大豆细胞质雄性不育系及其恢复系的比较转录组分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0219

生物技术通报 ›› 2024, Vol. 40 ›› Issue (7): 137-149.doi: 10.13560/j.cnki.biotech.bull.1985.2024-0219

大豆细胞质雄性不育系及其恢复系的比较转录组分析

高萌萌¹^,²^,³(), 赵天宇¹^,²^,³, 焦馨悦¹^,²^,³, 林春晶²^,³, 关哲允²^,³, 丁孝羊²^,³, 孙妍妍²^,³(), 张春宝²^,³()

1.吉林农业大学农学院，长春 130118
2.吉林省农业科学院大豆研究所，长春 130033
3.农业农村部杂交大豆育种重点实验室，长春 130033

收稿日期:2024-03-07 出版日期:2024-07-26 发布日期:2024-07-30
通讯作者: 张春宝，男，博士，研究员，研究方向：大豆杂种优势利用及分子机理；E-mail: cbzhang@cjaas.com；
孙妍妍，女，博士，副研究员，研究方向：大豆杂种优势利用及分子机理；E-mail: 15929800833@163.com
作者简介:高萌萌，女，硕士研究生，研究方向：大豆杂种优势利用及分子机理；E-mail: 1757753098@qq.com
基金资助:
基本科研经费项目(KYJF2021ZR110);基本科研经费项目(KYJF2023JJ101);国家自然科学基金项目(32372149);国家自然科学基金项目(32101766);国家现代农业产业技术体系建设项目(CARS-04);吉林省农业科技创新工程项目(CXGC2022RCY015)

Comparative Transcriptome Analysis of Cytoplasmic Male Sterile Line and Its Restorer Line in Soybean

GAO Meng-meng¹^,²^,³(), ZHAO Tian-yu¹^,²^,³, JIAO Xin-yue¹^,²^,³, LIN Chun-jing²^,³, GUAN Zhe-yun²^,³, DING Xiao-yang²^,³, SUN Yan-yan²^,³(), ZHANG Chun-bao²^,³()

1. College of Agronomy, Jilin Agricultural University, Changchun 130118
2. Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033
3. Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033

Received:2024-03-07 Published:2024-07-26 Online:2024-07-30

摘要/Abstract

摘要：

【目的】 “三系”法是选育杂交大豆的主要途径，但恢复系中仅有少数大豆恢复基因被克隆，为挖掘更多新恢复基因，从而促进多基因聚合的强恢复系选育，提高杂种F₁的育性稳定性。【方法】 以大豆细胞质雄性不育系JLCMS5A和其恢复系JLR2为材料，采用转录组测序技术分析JLCMS5A和JLR2花蕾不同时期的转录水平变化，挖掘调控育性恢复和花蕾发育进程的相关基因和通路。进一步对具有恢复基因特征编码PPR（pentatricopeptide repeat）蛋白的差异表达基因（differentially expressed genes，DEGs）进行基因注释、序列差异分析、RT-qPCR验证、系统进化分析及蛋白结构预测，挖掘育性恢复相关基因。【结果】 转录组测序鉴定到17 181个DEGs，其中有3 856个DEGs与发育时期相关，2 808个DEGs与育性相关。GO（gene ontology）功能注释表明，与育性相关的DEGs主要富集在ADP结合、核酸结合转录因子活性和蛋白激酶活性等功能类别，与发育时期相关的DEGs主要富集在蛋白质异源二聚化活性、DNA复制和DNA结合等功能类别。KEGG（kyoto encyclopedia of genes and genomes）富集分析表明，育性相关DEGs主要参与内质网蛋白质加工、葡萄糖苷酸生物合成和植物激素信号转导等与蛋白质、糖类和信号转导密切相关的代谢通路，发育时期相关DEGs主要参与DNA复制、错配修复、淀粉和蔗糖代谢等与细胞分裂和能量物质降解密切相关的代谢通路。育性恢复候选基因分析发现，JLR2中的Glyma.09G176400可能在调控大豆细胞质雄性不育育性恢复过程中起到一定作用。【结论】 共鉴定到3 856个与发育时期相关的DEGs，2 808个与育性相关的DEGs；鉴定出具有恢复基因特征编码PPR蛋白的DEGs 15个；挖掘了1个育性恢复相关基因Glyma.09G176400。

关键词: 大豆, 细胞质雄性不育, 育性恢复基因, 转录组测序, 差异表达基因

Abstract:

【Objective】 The “three line” method is the main way to breed hybrid soybeans. At present, only a few soybean restoration genes have been cloned. Thus it will be helpful in the breeding strong restorer lines with multi genes aggregation, thereby improving the fertility stability of hybrid F_1,if more new Rf genes can be discovered. 【Method】 Using soybean cytoplasmic male sterile line JLCMS5A and its restorer line JLR2 as materials, transcriptome sequencing technology was used to analyze the transcriptional level changes of JLCMS5A and JLR2 flower buds at different stages, and to explore the relevant genes and pathways regulating restorer of fertility and flower bud development processes. Further gene annotation, sequence difference analysis, RT-qPCR validation, phylogenetic analysis, and protein structure prediction were performed on differentially expressed genes（DEGs） with Rf gene features encoding PPR（pentatrioptide repeat）proteins to explore Rf related genes. 【Result】 Transcriptome sequencing identified 17 181 DEGs, of which 3 856 were related to developmental stage and 2 808 were related to fertility. GO（gene ontology）functional annotation indicated that fertility-related DEGs were mainly enriched in functional categories such as ADP binding, nucleic acid binding transcription factor activity, and protein kinase activity, while developmental stage-related DEGs were mainly enriched in functional categories such as protein heterodimerization activity, DNA replication, and DNA binding. KEGG（kyoto encyclopedia of genes and genes）enrichment analysis showed that fertility-related DEGs mainly participate in metabolic pathways closely related to protein, carbohydrates, and signal transduction, such as endoplasmic reticulum protein processing, glucoside biosynthesis, and plant hormone signal transduction. Development-related DEGs mainly participated in metabolic pathways closely related to DNA replication, mismatch repair, starch and sucrose metabolism, and cell division and energy degradation. Analysis of candidate Rf genes revealed that the Glyma.09G176400 in JLR2 may play a certain role in regulating the restorer-of-fertility process of soybean cytoplasmic male sterility. 【Conclusion】 3 856 DEGs and 2 808 DEGs which respectively related to developmental stage and fertility were identified by transcriptomic techniques and molecular biological methods. Whereafter, a total of 15 DEGs encoding PPR protein were identified, which had the characteristics of restorer-of-fertility gene. Finally, a restorer-of-fertility related gene Glyma.09G176400 was excavated.

Key words: soybean, cytoplasmic male sterility, restorer-of-fertility gene, transcriptome sequencing, differentially expressed gene

高萌萌, 赵天宇, 焦馨悦, 林春晶, 关哲允, 丁孝羊, 孙妍妍, 张春宝. 大豆细胞质雄性不育系及其恢复系的比较转录组分析[J]. 生物技术通报, 2024, 40(7): 137-149.

GAO Meng-meng, ZHAO Tian-yu, JIAO Xin-yue, LIN Chun-jing, GUAN Zhe-yun, DING Xiao-yang, SUN Yan-yan, ZHANG Chun-bao. Comparative Transcriptome Analysis of Cytoplasmic Male Sterile Line and Its Restorer Line in Soybean[J]. Biotechnology Bulletin, 2024, 40(7): 137-149.

图/表 11

图1 两个发育阶段的花蕾表型

Fig. 1 Flower bud phenotypes at two developmental stages

表1 RT-qPCR引物序列信息

Table 1 Information of RT-qPCR primer sequences

基因名称Gene name	上游引物Forward primer（5'-3'）	下游引物Reverse primer（5'-3'）
Cons4	GATCAGCAATTATGCACAACG	CCGCCACCATTCAGATTATGT
Glyma.01G235800	CGTGAGAGATGTGGTGACATAC	ACGACCCATCTTCCATTTCC
Glyma.08G233900	TGAGAGATGTGGTGCTTTGG	:GTTTCCCTCCATCCTCCTAAAC
Glyma.09G160300	GATTGGTAGAAGAGCGACTGAA	CGACCGAGAAGATCGATCAAA
Glyma.09G176400	GGTCAACCCGCAGATGTAAT	CGGTCGAATTCCCTGATCTTT
Glyma.09G176600	GTCGCTGCAAACAAGGTTAAG	GGCTGAGAGTGAAAGTGAGAAT
Glyma.09G209700	CAGGACAAGTCTCAACCACAA	CTGTGACATGTCTGGCGTATAA
Glyma.10G047150	CTTCGTGAAGGAGAGTGGAATC	CAAACAGCTCCCGCGTATAA
Glyma.13G135000	CGCGGGTTGTACTCTGATATT	GTTCCACGTTACGATATCTCTCTC
Glyma.15G019900	TGAGCCGGATATTGTGGTTTAC	ACCTCTTCCTCCTCATCTCTTT
Glyma.15G091700	GTTGTATGGGTGTGAGCCTAAT	CCTTCCCTCTCATCTCCCTATAA
Glyma.16G034600	CCGAGGAGTTCAAGTCTTCTTC	CCTGGTTCTTTCGCTGGTAATA
Glyma.16G195700	CTAGGAGATGCCTGTGATTTGT	AAAGCCATGGATCAGAGTAGTG
Glyma.16G195900	CCGGATGCAATTACCCTCAA	ACCCTTGAGCTACGACCTTA
Glyma.17G220100	GTGCCCATAGGAGTCAGAAATAC	CGCGGAGATTCTTCGTTACTT
Glyma.18G108202	GCGGCTTGAGGAAGGTAATAA	TCATGCATCCAGCCTCTTAATC

图2 花蕾总RNA琼脂糖凝胶电泳检测结果 M: Maker Ⅲ；1-3分别为FLB_1-FLB_3；4-6分别为FSB_1-FSB_3；7-9分别为SLB_1-SLB_3；10-12分别为SSB_1-SSB_3

Fig. 2 Result of total RNA in flower bud by agarose gel electrophoresis M: Maker Ⅲ. Lane 1-3: FLB_1 - FLB_3; respectively. Lane 4-6: FSB_1 - FSB_3; respectively. Lane 7-9: SLB_1 -SLB_3; respectively. Lane 10-12: SSB_1 - SSB_3; respectively

图3 样本间相关性检验 A：不同育性花蕾不同发育时期样本Pearson相关性分析；B：不同育性花蕾不同发育时期样本基因表达量PCA分析；C：样本间基因表达水平热图

Fig. 3 Correlation analysis among samples A: Pearson correlation analysis of fertile and sterile samples at different developmental stages. B: PCA analysis of gene expression levels in fertile and sterile samples at different developmental stages. C: Heat map of gene expressions among samples

图4 差异表达基因的统计分析 A：差异表达基因数量统计；B：差异表达基因韦恩图

Fig. 4 Statistics and analysis of differentially expressed genes A: Statistics of differentially expressed genes. B: Venn diagram of differentially expressed genes

图5 GO富集分析散点图

Fig. 5 Rich distribution point diagram for GO A：F_LB vs F_SB；B：S_LB vs S_SB；C：F_LB vs S_LB；D：F_SB vs S_SB；E：F_LB vs S_LB和F_SB vs S_SB；F：F_LB vs F_SB和S_LB vs S_SB, the same below

图6 KEGG富集分析散点图

Fig. 6 Rich distribution point diagram for KEGG

图7 编码PPR蛋白的差异表达基因统计分析 A：编码PPR蛋白的差异表达基因数量统计；B：编码PPR蛋白的差异表达基因Venn图；C：F_LB vs S_LB上调表达基因GO富集图；D：F_LB vs S_LB下调表达基因GO富集图；E：F_SB vs S_SB上调表达基因GO富集图；F：F_SB vs S_SB下调表达基因GO富集图

Fig. 7 Statistical analysis of differentially expressed genes encoding PPR proteins A: Statistics of differentially expressed genes encoding PPR protein. B: Venn diagram of differentially expressed genes encoding PPR protein. C: Map of GO enrichment of up-regulated DEGs in F_LB vs S_LB. D: Map of GO enrichment of down-regulated DEGs in F_LB vs S_LB. E: Map of GO enrichment of up-regulated DEGs in F_SB vs S_SB. F: Map of GO enrichment of down-regulated DEGs in F_SB vs S_SB

图8 候选基因RNA-Seq与RT-qPCR结果分析

Fig. 8 RNA-Seq and RT-qPCR analysis of candidate genes

图9 候选基因编码PPR蛋白进化分析红色分支代表豆科植物中的PPR蛋白；利用Maximum-Likelihood法构建进化树，设置Bootstrap为500次重复

Fig. 9 Phylogenetic analysis of candidate genes encoding PPR proteins The red branches indicate PPR proteins in leguminous plants. Phylogenetic analysis was constructed using Maximum-Likelihood, and Bootstrap values of 500 were used

图10 Glyma.09G176400编码蛋白结构预测绿色图形代表信号肽；橙色图形代表PPR，黄色图形代表氨基酸变异位点

Fig. 10 Structure prediction for Glyma.09G176400 encoded protein Green graphic indicates signal peptides. The orange graphics indicate pentatricopeptide repeat. The yellow graphic indicate amino acid mutation site

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大豆细胞质雄性不育系及其恢复系的比较转录组分析

Comparative Transcriptome Analysis of Cytoplasmic Male Sterile Line and Its Restorer Line in Soybean

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