Natural Variations in Sdr1 Improve Resistance to Preharvest Sprouting Through Involvement of Mitogen-Activated Protein Kinase Kinase Kinase in Rice

Resistance to preharvest sprouting (PHS) is an important agronomic trait in rice, because PHS reduces grain quality. We performed map-based cloning of a PHS resistance gene, Seed dormancy 1 (Sdr1), on chromosome 3. High-resolution mapping of 2375 BC₄F₂ plants derived from a cross between ‘Kasalath’ (resistant to PHS) and ‘Nipponbare’ (susceptible to PHS) delimited the candidate genomic region to a 2528-bp region of the Nipponbare sequence as the candidate Sdr1 locus. Sequencing analysis of the Kasalath candidate region identified a 9-bp substitution and a 1-bp insertion relative to Nipponbare. A transformant incorporating the Kasalath candidate region showed no phenotypic difference, but one incorporating the candidate region and an adjacent ORF, encoding a MAPKKK, showed higher germination rates. A MAPKKK overexpressor also showed higher germination rates. Furthermore, knockdown of the MAPKKK resulted in lower germination rates. These results indicate that this MAPKKK is a germination promoter. Expression analysis using Nipponbare and Nipponbare NIL[Sdr1] showed that MAPKKK expression was highly induced by seed imbibition; furthermore, the expression level of the Kasalath allele of MAPKKK was lower than that of the Nipponbare allele. These results indicate that Sdr1 is this MAPKKK, which promotes germination, and that the resistance to PHS conferred by the Kasalath allele of Sdr1 is due to its lower level of expression, probably through the effect of an SNP or an insertion in the candidate region of MAPKKK promoter. 

This work was supported by a grant from the MAFF of Japan (Genomics-based Technology for Agricultural Improvement, IVG3003).