Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.)
Abstract Background Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativ...
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09528-6 |
| _version_ | 1827635505523589120 |
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| author | Yadong Li Xiaobo Luo Xiao Peng Yueyue Jin Huping Tan Linjun Wu Jingwei Li Yun Pei Xiuhong Xu Wanping Zhang |
| author_facet | Yadong Li Xiaobo Luo Xiao Peng Yueyue Jin Huping Tan Linjun Wu Jingwei Li Yun Pei Xiuhong Xu Wanping Zhang |
| author_sort | Yadong Li |
| collection | DOAJ |
| description | Abstract Background Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativus L.). Results In this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome resequencing between ‘YZH’ and ‘XHT’. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome sequencing. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. The 100 polymorphic InDels markers generated 207 alleles among 200 Chinese radish germplasm, with an average 2.07 of the number of alleles (Na) and with an average 0.33 of the polymorphism information content (PIC). Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 11,003 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained. Conclusions The large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The SNPs and InDels within flowering time-related DGEs provide fundamental insight into for dissecting molecular mechanism of bolting and flowering in radish. |
| first_indexed | 2024-03-09T15:28:38Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T15:28:38Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-ce46a651a13749fca6f111c67abaeb362023-11-26T12:25:22ZengBMCBMC Genomics1471-21642023-08-0124111210.1186/s12864-023-09528-6Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.)Yadong Li0Xiaobo Luo1Xiao Peng2Yueyue Jin3Huping Tan4Linjun Wu5Jingwei Li6Yun Pei7Xiuhong Xu8Wanping Zhang9College of Agriculture, Guizhou UniversityGuizhou Province Academy of Agricultural Sciences, Guizhou Institute of BiotechnologyCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityAbstract Background Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativus L.). Results In this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome resequencing between ‘YZH’ and ‘XHT’. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome sequencing. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. The 100 polymorphic InDels markers generated 207 alleles among 200 Chinese radish germplasm, with an average 2.07 of the number of alleles (Na) and with an average 0.33 of the polymorphism information content (PIC). Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 11,003 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained. Conclusions The large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The SNPs and InDels within flowering time-related DGEs provide fundamental insight into for dissecting molecular mechanism of bolting and flowering in radish.https://doi.org/10.1186/s12864-023-09528-6RadishInDelGenetic diversityPopulation structureTranscriptomeFlowering |
| spellingShingle | Yadong Li Xiaobo Luo Xiao Peng Yueyue Jin Huping Tan Linjun Wu Jingwei Li Yun Pei Xiuhong Xu Wanping Zhang Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.) BMC Genomics Radish InDel Genetic diversity Population structure Transcriptome Flowering |
| title | Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.) |
| title_full | Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.) |
| title_fullStr | Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.) |
| title_full_unstemmed | Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.) |
| title_short | Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.) |
| title_sort | development of snp and indel markers by genome resequencing and transcriptome sequencing in radish raphanus sativus l |
| topic | Radish InDel Genetic diversity Population structure Transcriptome Flowering |
| url | https://doi.org/10.1186/s12864-023-09528-6 |
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