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Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress
BACKGROUND: Rice growth is frequently affected by salinity. When exposed to high salinity, rice seed germination and seedling establishment are significantly inhibited. With the promotion of direct-seeding in Asia, improving rice seed germination under salt stress is crucial for breeding. RESULTS: I...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7797128/ https://www.ncbi.nlm.nih.gov/pubmed/33422012 http://dx.doi.org/10.1186/s12870-020-02820-7 |
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author | Zeng, Peng Zhu, Peiwen Qian, Luofeng Qian, Xumei Mi, Yuxin Lin, Zefeng Dong, Shinan Aronsson, Henrik Zhang, Hongsheng Cheng, Jinping |
author_facet | Zeng, Peng Zhu, Peiwen Qian, Luofeng Qian, Xumei Mi, Yuxin Lin, Zefeng Dong, Shinan Aronsson, Henrik Zhang, Hongsheng Cheng, Jinping |
author_sort | Zeng, Peng |
collection | PubMed |
description | BACKGROUND: Rice growth is frequently affected by salinity. When exposed to high salinity, rice seed germination and seedling establishment are significantly inhibited. With the promotion of direct-seeding in Asia, improving rice seed germination under salt stress is crucial for breeding. RESULTS: In this study, an indica landrace Wujiaozhan (WJZ) was identified with high germinability under salt stress. A BC(1)F(2) population derived from the crossing WJZ/Nip (japonica, Nipponbare)//Nip, was used to quantitative trait loci (QTL) mapping for the seed germination rate (GR) and germination index (GI) under H(2)O and 300 mM NaCl conditions. A total of 13 QTLs were identified, i.e. ten QTLs under H(2)O conditions and nine QTLs under salt conditions. Six QTLs, qGR6.1, qGR8.1, qGR8.2, qGR10.1, qGR10.2 and qGI10.1 were simultaneously identified under two conditions. Under salt conditions, three QTLs, qGR6.2, qGR10.1 and qGR10.2 for GR were identified at different time points during seed germination, which shared the same chromosomal region with qGI6.2, qGI10.1 and qGI10.2 for GI respectively. The qGR6.2 accounted for more than 20% of phenotypic variation under salt stress, as the major effective QTL. Furthermore, qGR6.2 was verified via the BC(2)F(2) population and narrowed to a 65.9-kb region with eleven candidate genes predicted. Based on the microarray database, five candidate genes were found with high transcript abundances at the seed germination stage, of which LOC_Os06g10650 and LOC_Os06g10710 were differentially expressed after seed imbibition. RT-qPCR results showed the expression of LOC_Os06g10650 was significantly up-regulated in two parents with higher levels in WJZ than Nip during seed germination under salt conditions. Taken together, it suggests that LOC_Os06g10650, encoding tyrosine phosphatase family protein, might be the causal candidate gene for qGR6.2. CONCLUSIONS: In this study, we identified 13 QTLs from a landrace WJZ that confer seed germination traits under H(2)O and salt conditions. A major salt-tolerance-specific QTL qGR6.2 was fine mapped to a 65.9-kb region. Our results provide information on the genetic basis of improving rice seed germination under salt stress by marker-assisted selection (MAS). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-020-02820-7. |
format | Online Article Text |
id | pubmed-7797128 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-77971282021-01-11 Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress Zeng, Peng Zhu, Peiwen Qian, Luofeng Qian, Xumei Mi, Yuxin Lin, Zefeng Dong, Shinan Aronsson, Henrik Zhang, Hongsheng Cheng, Jinping BMC Plant Biol Research Article BACKGROUND: Rice growth is frequently affected by salinity. When exposed to high salinity, rice seed germination and seedling establishment are significantly inhibited. With the promotion of direct-seeding in Asia, improving rice seed germination under salt stress is crucial for breeding. RESULTS: In this study, an indica landrace Wujiaozhan (WJZ) was identified with high germinability under salt stress. A BC(1)F(2) population derived from the crossing WJZ/Nip (japonica, Nipponbare)//Nip, was used to quantitative trait loci (QTL) mapping for the seed germination rate (GR) and germination index (GI) under H(2)O and 300 mM NaCl conditions. A total of 13 QTLs were identified, i.e. ten QTLs under H(2)O conditions and nine QTLs under salt conditions. Six QTLs, qGR6.1, qGR8.1, qGR8.2, qGR10.1, qGR10.2 and qGI10.1 were simultaneously identified under two conditions. Under salt conditions, three QTLs, qGR6.2, qGR10.1 and qGR10.2 for GR were identified at different time points during seed germination, which shared the same chromosomal region with qGI6.2, qGI10.1 and qGI10.2 for GI respectively. The qGR6.2 accounted for more than 20% of phenotypic variation under salt stress, as the major effective QTL. Furthermore, qGR6.2 was verified via the BC(2)F(2) population and narrowed to a 65.9-kb region with eleven candidate genes predicted. Based on the microarray database, five candidate genes were found with high transcript abundances at the seed germination stage, of which LOC_Os06g10650 and LOC_Os06g10710 were differentially expressed after seed imbibition. RT-qPCR results showed the expression of LOC_Os06g10650 was significantly up-regulated in two parents with higher levels in WJZ than Nip during seed germination under salt conditions. Taken together, it suggests that LOC_Os06g10650, encoding tyrosine phosphatase family protein, might be the causal candidate gene for qGR6.2. CONCLUSIONS: In this study, we identified 13 QTLs from a landrace WJZ that confer seed germination traits under H(2)O and salt conditions. A major salt-tolerance-specific QTL qGR6.2 was fine mapped to a 65.9-kb region. Our results provide information on the genetic basis of improving rice seed germination under salt stress by marker-assisted selection (MAS). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-020-02820-7. BioMed Central 2021-01-09 /pmc/articles/PMC7797128/ /pubmed/33422012 http://dx.doi.org/10.1186/s12870-020-02820-7 Text en © The Author(s) 2021 Open AccessThis 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/. 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 in a credit line to the data. |
spellingShingle | Research Article Zeng, Peng Zhu, Peiwen Qian, Luofeng Qian, Xumei Mi, Yuxin Lin, Zefeng Dong, Shinan Aronsson, Henrik Zhang, Hongsheng Cheng, Jinping Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress |
title | Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress |
title_full | Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress |
title_fullStr | Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress |
title_full_unstemmed | Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress |
title_short | Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress |
title_sort | identification and fine mapping of qgr6.2, a novel locus controlling rice seed germination under salt stress |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7797128/ https://www.ncbi.nlm.nih.gov/pubmed/33422012 http://dx.doi.org/10.1186/s12870-020-02820-7 |
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