Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (7): 1626-1637.DOI: 10.3969/j.issn.1004-1524.20220927
• Horticultural Science • Previous Articles Next Articles
Genome-wide identification and expression analysis of key genes response to vernalization in radish (Raphanus sativus)
CHEN Guohu1(
), LI Guang1, WEN Hongwei1, YIN Qian1, WU Siwen1, WANG Ying1, LIU Xueqing1, ZHAO Longlong1, KHAN Afrasyab1, GUI Shangzhi1, TANG Xiaoyan1, WANG Chenggang1,2,*()
- 1. Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
2. Wanjiang Vegetable Industrial Technology Institute of Anhui Province, Ma‘anshan 238253, Anhui, China
-
Received:2022-06-22Online:2023-07-25Published:2023-08-17 -
Contact:WANG Chenggang
CLC Number:
Cite this article
CHEN Guohu, LI Guang, WEN Hongwei, YIN Qian, WU Siwen, WANG Ying, LIU Xueqing, ZHAO Longlong, KHAN Afrasyab, GUI Shangzhi, TANG Xiaoyan, WANG Chenggang. Genome-wide identification and expression analysis of key genes response to vernalization in radish (Raphanus sativus)[J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1626-1637.
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| 基因名称 Gene name | 引物序列 Primer sequences (5'→3') | 退火温度 Annealing temperature/℃ |
|---|---|---|
| RsGI | F:GCATCTGGTGTAAGGATAGAAGTT R:AGGGATCAATCCATAGGCAG | 57.0 |
| RsGA3ox2 | F:ATGGTGAGTGGACAGTGGTCTTA R:CTTTACTCTTGCTTGCCTCTGC | 58.0 |
| RsKS | F:GGCTATGATGTGACTTACGATC R:TGCTTAGTCCACAGACACTGC | 58.0 |
| RsPRR5 | F:GCCTCTGCTTTCACACGGT R:GCACTTTGAGGTGGTTCAGATA | 58.5 |
| RsGID1B | F:ATGCAAGATCATTTCCCCGT R:AGGAGGTTGGTGGAGGTGTG | 59.0 |
| RsFLC3 | F:GCCTTGCAGGATCTTCAGTCA R:AACGAGGGTGTCCACGCTTA | 55.0 |
| RsTEM1 | F:ACGACCAACGCTAAAC R:TGGAACATCCTAACGCAAAC | 58.0 |
| RsGA2ox1 | F:GAGTTGAGCCACTAGGGAAG R:TTCACTACTCTGTCTTTTTTCGG | 58.1 |
| RsTOC1 | F:GAAGCACTAATCCAGCG R:CAGAGGACTCTCCAATCTTCAAC | 59.0 |
| RsFLC2 | F:CGGCGATAACTTGGTCAAGA R:AGGGCAGTCTCAAGGTGGTC | 59.5 |
| RsPRR9 | F:TGTAAGTGGTGCTCAGGCTAAC R:GATTCCACCGATCAAGTCCA | 56.0 |
| RsCHE | F:GAGACGGATTCGTATGCCAA R:TAGAAGGCTCGGCTTGACG | 60.5 |
| RsCDF1 | F:GATGAATTATCCGCAGAGC R:CTTCGTTTCCATACTGTTGC | 59.0 |
| RsPHYA | F:CATTGAAGGGTGCTTGGATC R:CTGACCTCCAGATGGTGTAAAGT | 57.0 |
| RsPHYB | F:GAGAGGGGACGAGGACAAGA R:GACTATGGACGATTGCTCTGTAGT | 56.5 |
| RsGA2ox6 | F:TCCCTTCAAGTTCAGTTCGG R:GATTGAGTCGCTACGGACG | 55.0 |
| actin | F:TACCGCAAAGAGCAGTTCGTCAGTG R:GAGCGATGGCTGGAACAGTACTTCAG | 57.5 |
Table 1 Primer sequences used for qRT-PCR
| 基因名称 Gene name | 引物序列 Primer sequences (5'→3') | 退火温度 Annealing temperature/℃ |
|---|---|---|
| RsGI | F:GCATCTGGTGTAAGGATAGAAGTT R:AGGGATCAATCCATAGGCAG | 57.0 |
| RsGA3ox2 | F:ATGGTGAGTGGACAGTGGTCTTA R:CTTTACTCTTGCTTGCCTCTGC | 58.0 |
| RsKS | F:GGCTATGATGTGACTTACGATC R:TGCTTAGTCCACAGACACTGC | 58.0 |
| RsPRR5 | F:GCCTCTGCTTTCACACGGT R:GCACTTTGAGGTGGTTCAGATA | 58.5 |
| RsGID1B | F:ATGCAAGATCATTTCCCCGT R:AGGAGGTTGGTGGAGGTGTG | 59.0 |
| RsFLC3 | F:GCCTTGCAGGATCTTCAGTCA R:AACGAGGGTGTCCACGCTTA | 55.0 |
| RsTEM1 | F:ACGACCAACGCTAAAC R:TGGAACATCCTAACGCAAAC | 58.0 |
| RsGA2ox1 | F:GAGTTGAGCCACTAGGGAAG R:TTCACTACTCTGTCTTTTTTCGG | 58.1 |
| RsTOC1 | F:GAAGCACTAATCCAGCG R:CAGAGGACTCTCCAATCTTCAAC | 59.0 |
| RsFLC2 | F:CGGCGATAACTTGGTCAAGA R:AGGGCAGTCTCAAGGTGGTC | 59.5 |
| RsPRR9 | F:TGTAAGTGGTGCTCAGGCTAAC R:GATTCCACCGATCAAGTCCA | 56.0 |
| RsCHE | F:GAGACGGATTCGTATGCCAA R:TAGAAGGCTCGGCTTGACG | 60.5 |
| RsCDF1 | F:GATGAATTATCCGCAGAGC R:CTTCGTTTCCATACTGTTGC | 59.0 |
| RsPHYA | F:CATTGAAGGGTGCTTGGATC R:CTGACCTCCAGATGGTGTAAAGT | 57.0 |
| RsPHYB | F:GAGAGGGGACGAGGACAAGA R:GACTATGGACGATTGCTCTGTAGT | 56.5 |
| RsGA2ox6 | F:TCCCTTCAAGTTCAGTTCGG R:GATTGAGTCGCTACGGACG | 55.0 |
| actin | F:TACCGCAAAGAGCAGTTCGTCAGTG R:GAGCGATGGCTGGAACAGTACTTCAG | 57.5 |
Fig.1 Chromosomal mapping of flowering related genes in radish
Fig.2 Tissue expression pattern of flowering related genes based on transcriptomes of radish The color scale bar of the figure represents log2 transformed FPKM values.
Fig.3 Correlation analysis of RNA-Seq data among different radish ls and vernalization time
Fig.4 Identification and expression analysis of vernalization responded genes in radish A, Differentially expressed genes (DEG) analysis by RNA-Seq data. B, Ween of DEGs between differential materials. C, VRG, Vernalization responded genes; FRG, Flowering related genes; T-DEG, DEGs between differential materials. D, Expression trend of vernalization related gene (VRG); RT, Room temperature treatment; VE, Early vernalization treatment; VL, Late vernalization treatment.
Fig.5 META analysis and identification of vernalization key genes A, Venn diagram of META analysis; RT, Room temperature treatment; VE, Early vernalization treatment; VL, Late vernalization treatment. B, Venn diagram of key genes responded vernalization; FRG, Flowering related genes; VRG, Vernalization related genes found by transcriptome analysis; M-DEG, Differentially expressed genes obtained by META-analysis.
Fig.6 Functional enrichment analyses of key genes responded vernalization A, GO enrichment; B, KEGG enrichment; C, The pathway of gibberellin biosynthesis. In A and B, the first circle represents the enriched GO entries and KO numbers, the second circle represents the background genes enriched in this pathway, the third circle represents the number of down-regulated genes enriched in this pathway, and the fourth circle represents the enrichment factor.
Fig.7 PPI networks of key genes responded vernalization (A), vernalization pathway (B) and gibberellin pathway (C) Red represents up-regulated protein/gene and green represents down-regulated protein/gene. The size of the circle represents the degree of connection, and the larger the circle, the more connection it is.
| 序号 | 萝卜基因ID Rs gene ID | 拟南芥基因ID At gene ID | 基因名称 Gene name | 注释 Annotation | GO | KEGG |
|---|---|---|---|---|---|---|
| 1 | Rsa10019598 | AT5G62430 | RsCDF1 | CYCLING DOF FACTOR 1 | GO:0050789 | K16222 |
| 2 | Rsa10024990 | AT5G10140 | RsFLC1 | FLOWERING LOCUS C-like | GO:0010219 | |
| 3 | Rsa10036313 | AT5G10140 | RsFLC2 | FLOWERING LOCUS C-like | GO:0010219 | |
| 4 | Rsa10009519 | AT4G02780 | RsGA1 | ENT-COPALYL DIPHOSPHATE SYNTHETASE 1 | GO:0009739 | K04120 |
| 5 | Rsa10027754 | AT3G63010 | RsGID1B | GA INSENSITIVE DWARF1B | GO:0007165 | K14493 |
| 6 | Rsa10036693 | AT4G25420 | RsGA20ox1 | GIBBERELLIN 20-OXIDASE 1 | GO:0009937 | K05282 |
| 7 | Rsa10012570 | AT1G02400 | RsGA2ox6 | GIBBERELLIN 2-OXIDASE 6 | GO:0009685 | K04125 |
| 8 | Rsa10003234 | AT1G80340 | RsGA3ox2 | GIBBERELLIN 3-OXIDASE 2 | GO:0009685 | K04124 |
| 9 | Rsa10001141 | AT1G22770 | RsGI | GIGANTEA | GO:0009648 | K12124 |
| 10 | Rsa10014915 | AT1G79460 | RsKS | GA REQUIRING 2/ENT-KAURENE SYNTHASE | GO:0010476 | K04121 |
| 11 | Rsa10018279 | AT5G24470 | RsPRR5 | PSEUDO-RESPONSE REGULATOR 5 | GO:0048571 | K12130 |
| 12 | Rsa10009861 | AT2G46790 | RsPRR9 | PSEUDO-RESPONSE REGULATOR 9 | GO:0048511 | K12128 |
| 13 | Rsa10040564 | AT1G25560 | RsTEM1 | TEMPRANILLO 1 | GO:0009908 | |
| 14 | Rsa10017933 | AT5G61380 | RsTOC1 | PRR1/TOC1 | GO:0009648 | K12127 |
| 15 | Rsa10028588 | AT1G09570 | RsPHYA | PHYTOCHROME A | GO:0009416 | K12120 |
| 16 | Rsa10042572 | AT2G18790 | RsPHYB | PHYTOCHROME B | K12121 | |
| 17 | Rsa10036371 | AT5G08330 | RsCHE | CHE | GO:0050789 | K16221 |
Table 2 Vernalization response key genes in photoperiod, vernalization, gibberellin biosynthesis and signal transduction pathway
| 序号 | 萝卜基因ID Rs gene ID | 拟南芥基因ID At gene ID | 基因名称 Gene name | 注释 Annotation | GO | KEGG |
|---|---|---|---|---|---|---|
| 1 | Rsa10019598 | AT5G62430 | RsCDF1 | CYCLING DOF FACTOR 1 | GO:0050789 | K16222 |
| 2 | Rsa10024990 | AT5G10140 | RsFLC1 | FLOWERING LOCUS C-like | GO:0010219 | |
| 3 | Rsa10036313 | AT5G10140 | RsFLC2 | FLOWERING LOCUS C-like | GO:0010219 | |
| 4 | Rsa10009519 | AT4G02780 | RsGA1 | ENT-COPALYL DIPHOSPHATE SYNTHETASE 1 | GO:0009739 | K04120 |
| 5 | Rsa10027754 | AT3G63010 | RsGID1B | GA INSENSITIVE DWARF1B | GO:0007165 | K14493 |
| 6 | Rsa10036693 | AT4G25420 | RsGA20ox1 | GIBBERELLIN 20-OXIDASE 1 | GO:0009937 | K05282 |
| 7 | Rsa10012570 | AT1G02400 | RsGA2ox6 | GIBBERELLIN 2-OXIDASE 6 | GO:0009685 | K04125 |
| 8 | Rsa10003234 | AT1G80340 | RsGA3ox2 | GIBBERELLIN 3-OXIDASE 2 | GO:0009685 | K04124 |
| 9 | Rsa10001141 | AT1G22770 | RsGI | GIGANTEA | GO:0009648 | K12124 |
| 10 | Rsa10014915 | AT1G79460 | RsKS | GA REQUIRING 2/ENT-KAURENE SYNTHASE | GO:0010476 | K04121 |
| 11 | Rsa10018279 | AT5G24470 | RsPRR5 | PSEUDO-RESPONSE REGULATOR 5 | GO:0048571 | K12130 |
| 12 | Rsa10009861 | AT2G46790 | RsPRR9 | PSEUDO-RESPONSE REGULATOR 9 | GO:0048511 | K12128 |
| 13 | Rsa10040564 | AT1G25560 | RsTEM1 | TEMPRANILLO 1 | GO:0009908 | |
| 14 | Rsa10017933 | AT5G61380 | RsTOC1 | PRR1/TOC1 | GO:0009648 | K12127 |
| 15 | Rsa10028588 | AT1G09570 | RsPHYA | PHYTOCHROME A | GO:0009416 | K12120 |
| 16 | Rsa10042572 | AT2G18790 | RsPHYB | PHYTOCHROME B | K12121 | |
| 17 | Rsa10036371 | AT5G08330 | RsCHE | CHE | GO:0050789 | K16221 |
Fig.8 Relative expression levels of vernalization key genes enriched in photoperiod, vernalization, gibberellin biosynthesis and signal transduction pathways Different lowercase letters indicate significant difference (P<0.05).
Fig.9 Vernalization responded key genes regulate bolting and flowering in radish
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