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Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.)
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.)....
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10408230/ https://www.ncbi.nlm.nih.gov/pubmed/37553577 http://dx.doi.org/10.1186/s12864-023-09528-6 |
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author | Li, Yadong Luo, Xiaobo Peng, Xiao Jin, Yueyue Tan, Huping Wu, Linjun Li, Jingwei Pei, Yun Xu, Xiuhong Zhang, Wanping |
author_facet | Li, Yadong Luo, Xiaobo Peng, Xiao Jin, Yueyue Tan, Huping Wu, Linjun Li, Jingwei Pei, Yun Xu, Xiuhong Zhang, Wanping |
author_sort | Li, Yadong |
collection | PubMed |
description | 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09528-6. |
format | Online Article Text |
id | pubmed-10408230 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-104082302023-08-09 Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.) Li, Yadong Luo, Xiaobo Peng, Xiao Jin, Yueyue Tan, Huping Wu, Linjun Li, Jingwei Pei, Yun Xu, Xiuhong Zhang, Wanping BMC Genomics Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09528-6. BioMed Central 2023-08-08 /pmc/articles/PMC10408230/ /pubmed/37553577 http://dx.doi.org/10.1186/s12864-023-09528-6 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Li, Yadong Luo, Xiaobo Peng, Xiao Jin, Yueyue Tan, Huping Wu, Linjun Li, Jingwei Pei, Yun Xu, Xiuhong Zhang, Wanping Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.) |
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 | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10408230/ https://www.ncbi.nlm.nih.gov/pubmed/37553577 http://dx.doi.org/10.1186/s12864-023-09528-6 |
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