(A) The distribution of sRNAs across the IMF2 population. (B) The distribution of sRNAs aligned to the genic region, 2-kb upstream, and 500-bp downstream of annotated genes, as well as intergenic …
The number of sRNAs with specific length for all the IMF2s is shown as box plot.
The number of sRNAs of specific length in the IMF2 population is shown as box plot.
The distribution of the distance between sRNAs and transcription start site (TSS) (2-kb upstream) (A) and transcription termination site (TTS) (500-bp downstream) (B).
(A) The distribution of expression correlations between s-traits originating from the same genes. (B) The distribution of expression correlations between s-traits originating from LOC_Os03g01360. (C)…
The s-traits originated from same genes were grouped by their sizes. The expression correlations between s-traits from pairs of groups were calculated, and results with more than 2000 correlations …
(A) The distribution of expression correlations between s-traits originating from introns of the same mother genes. (B) The distribution of expression correlations between s-traits originating from …
The structure of LOC_Os03g01360 is shown by the bars in the left and bottom of the plot. Each point represents the expression correlation between a pair of s-traits.
(A) Distribution of the sizes of all 80,362 sRNA clusters. (B) Distribution of the sizes of sRNA clusters not longer than 10 kb. (C) Distribution of the sizes of sRNA clusters not longer than 1 kb. …
(A) The distribution of expression correlations between s-traits originating from the same sRNA clusters. (B) The distribution of expression correlations between s-traits originating from …
(A) Correlations between s-traits and e-traits derived from LOC_Os03g01360. (B) Correlations between s-traits and e-traits derived from LOC_Os07g01240. (C) Correlations between s-traits and e-traits …
The read number of all IMF2s in each step is shown as box plot.
The color key shows the LOD value. X-axis, the physical position of sQTLs along the genome of 12 chromosomes. Y-axis, the physical position of s-traits. QTLs with LOD value <5 are not included in …
Each row represents an IMF2, while each column represents a bin. Different color indicates different genotype. The 12 chromosomes were separated by black vertical lines.
(A) The LOD values for local-sQTLs. (B) The LOD values for distant-sQTLs. (C) Expression variation explained by local-sQTL. (D) Expression variation explained by distant-sQTL.
The color key shows the LOD value. X-axis shows the physical position of scQTLs along the genome. Y-axis shows the physical position of sc-traits. QTLs with LOD value <5 are not included in the …
(A) The LOD values for local-scQTLs. (B) The LOD values for distant-scQTLs. (C) Expression variation explained by local-scQTL. (D) Expression variation explained by distant-scQTL.
The color key shows the LOD value. X-axis shows the physical position of eQTLs along the genome. Y-axis shows the physical position of e-traits. QTLs with LOD value <5 are not included in the …
(A) The LOD values for local-eQTLs. (B) The LOD values for distant-eQTLs. (C) Expression variation explained by local-eQTL. (D) Expression variation explained by distant-eQTL.
The expression value (reads per millions [RPM]) of each s-trait in the IMF2 population is shown as box plot. IMF2s with different genotypes as determined by the genotype of the bin harboring these …
(A) s-traits and sQTLs. (B) sc-traits and scQTLs. (C) e-traits and e-QTLs. The 1568 bins are arranged from left to right according to their genomic position. The width of bar represents the size of …
(A) SNPs in sRNA biogenesis genes between Zhenshan 97 and Minghui 63. (B) Indels in sRNA biogenesis genes between Zhenshan 97 and Minghui 63.
(A) Expression correlations between s-traits regulated by Bin632–Bin637 and the e-traits in these bins. (B) Expression correlations between s-traits regulated by Bin632–Bin637 and the e-traits of OsR…
(A) Expression correlations between pairs of s-traits originating from the same mother genes and both regulated by local-sQTLs. (B) Expression correlations between pairs of s-traits originating from …
(A) Expression correlations between s-traits and their mother genes that were both controlled by local-QTLs. (B) Expression correlations between s-traits regulated by distant-sQTLs and their mother …
(A) The structure of LOC_Os03g01360 is shown in the top panel, with black color representing exons and red color indicating introns and UTRs. The number of mRNA reads is shown in blue color. The …
Average number of reads obtained for the 104 libraries from flag leaves of the IMF2 population and the parental lines
Quality filtering* | Size filtering† | NcRNA filtering‡ | Genome mapping§ | Total# | |
---|---|---|---|---|---|
Redundant reads | 22,864,067 | 22,318,928 | 19,968,566 | 9,816,933 | 1,020,961,021 |
Distinct reads | 5,106,654 | 5,035,073 | 4,986,184 | 2,499,233 | 53,613,739 |
Reads after filtering out low-quality reads.
Reads of 18–26 nt in length.
Reads after eliminating ones matching tRNAs, rRNAs, snRNAs, and snoRNAs.
Reads mapped to the SNP-replaced reference genomes of the parents with unique locations allowing no mismatch.
The total reads of 104 libraries used to identify s-traits.