In this study,we screened and confirmed the candidate gene of iga-1 in the fine mapping region,which controls the dwarf phenotype of mutation of cha-2,made clear the sequence variation and expression patterns of the gene,and explored its molecular mechanism of genetic regulation.Candidate gene in the mapping region was predicted using rice annotation database,and sequence variations of the ORF,upstream and downstream were analyzed based on sequencing and sequence alignment.Furthermore,meta-analysis of the crucial motif was performed.And expression pattern was investigated using semi-quantitative PCR.(1)On the basis of early studies of fine mapping of the nuclear genes iga-1,3 ORF were predicted in this study,including 2 dnaJ chaperones LOC_Os05g26902 and LOC_Os05g26926,and another one is the dwarf gene,RGA1( LOC_Os05g26890).(2)It is found that only several SNP were detected in the LOC_Os05g26890 in the mapping region between cha-2 and wild type by sequencing of ORFs,which appear to have no alteration of amino acid coding.(3)Expression analysis results show that RGA1 was unable to express in four developmental stages of cha-2 and was revealed inactivation in genetic background of ‘Zhonghua 11’ or ‘Shisoubaimao’ with genetic stability,which therefore was identified as candidate gene of iga-1.(4)The sequences in upstream and downstream of the RGA1 were examined,and 865 bp deletion was found in the upstream of RGA1 in cha-2,which was induced the whole exon 1,part of intron 1 and upstream region of transcription initiation.We concluded that the iga-1 in mutation of cha-2 was the inactivated RGA1 without normal expression,which was caused by a large fragment deletion in the key region of transcription.