Table 3 Mean yield and RCA for all genotypes. Mean yield (t/ha) Mean RCA (%) Total mean yield (t/ha) Total mean RCA (%) Year 2019 2020 2019 2020 2019 & 2020 2019 & 2020 Treatment CON WL CON WL CON WI CON WI CON WL CON WL Macq+ 9.64 8.92 9.62 7.26 0.00 78 0.00 75 9.63 8.09 Macq 10.69 0.00 7.24 76.5 10.06 6.12 0.00 14 0.00 13 10.38 6.68 0.00 13.5 Macq- 9.92 7.31 9.75 5.96 0.00 15 0.00 32 9.84 6.64 Planet+ 0.00 23.5 12.83 7.74 0.00 73 12.83 7.74 0.00 73 Planet 11.82 5.74 12.84 6.09 0.00 19 0.00 17 12.33 5.92 Planet- 0.00 18 NA NA 13.12 6.32 0.00 27 13.12 6.32 West+ 0.00 9.99 27 9.83 9.80 7.78 0.00 73 0.00 70 9.90 8.81 West 0.00 11.36 8.62 71.5 10.31 6.78 0.00 36 0.00 35 10.84 7.70 West- 0.00 10.22 35.5 9.11 9.39 6.25 0.00 28 0.00 32 9.81 7.68 0.00 Yerong 12.37 30 10.65 8.60 6.79 0.00 89 0.00 90 10.49 8.72 TAM169 0.00 12.09 89.5 10.33 11.61 8.69 0.00 76 0.00 75 11.85 9.51 YF163 0.00 10.37 75.5 3.03 9.14 3.86 0.00 5 0.00 7 9.76 Frank 3.45 0.00 11.12 6 4.18 11.12 5.69 0.00 8 0.00 7 11.12 4.94 YF225 0.00 7.5 11.11 10.56 9.84 6.90 0.00 10 0.00 10 10.48 8.73 0.00 10 In each case n = 4 in 2019 and n = 3 in 2020; CON=control, WL=waterlogging; RCA= Root cortical aerenchyma. Macq*, Planet* and West* had the RCA-QTL introgressed.Table 4 Detailed contrasts for yields (t/ha) between main genotypes, according to linear regression models (A and B). Estimate 95% confidence P- interval value WL Macq versus (Macq + Macq )* .5 2.04 (1.26,2.83) 0.000 Planet versus (Planet + Planet) 1.81 (0.77,2.86) 0.001 * .5 West versus (West + West )* .5 1.64 (0.86,2.42) 0.000 Overall 1.83 (1.32,2.34) 0.000 CON Macq versus (Macq + Macq )* .5 -0.5 (-1.32,0.32) 0.223 Planet* versus (Planet + Planet ) 0.22 (-0.99,1.42) 0.719 * .5 West versus (West + West )* .5 -0.47 (-1.30,0.35) 0.250 Overall -0.25 (-0.81,0.30) 0.363 The estimate column is the point estimate of the average difference between variety groups within the respective regression model. For example, the esti- mated average yield of Macq+ compared to the average of its varietal coun- terparts (Macq and Macq ) is 2.04, with a 95% confidence interval of 1.26-2.83 (this is evidence that the introgression of the waterlogging QTL has a strong and positive effect on the original Macquarie commercial variety). The rows denoted "overall" pool the three tolerant ("+") varieties and contrasts them to an equally weighted average of their six counterparts (the results for the overall rows are analogous to an "average introgression" effect). Other table details include: the data is for both 2019 and 2020; CON=control, WL=waterlogging; the p-values are unadjusted for multiple hypothesis corrections (all these contrasts were prespecified at our study design phase); the WL model corresponds to Model A and the CON model to Model B; and the degrees of freedom for the regressions are 44 for WL and 45 for CON