中国水稻科学 ›› 2022, Vol. 36 ›› Issue (5): 447-458.DOI: 10.16819/j.1001-7216.2022.210714
伏荣桃1,2, 王剑1,2, 陈诚1,2, 赵黎宇1, 陈雪娟1, 卢代华1,2()
收稿日期:
2021-09-06
修回日期:
2021-11-10
出版日期:
2022-09-10
发布日期:
2022-09-09
通讯作者:
卢代华
基金资助:
FU Rongtao1,2, WANG Jian1,2, CHEN Cheng1,2, ZHAO Liyu1, CHEN Xuejuan1, LU Daihua1,2()
Received:
2021-09-06
Revised:
2021-11-10
Online:
2022-09-10
Published:
2022-09-09
Contact:
LU Daihua
摘要:
【目的】由稻曲病菌引起的稻曲病不仅造成水稻减产,而且还会产生对动物和植物有毒的真菌毒素。探明水稻幼穗对稻曲病菌毒素胁迫响应的分子机制,可为发掘水稻抗稻曲病基因以及抗病分子育种开辟新的思路。【方法】用稻曲病菌毒素处理水稻幼穗,采用转录组测序技术对水稻幼穗进行转录组测序,以水稻9311基因组作为参考基因组进行对比,利用TPM法计算基因表达量,设定参数(差异倍数的绝对值不小于2,且q值不大于0.05)筛选差异表达基因。结合基因差异表达分析、富集功能分析,鉴定水稻响应胁迫的关键基因,并利用实时荧光定量PCR技术对差异表达基因进行验证。【结果】在稻曲病菌毒素胁迫12 h后,水稻幼穗出现2526个差异表达基因(DEG);通过GO富集、KEGG代谢途经和KOG功能分析,将差异基因划分为GO功能下的64个条目、32个代谢途径和KOG功能下23个类别,包括淀粉和蔗糖代谢、苯丙类生物合成、碳代谢、糖酵解/糖异生、氨基糖和核苷酸糖代谢等生物学过程。DEG中有66个植物转录因子,分属7种植物转录因子家族,包括WRKY和Myb两大转录因子。分析二萜类生物合成与淀粉和蔗糖代谢途径相关基因发现,OsCPS2、OsKSL4和细胞色素P450等基因表达量上调,而淀粉酶、β-呋喃果糖苷酶和UDP-焦磷酸化酶等基因表达量下调,推测这些基因在水稻响应稻曲病菌毒素胁迫时发挥重要的作用。【结论】稻曲病菌毒素作为非生物胁迫因素对水稻幼穗具有毒性;通过干扰淀粉和蔗糖代谢等途径而影响种子营养物质的合成,降低水稻抵抗病原菌侵染水稻的能力。
伏荣桃, 王剑, 陈诚, 赵黎宇, 陈雪娟, 卢代华. 水稻幼穗响应稻曲病菌毒素胁迫早期的转录组分析[J]. 中国水稻科学, 2022, 36(5): 447-458.
FU Rongtao, WANG Jian, CHEN Cheng, ZHAO Liyu, CHEN Xuejuan, LU Daihua. Transcriptome Analysis of Young Rice Panicles in Early Response to Exposure to Mycotoxin of Ustilaginoidea virens[J]. Chinese Journal OF Rice Science, 2022, 36(5): 447-458.
样品名 Sample | 过滤前数据 Total raw reads / bp | 过滤后数据 Total clean reads / bp | 过滤后数据Clean bases(G) / bp | Q30/% | N/% | GC/% | 总对比数据 Total mapped reads /% |
---|---|---|---|---|---|---|---|
CK1-1 | 43 418 126 | 41 710 168 | 5.82 | 90.75 | 0.01 | 50.07 | 36 532 652(94.56%) |
CK1-2 | 38 359 472 | 35 721 996 | 4.98 | 87.46 | 0.01 | 52.25 | 32 694 216(94.92%) |
CK1-3 | 49 946 750 | 47 116 642 | 6.53 | 86.91 | 0.01 | 52.26 | 42 564 507(94.74%) |
CL1-1 | 44 766 290 | 43 134 338 | 6.11 | 90.88 | 0.01 | 49.21 | 38 396 232(95.14%) |
CL1-2 | 43 990 022 | 42 300 572 | 5.84 | 89.18 | 0.01 | 48.86 | 35 673 451(93.65%) |
CL1-3 | 44 322 824 | 42 304 834 | 5.97 | 89.59 | 0.01 | 49.82 | 39 456 359(94.76%) |
表1 样本测序数据质量控制数据统计
Table 1. Statistics of transcriptone sequencing data.
样品名 Sample | 过滤前数据 Total raw reads / bp | 过滤后数据 Total clean reads / bp | 过滤后数据Clean bases(G) / bp | Q30/% | N/% | GC/% | 总对比数据 Total mapped reads /% |
---|---|---|---|---|---|---|---|
CK1-1 | 43 418 126 | 41 710 168 | 5.82 | 90.75 | 0.01 | 50.07 | 36 532 652(94.56%) |
CK1-2 | 38 359 472 | 35 721 996 | 4.98 | 87.46 | 0.01 | 52.25 | 32 694 216(94.92%) |
CK1-3 | 49 946 750 | 47 116 642 | 6.53 | 86.91 | 0.01 | 52.26 | 42 564 507(94.74%) |
CL1-1 | 44 766 290 | 43 134 338 | 6.11 | 90.88 | 0.01 | 49.21 | 38 396 232(95.14%) |
CL1-2 | 43 990 022 | 42 300 572 | 5.84 | 89.18 | 0.01 | 48.86 | 35 673 451(93.65%) |
CL1-3 | 44 322 824 | 42 304 834 | 5.97 | 89.59 | 0.01 | 49.82 | 39 456 359(94.76%) |
图2 差异表达基因的火山图分布 横轴为基因在不同组样本间的差异表达倍数(Log2 B/A);纵轴为基因表达量变化的统计学显著程度(P值);图中每个点代表一个基因,其中红色表示上调基因,绿色表示下调基因,黑色表示非差异基因。
Fig. 2. Volcano-plot distribution of DEGs. Horizontal axis represents the multiple value of differetially expressed gene between different groups of samples; Vertical axis represents statistically significant degree(P value) of gene expression changes; Red, Up-regulated DEGs; Blue, Down-regulated DEGs; Black, Non-DEGs.
图3 差异表达基因的GO功能分类 纵轴为功能分类; 横轴为该分类内基因个数(下)及其占被注释上基因总数的百分比(上)。不同颜色代表不同的分类。柱状图和坐标轴上浅色代表差异基因,深色代表所有基因。
Fig. 3. GO function classification of DEGs. Vertical axis is function classification; Horizontal axis is the number of genes in the classification (bottom) and their percentage in the total number of annotated genes (top). Light colors represent differentially expressed genes and dark colors represent all genes.
图4 差异表达基因KEEG代谢途径分类 横轴代表的是不同的通路,左侧纵轴代表该通路内基因个数占被注释上基因总数的百分比(左),右侧纵轴代表基因数目(浅色字体代表差异基因,深色字体代表所有基因)。
Fig. 4. KEGG pathway classification of DEGs. The horizontal axis represents different pathways; The left vertical axis represents the percentage of the number of genes in this pathway in the total number of annotated genes (left), the right vertical axis represents the number of genes (light color represents differentially expressed genes, dark color represents all genes).
图5 差异基因通路富集散点图 纵轴表示功能注释信息,横轴表示通路对应的富集因子(Rich factor), 富集因子越大,表示富集的程度越高。点的颜色表示q值的大小,q值越小则颜色越接近红色。点的大小表示每个条目下包含的差异基因的个数,点越大则基因越多(富集程度最高的前30个通路)。
Fig. 5. Scatter plot of enriched KEGG pathways for DEGs. Vertical axis represents functional information; Horizontal axis shows the rich factor corresponding to pathway, and the greater the rich factor, the greater the enrichment degree. The size of the dots represents the number of DEGs under the term, and the larger the dots, the more genes (the top 30 pathways with the highest enrichment).
图6 差异基因KOG功能分类 横轴每种颜色代表一个KOG的功能分类;纵轴为注释到该分类下的基因数目。
Fig. 6. KOG function classification of DEGs. Each color on the horizontal axis represents a functional classification of KOG; Vertical axis is number of genes annotated under the classification.
转录因子家族 Transcription factor family | 受影响的转录因子数量 Number of affected transcription factors | 主要的植物调控功能 Main regulatory functions in plants | ||
---|---|---|---|---|
上调 Up-regulated | 下调 Down-regulated | 总数 Total | ||
Myb | 8 | 7 | 15 | 植物生长发育,抵御生物、非生物胁迫a, b, c |
WRKY | 2 | 0 | 2 | 植物生长发育,抵御生物、非生物胁迫a, b, c |
HSF(Heat shock transcription factor) | 6 | 3 | 9 | 抵御生物、非生物胁迫b, c |
bHLH(basic Helix loop helix) | 1 | 3 | 4 | 植物生长发育,抵御生物、非生物胁迫a, b, c |
MADS-box | 3 | 9 | 12 | 植物生长发育,抵御非生物胁迫a, c |
GATA | 2 | 7 | 9 | 植物生长发育,抵御非生物胁迫a, c |
HOX | 6 | 9 | 15 | 植物生长发育,抵御非生物胁迫a, c |
总数Total | 28 | 38 | 66 |
表2 稻曲菌毒素影响的植物转录因子
Table 2. Plant transcription factors affected by mycotoxin from U. virens.
转录因子家族 Transcription factor family | 受影响的转录因子数量 Number of affected transcription factors | 主要的植物调控功能 Main regulatory functions in plants | ||
---|---|---|---|---|
上调 Up-regulated | 下调 Down-regulated | 总数 Total | ||
Myb | 8 | 7 | 15 | 植物生长发育,抵御生物、非生物胁迫a, b, c |
WRKY | 2 | 0 | 2 | 植物生长发育,抵御生物、非生物胁迫a, b, c |
HSF(Heat shock transcription factor) | 6 | 3 | 9 | 抵御生物、非生物胁迫b, c |
bHLH(basic Helix loop helix) | 1 | 3 | 4 | 植物生长发育,抵御生物、非生物胁迫a, b, c |
MADS-box | 3 | 9 | 12 | 植物生长发育,抵御非生物胁迫a, c |
GATA | 2 | 7 | 9 | 植物生长发育,抵御非生物胁迫a, c |
HOX | 6 | 9 | 15 | 植物生长发育,抵御非生物胁迫a, c |
总数Total | 28 | 38 | 66 |
序号No. | 基因名称 Gene name | 基因登录号 Gene ID | 引物序列 Primer sequence (5′-3′) |
---|---|---|---|
1 | WRKY71 | BGIOSGA007670 | F: TGCAGGTGGTGAAAGATGGG |
R: GAAACAGGCTCGAATTTGCACT | |||
2 | WRKY24 | BGIOSGA004722 | F: AGAGATGGTGAGTGCCCTGT |
R: CGATGTCGCTCATGGTTTGG | |||
3 | Myb | BGIOSGA004072 | F: CATCTCGCAAAACGGCGAAG |
R: GTTCGGACATCACATAGTCGC | |||
4 | Myb | BGIOSGA006005 | F: TGCCTTGGATACGCGAAAGA |
R: CCGCTTCTTGAGGTGAGTGT | |||
5 | UGPase | BGIOSGA007245 | F: TCTGGGATGGCCATAGAAAAACA |
R: GTACTGGACCAACAACGTGC | |||
6 | Chitinase | BGIOSGA006087 | F: GTACTGGACCAACAACGTGC |
R: TTAGCAGGTGAGGTTGCTGC | |||
7 | Peroxidase | BGIOSGA037333 | F: GGGATTTGCCATAAGCGAAACA |
R:CCACATTCTCGGTTGTTGCC | |||
8 | SBEII | BGIOSGA018719 | F: GAGTCGAGCTGGAATTGTGTTG |
R: GCAGAGTGCCCACATTCATC | |||
9 | NADPH oxidase | BGIOSGA037531 | F: AGATGAATTCGCTCCAATGATTTGT |
R: GGCCAAGCTGAAATTGTGGC | |||
UBI | F: CGCAAGAAGAAGTGTGGTCA | ||
R: ACGATTGATTTAACCAGTCCATGA |
表3 qRT-PCR验证引物
Table 3. Primers used for qRT-PCR verifying.
序号No. | 基因名称 Gene name | 基因登录号 Gene ID | 引物序列 Primer sequence (5′-3′) |
---|---|---|---|
1 | WRKY71 | BGIOSGA007670 | F: TGCAGGTGGTGAAAGATGGG |
R: GAAACAGGCTCGAATTTGCACT | |||
2 | WRKY24 | BGIOSGA004722 | F: AGAGATGGTGAGTGCCCTGT |
R: CGATGTCGCTCATGGTTTGG | |||
3 | Myb | BGIOSGA004072 | F: CATCTCGCAAAACGGCGAAG |
R: GTTCGGACATCACATAGTCGC | |||
4 | Myb | BGIOSGA006005 | F: TGCCTTGGATACGCGAAAGA |
R: CCGCTTCTTGAGGTGAGTGT | |||
5 | UGPase | BGIOSGA007245 | F: TCTGGGATGGCCATAGAAAAACA |
R: GTACTGGACCAACAACGTGC | |||
6 | Chitinase | BGIOSGA006087 | F: GTACTGGACCAACAACGTGC |
R: TTAGCAGGTGAGGTTGCTGC | |||
7 | Peroxidase | BGIOSGA037333 | F: GGGATTTGCCATAAGCGAAACA |
R:CCACATTCTCGGTTGTTGCC | |||
8 | SBEII | BGIOSGA018719 | F: GAGTCGAGCTGGAATTGTGTTG |
R: GCAGAGTGCCCACATTCATC | |||
9 | NADPH oxidase | BGIOSGA037531 | F: AGATGAATTCGCTCCAATGATTTGT |
R: GGCCAAGCTGAAATTGTGGC | |||
UBI | F: CGCAAGAAGAAGTGTGGTCA | ||
R: ACGATTGATTTAACCAGTCCATGA |
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