this study, we detected 12 QTLs regulating grain size and weight using an introgression line from a cross between  Oryza sativa  and  Oryza minuta . Of these loci, we confirmed and delimited the  qGL7  to a ~ 261 kb region. Three putative genes,  LOC_Os07g36830 ,  LOC_Os07g36900  and  LOC_Os07g36910  encoding F-box domain-containing proteins may be the candidate genes for  qGL7 . These results provide a basis for map-based cloning of the  qGL7  gene and useful information for marker assisted selection in rice grain quality improvement.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12284-021-00472-1.

Validation of a QTL for Grain Size and Weight Using an Introgression Line from a Cross between Oryza sativa and Oryza minuta