JIA-2019-11

2462 XU Bing-qin et al. Journal of Integrative Agriculture 2019, 18(11): 2457–2471 of the foxtail millet response to short-term water deficit, we compared the DEGs of DM1<DM2(+) and HN1<HN2(+). From the Venn plot (Fig. 5-A), 938 (20.32%) genes were co-modulated in the two cultivars, and they mostly stayed in step with respect to up- or down-regulation (97.44%). The large amount of genotype-specific DEGs in the two cultivars showed their differential regulatory profiles to drought stress. By contrast, co-modulated DEGs, which were more likely to be involved in foxtail millet regulatory network responses to drought stress, were exclusively Fig. 2 The distribution of differentially expressed genes in two groups. A, the statistics data of differentially expressed genes in each pair. The black color column stands for up-regulated genes number that the latter treatment compared with the former. And the white color column stands for down-regulated genes number that the latter treatment compared with the former. B, Volcano plot to display the different expressed genes. The abscissa indicates the value of the Log 10 (fold-change) difference between the two groups; the ordinate indicates the negative log 10 value of the FDR of the two groups. The red (the gene expression of group 2 is up-regulated relative to the group 1) and the green (the expression is down-regulated) points indicate the expression of the gene is different (the criterion is FDR<0.05, and the difference is more than twice), and the black point means no difference. Table 1 Number of reads sequenced and mapped with Tophat 1) Sample 2) Clean reads no. HQ clean reads no. Total HQ clean reads after removing rRNA Mapped reads Unique mapped reads Multiple mapped DM1 27 757 220 24 343 082 (87.70%) 23 815 945 (85.80%) 24 995 367 (87.60%) 24 455 705 (85.70%) 540512 (1.89%) DM2 29 171 928 25 531 271 (87.52%) 24 983 169 (85.64%) 24 386 742 (87.61%) 23 646 538 (84.69%) 740579 (2.66%) HN1 28 676 200 25 111 748 (87.57%) 24 568 000 (85.67%) 25 176 160 (86.99%) 24 548 974 (85.40%) 457044 (1.59%) HN2 27 030 722 23 614 039 (87.36%) 22 954 972 (84.92%) 23 282 693 (85.92%) 22 492 226 (82.99%) 790847 (2.93%) 1) The number of unique mapping reads plus multimapping reads equals the total number of alignments. Uniquely mapped reads are those that map to only one position in the genome, and multimapping reads are those that map to more than one position in the reference genome. Every sample has three biological replicates. Data in brackets mean percentage. 2) DM1 and DM2 stand for foxtail millet cultivar DM, short-term drought treatment 0 and 24 h , respectively; HN1 and HN2 stand for foxtail millet cultivar DM, short-term drought treatment 0 and 24 h, respectively. 0 200 400 600 800 1 000 1 200 1 400 1 600 1 800 2 000 A DM1- vs. -DM2 HN1- vs. -HN2 Numner of genes DiffGene (up-regulated) DiffGene (down-regulated) B 30 25 20 15 10 5 0 –4 –2 0 log 2 FC Volcano plot Volcano plot –1*log 10 FDR –1*log 10 FDR log 2 FC 2 4 –4 –2 0 2 4 30 25 20 15 10 5 0