基于RNA-Seq筛选调控马铃薯熟性的候选基因

doi:10.16420/j.issn.0513-353x.2024-0315

园艺学报 ›› 2025, Vol. 52 ›› Issue (6): 1505-1518.doi: 10.16420/j.issn.0513-353x.2024-0315

• 遗传育种·种质资源·分子生物学 • 上一篇下一篇

基于RNA-Seq筛选调控马铃薯熟性的候选基因

李姿燕¹^,², 陈炜曦¹^,², 李子涵¹^,², 黎茵¹^,², 梁峰铭⁵, 曾祥利⁵, 荐红举¹^,²^,³^,⁴^,^*(), 吕典秋¹^,²^,³^,⁴^,^*()

¹ 西南大学，西部（重庆）科学城种质创制大科学中心，重庆 400715
² 西南大学农学与生物科技学院，重庆 400715
³ 西南大学，南方山地农业教育部工程研究中心，重庆 400715
⁴ 西南大学，薯类生物学与遗传育种重庆市重点实验室，重庆 400715
⁵ 巫溪县薯光农业科技发展有限公司，重庆 405899

收稿日期:2025-01-20 修回日期:2025-03-06 出版日期:2025-06-20 发布日期:2025-06-20
通讯作者:
*E-mail：hjjian518@swu.edu.cn；
smallpotatoes@126.com
基金资助:
国家重点研发计划项目(2022YFD1201600); 国家自然科学基金项目(32101659); 重庆市现代农业产业技术体系项目(CQMAITS202303); 西南大学人才引进项目(SWU019008); 中央高校基本科研业务费专项(SWU-KT22036)

Screening Candidate Genes Controlling Potato Maturation Time Based on RNA-Seq

LI Ziyan¹^,², CHEN Weixi¹^,², LI Zihan¹^,², LI Yin¹^,², LIANG Fengming⁵, ZENG Xiangli⁵, JIAN Hongju¹^,²^,³^,⁴^,^*(), and LÜ Dianqiu¹^,²^,³^,⁴^,^*()

¹ Integrative Science Center of Germplasm Creation in Western China（Chongqing）Science City，Southwest University，Chongqing 400715，China
² College of Agronomy and Biotechnology，Southwest University，Chongqing 400715，China
³ Engineering Research Center of South Upland Agriculture，Ministry of Education，Southwest University，Chongqing 400715，China
⁴ Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops，Southwest University，Chongqing 400715，China
⁵ Wuxi County Shuguang Agricultural Science and Technology Development Co.，Ltd.，Chongqing 405899，China

Received:2025-01-20 Revised:2025-03-06 Published:2025-06-20 Online:2025-06-20

摘要/Abstract

摘要： 以早熟品种‘早大白’‘中薯5号’‘鄂马铃薯3号’与中晚熟品种‘大西洋’和‘青薯9号’为材料，分析了马铃薯顶端分生组织发育与结薯时间的关系，并利用RNA-Seq技术研究早大白与青薯9号差异表达基因的功能及可能参与的调控通路。结果表明，相比晚熟品种，早熟品种的顶端分生组织向生殖生长转变更早。转录组测序共鉴定出差异表达基因2 842个，其中与激素相关的基因85%集中在激素信号转导途径，特别是生长素（IAA）、脱落酸（ABA）和茉莉酸（JA）等通路；另外，筛选到127个差异表达基因编码转录因子，分布在35个转录因子家族。GO和KEGG富集分析发现差异表达基因主要富集在光合作用、对激素的响应、植物昼夜节律、淀粉和蔗糖代谢、植物激素信号转导等过程。挑选20个可能影响马铃薯结薯早晚的候选基因进行荧光定量PCR验证。其中参与昼夜节律通路的基因FT、HY5，参与淀粉和蔗糖代谢通路的基因BGLU17、CWIN2、GH9B13在早大白中高表达；参与植物激素信号转导或合成代谢的基因GH3、RD22、HB16、CYP74A在早大白中高表达，而IAA17、MES1、RCA在青薯9号中高表达。此外，在早大白中高表达的GRP3可能通过影响生长发育从而调控马铃薯结薯早晚。这些基因可能通过调控光周期响应、激素信号转导、蔗糖水平等在马铃薯中发挥作用，从而影响马铃薯熟性。

关键词: 马铃薯, 转录组测序, 熟性, 顶端分生组织, 差异基因, 光周期, 激素, 蔗糖

Abstract:

In this study，early maturing cultivars‘Zaodabai’‘Zhongshu5’‘Eshu3’，middle late maturing cultivar ‘Atlantic’and late maturing cultivar‘Qingshu 9’were used to analyze the relationship between potato apical meristem development and tuberization time，Zaodabai and Qingshu 9 were also taken to study the function of differentially expressed genes as well as the possible regulatory pathways involved by RNA-Seq. Results showed that the apical meristem turned to reproductive growth earlier in early maturing cultivars than late maturing cultivars. A total of 2 842 differentially expressed genes were identified in transcriptome sequencing，85% of which related to hormones were concentrated in hormone signal transduction pathways and showed rich expression differences，especially in IAA，ABA，JA and other pathways. Besides，a total of 127 differentially expressed transcription factor genes were identified，distributed in 35 transcription factor families. GO and KEGG enrichment analysis showed that differentially expressed genes were mainly concentrated in photosynthesis，hormone response，plant circadian rhythm，starch and sucrose metabolism，and plant hormone signal transduction. The 20 candidate genes that may affect the early and late tuberization of potato were selected for qRT-PCR verification. The genes involved in the circadian rhythm pathway，FT and HY5，were highly expressed in Zaodabai. Genes involved in the starch and sucrose metabolic pathway，BGLU17，CWIN2 and GH9B13 were highly expressed in Zaodabai. GH3，RD22，HB16 and CYP74A involved in plant hormone signal transduction or anabolism were highly expressed in Zaodabai，while IAA17，MES1 and RCA were highly expressed in Qingshu 9. In addition，GRP3 which highly expressed in Zaodabai may also affect tuberization time. These genes may play a role in potato by regulating photoperiodic response，hormone signal transduction，sucrose level，etc.，thus affecting potato tuberization time.

Key words: potato, transcriptome sequencing, maturation, apical meristem, differential expressed gene, photoperiod, hormone, sucrose

李姿燕, 陈炜曦, 李子涵, 黎茵, 梁峰铭, 曾祥利, 荐红举, 吕典秋. 基于RNA-Seq筛选调控马铃薯熟性的候选基因[J]. 园艺学报, 2025, 52(6): 1505-1518.

LI Ziyan, CHEN Weixi, LI Zihan, LI Yin, LIANG Fengming, ZENG Xiangli, JIAN Hongju, and LÜ Dianqiu. Screening Candidate Genes Controlling Potato Maturation Time Based on RNA-Seq[J]. Acta Horticulturae Sinica, 2025, 52(6): 1505-1518.

图/表 8

表1 候选基因qRT-PCR引物序列

Table 1 qRT-PCR primer sequences of candidate genes

名称Name	基因ID Gene ID	正向引物（5′-3′）Forward primer	反向引物（3′-5′）Reverse primer
GH3	Soltu.DM.10G002010	TGAAGCCATTCTCTGCCTAGACTC	AGCCAACACGAACGACTTCTCTG
SAUR79	Soltu.DM.08G022860	GGTAGCAATCTTGACAAGGCGATG	TTCCTTTCCCACCAGCACAGTTAC
IAA17	Soltu.DM.03G035030	GATGGAGACTGGATGCTTGTTGGA	CCTCCGTGCTCTTCATCAACCTAA
RD22	Soltu.DM.08G017220	GGTGTCTATGGTGGGTGCTGATG	ATAGGCTTGTCTCCAGGCTTAACG
HB16	Soltu.DM.11G003380	GGTTGGTTGTTCATCTCCGTTGA	TGTTGTTGTTGTTGTTGACGAAGG
CYP74A	Soltu.DM.10G003720	TGGATTGGAACATCAGGACCTAGT	ACCACAGACTTAACAAGAGGCATT
MES1	Soltu.DM.02G008550	CCTGAAGAGCCTCGGACATCCA	GGTCTCACCAACGACGATGCTAAT
MES3	Soltu.DM.01G048330	TGCCAATCCTCCAACAACCTTCAT	GTAGTAGCCAGTGCCCAGTCCT
RCA	Soltu.DM.10G023180	ACTCACCATCCTGTCTTGTCATCA	ATCCATCCAGCGTGTTGTCCAG
GIM2	Soltu.DM.08G001760	ACTTGGTATGCCACCTCATTCAGA	TCGAGATGGTCGCCGGTATTG
FT	Soltu.DM.05G026370	CAAGCCCAAGCGACCCTAACTT	CGTAGGTGTTGGATTCTCGTAGCA
COP1	Soltu.DM.11G001010	AGGAGGAAGAGGAAGAGGAAGAGG	AACTATGTCCACACGCCGTTAGAA
HY5	Soltu.DM.08G011730	TGCCGCTAGTTCACTACCTTCAAG	ACATCGTTCCCGTCGCTTCTC
GRP3	Soltu.DM.09G030440	ATTATGGAGGCGGCTATGGTAAGG	AGTCTGGGCAGCCACATATTCTTC
RBCS3B	Soltu.DM.02G025840	AGGTCTTGGCTGAGGTGGAGGA	AACTGATGCACTGCACTTGACGAA
GH9B13	Soltu.DM.09G023670	ACGAGCGATCAGATTACGAGCAAT	TGAGCAAGGTAAGTGAGTGTTCCA
BGLU45	Soltu.DM.07G024580	ACAAGGTGGAACGATAGGAATGGT	AGGATCAAGAAGCCAGGCAACAT
ADG2	Soltu.DM.01G024440	GCAGGTGAGGCTAAGTTGAAGGAT	CCCATTGGAACGGCAGGCTTA
BGLU17	Soltu.DM.10G010830	GTCGGCTCCCAAGATTCACAGTT	CAGCATGATTGTCAGTGGTGTAGC
CWIN2	Soltu.DM.10G025030	ATGTTGGTTGGGTCAGGATGGTT	CCGTCAACTGAATGAAGTGGATGT

图1 不同马铃薯品种在长日照（A、B）和短日照（C、D）条件下微型薯结薯时间和数量统计早熟：早大白、中薯5号、鄂马铃薯3号；中晚熟：大西洋；晚熟：青薯9号。使用最小显著差异法对数据进行多重比较分析，不同小写字母表示差异显著，（P < 0.05）

Fig. 1 Statistics of tuberization time and number of microtuber in different potato cultivars under long day(A，B)and short day(C，D)condition Early maturing：Zaodabai，Zhongshu5，Eshu3；middle late maturing：Atlantic；late maturing：Qingshu9. The minimum significant difference method was used for multiple comparative analysis of the data. Different lowercase letters indicate significant differences at 0.05 level

图2 长日照条件下马铃薯不同品种组培苗茎顶端分生组织发育绿色箭头代表顶端分生组织进行营养生长，红色箭头代表顶端分生组织已转向生殖生长

Fig. 2 Stem apical meristem development of plantlet of various potato cultivars under long day condition The green arrows indicates that the apical meristem has undergone vegetative growth，the red arrow indicates that the apical meristem has shifted to reproductive growth

图3 马铃薯品种早大白与青薯9号差异基因表达模式聚类分析（A）和表达量差异统计（B）

Fig. 3 Cluster analysis of differential gene expression pattern（A）and statistical difference of expression level（B） between potato cultivars Zaodabai and Qingshu 9

图4 马铃薯品种早大白和青薯9号中植物激素相关基因的表达

Fig. 4 Expression of hormone-related genes in potato cultivars Zaodabai and Qingshu 9

图5 马铃薯品种早大白和青薯9号的差异表达基因中各转录因子家族基因分布

Fig. 5 Distribution of transcription factor family genes in DEGs of potato cultivars Zaodabai and Qingshu 9

图6 马铃薯品种早大白与青薯9号差异表达基因GO（A）和KEGG（B）富集分析

Fig. 6 GO(A)and KEGG(B)enrichment analysis of differentially expressed genes of potato cultivars Zaodabai and Qingshu 9

图7 马铃薯熟性相关候选基因表达模式分析使用t检验对数据进行分析，*代表显著性水平P ≤ 0.05；**代表显著性水平P ≤ 0.01；ns代表无显著性

Fig. 7 Analysis of candidate gene expression patterns related to potato maturation time t-Test was used to analyze the data，* represents a significance level of P ≤ 0.05，** represents a significance level of P ≤ 0.01，ns represents no significance

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基于RNA-Seq筛选调控马铃薯熟性的候选基因

Screening Candidate Genes Controlling Potato Maturation Time Based on RNA-Seq

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基于RNA-Seq筛选调控马铃薯熟性的候选基因

Screening Candidate Genes Controlling Potato Maturation Time Based on RNA-Seq

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相关文章 15

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