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Re-sequencing and genetic variation identification of a rice line with ideal plant architecture
BACKGROUND: The ideal plant architecture (IPA) includes several important characteristics such as low tiller numbers, few or no unproductive tillers, more grains per panicle, and thick and sturdy stems. We have developed an indica restorer line 7302R that displays the IPA phenotype in terms of tille...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer New York
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5520836/ https://www.ncbi.nlm.nih.gov/pubmed/27234240 http://dx.doi.org/10.1186/1939-8433-5-18 |
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author | Li, Shuangcheng Xie, Kailong Li, Wenbo Zou, Ting Ren, Yun Wang, Shiquan Deng, Qiming Zheng, Aiping Zhu, Jun Liu, Huainian Wang, Lingxia Ai, Peng Gao, Fengyan Huang, Bin Cao, Xuemei Li, Ping |
author_facet | Li, Shuangcheng Xie, Kailong Li, Wenbo Zou, Ting Ren, Yun Wang, Shiquan Deng, Qiming Zheng, Aiping Zhu, Jun Liu, Huainian Wang, Lingxia Ai, Peng Gao, Fengyan Huang, Bin Cao, Xuemei Li, Ping |
author_sort | Li, Shuangcheng |
collection | PubMed |
description | BACKGROUND: The ideal plant architecture (IPA) includes several important characteristics such as low tiller numbers, few or no unproductive tillers, more grains per panicle, and thick and sturdy stems. We have developed an indica restorer line 7302R that displays the IPA phenotype in terms of tiller number, grain number, and stem strength. However, its mechanism had to be clarified. FINDINGS: We performed re-sequencing and genome-wide variation analysis of 7302R using the Solexa sequencing technology. With the genomic sequence of the indica cultivar 9311 as reference, 307 627 SNPs, 57 372 InDels, and 3 096 SVs were identified in the 7302R genome. The 7302R-specific variations were investigated via the synteny analysis of all the SNPs of 7302R with those of the previous sequenced none-IPA-type lines IR24, MH63, and SH527. Moreover, we found 178 168 7302R-specific SNPs across the whole genome and 30 239 SNPs in the predicted mRNA regions, among which 8 517 were Non-syn CDS. In addition, 263 large-effect SNPs that were expected to affect the integrity of encoded proteins were identified from the 7302R-specific SNPs. SNPs of several important previously cloned rice genes were also identified by aligning the 7302R sequence with other sequence lines. CONCLUSIONS: Our results provided several candidates account for the IPA phenotype of 7302R. These results therefore lay the groundwork for long-term efforts to uncover important genes and alleles for rice plant architecture construction, also offer useful data resources for future genetic and genomic studies in rice. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1939-8433-5-18) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5520836 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Springer New York |
record_format | MEDLINE/PubMed |
spelling | pubmed-55208362017-07-27 Re-sequencing and genetic variation identification of a rice line with ideal plant architecture Li, Shuangcheng Xie, Kailong Li, Wenbo Zou, Ting Ren, Yun Wang, Shiquan Deng, Qiming Zheng, Aiping Zhu, Jun Liu, Huainian Wang, Lingxia Ai, Peng Gao, Fengyan Huang, Bin Cao, Xuemei Li, Ping Rice (N Y) Short Report BACKGROUND: The ideal plant architecture (IPA) includes several important characteristics such as low tiller numbers, few or no unproductive tillers, more grains per panicle, and thick and sturdy stems. We have developed an indica restorer line 7302R that displays the IPA phenotype in terms of tiller number, grain number, and stem strength. However, its mechanism had to be clarified. FINDINGS: We performed re-sequencing and genome-wide variation analysis of 7302R using the Solexa sequencing technology. With the genomic sequence of the indica cultivar 9311 as reference, 307 627 SNPs, 57 372 InDels, and 3 096 SVs were identified in the 7302R genome. The 7302R-specific variations were investigated via the synteny analysis of all the SNPs of 7302R with those of the previous sequenced none-IPA-type lines IR24, MH63, and SH527. Moreover, we found 178 168 7302R-specific SNPs across the whole genome and 30 239 SNPs in the predicted mRNA regions, among which 8 517 were Non-syn CDS. In addition, 263 large-effect SNPs that were expected to affect the integrity of encoded proteins were identified from the 7302R-specific SNPs. SNPs of several important previously cloned rice genes were also identified by aligning the 7302R sequence with other sequence lines. CONCLUSIONS: Our results provided several candidates account for the IPA phenotype of 7302R. These results therefore lay the groundwork for long-term efforts to uncover important genes and alleles for rice plant architecture construction, also offer useful data resources for future genetic and genomic studies in rice. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1939-8433-5-18) contains supplementary material, which is available to authorized users. Springer New York 2012-07-24 /pmc/articles/PMC5520836/ /pubmed/27234240 http://dx.doi.org/10.1186/1939-8433-5-18 Text en © Li et al.; licensee Springer. 2012 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Short Report Li, Shuangcheng Xie, Kailong Li, Wenbo Zou, Ting Ren, Yun Wang, Shiquan Deng, Qiming Zheng, Aiping Zhu, Jun Liu, Huainian Wang, Lingxia Ai, Peng Gao, Fengyan Huang, Bin Cao, Xuemei Li, Ping Re-sequencing and genetic variation identification of a rice line with ideal plant architecture |
title | Re-sequencing and genetic variation identification of a rice line with ideal plant architecture |
title_full | Re-sequencing and genetic variation identification of a rice line with ideal plant architecture |
title_fullStr | Re-sequencing and genetic variation identification of a rice line with ideal plant architecture |
title_full_unstemmed | Re-sequencing and genetic variation identification of a rice line with ideal plant architecture |
title_short | Re-sequencing and genetic variation identification of a rice line with ideal plant architecture |
title_sort | re-sequencing and genetic variation identification of a rice line with ideal plant architecture |
topic | Short Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5520836/ https://www.ncbi.nlm.nih.gov/pubmed/27234240 http://dx.doi.org/10.1186/1939-8433-5-18 |
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