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Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq
BACKGROUND: Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties. RESULTS: In this study, a recombinant inbred line (RIL) population derived from a cross bet...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506967/ https://www.ncbi.nlm.nih.gov/pubmed/31072298 http://dx.doi.org/10.1186/s12864-019-5741-y |
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author | Yang, Jing Sun, Kai Li, Dongxiu Luo, Lixin Liu, Yongzhu Huang, Ming Yang, Guili Liu, Hong Wang, Hui Chen, Zhiqiang Guo, Tao |
author_facet | Yang, Jing Sun, Kai Li, Dongxiu Luo, Lixin Liu, Yongzhu Huang, Ming Yang, Guili Liu, Hong Wang, Hui Chen, Zhiqiang Guo, Tao |
author_sort | Yang, Jing |
collection | PubMed |
description | BACKGROUND: Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties. RESULTS: In this study, a recombinant inbred line (RIL) population derived from a cross between YZX and 02428 exhibited obvious coleoptile phenotypic differences. Mapping analysis using a high-density bin map indicated that a total of 25 loci were detected across two cropping seasons, including 10 previously detected loci and a total of 13 stable loci. Analysis of the 13 stable loci demonstrated that the more elite alleles that were pyramided in an individual, the higher the values of these traits were in the two cropping seasons. Furthermore, some anaerobic germination-tolerant recombinant inbred lines, namely G9, G10, G16, and G151, were identified. A total of 84 differentially expressed genes were obtained from the 13 stable loci via genome-wide expression analysis of the two parents at three key periods. Among them, Os06g0110200, Os07g0638300, Os07g0638400, Os09g0532900, Os09g0531701 and Os12g0539751 constitute the best candidates associated with anaerobic germination. CONCLUSIONS: Both the anaerobic germination-tolerant recombinant inbred lines and the loci identified in this study will provide new genetic resources for improving the anaerobic germination tolerance of rice using molecular breeding strategies, as well as will broaden our understanding of the genetic control of germination tolerance under anaerobic conditions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5741-y) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6506967 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65069672019-05-13 Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq Yang, Jing Sun, Kai Li, Dongxiu Luo, Lixin Liu, Yongzhu Huang, Ming Yang, Guili Liu, Hong Wang, Hui Chen, Zhiqiang Guo, Tao BMC Genomics Research Article BACKGROUND: Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties. RESULTS: In this study, a recombinant inbred line (RIL) population derived from a cross between YZX and 02428 exhibited obvious coleoptile phenotypic differences. Mapping analysis using a high-density bin map indicated that a total of 25 loci were detected across two cropping seasons, including 10 previously detected loci and a total of 13 stable loci. Analysis of the 13 stable loci demonstrated that the more elite alleles that were pyramided in an individual, the higher the values of these traits were in the two cropping seasons. Furthermore, some anaerobic germination-tolerant recombinant inbred lines, namely G9, G10, G16, and G151, were identified. A total of 84 differentially expressed genes were obtained from the 13 stable loci via genome-wide expression analysis of the two parents at three key periods. Among them, Os06g0110200, Os07g0638300, Os07g0638400, Os09g0532900, Os09g0531701 and Os12g0539751 constitute the best candidates associated with anaerobic germination. CONCLUSIONS: Both the anaerobic germination-tolerant recombinant inbred lines and the loci identified in this study will provide new genetic resources for improving the anaerobic germination tolerance of rice using molecular breeding strategies, as well as will broaden our understanding of the genetic control of germination tolerance under anaerobic conditions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5741-y) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-09 /pmc/articles/PMC6506967/ /pubmed/31072298 http://dx.doi.org/10.1186/s12864-019-5741-y Text en © The Author(s). 2019 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 Yang, Jing Sun, Kai Li, Dongxiu Luo, Lixin Liu, Yongzhu Huang, Ming Yang, Guili Liu, Hong Wang, Hui Chen, Zhiqiang Guo, Tao Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq |
title | Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq |
title_full | Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq |
title_fullStr | Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq |
title_full_unstemmed | Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq |
title_short | Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq |
title_sort | identification of stable qtls and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and rna-seq |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506967/ https://www.ncbi.nlm.nih.gov/pubmed/31072298 http://dx.doi.org/10.1186/s12864-019-5741-y |
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