3.5 CNI in F2 population for clock rhythmicity
To examine the QTLs found in the B1K related to circadian photosynthetic rhythms, including testing the CNI, we generated F2 population from reciprocal crosses between two wild B1K accessions, B1K-05-07 and B1K-50-04. Interestedly, the elevation of B1K-05-07 (Neomi) is -245 meter and the elevation of B1K-50-04 (Mt. Hermon) is 1469 meter above sea level. These crosses allow the analysis of the clock output phenotype linked with segregation in the nuclear locus and comparison of this relationship in two differing chloroplast genetic backgrounds (see raw data at Table S8 ). We phenotyped and genotyped the two F2 populations (B1K-05-07 and B1K-50-04 plasmotypes; n=84 and 113, respectively) for the chr3H_67434330 near the GI gene (FigureS4 ). In the total F2 plants, without considering the plasmotype identity, the DOC3.2 allele of B1K-50-04 was associated with higher thermal plasticity for the period (accelerated clock in the transition to HT; delta=-1.34h) than B1K-05-07 allele (delta=-0.6h) (Figure 5a ). For the amplitude, there is no difference in plasticity between the two alleles (delta -0.006 and -0.008, respectively) and similar significant difference between temperatures (p=0.0003 and p=0.0006, respectively) (Figure 5b ).
When we split the analysis between the two F2 populations, based on the plasmotype, we could see relatively mild differences between the two. Statistical testing using two factorial ANOVA of the interaction between the DOC3.2 / chr3H_67434330 alleles and the plasmotypes for the period and the amplitude, we found significant interaction between the nucleotype and plasmotype loci only for the amplitude under OT (P=0.01) (Figure 5c, d and Table S9 ). The ”natural” combination of plamotype/GI of B1K-05-07/B1K-05-07 has the amplitude of 0.03 and the B1K-50-04/B1K-50-04 has the amplitude of 0.032, while the ”unnatural” arrangement of B1K-05-07/B1K-50-04 and B1K-50-04/B1K-05-07 has lower amplitude of 0.025. These results imply that combination of the plasmotype and DOC3.2 /chr3H_67434330 of the same origin (either B1K-05-07 or B1K-50-04) are associated with higher amplitude values. This could be viewed in the crisscross pattern where the mean amplitude values of two genotypic group is in opposite direction under OT (Figure 5d , right-bottom panel).