
Identification of miRNAs and their target genes in response to salt stress in Brassica napus
Yue WANG, Ting ZHOU, Cai-peng YUE, Jin-yong HUANG, Ying-peng HUA
CHINESE JOURNAL OF OIL CROP SCIENCES ›› 2022, Vol. 44 ›› Issue (1) : 103-115.
Identification of miRNAs and their target genes in response to salt stress in Brassica napus
Brassica napus L. is one of the important oil crops in the world. However soil salt stress severely inhibited its growth and development. Previous studies have shown that under salt stress, plants increase their own salt stress resistance by expressing some miRNAs and regulating the expression of their target genes. In this study, rapeseed was cultured under 200 mmol·L-1 NaCl treatment and control, and took the shoot and root to construct 12 small RNA libraries for high-throughput sequencing. Through the differential expression analysis of miRNAs in the whole genome, a total of 26 differentially expressed miRNAs were identified and 171 corresponding target genes were predicted. Combining the differential expression of genes in the early transcriptome and the results of the differential expression of miRNAs in this study, it is speculated that miRNA156-SPL15-WRKY, miRNA397-LAC12-xylogen, miR169-NFYA5 and miR399-UBC29-ubiquitination pathways might be involved in the regulation of salt stress resistance in B. napus.
Brassica napus / microRNAs / resistance to salt stress / target genes / transcriptome {{custom_keyword}} /
Table 1 Results of sRNA sequencing of B. napus library表1 油菜文库小RNA测序结果 |
Read type | Total | Known miRNA | Novel miRNA | Ribosomal RNA | Transfer RNA | Small Nucleolar RNA | Small Nuclear RNA | Repbase | Exon | Intron | Unknown |
---|---|---|---|---|---|---|---|---|---|---|---|
CR-1 | 10,671,419 | 724,524 (6.79%) | 8027 (0.08%) | 1,206,853 (11.31%) | 292,719 (2.74%) | 12,913 (0.12%) | 4415 (0.04%) | 196,833 (1.84%) | 71,915 (0.67%) | 58,371 (0.55%) | 8,094,849 (75.86%) |
CR-2 | 21,824,907 | 1,458,902 (6.68%) | 18,806 (0.09%) | 2,687,449 (12.31%) | 539,622 (2.47%) | 18,375 (0.08%) | 4948 (0.02%) | 155,441 (0.71%) | 135,205 (0.62%) | 109,721 (0.5%) | 16,696,438 (76.5%) |
CR-3 | 8,826,325 | 632,478 (7.17%) | 5302 (0.06%) | 889,018 (10.07%) | 196,670 (2.23%) | 6985 (0.08%) | 2830 (0.03%) | 59,018 (0.67%) | 56,971 (0.65%) | 47,288 (0.54%) | 6,929,765 (78.51%) |
CS-1 | 13,311,272 | 1,758,631 (13.21%) | 14,990 (0.11%) | 1,164,394 (8.75%) | 181,656 (1.36%) | 9785 (0.07%) | 4157 (0.03%) | 60,482 (0.45%) | 107,119 (0.8%) | 78,948 (0.59%) | 9,931,110 (74.61%) |
CS-2 | 19,907,571 | 2,758,297 (13.86%) | 25,686 (0.13%) | 1,731,062 (8.7%) | 263,914 (1.33%) | 19,987 (0.1%) | 5651 (0.03%) | 90,780 (0.46%) | 186,702 (0.94%) | 113,969 (0.57%) | 14,711,523 (73.9%) |
CS-3 | 12,740,023 | 1,827,330 (14.34%) | 13,004 (0.1%) | 1,071,149 (8.41%) | 154,355 (1.21%) | 11,518 (0.09%) | 3,750 (0.03%) | 54,815 (0.43%) | 113,233 (0.89%) | 74,717 (0.59%) | 9,416,152 (73.91%) |
TR-1 | 14,041,921 | 1,094,034 (7.79%) | 10,027 (0.07%) | 933,178 (6.65%) | 333,787 (2.38%) | 17,183 (0.12%) | 5482 (0.04%) | 114,748 (0.82%) | 96,049 (0.68%) | 83,830 (0.6%) | 11,353,603 (80.86%) |
TR-2 | 15,453,219 | 1,334,615 (8.64%) | 10,345 (0.07%) | 1,028,761 (6.66%) | 286,273 (1.85%) | 20,802 (0.13%) | 5192 (0.03%) | 230,234 (1.49%) | 113,410 (0.73%) | 90,019 (0.58%) | 12,333,568 (79.81%) |
TR-3 | 11,482,398 | 1,022,945 (8.91%) | 6952 (0.06%) | 802,521 (6.99%) | 206,254 (1.8%) | 14,802 (0.13%) | 3615 (0.03%) | 115,120 (1.0%) | 85,078 (0.74%) | 66,935 (0.58%) | 9,158,176 (79.76%) |
TS-1 | 13,420,039 | 1,681,408 (12.53%) | 12,961 (0.1%) | 1,279,250 (9.53%) | 442,353 (3.3%) | 16,170 (0.12%) | 3583 (0.03%) | 71,301 (0.53%) | 109,646 (0.82%) | 82,047 (0.61%) | 9,721,320 (72.44%) |
TS-2 | 11,799,897 | 1,607,229 (13.62%) | 9271 (0.08%) | 1,415,308 (11.99%) | 229,078 (1.94%) | 15,229 (0.13%) | 2582 (0.02%) | 66,275 (0.56%) | 112,288 (0.95%) | 64,245 (0.54%) | 8,278,392 (70.16%) |
TS-3 | 10,484,620 | 1,495,122 (14.26%) | 9063 (0.09%) | 853,612 (8.14%) | 190,008 (1.81%) | 10,073 (0.1%) | 2831 (0.03%) | 74,202 (0.71%) | 77,089 (0.74%) | 64,089 (0.61%) | 7,708,531 (73.52%) |
Table 2 Annotation classification of small RNA表2 小RNA注释分类 |
Category | Total reads | Total bases | Error rate /% | Q20 /% | Q30 /% | GC content /% | Useful reads | Clean reads | Clean bases |
---|---|---|---|---|---|---|---|---|---|
CR-1 | 13 154 604 | 291 035 914 | 0.0235 | 98.69 | 95.55 | 43.12 | 10 671 419 | 10 681 492 | 239 019 646 |
CR-2 | 26 957 726 | 598 132 265 | 0.0236 | 98.66 | 95.49 | 43.22 | 21 824 907 | 21 844 428 | 491 159 419 |
CR-3 | 11 034 556 | 243 176 274 | 0.0236 | 98.67 | 95.53 | 42.43 | 8 826 325 | 8 835 328 | 197 239 995 |
CS-1 | 15 806 746 | 359 492 264 | 0.0234 | 98.73 | 95.76 | 39.34 | 13 311 272 | 13 318 196 | 303 252 592 |
CS-2 | 23 759 486 | 538 885 516 | 0.0234 | 98.72 | 95.67 | 39.98 | 19 907 571 | 19 919 184 | 452 987 087 |
CS-3 | 15 091 694 | 343 031 941 | 0.0235 | 98.67 | 95.56 | 39.58 | 12 740 023 | 12 746 750 | 289 962 903 |
TR-1 | 16 854 778 | 383 270 232 | 0.0235 | 98.69 | 95.59 | 39.74 | 14 041 921 | 14 050 220 | 319 345 392 |
TR-2 | 18 649 198 | 419 597 126 | 0.0236 | 98.67 | 95.54 | 41.00 | 15 453 219 | 15 464 404 | 348 639 253 |
TR-3 | 13 925 993 | 312 629 146 | 0.0234 | 98.71 | 95.68 | 41.26 | 11 482 398 | 11 490 602 | 259 040 892 |
TS-1 | 16 299 805 | 377 200 623 | 0.0234 | 98.73 | 95.69 | 40.45 | 13 420 039 | 13 426 808 | 306 419 825 |
TS-2 | 14 532 333 | 330 847 865 | 0.0123 | 99.63 | 98.74 | 42.15 | 11 799 897 | 11 801 873 | 267 923 980 |
TS-3 | 12 764 861 | 288 123 155 | 0.0235 | 98.68 | 95.61 | 40.40 | 10 484 620 | 10 491 199 | 235 944 750 |
Fig. 1 Base length distribution of miRNAs (A), numbers of miRNAs (B), preference distribution of the first base of different length miRNAs (C), base preference distribution of miRNAs (D) in shoots and roots of B. napus under different treatments图1 不同处理条件下油菜地上部和根中miRNA碱基长度分布(A)、数量(B)、首位碱基偏好性(C)、各位点碱基偏好性(D) |
Fig. 2 Number of conserved miRNAs of each miRNA family in shoots and roots of B. napus图2 油菜地上部和根中每个miRNA家族的保守miRNA数量 |
Fig. 3 Proportion of miRNA in shoots and roots of the top 15 with differential expression under different treatments (A), differential expressions of miRNA between treatment shoot and control shoot (B), and differential expressions of miRNA between control root and treatment root (C)图3 不同处理下差异表达量前15的miRNA在地上部和根中所占的比例(A),地上部处理组和对照组之间差异表达miRNA的表达量(B)和根部处理组和对照组之间差异表达miRNA的表达量(C) |
Fig. 4 Numbers of target genes of miRNAs图4 差异表达miRNA的靶基因数量 |
Fig. 5 Functional classification of different expression miRNA targets图5 差异表达miRNA靶基因功能分类 |
Fig. 6 Pathway involved in differentially expressed miRNAs target genes图6 差异表达miRNA靶基因参与的pathway通路 |
Fig. 7 Differentially expressed miRNAs in B. napus under salt stress图7 盐胁迫条件下油菜的差异表达miRNA |
Fig. 8 Impact on miRNA397 target gene LAC (A), miRNA156 target gene SPL (B), miRNA169 target gene NFY (C), and miRNA399 target gene UBC (D) under salt stress图8 盐胁迫条件下对miRNA397靶基因LAC的影响(A)、miRNA156靶基因SPL的影响(B)、miRNA169靶基因NFY的影响(C)、miRNA399靶基因UBC的影响(D) |
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