TOWARDS POSITIONAL CLONING OF THE SUBMERGENCE TOLERANCE GENES BASED ON RICE GENOMIC SEQUENCES

¹ DNA Fingerprinting Unit, National Center for Genetic Engineering and Biotechnology, at Kasetsart University, Kamphangsaen, Nakorn Pathom 73140, P.O.Box 7, Thailand.

² Agronomy Department, Kasetsart Univerisity and DNA Fingerprinting Unit

Submergence tolerance is important trait for rice farming in the tropical lowland where flash flooding is unavoidable. Recently, the major QTL was located within the 16 cM region flanked by two RFLP markers, R1164 and RZ698. Fine map was constructed near R1164 using two YAC ends, 7 BAC ends and a SSCP. Subsequently a sequence-ready map was constructed using four contiguous PAC clones from Nipponbare. The 136 kb PAC clone was identified to cover the whole submergence tolerance QTL by the flanking markers. Shot gun sequencing was conducted from 2 and 5 kb plasmid subclones from this PAC. Two approaches were used to identify candidate genes for submergence tolerance. Putative genes were predicted from the expected location of submergence QTL and the expression pattern was tested in submerged tolerance rice. The second approach, cDNA from 3, 6, 9, 12 days submerged tolerance rice were enriched against the 136 kb PAC clone. The cDNAs located within the QTL peak were evaluated for expression under submergence conditions. Based on both position and differential expression, a molecular mechanism involving genes responsible for submergence tolerance is proposed and discussed. The positional candidate gene approach greatly hastens the pace of gene discovery by using the genome sequence information.