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作物学报

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   

  1. 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   

  1. 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)

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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

图1

3种生态型甘蓝型油菜同时期形态 在武汉半冬性环境下, 2021-2022年度, 播种约110 d时, 3种生态型甘蓝型油菜形态差异明显。A: Westar; B: 中双11号; C: Tapidor。标尺为20 cm。"

图2

3种生态型6个甘蓝型油菜品种mRNA-seq分析相关结果 A: 6种甘蓝型油菜品种12个样本mRNA-seq主成分分析; B: 在6个甘蓝型油菜品种和3种生态型中甘蓝型油菜全部基因表达情况; C: 甘蓝型油菜3种生态型两两之间差异表达基因数量; D: 甘蓝型油菜3种生态型两两之间差异表达基因韦恩图。SOR: 春油菜; SWOR: 半冬性油菜; WOR: 冬油菜。"

图3

3种生态型甘蓝型油菜差异表达基因GO功能和KEGG通路富集分析 A: 3种生态型甘蓝型油菜差异表达基因GO功能富集分析; B: 3种生态型甘蓝型油菜差异表达基因KEGG通路富集分析。"

图4

3种生态型6个甘蓝型油菜品种LncRNA-seq分析相关结果 A: 6种甘蓝型油菜品种12个样本LncRNA-seq主成分分析; B: 在6个甘蓝型油菜品种和3种生态型中存在表达的LncRNA数量; C: 甘蓝型油菜3种生态型之间LncRNA表达情况韦恩图; D: 在3种生态型甘蓝型油菜中共鉴定到了LncRNA在19条染色体以及An/Cn亚基因组上的分布。SOR: 春油菜; SWOR: 半冬性油菜; WOR: 冬油菜。"

图5

3种生态型甘蓝型油菜差异表达LncRNA候选靶基因GO功能和KEGG通路富集分析 A: 3种生态型甘蓝型油菜差异表达LncRNA候选靶基因GO功能富集分析; B: 3种生态型甘蓝型油菜差异表达LncRNA候选靶基因KEGG通路富集分析。"

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2

差异表达LncRNA涉及到的开花基因"

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
AT4G14690 ELIP2 A01p22980.1_BnaDAR 光信号途径 Light singnalling
AT5G15970 KIN2 A02p03320.1_BnaDAR 春化途径 Vernalization
AT1G69120 AP1 A02p15620.1_BnaDAR 花分化和发育途径 Floral meristems and development
AT1G78440 GA2OX1 A02p22190.1_BnaDAR 赤霉素途径 Gibberellin
AT2G42530 COR15b A03p23680.1_BnaDAR 春化途径 Vernalization
AT2G42530 COR15b A03p23700.1_BnaDAR 春化途径 Vernalization
AT2G45660 SOC1 A03p25280.1_BnaDAR 开花整合基因 Floral integrator
AT2G45660 SOC1 A05p05620.1_BnaDAR 开花整合基因 Floral integrator
AT5G11260 HY5 A10p26460.1_BnaDAR 光信号途径 Light singnalling
AT5G15970 KIN2 C02p08090.1_BnaDAR 春化途径 Vernalization
AT1G69120 AP1 C02p17480.1_BnaDAR 花分化和发育途径 Floral meristems and development
AT4G25470 CBF2 C03p19680.1_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 C08p47250.1_BnaDAR 赤霉素途径 Gibberellin
AT5G20730 NPH4 C09p55450.1_BnaDAR 光信号途径 Light singnalling

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

图6

差异表达mRNA-LncRNA互作模块及基因在甘蓝型群体中的达量 A: 差异表达mRNA-LncRNA互作模块, 包含8个基因和23个LncRNA序列; B: 差异表达mRNA-LncRNA互作模块中, COR15b、KIN2和SOC1基因(多个拷贝)在甘蓝型油菜不同生态型群体中的表达量。FPKM (Fragments Per Kilobase of exon model per Million mapped fragments): 每千个碱基的转录每百万映射读取的片段数, *表示在P < 0.05水平差异显著, **表示在P < 0.01水平差异显著, ns表示差异不显著P > 0.05。SOR: 春油菜, SWOR: 半冬性油菜, WOR: 冬油菜。"

附表4

甘蓝型油菜收集的QTL信息汇总"

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

图7

甘蓝型油菜QTL和鉴定到的LncRNA共线性分布"

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