| 引用本文: | 田怀志, 郭 豪, 田 浩, 熊兴伟, 张素勤, 耿广东.水涝胁迫下辣椒转录组特征分析及EST-SSR标记开发[J].广西植物,2023,43(11):2055-2064.[点击复制] |
| TIAN Huaizhi, GUO Hao, TIAN Hao, XIONG Xingwei,
ZHANG Suqin, GENG Guangdong.Transcriptome characteristic analysis and EST-SSR marker development of Capsicum annuum under waterlogging stress[J].Guihaia,2023,43(11):2055-2064.[点击复制] |
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| 水涝胁迫下辣椒转录组特征分析及EST-SSR标记开发 |
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田怀志1, 郭 豪1, 田 浩2, 熊兴伟1, 张素勤1, 耿广东1,3*
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1. 贵州大学 农学院, 贵阳 550025;2. 遵义市农业科学研究院, 贵州 遵义 563000;3. 贵州大学辣椒产业技术研究院, 贵阳 550025
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| 摘要: |
| 为开发适当的生物学工具以探索辣椒对水涝胁迫应答的分子机制,该研究对不同淹水处理的辣椒样本进行转录组分析,获得了丰富的序列数据,并在此基础上对SSR分子标记进行挖掘。结果表明:(1)辣椒转录组检测共获得128 939个Unigene,其总长度平均长度和GC含量分别是55 082 725、1 101 bp和40.57%。与七大功能数据库进行比较,分别有102 123个(NR: 79.20%)、110 157个(NT: 85.43%)、70 203个(SwissProt: 54.45%)、73 539个(KOG: 57.03%)、77 646个(KEGG: 60.22%)、77 442个(GO: 60.06%)以及68 216个(Pfam: 52.91%)个Unigene获得功能注释。发现脂质代谢、碳水化合物代谢、氨基酸代谢、环境适应、次级代谢物生物合成、信号转导和翻译等途径在辣椒水涝胁迫应答中起重要作用。(2)从辣椒转录组数据中发掘到26 574个SSR位点分布在24 889个Unigene中。SSR的出现频率为20.61%,其中单核苷酸重复所占比例(37.26%)最高,其次是三核苷酸(31.00%)和二核苷酸(25.44%)重复类型,三者占EST-SSR总数的93.70%。在单核苷酸与二核苷酸中最多的基序类型为A/T、AG/CT和TC/GA,然后是AT和TA; 三核苷酸中最常见的基序类型是TTG/CAA和ACA/TGT。(3)用Primer 3在线工具设计了10 002对EST-SSR引物,随机选择30对引物进行PCR扩增,均可获得有效扩增。对3份辣椒材料进行扩增,其中7对引物可以扩增出目标条带。综上所述,在辣椒中优势SSR重复类型的基序结构和其他品种基本相近,并初步探索了辣椒水涝胁迫应答的分子机制,开发了EST-SSR标记,为辣椒耐涝遗传育种提供了参考。 |
| 关键词: 辣椒, 水涝胁迫, 响应机制, 转录组, EST-SSR |
| DOI：10.11931/guihaia.gxzw202207044 |
| 分类号:Q943 |
| 文章编号:1000-3142(2023)11-2042-13 |
| 基金项目:国家自然科学基金(32260760); 贵州省科技计划资助项目(2022050, 20201Z002, 2021063, 20202102); 贵州省农业农村厅资助项目(黔财农[2022]89号)。 |
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| Transcriptome characteristic analysis and EST-SSR marker development of Capsicum annuum under waterlogging stress |
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TIAN Huaizhi1, GUO Hao1, TIAN Hao2, XIONG Xingwei1,
ZHANG Suqin1, GENG Guangdong1,3*
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1. College of Agriculture, Guizhou University, Guiyang 550025, China;2. Zunyi Academy of Agricultural Sciences, Zunyi 563000,
Guizhou, China;3. Industrial Technology Institute of Pepper, Guizhou University, Guiyang 550025, China
1. College of Agriculture, Guizhou University, Guiyang 550025, China; 2. Zunyi Academy of Agricultural Sciences, Zunyi 563000,
Guizhou, China; 3. Industrial Technology Institute of Pepper, Guizhou University, Guiyang 550025, China
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| Abstract: |
| SSR molecular markers were obtained based on abundant transcriptome data under different waterlogging conditions in order to develop appropriate biological tools and explore the molecular mechanism of hot pepper response to waterlogging stress in this experiment. The results were as follows:(1)A total of 128 939 Unigenes were obtained from transcriptome analysis of hot pepper. The total length, average length, and GC content were 55 082 725 bp, 1 101 bp and 40.57%, respectively. Compared with seven major functional databases, 102 123(NR: 79.20%), 110 157(NT: 85.43%), 70 203(SwissProt: 54.45%), 73 539(KOG: 57.03%), 77 646(KEGG: 60.22%), 77 442(GO: 60.06%)and 68 216(Pfam: 52.91%)Unigenes obtained functional annotations. It was found that lipid metabolism, carbohydrate metabolism, amino acid metabolism, environmental adaptation, secondary metabolite biosynthesis, signal transduction and translation played important roles in the response to waterlogging stress.(2)A total of 26 574 SSR loci were found in 24 889 Unigenes from hot pepper transcriptome data. The frequency of SSR was 20.61%, of which single nucleotide repeat accounted for the highest ratio(37.26%), followed by tri-nucleotide(31.00%)and di-nucleotide(25.44%)repeat types, accounting for 93.70% of the total EST-SSR. The motifs A/T, AG/CT and TC/GA, followed by AT and TA, were the most abundant in mono-nucleotide and di-nucleotide. The most common types of tri-nucleotides were TTG/CAA and ACA/TGT.(3)10 002 pairs of EST-SSR primers were designed with Primer 3. A total of 30 pairs of primers were randomly selected for amplification test, and all of them were effective. Seven pairs of primers could amplify the target bands in three hot pepper germplasms. To sum up, the motif structure of the most dominant SSR repeat type in hot pepper is basically similar to that of other varieties, and the molecular mechanism of hot pepper waterlogging stress response is preliminarily explored. The EST-SSR markers are developed to provide reference for hot pepper waterlogging-tolerant genetics breeding. |
| Key words: Capsicum annuum(hot pepper), waterlogging stress, response mechanism, transcriptome, EST-SSR |
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