Identifying optimal haplotypes for future climates
To ensure adaptation to future climates, exploiting genetic variation for phenotypic plasticity is crucial. To identify genotypes suitable for various planting sites with different possible future climates, we examined the plasticity of SOC as a function of the genotype at the candidate plasticity genes in the eight environments. Here, we used PR166–195 as a critical environmental index due to data unavailability and the absence of noticeable change in the other two indices (Fig S11). We observed changes in the ranking of gene–environment interactions for all candidate genes (MYB106 ,MIPS3 , HAD , DGD1 and PSD1 ) in response to PR166–195 (Fig S12). To achieve high SOC, the allele with greater plasticity (as defined by higher slope) should be preferred in environments with higher precipitation, while the allele with lower plasticity should be favored in environments with lower precipitation.
We further examined SOC plasticity when considering the two possible alleles for all five candidate plasticity genes. From the 32 possible haplotypes, we focused on the 10 most abundant among the 505 B. napus lines and calculated the reaction norms for each haplotype in response to the environmental index PR166–195. We observed varied plasticity levels among the 10 major haplotypes (Fig. 6a, b). Haplotype 1 (with the allele combination AAGTA forMYB106 , MIPS3 , HAD , DGD1 and PSD1 ), consisting of 329 lines and representing 65% of the entire population, displays the lowest plasticity, as illustrated by the lowest slope of its regression with PR166–195. It performs well in environments with lower precipitation but lags behind in environments with higher precipitation. By contrast, Haplotype 10 (allele combination CGAAA), composed of only five lines, presents the highest plasticity. It significantly outperforms the other haplotypes in terms of SOC, particularly in response to extremely high precipitation. This comparison suggests that most of the preserved germplasm has the potential to thrive in relatively dry environments, based on their SOC. However, we have a limited number of germplasms with rare haplotypes that are well suited to wet environments.
To develop varieties for future climates, we initially examined the precipitation patterns in major oilseed producing areas. We collected PR166–195 data from seven planting sites, including tested and untested sites, from 1960 to 2080. Based on this data, we identified three distinct categories of precipitation conditions. The first category comprises the sites CD and ZZ, with an average precipitation of 1.0 mm per day with no significant change over time. The second category includes the sites WH, HF and NJ, with average precipitation increasing from 2.0 to 3.9 mm per day throughout the years. The third category involves the sites CS and NC, experiencing an increase in precipitation from 5.0 to 7.7 mm per day on average (Fig. 6c). We then determined the optimal haplotype with the highest SOC for the past and future PR166–195 level at each site. In drier regions (CD and ZZ), haplotype 5 consistently demonstrated the highest SOC in both past and future scenarios. For more humid areas (WH, HF and NJ), haplotype 2 was the best performer in the past but is predicted to be replaced by haplotype 10 in future climates. In high-humidity regions (CS and NC), haplotype 10 was beneficial in both the past and future scenarios (Fig. 6d). Increasing the prevalence of haplotype 10 in future germplasms could be a viable approach to developing varieties that are well adapted to future climates.