Comparative analysis of nine different small heat shock protein gene promoters in Oryza sativa L. subsp indica

Small heat shock proteins (sHSPs), the intra cellular chaperons respond to high temperatures and other stresses, are expressed under the control of the heat shock factors, which recognize highly conserved cis-regulatory elements (CREs). The present study was designed to identify and compare nine different sHSP gene promoters from rice on the basis of their location on chromosomes, sequence similarities, evolutionary relationship and putative binding sites of transcription factors. Additionally, they were analyzed for their functional importance in the regulation of sHSP genes. For this, 5' upstream region of nine sHSP genes from Oryza sativa was amplified, sequenced and analyzed. RFLP mapping approach using molecular linkage maps of three-way cross-population showed that OsHSP 16.9A, OsHSP 16.9B, OsHSP 16.9C and OsHSP C-II genes were clustered on the short arm of chromosome 1 with a 1238-bp overlapped sequence between OsHSP 16.9A and OsHSP 16.9B, whereas OsHSP 17.3, OsHSP 17.7, OsHSP 17.9, OsHSP 18.0 and OsHSP 26 genes were clustered on chromosome 3 with a 420-bp overlapped sequence between OsHSP 17.3 and OsHSP 18.0. Evolutionary analysis revealed that sHSPs that clustered on different chromosomes in the same specie showed high sequence similarity and evolved prior to the divergence of their localization. Eighteen CREs remained conserved among all sHSP gene promoters during evolution. These common regulatory elements are related to disease resistance, hormonal responses, light responses, seed storage proteins, tissue-specific expression, pollen development and other environmental stresses. Moreover, CCAATBOX1 was also found in all sHSP gene promoters involved in the regulation of heat shock response. Conclusively, promoter region of sHSP genes seems to be capable of driving genes expression during stress and genetic manipulation might be helpful in producing better quality rice.