Supplementary Figures
Figure S1. Proportion of small RNAs generated from different categories of genomic loci in the two small RNA libraries ofBrassica rapa .
Figure S2. Cis-element analysis of bra-MIR1885 promoter. G-box, GA-motif, P-box, TC, TCT, AAAC, ATCT, Box 4, I-box and LTR represent cis -elements. A06: chrA06. 24219516 and 24221516: Location information. Red or green bar represent position.
Figure S3. Analysis of the single nucleotide polymorphism (SNP) density distribution, principal component analysis (PCA), and linkage disequilibrium (LD) of B. napus population. (A ) SNP density distribution (number of SNPs in 0.1 Mb sliding windows across each chromosome). (B ) PCA analysis. Blue, green, and red points represent winter (W), semi-winter (SW) and spring (S) ecotypes, respectively. (C ) Genome-wide average LD decay estimated fromB. napus . (D ) LD heatmap of SNPs in bna-MIR1885promoter. Numbers indicate physical position where bna-MIR1885promoter locates. Deeper red color indicates stronger linkage relationship. (E ) Comparison of the miR1885 relative expression abundance between the two groups with extremely different phenotypes. ES: Low-temperature sensitive accessions; ER: Low-temperature resistant accessions. U6 was used as an internal control. Data are presented as boxplot. Significant differences were determined by Student’s t-test: * indicates p < 0.05 . (F-I ) The local LD heatmap of SNPs in bna-MIR166C , bna-MIR168A andbna-MIR845A gene loci.
Figure S4. 5’-RACE assays of Bn. TIR.A09 (BnaA09g14980D) and Bn. TNL.A03 (BnaA03g56180D). PCR products ofBn.A09.TIR and Bn.A03.TNL were separated in 2% agarose gel. DNA ladders are labeled on the side. PCR products were cloned into T vectors for Sanger sequencing. Red line represents target fragment; black line represents inner primer.