This integrated genetic map was obtained using JoinMap software version 2.0, based on three separate populations and maps. The final integrated map included 298 markers: 96 RFLPs, 166 SSLPs, seven SSCPs, 16 AFLPs, one STS, seven RGAs, two RAPDs, two BAC ends and one YAC end, with an average distance of 4.9 cM between markers.

For three mapping populations, the first was the F1-derived doubled haploid lines (DHLs) from a cross between IR49830-7-1-2-2 [IR49830; a submergence-tolerant breeding line] and CT6241-17-1-5-1 [CT6241; a submergence intolerant line]. This population consists of 65 DHLs and was developed using an anther culture method. The second population, derived from the cross between FR13A (an Indian land race cultivar and one of the most submergence-tolerant lines) and CT6241, consists of 172 recombinant inbred lines (RILs). This population was developed via single seed descent (SSD) at IRRI. The third population consists of 188 F2 plants developed from a cross between Jao Hom Nin (a black rice with moderate tolerance to submergence) and Khaow Dawk Mali 105 (KDML105; an aromatic traditional cultivar from Thailand but that is intolerant of submergence).

A 1235 cM-linkage map of the DHLs was constructed using 105 markers including 72 RFLPs, 13 SSLPs, two randon amplified polymorphic DNAs (RAPDs) and 18 AFLPs. The RIL linkage map was constructed using 183 markers including 46 RFLPs, 128 SSLPs, four single stranded conformation polymorphisms (SSCPs), one AFLP, one sequence tag site (STS), two bacterial artificial chromosome (BAC) ends, and one yeast artificial chromosome (YAC) end. The F2 linkage map consisted of 111 markers including 99 SSLPs, two SSCPs, three STSs and seven resistance gene analogue polymorphisms (RGAPs).