3.4 CNI and linkage disequilibrium between chloroplastic RpoC1 and DOC loci
One primary goal of this study was to explore the plasmotype variation’s contribution to the circadian photosynthetic rhythm plasticity and growth together with the possibility of epistatic interaction with nuclear loci relevant to the clock output. Since earlier we identified variation within chloroplastic rpoC1 as possible causal variation between B1K-09-07 and B1K-50-04 (Bdolach et al., 2019), we performed an additional long-range Nanopore sequencing of the RpoC1 region with chloroplast DNA isolated from 75 B1K accessions (selected from the 285 GWAS panel).
Table S7 includes the identified SNP within the panel of 75 B1K accessions. In RpoC1 , there is one distinct SNP (positionRpoC1G1713T ) that divides the sequenced B1Ks into 51 accessions that carry the RpoC11713Tallele, while the other 24 accessions carry theRpoC11713G allele. Notably, this SNP is a non-synonymous mutation of the RpoC1 chloroplastic gene (changes N:AAT to K:AAG ; Table S4 ).
We tested the effects of two main QTLs, i.e. DOC3.2 for the amplitude and DOC5.1 for the period (Figure 4a, b ), in the complete and in the smaller panels (n=285 and 75, respectively), while considering RpoC1 variation in the later (TableS7 ). For DOC3.2 , we noticed segregation at chr3H_67267835 between A and G only for the 51 out of 75RpoC1 -sequenced B1K that carry theRpoC11713T allele (Figure 4c ). This is compared to the other 24 carriers of theRpoC11713G where no segregation is found for chr3H_67267835. A strong CNI is also found between the RpoC1 andDOC5.1 (chr5H_648981054), a locus with significant effects on the period (Figure 4b ). While in theRpoC11713G background there is mild difference in the period thermal plasticity between carriers of the twoDOC5.1 allele, a more significant and even opposite directionality is found for the nuclear locus in the background ofRpoC11713T (Figure 4b, d ).