Selection for flood‐tolerance in soybean [Glycine max (L.) Merr.] is mainly phenotypic. With the development of new molecular breeding tools, our research objective was to assess the effect of different selection methods at the F4:5 and F4:6 stages on the response to flood tolerance and yield at F4:6 stage. Four breeding populations were subjected to six selection treatments: (a) flood tolerance screening using hill‐plots (VIShill); (b) flood tolerance screening using long rows (VISrow); (c) genomic selection using population‐specific training (GShill); (d) genomic selection using broad‐based training population (GSrow); (e) marker‐assisted selection (MAS); (f) advanced based on agronomic adaptation under nonflooded conditions (random selection, RND). The top 15% lines within were tagged for selection, except for MAS that was adjusted based on recovery of desired haplotype. The complete base populations (BP) were advanced into flood and yield trials to determine probability of discard (POD), tolerance index (TOL), and seed yield. Analysis of variance was conducted across populations, and means were separated via Dunnett to the BP. Results indicated significantly different responses for flood tolerance (POD and TOL) across selection methods (p < .0001), with VISrow and GSrow consistently having better tolerance selections than the BP (p < .0001). In addition, lines selected by RND had lower tolerance than BP (p = .0053 and .0618 for POD and TOL, respectively). Moreover, no significant differences were observed among selection treatments (p = .6797) for yield. In conclusion, when breeding for flood tolerance, selections under standard agronomic practices are inadequate, and genomic selection (GSrow) or field screening using long rows (VISrow) are favored selection methods.

Current field screening methods for soybean [Glycine max L. (Merr.)] flood tolerance are time-and labor-intensive. The purpose of this research was to develop a method of screening soybean in a low-O 2 and CO 2 -rich treatment using hydroponic culture in a greenhouse setting. Growth media, solution, and plant response were evaluated at various days after termination of gas treatment (DAT). Initially, a flood-susceptible genotype at early vegetative stage was subjected to a hypoxic treatment, displacing O 2 by bubbling CO 2 into the system for 5 d. The methodology was tested with 33 soybean genotypes, and normalized difference vegetation index (NDVI), soil-plant analysis development (SPAD), and foliar damage score (FDS) were measured. Then, the reaction of 17 genotypes was compared between hydroponic and field conditions. Expanded clay pebbles were identified as the best substrate for the screening method, as germination rate was not different from control. Gas treatment was shown to affect the level of dissolved O 2 in solution and to elicit phenotypic responses, of which NDVI was the most effective for differentiating germplasm, with an average of 0.29 and 0.69 for the CO 2 treatment and ambient air control, respectively (p < .0001). Also, repeatability of NDVI response across genotypes was 94.5%. Finally, preliminary field validation supported the ability of this new hydroponic methodology to separate susceptible and tolerant genotypes under hypoxia and water-logged conditions.