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作物学报

作物学报 ›› 2022, Vol. 48 ›› Issue (7): 1645-1657.doi: 10.3724/SP.J.1006.2022.14107

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于WGCNA发掘谷子穗部类黄酮合成途径调控关键基因

韩尚玲1(), 霍轶琼1,2, 李辉1, 韩华蕊1, 侯思宇1,2,3, 孙朝霞1,2,3, 韩渊怀1,2,3, 李红英1,2,3,*()   

  1. 1山西农业大学农学院, 山西太谷 030801
    2山西农业大学农业生物工程研究所, 山西太谷 030801
    3杂粮种质创新与分子育种山西省重点实验室, 山西太谷 030801
  • 收稿日期:2021-06-22 接受日期:2021-10-19 出版日期:2022-07-12 网络出版日期:2021-11-01
  • 通讯作者: 李红英
  • 作者简介:E-mail: 1438989621@qq.com
  • 基金资助:
    国家自然科学基金项目(31771810);国家自然科学基金项目(32070366);国家重点研发计划项目(2018YFD1000705-2);山西省优秀博士来晋工作奖励资金科研项目(SXYBKY2019042);山西省研究生创新项目(2020SY209);山西省高等学校科学研究优秀成果培育项目(2019KJ020);山西农谷建设科研专项(SXNGJSKYZX201702);杂粮种质创新与分子育种山西省重点实验室资助

Identification of regulatory genes related to flavonoids synthesis by weighted gene correlation network analysis in the panicle of foxtail millet

HAN Shang-Ling1(), HUO Yi-Qiong1,2, LI Hui1, HAN Hua-Rui1, HOU Si-Yu1,2,3, SUN Zhao-Xia1,2,3, HAN Yuan-Huai1,2,3, LI Hong-Ying1,2,3,*()   

  1. 1College of Agriculture, Shanxi Agricultural University, Taigu 030801, Shanxi, China
    2Institute of Agricultural Bioengineer, Shanxi Agricultural University, Taigu 030801, Shanxi, China
    3Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding in Minor Crops, Taigu 030801, Shanxi, China
  • Received:2021-06-22 Accepted:2021-10-19 Published:2022-07-12 Published online:2021-11-01
  • Contact: LI Hong-Ying
  • Supported by:
    National Natural Science Foundation of China(31771810);National Natural Science Foundation of China(32070366);National Key Research and Development Project(2018YFD1000705-2);Scientific Research Project of Shanxi Province Outstanding Doctoral Work Award Fund(SXYBKY2019042);Shanxi Graduate Innovation Project(2020SY209);Cultivation Project of Excellent Scientific Research Achievements in Shanxi Universities(2019KJ020);Shanxi Agricultural Valley Construction Research Project(SXNGJSKYZX201702);and the Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding

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摘要：

类黄酮是植物重要的次生代谢物质, 在植物生长发育中发挥着重要的作用, 此外, 类黄酮具有抗氧化活性, 对人体十分有益。谷子籽粒营养丰富全面, 是一种保健型杂粮, 深受我国人民喜爱。谷子作为C4模式植物, 正在受到越来越多的关注。目前谷子籽粒类黄酮代谢及调控机制研究较少。本研究利用高类黄酮品种晋谷21 (JG21)及低类黄酮品种牛毛白(NMB)谷穗为材料, 分析JG21与NMB小穗发育不同阶段类黄酮靶向代谢组及JG21小穗发育不同阶段转录组, 结合加权基因共表达网络分析挖掘可能参与调控类黄酮代谢的转录因子, 并在不同水平的类黄酮品种中进行表达分析初步验证。结果发现, 2个品种小穗中主要富集的类黄酮组分为芹菜素、牡荆素及柚皮素, 三者共占总类黄酮含量的79%以上。类黄酮代谢基因共表达网络中包含38,921个基因, 共划分为32个模块, 其中turquoise模块、green模块及magenta模块与类黄酮代谢显著相关。利用类黄酮代谢通路差异表达基因作为关键基因筛选出与类黄酮代谢调控相关的27个转录因子家族, 并通过启动子结合基序分析筛选获得11个转录因子。Pearson相关性分析表明, 11个转录因子中有7个候选转录因子可能参与类黄酮代谢, 分别为WRKY38、MYB4a、PI、WRKY15、WRKY62、MYB46、WRKY23。以上结果为研究谷子类黄酮代谢通路转录调控机制提供了新的候选基因, 为深入揭示类黄酮代谢调控机制奠定基础。

关键词: 谷子, 类黄酮, 权重基因共表达网络, 转录因子

Abstract:

Flavonoids are important secondary metabolites in plants and play significant roles in plant growth and development. They have antioxidant activity and are beneficial to human health. Foxtail millet is rich in nutrients, making it a healthy grain and popular among consumers. The crop is gaining more and more attention as a C4 model plant. However, there are few studies on the metabolic regulatory mechanism of flavonoids in foxtail millet. In this study, the panicles of flavonoid-rich variety JG21 and flavonoid-less variety NMB were analyzed on the flavonoid metabolomic profiles. Transcriptome sequencing was performed on the panicles of JG21 at different developmental stages. Transcription factors involved in regulating flavonoid metabolism were identified by weighted gene correlation network analysis (WGCNA). The expression patterns of these genes were verified by qRT-PCR. The results showed that the main flavonoid components enriched in the spikelets of foxtail millet were apigenin, vitexin, and naringenin, accounting for more than 79% of the total flavonoids. The flavonoid-related network of JG21 contained 38,921 genes, which were divided into 32 modules. Among them, the turquoise module, green module, and magenta module were significantly correlated with flavonoid metabolism. A total of 27 transcription factor families related to the regulation of flavonoid metabolism were identified by using differentially expressed genes related to flavonoid metabolism pathway as the hubs, and 11 transcription factors were obtained through promoter binding motif analysis. Pearson correlation analysis showed that 7 out of the 11 transcription factors might be involved in flavonoid metabolism, which were WRKY38, MYB4a, PI, WRKY15, WRKY62, MYB46, and WRKY23, respectively. The above results provide new candidate genes for studying the transcriptional regulation mechanism of flavonoids and lay a foundation for further investigation of the flavonoid metabolism regulation mechanism in foxtail millet.

Key words: foxtail millet, flavonoids, WGCNA, transcription factor

图1

代表性品种JG21穗发育时期(S1、S3和S5) S1外观呈鲜绿色, 内含物呈水乳状; S3外观呈黄绿色或浅绿色, 营养物质积累, 内含物固化, 胚与粉状内含物可分离; S5外观呈深黄色或灰白色, 稃壳干燥变脆, 籽粒成熟。"

附表1

本试验所用引物"

基因
Gene		 上游引物
Forward primer (5'-3')		 下游引物
Reverse primer (5'-3')
Seita.4G268200 ACCTCAAGGACGAACAGCAG TTCACGTTCAGGAGGTACGC
Seita.3G350800 CGGTGGATCAACTACCTCCG GCGATCTGAGACCACCTGTT
Seita.7G284800 CACCGAGGAAGAAGACGACC TTGATCTCGTTGTCCGTCCG
Seita.7G201000 GACCTGACGGGCATCAAGAA TTGGAGCACTTGTCGCACTT
Seita.3G236800 GAGCCTGAGTGCAGAGATCG ATCCTCGCCTTTCAGATGCC
Seita.6G239700 CAGAGGAGCACTCTGCTTCG AGGCCTCTGAAGTCGAGCAT
Seita.5G362000 AGGAGATCAACGGGCACAAG CTCCCCGTAGTAGGCGATCT
Seita.5G361900 AGCATCCCCAGAGAGCAAAC GTGGAAGCTGCACCTGTAGT
Seita.3G164900 TTCTGGACGACGGCTACAAG TCTTCACGTTGCACCCTTCC
Seita.7G203300 AGACGTGCACCGACAAATCT TGATGGCAAGAGTGCCACAT
Seita.1G154200 TCGACGATCTGATGAGCTGC CCATCATTTGCTGCCACGAC

图2

谷子穗发育不同时期类黄酮各组分含量 柱上不同小写字母表示在P < 0.05水平差异显著。"

表1

样品转录组测序情况统计"

样本名称
Sample name		 总序列数量
Total reads		 匹配序列数量
Mapped reads		 匹配比例
Mapped ratio
(%)		 GC含量
GC content (%)		 Q30比例
Q30 ratio
(%)		 基因间序列比例
Intergenic ratio
(%)		 外显子序列比例
Exon ratio
(%)		 内含子序列比例
Intron ratio
(%)
JG21-S1-1 47,381,498 43,109,022 90.98 53.30 93.50 9.95 86.55 3.50
JG21-S1-2 49,046,244 44,551,756 90.84 53.49 93.28 10.04 86.50 3.46
JG21-S1-3 46,450,810 41,656,468 89.68 53.54 94.01 10.22 86.35 3.43
JG21-S3-1 43,629,752 41,008,492 93.99 54.21 93.48 10.33 86.91 2.76
JG21-S3-2 51,156,392 48,064,045 93.96 54.11 93.70 10.31 86.91 2.78
JG21-S3-3 47,754,204 44,808,816 93.83 53.96 93.61 10.26 86.87 2.87
JG21-S5-1 45,693,728 38,155,584 83.50 53.90 93.63 11.09 85.30 3.61
JG21-S5-2 43,824,250 36,414,881 83.09 53.78 93.48 11.10 85.30 3.60
JG21-S5-3 46,573,564 38,830,068 83.37 53.93 93.52 11.13 85.32 3.55

图3

基于欧氏距离法的谷子转录组样本表达量层次聚类图"

图4

谷穗转录本聚类及模块识别 a: 基于拓扑相异矩阵构建的基因聚类树。b: 使用动态剪切算法得到的基因模块, 不同颜色代表不同模块。"

图5

类黄酮代谢相关模块鉴定 每行代表一个模块, 每列代表一种性状。矩形框里的数字代表模块与性状之间的相关系数及相应P值。"

附图1

类黄酮差异表达基因表达分析"

表2

类黄酮合成通路差异表达基因与3种类黄酮物质相关性"

基因
Gene		 牡荆素
Vitexin		 柚皮素
Naringenin		 芹菜素
Apigenin
CHIL_Seita.7G301600 0.933** 0.992** -0.436
F3H2_Seita.9G561700 0.391 -0.033 0.858**
F3'H6_Seita.2G219600 0.944** 0.987** -0.398
F3'H8_Seita.3G327200 0.921** 0.994** -0.464
ANR2_Seita.7G249100 0.862** 0.994** -0.567
CHSC2_Seita.8G140200 0.954** 0.984** -0.368
4CL1_Seita.6G093400 -0.688* -0.314 -0.642
4CL5_Seita.6G167900 0.974** 0.965** -0.280
4CL2_Seita.1G283300 0.663 0.917** -0.797*
PAL5_Seita.1G240600 0.928** 0.992** -0.442
PAL3_Seita.1G240400 0.919** 0.946** -0.382
PAL4_Seita.1G240500 0.951** 0.984** -0.373
PAL2_Seita.1G240300 0.956** 0.981** -0.352
PAL1_Seita.1G240200 0.953** 0.983** -0.367
PAL7_Seita.6G181000 0.971** 0.969** -0.296

图6

3个模块类黄酮合成基因局部调控网络 红色圆圈表示存在差异表达的类黄酮合成基因, 蓝色方块表示与类黄酮合成基因存在互作的差异表达转录因子。A: turquoise模块; B: green模块; C: magenta模块。"

附表2

类黄酮代谢基因与候选转录因子结合基序分析"

转录因子
Transcription factor		 结合基序
Motif ID		 E值
E-value		 靶基因
Target gene		 模板链
Strand		 起始位置
Start		 终止位置
End		 p值
p-value		 q值
q-value		 匹配序列
Matched Sequence
Seita.4G268200 MA0940.1
(AP1)		 3.23722E-30 Seita.7G301600_CHIL - 361 373 0.0000404 0.119 ATAAAAAAATAAA
Seita.7G301600_CHIL + 765 777 0.0000413 0.119 CTAAATAAGAAAA
Seita.7G301600_CHIL + 1004 1016 0.0000417 0.119 ATAAAAATATAAA
Seita.1G240300_PAL2 + 695 707 0.0000676 0.153 ACAGAAAAAAAAA
Seita.7G301600_CHIL - 367 379 0.0000686 0.153 ACTAAAATAAAAA
Seita.2G219600_F3'H6 + 307 319 0.0000880 0.156 ACGAAAAAGGGAA
Seita.3G350800 MA1040.1(MYB46) 3.80676E-67 Seita.7G301600_CHIL - 1790 1797 0.0000179 0.293 GTTAGGTA
Seita.7G301600_CHIL - 1685 1692 0.0000593 0.293 GGTAGGTG
Seita.8G140200_CHSC2 + 1015 1022 0.0000772 0.293 GTTTGGTA
Seita.7G284800 MA1039.1(MYB4a) 1.80221E-92 Seita.7G301600_CHIL - 1685 1692 0.0000121 0.096 GGTAGGTG
Seita.1G240300_PAL2 - 1435 1442 0.0000241 0.096 GGTTGGTG
Seita.1G240300_PAL2 + 93 100 0.0000241 0.096 GGTTGGTG
Seita.2G219600_F3'H6 + 682 689 0.0000241 0.096 GGTTGGTG
Seita.1G240300_PAL2 - 665 672 0.0000535 0.155 GGTTGGTA
Seita.2G219600_F3'H6 + 375 382 0.0000681 0.181 AGTAGGTG
Seita.1G240300_PAL2 + 905 912 0.0000975 0.183 AGTAGGTG
Seita.7G301600_CHIL + 1220 1227 0.0000975 0.183 AGTAGGTG
Seita.7G201000 MA0120.1(id1) 2.69525E-87 Seita.1G240300_PAL2 - 1350 1361 0.0000238 0.185 TGGTCCCTTCCG
Seita.7G301600_CHIL + 553 564 0.0000644 0.232 TTTCCCTTCTCT
Seita.1G240300_PAL2 - 490 501 0.0000684 0.232 TTTTCCCTCTCT
Seita.2G219600_F3'H6 - 308 319 0.0000694 0.232 TTCCCTTTTTCG
Seita.3G236800 MA0559.1(PI) 4.96687E-74 Seita.8G140200_CHSC2 + 1243 1256 0.00000786 0.123 ACAAAACAGGAAAA
Seita.7G301600_CHIL + 1630 1643 0.0000174 0.146 ACAAAACAGGAAAA
Seita.8G140200_CHSC2 + 1261 1274 0.0000234 0.146 ACAAAAATAGAATA
Seita.8G140200_CHSC2 + 499 512 0.0000354 0.172 CTAGAAGAAGAAGG
Seita.8G140200_CHSC2 + 1219 1232 0.0000809 0.172 AAGAATAAGGAAAG
Seita.8G140200_CHSC2 + 710 723 0.0000885 0.172 ACAGAACTAGAAAA
Seita.6G239700 MA1039.1(MYB4) 1.85497E-89 Seita.9G561700_F3H2 + 277 284 0.0000975 0.183 AGTTGGTG
Seita.5G362000 MA1084.1(WRKY38) 2.75933E-17 Seita.6G167900_4CL5 + 176 183 0.0000414 0.660 AGTTGACC
Seita.6G167900_4CL5 - 1533 1540 0.0000828 0.880 CATTGACC
Seita.5G361900 MA1091.1(WRKY62) 1.26504E-15 Seita.6G167900_4CL5 - 177 184 0.0000147 0.468 TGGTCAAC
Seita.3G164900 MA1080.1(WRKY23) 2.98528E-34 Seita.1G240500_PAL4 - 947 954 0.0000593 0.820 AGTCAAAG
Seita.7G203300 MA0990.1(EDT1) 0 Seita.6G167900_4CL5 + 662 671 0.0000346 0.366 AAATAAATGC
Seita.6G167900_4CL5 - 330 339 0.0000779 0.618 CTTTTAATGC
Seita.1G154200 MA1076.1(WRKY15) 3.76677E-45 Seita.1G240500_PAL4 - 955 964 0.0000855 0.907 GAGTCAACTC

表3

候选转录因子功能"

转录因子
Transcription factor		 功能
Function
AP1 拟南芥: 参与花的形成[20⇓-22]
Arabidopsis thaliana: participate in flower formation[20⇓-22]
MYB46 拟南芥: 参与木质素生物合成[23⇓-25]
Arabidopsis thaliana: participate in lignin biosynthesis[23⇓-25]
MYB4a/b 拟南芥: 参与类黄酮生物合成[26]
Arabidopsis thaliana: participate in flavonoid biosynthesis[26]
id1 玉米: 参与开花过程[27-28]
Zea mays: participate in flowering process[27-28]
PI 拟南芥: 参与开花过程[29]
Arabidopsis thaliana: participate in flowering process[29]
WRKY38 拟南芥: 基础防御的负调节剂[30]
Arabidopsis thaliana: negative regulator of basal defense[30]
WRKY62 拟南芥: 基础防御的负调节剂; 参与水杨酸诱导的反应[30-31]
Arabidopsis thaliana: negative regulator of basal defense; participate in the response induced by salicylic acid[30-31]
WRKY23 拟南芥: 介导黄酮醇合成的局部调控, 调节生长素的转运[32]; 参与生长素介导的PIN蛋白的重排[33]
Arabidopsis thaliana: participate in local regulation of flavonol biosynthesis and auxin transport[32]; participate in auxin-mediated PIN polarity rearrangements[33]
EDT1 拟南芥: 增加陆地棉抗旱性和耐盐性[34⇓-36]
Arabidopsis thaliana: increase drought and salt tolerance of upland cotton[34⇓-36]
WRKY15 拟南芥: 调节植物的生长和盐/渗透胁迫反应[37]; 抑制木质部形成期间VND7上游的导管分子分化[38]
Arabidopsis thaliana: modulates plant growth and salt/osmotic stress responses[37]; suppresses tracheary element differentiation upstream of VND7 during xylem formation[38]

表4

11个转录因子与3种类黄酮物质相关性"

转录因子
Transcription factors		 JG21 NMB
牡荆素
Vitexin		 柚皮素
Naringenin		 芹菜素
Apigenin		 牡荆素
Vitexin		 柚皮素
Naringenin		 芹菜素
Apigenin
WRKY38 0.948** 0.984** -0.378 0.595 0.715 -0.975**
EDT1 0.976** 0.962** -0.275 -0.983** -0.887* 0.993**
AP1 -0.922** -0.975** 0.422 0.927** 0.995** -0.717
MYB4a 0.926** 0.975** -0.401 0.879* 0.811* -0.991**
PI 0.886** 0.997** -0.534 0.805* 0.919* -0.889*
MYB4b -0.051 -0.472 0.994** 0.939** 0.984** -0.936**
WRKY15 0.980** 0.917** -0.136 0.738 0.801* -0.755
id1 -0.969** -0.973** 0.304 0.998** 0.998** -0.976**
WRKY62 0.946** 0.988** -0.392 0.497 0.773 -0.834*
MYB46 0.840** 0.986** -0.605 0.911** 0.915** -0.944**
WRKY23 0.983** 0.944** -0.228 0.874* 0.890* -0.937**
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