3.6 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. 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. 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 (Figure S5 ). In the total F2 plants, without
considering the plasmotype identity, the DOC3.2 allele of the
B1K-50-04 was associated with higher thermal plasticity for the period
(accelerated clock in the transition to HT; delta=-1.34h) than the
B1K-05-07 allele (delta=-0.6h) (Figure 5a ). For the amplitude,
there is no difference in plasticity between B1K-05-07 and B1K-50-04
alleles (delta -0.006 and -0.008, respectively) and similar significant
difference between temperatures (p=0.0003 and p=0.0006, respectively)
(Figure 5b ; Table S8 ).
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 found significant interaction between the
nucleotype and plasmotype loci only for the amplitude under OT (P=0.01)
(Table S9 ). The ”natural” combination of plamotype/GI of
B1K-05-07/05-07 has the amplitude of 0.03 and the B1K-50-04/50-04 has
the amplitude of 0.032, while the ”unnatural” arrangement of
B1K-05-07/50-04 and B1K-50-04/05-07 has lower amplitude of 0.025. These
results imply that combination of the plasmotype andDOC3.2 /chr3H_67434330 of the same origin (either B1K-50-04 or
B1K-05-07) 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 5c ,
right-bottom panel).