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Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)

BACKGROUND: Alternative splicing (AS) plays important roles in gene expression and proteome diversity. Single nucleotide polymorphism (SNP) and insertion/deletion (InDel) are abundant polymorphisms and co-dominant inheritance markers, which have been widely used in germplasm identification, genetic...

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Autores principales: Luo, Xiaobo, Xu, Liang, Liang, Dongyi, Wang, Yan, Zhang, Wei, Zhu, Xianwen, Zhu, Yuelin, Jiang, Haiyan, Tang, Mingjia, Liu, Liwang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5496183/
https://www.ncbi.nlm.nih.gov/pubmed/28673249
http://dx.doi.org/10.1186/s12864-017-3874-4
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author Luo, Xiaobo
Xu, Liang
Liang, Dongyi
Wang, Yan
Zhang, Wei
Zhu, Xianwen
Zhu, Yuelin
Jiang, Haiyan
Tang, Mingjia
Liu, Liwang
author_facet Luo, Xiaobo
Xu, Liang
Liang, Dongyi
Wang, Yan
Zhang, Wei
Zhu, Xianwen
Zhu, Yuelin
Jiang, Haiyan
Tang, Mingjia
Liu, Liwang
author_sort Luo, Xiaobo
collection PubMed
description BACKGROUND: Alternative splicing (AS) plays important roles in gene expression and proteome diversity. Single nucleotide polymorphism (SNP) and insertion/deletion (InDel) are abundant polymorphisms and co-dominant inheritance markers, which have been widely used in germplasm identification, genetic mapping and marker-assisted selection in plants. So far, however, little information is available on utilization of AS events and development of SNP and InDel markers from transcriptome in radish. RESULTS: In this study, three radish transcriptome datasets were collected and aligned to the reference radish genome. A total of 56,530 AS events were identified from three radish genotypes with intron retention (IR) being the most frequent AS type, which accounted for 59.4% of the total expressed genes in radish. In all, 22,412 SNPs and 9436 InDels were identified with an average frequency of 1 SNP/17.9 kb and 1 InDel/42.5 kb, respectively. A total of 43,680 potential SSRs were identified in 31,604 assembled unigenes with a density of 1 SSR/2.5 kb. The ratio of SNPs with nonsynonymous/synonymous mutations was 1.05:1. Moreover, 35 SNPs and 200 InDels were randomly selected and validated by Sanger sequencing, 83.9% of the SNPs and 70% of the InDels exhibited polymorphism among these three genotypes. In addition, the 15 SNPs and 125 InDels were found to be unevenly distributed on 9 linkage groups. Furthermore, 40 informative InDel markers were successfully used for the genetic diversity analysis on 32 radish accessions. CONCLUSIONS: These results would not only provide new insights into transcriptome complexity and AS regulation, but also furnish large amount of molecular marker resources for germplasm identification, genetic mapping and further genetic improvement of radish in breeding programs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3874-4) contains supplementary material, which is available to authorized users.
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spelling pubmed-54961832017-07-05 Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.) Luo, Xiaobo Xu, Liang Liang, Dongyi Wang, Yan Zhang, Wei Zhu, Xianwen Zhu, Yuelin Jiang, Haiyan Tang, Mingjia Liu, Liwang BMC Genomics Research Article BACKGROUND: Alternative splicing (AS) plays important roles in gene expression and proteome diversity. Single nucleotide polymorphism (SNP) and insertion/deletion (InDel) are abundant polymorphisms and co-dominant inheritance markers, which have been widely used in germplasm identification, genetic mapping and marker-assisted selection in plants. So far, however, little information is available on utilization of AS events and development of SNP and InDel markers from transcriptome in radish. RESULTS: In this study, three radish transcriptome datasets were collected and aligned to the reference radish genome. A total of 56,530 AS events were identified from three radish genotypes with intron retention (IR) being the most frequent AS type, which accounted for 59.4% of the total expressed genes in radish. In all, 22,412 SNPs and 9436 InDels were identified with an average frequency of 1 SNP/17.9 kb and 1 InDel/42.5 kb, respectively. A total of 43,680 potential SSRs were identified in 31,604 assembled unigenes with a density of 1 SSR/2.5 kb. The ratio of SNPs with nonsynonymous/synonymous mutations was 1.05:1. Moreover, 35 SNPs and 200 InDels were randomly selected and validated by Sanger sequencing, 83.9% of the SNPs and 70% of the InDels exhibited polymorphism among these three genotypes. In addition, the 15 SNPs and 125 InDels were found to be unevenly distributed on 9 linkage groups. Furthermore, 40 informative InDel markers were successfully used for the genetic diversity analysis on 32 radish accessions. CONCLUSIONS: These results would not only provide new insights into transcriptome complexity and AS regulation, but also furnish large amount of molecular marker resources for germplasm identification, genetic mapping and further genetic improvement of radish in breeding programs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3874-4) contains supplementary material, which is available to authorized users. BioMed Central 2017-07-03 /pmc/articles/PMC5496183/ /pubmed/28673249 http://dx.doi.org/10.1186/s12864-017-3874-4 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Luo, Xiaobo
Xu, Liang
Liang, Dongyi
Wang, Yan
Zhang, Wei
Zhu, Xianwen
Zhu, Yuelin
Jiang, Haiyan
Tang, Mingjia
Liu, Liwang
Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)
title Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)
title_full Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)
title_fullStr Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)
title_full_unstemmed Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)
title_short Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)
title_sort comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (raphanus sativus l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5496183/
https://www.ncbi.nlm.nih.gov/pubmed/28673249
http://dx.doi.org/10.1186/s12864-017-3874-4
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