Identification of QTLs underlying water-logging tolerance in soybean

Soil water-logging can cause severe damage to soybean [Glycine max (L.) Merr.] and results in significant yield reduction. The objective of this study was to identify quantitative trait loci (QTL) that condition water-logging tolerance (WLT) in soybean. Two populations with 103 and 67 F-6:11 recombinant inbred lines (RILs) from A5403 x Archer (Population 1) and P9641 x Archer (Population 2), respectively, were used as the mapping populations. The populations were evaluated for WLT in manually flooded fields in 2001, 2002, and 2003. Significant variation was observed for WLT among the lines in the two populations. No transgressive tolerant segregants were observed in either population. Broad-sense heritability of WLT for populations 1 and 2 were 0.59 and 0.43, respectively. The tolerant and sensitive RILs from each population were selected to create a tolerant bulk and a sensitive bulk, respectively. The two bulks and the parents of each population were tested with 912 simple sequence repeat (SSR) markers to select candidate regions on the linkage map that were associated with WLT. Markers from the candidate regions were used to genotype the RILs in both populations. Both single marker analysis (SMA) and composite interval mapping (CIM) were used to identify QTL for WLT. Seventeen markers in Population 1 and 15 markers in Population 2 were significantly (p < 0.0001) associated with WLT in SMA. Many of these markers were linked to Rps genes or QTL conferring resistance to Phytophthora sojae Kaufmann and Gerdemann. Five markers, Satt599 on linkage group (LG) A1, Satt160, Satt269, and Satt252 on LG F, and Satt485 on LG N, were significant (p < 0.0001) for WLT in both populations. With CIM, a WLT QTL was found close to the marker Satt385 on LG A1 in Population 1 in 2003. This QTL explained 10% of the phenotypic variation and the allele that increased WLT came from Archer. In Population 2 in 2002, a WLT QTL was located near the marker Satt269 on LG F. This QTL explained 16% of the phenotypic variation and the allele that increased WLT also came from Archer.