初步探究LncRNA在甘蓝型油菜生态型分化中的作用

doi:10.3724/SP.J.1006.2023.24105

作物学报 ›› 2023, Vol. 49 ›› Issue (5): 1197-1210.doi: 10.3724/SP.J.1006.2023.24105

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

初步探究LncRNA在甘蓝型油菜生态型分化中的作用

杨太桦(), 杨福权, 郜耿东, 殷帅, 金庆东, 徐林珊, 蒯婕, 汪波, 徐正华, 葛贤宏, 王晶(), 周广生

华中农业大学植物科学技术学院, 湖北武汉 430070

收稿日期:2022-04-27 接受日期:2022-09-05 出版日期:2023-05-12 网络出版日期:2022-09-15
通讯作者: *王晶, E-mail: wangjing@mail.hzau.edu.cn
作者简介:E-mail: taihua1996@gmail.com
基金资助:
国家重点研发计划项目“大田经济作物优质丰产的生理基础与调控”(2018YFD1000900)

Preliminary exploration of the role of LncRNA in the ecotype differentiation of Brassica napus L.

YANG Tai-Hua(), YANG Fu-Quan, GAO Geng-Dong, YIN Shuai, JIN Qing-Dong, XU Lin-Shan, KUAI Jie, WANG Bo, XU Zheng-Hua, GE Xian-Hong, WANG Jing(), ZHOU Guang-Sheng

College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China

Received:2022-04-27 Accepted:2022-09-05 Published:2023-05-12 Published online:2022-09-15
Contact: *E-mail: wangjing@mail.hzau.edu.cn
Supported by:
National Key Research and Development Program of China “Physiological Basis and Agronomic Management for High-quality and High-yield of Field Cash Crops”(2018YFD1000900)

摘要/Abstract

摘要：

甘蓝型油菜是我国重要的油料作物之一, 根据其成花转变过程中对低温春化时间需求的不同分为3种生态型: 春性、半冬性和冬性。前人研究发现, 长链非编码RNA (LncRNA)可在多层面上调控基因的表达, 参与对植物生长发育的调控。在拟南芥中, LncRNA可以通过调控春化途径相关基因的表达来影响开花。本研究以3种生态型甘蓝型油菜为材料, 利用高通量测序技术进行苗期叶片的mRNA和LncRNA测序, 初步探究LncRNA在油菜生态型分化及适应性形成中的作用。3种生态型甘蓝型油菜共差异表达基因的GO及KEGG富集分析表明, 不同生态型甘蓝型油菜之间存在大量基础化合物合成代谢差异, 特别是脂质类化合物。3种生态型甘蓝型油菜中共鉴定获得3775个LncRNA, 其中285个在2个及以上生态型组合中存在差异表达, 涉及到1517个候选靶基因。这些差异表达LncRNA涉及到的靶基因也富集到大量基础化合物合成代谢途径。通过mRNA-LncRNA联合分析, 我们预测到了一个开花基因的调控网络, 包含8个开花基因和23个LncRNA, 涉及到温度和光信号调控通路。通过比较鉴定得到的LncRNA和972个甘蓝型油菜重要农艺性状QTL位置信息发现约90%的LncRNA位点和QTL区间存在重叠, 且差异表达LncRNA和QTL的重叠位点在不同生态型油菜中的分布具有差异。结果说明LncRNA在油菜生态型分化及重要农艺性状形成中具有重要作用。

关键词: 甘蓝型油菜, 生态型, 长链非编码RNA, 开花基因, 农艺性状位点

Abstract:

Brassica napus L. is one of the important oil crops in China. Based on its different requirements for vernalization temperature during flower transition, Brassica. napus can be divided into three ecotypes (spring, semi-winter, and winter ecotype). Previous studies found that long non-coding RNA (LncRNA) can regulate gene expression level in multiple levels and participate in the regulation of plant growth and development. In Arabidopsis thaliana, LncRNA can regulate flowering time by regulating the expression of genes related to vernalization pathway. In this study, to preliminarily explore the ecotype differentiation and adaptive formation among the three ecotypes of Brassica napus, three different ecotypes of Brassica. napus were used as the materials and high-throughput sequencing technology was used to sequence mRNA and LncRNA in seeding leaves. The GO and KEGG enrichment analysis of co-differential expression genes of three ecotypes of Brassica napus showed that there were a lot of differences in the anabolism of basic compounds, especially lipid compounds. A total of 3775 LncRNA sequences were identified from the three ecotypes of Brassica napus, among which 285 LncRNA were differentially expressed in two or three ecotype combinations, and 1517 candidate target genes were involved. The candidate target genes of these differential expression LncRNA were also enriched in large number of anabolism related pathways of basic compounds. Based on conjoint analysis of mRNA and LncRNA, we predicted a putative regulatory network in the flowering genes, included eight flowering time genes and 23 LncRNA, which were involved in the regulation of temperature and light signal pathways. By analyzing the location of QTLs for important agronomic traits in B. napus, we found that about 90% of LncRNA and QTLs intervals were overlapped. The distribution of different expression LncRNA and the location of QTLs were different in three ecotypes of Brassica napus, which suggesting that LncRNA played an important role in ecotype differentiation and formation of important agronomic traits in Brassica napus.

Key words: Brassica napus, ecotype, long non-coding RNA, flowering genes, QTLs

杨太桦, 杨福权, 郜耿东, 殷帅, 金庆东, 徐林珊, 蒯婕, 汪波, 徐正华, 葛贤宏, 王晶, 周广生. 初步探究LncRNA在甘蓝型油菜生态型分化中的作用[J]. 作物学报, 2023, 49(5): 1197-1210.

YANG Tai-Hua, YANG Fu-Quan, GAO Geng-Dong, YIN Shuai, JIN Qing-Dong, XU Lin-Shan, KUAI Jie, WANG Bo, XU Zheng-Hua, GE Xian-Hong, WANG Jing, ZHOU Guang-Sheng. Preliminary exploration of the role of LncRNA in the ecotype differentiation of Brassica napus L.[J]. Acta Agronomica Sinica, 2023, 49(5): 1197-1210.

图/表 11

图1

图2

图3

图4

图5

附表1

差异表达开花基因"

拟南芥基因 Arabidopsis thaliana gene-ID	基因缩写 Symbol	甘蓝型油菜基因ID Brassica napus gene-ID	开花调控途径 Flowering regulation pathway
AT4G11880	AGL14	A09p27210.1_BnaDAR	其他途径 Other
AT5G13790	AGL15	C09p63310.1_BnaDAR	开花整合基因 Floral integrator
AT1G69120	AP1	A02p15620.1_BnaDAR	花分化和发育途径 Floral meristems and development
AT1G69120	AP1	C02p17480.1_BnaDAR	花分化和发育途径 Floral meristems and development
AT3G21320	AT3G21320	A03p42190.1_BnaDAR	其他途径 Other
AT5G37780	CAM1	C09p30310.1_BnaDAR	其他途径 Other
AT4G17640	CKB2	C01p11310.1_BnaDAR	光信号途径 Light singnalling
AT2G42530	COR15b	A03p23680.1_BnaDAR	春化途径 Vernalization
AT2G42530	COR15b	A03p23700.1_BnaDAR	春化途径 Vernalization
AT2G42530	COR15b	C03p28240.1_BnaDAR	春化途径 Vernalization
AT2G42530	COR15b	C03p28260.1_BnaDAR	春化途径 Vernalization
AT1G12610	DDF1	A06p09040.1_BnaDAR	赤霉素途径 Gibberellin
AT1G12610	DDF1	A08p32730.1_BnaDAR	赤霉素途径 Gibberellin
AT1G12610	DDF1	C05p10640.1_BnaDAR	赤霉素途径 Gibberellin
AT1G12610	DDF1	C08p15540.1_BnaDAR	赤霉素途径 Gibberellin
AT1G12610	DDF1	C08p47250.1_BnaDAR	赤霉素途径 Gibberellin
AT5G54510	DFL1	A02p10230.1_BnaDAR	其他途径 Other
AT4G14690	ELIP2	A01p22980.1_BnaDAR	光信号途径 Light singnalling
拟南芥基因 Arabidopsis thaliana gene-ID	基因缩写 Symbol	甘蓝型油菜基因ID Brassica napus gene-ID	开花调控途径 Flowering regulation pathway
AT4G14690	ELIP2	C01p28420.1_BnaDAR	光信号途径 Light singnalling
AT5G10140	FLC	A02p00340.1_BnaDAR	春化途径 Vernalization
AT5G10140	FLC	A03p16730.1_BnaDAR	春化途径 Vernalization
AT5G10140	FLC	C03p04920.1_BnaDAR	春化途径 Vernalization
AT5G10140	FLC	C09p67350.1_BnaDAR	春化途径 Vernalization
AT5G10140	FLC	C09p67380.1_BnaDAR	春化途径 Vernalization
AT1G30040	GA2OX2	C03p76330.1_BnaDAR	赤霉素途径 Gibberellin
AT5G67100	ICU2	A02p33280.1_BnaDAR	花分化和发育途径 Floral meristems and development
AT5G15970	KIN2	A02p03320.1_BnaDAR	春化途径 Vernalization
AT5G15970	KIN2	C02p08090.1_BnaDAR	春化途径 Vernalization
AT4G32040	KNAT5	C01p06890.1_BnaDAR	赤霉素途径 Gibberellin
AT5G65060	MAF3	A02p43650.1_BnaDAR	春化途径 Vernalization
AT5G65060	MAF3	C02p63700.1_BnaDAR	春化途径 Vernalization
AT3G01460	MBD9	C09p75140.1_BnaDAR	光周期和生物钟途径Photoperiod and circadian clock
AT3G62090	PIL2	C08p37050.1_BnaDAR	光信号途径 Light singnalling
AT1G13260	RAV1	A09p63190.1_BnaDAR	光周期和生物钟途径Photoperiod and circadian clock
AT2G03710	SEPALLATA4	A02p33530.1_BnaDAR	花分化和发育途径 Floral meristems and development
AT2G45660	SOC1	A05p05620.1_BnaDAR	开花整合基因 Floral integrator
AT2G45660	SOC1	C03p30160.1_BnaDAR	开花整合基因 Floral integrator
AT2G33810	SPL3	C04p15220.1_BnaDAR	花分化和发育途径 Floral meristems and development
AT3G16640	TCTP	C01p47690.1_BnaDAR	花分化和发育途径 Floral meristems and development

附表1

附表2

附表3

差异表达基因与差异表达LncRNA候选靶基因"

基因缩写 Symbol	拟南芥基因 Arabidopsis thaliana gene	甘蓝型油菜基因 Brassica napus gene	非编码RNA LncRNA
COR15b	AT2G42530	A03p23680.1_BnaDAR	BnaLncA02_026, BnaLncA02_041, BnaLncA03_157, BnaLncC02_051, BnaLncC03_115, BnaLncC03_185, BnaLncC03_268, BnaLncC05_059, BnaLncC05_060, BnaLncC06_126, BnaLncC06_146
COR15b	AT2G42530	A03p23700.1_BnaDAR	BnaLncA02_026, BnaLncA02_041, BnaLncA03_157, BnaLncC02_051, BnaLncC03_115, BnaLncC03_185, BnaLncC03_268, BnaLncC05_059, BnaLncC05_060, BnaLncC06_126, BnaLncC06_146
COR15b	AT2G42530	C03p28240.1_BnaDAR	BnaLncA02_026, BnaLncA02_041, BnaLncA03_109, BnaLncA03_157, BnaLncA03_168, BnaLncC02_040, BnaLncC02_051, BnaLncC03_115, BnaLncC03_185, BnaLncC03_268, BnaLncC05_059, BnaLncC05_060, BnaLncC06_126, BnaLncC06_146, BnaLncC07_243
COR15b	AT2G42530	C03p28260.1_BnaDAR	BnaLncA02_026, BnaLncA02_041, BnaLncA03_109, BnaLncA03_157, BnaLncA03_168, BnaLncC02_040, BnaLncC02_051, BnaLncC03_115, BnaLncC03_164, BnaLncC03_185, BnaLncC03_268, BnaLncC05_059, BnaLncC05_060, BnaLncC06_126, BnaLncC06_146, BnaLncC07_243
AP1	AT1G69120	A02p15620.1_BnaDAR	BnaLncA02_044, BnaLncA06_211, BnaLncC08_129
AP1	AT1G69120	C02p17480.1_BnaDAR	BnaLncA01_118, BnaLncA08_034, BnaLncA08_093, BnaLncA10_078, BnaLncC01_179, BnaLncC03_247, BnaLncC04_029
KIN2	AT5G15970	A02p03320.1_BnaDAR	BnaLncA02_027, BnaLncA02_142, BnaLncA03_109, BnaLncA03_168, BnaLncA06_218, BnaLncA09_045, BnaLncA09_161, BnaLncC02_040, BnaLncC03_164, BnaLncC05_060, BnaLncC06_146, BnaLncC07_243, BnaLncC08_166
KIN2	AT5G15970	C02p08090.1_BnaDAR	BnaLncA02_027, BnaLncA02_142, BnaLncA03_109, BnaLncA03_168, BnaLncA06_218, BnaLncA09_045, BnaLncA09_161, BnaLncC02_016, BnaLncC02_040, BnaLncC03_164, BnaLncC05_060, BnaLncC07_243, BnaLncC08_166
DDF1	AT1G12610	C08p47250.1_BnaDAR	BnaLncC08_081
ELIP2	AT4G14690	A01p22980.1_BnaDAR	BnaLncA02_026, BnaLncA02_041, BnaLncA03_109, BnaLncA03_157, BnaLncA03_168, BnaLncC02_040, BnaLncC02_051, BnaLncC03_115, BnaLncC03_164, BnaLncC03_185, BnaLncC03_268, BnaLncC05_059, BnaLncC05_060, BnaLncC06_126, BnaLncC06_146, BnaLncC07_243
SOC1	AT2G45660	A05p05620.1_BnaDAR	BnaLncA02_027, BnaLncA03_109, BnaLncA03_168, BnaLncA06_218, BnaLncA09_161, BnaLncC02_040, BnaLncC08_166

附表3

图6

附表4

图7

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QTL性状 QTL trait	数目Number
开花时间Flowering times	181
千粒重Thousand seed weight	160
株高Plant height	124
种子产量Seed yield	89
成熟时间Maturity time	73
第一分支数Number of primary branches	53
其他Others	292
A基因组数目A genome numbers	624
C基因组数目C genome numbers	348
总计Total	972

初步探究LncRNA在甘蓝型油菜生态型分化中的作用

Preliminary exploration of the role of LncRNA in the ecotype differentiation of Brassica napus L.

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