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Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

Low-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment su...

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Autores principales: Pan, Zhaoyuan, Tan, Bin, Cao, Guiyuan, Zheng, Rongqi, Liu, Meng, Zeng, Ruizhen, Wang, Shaokui, Zhu, Haitao, Ye, Heng, Zhao, Guangmiao, Cao, Wei, Liu, Guifu, Zhang, Guiquan, Zhou, Yuliang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8674402/
https://www.ncbi.nlm.nih.gov/pubmed/34910270
http://dx.doi.org/10.1186/s12284-021-00544-2
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author Pan, Zhaoyuan
Tan, Bin
Cao, Guiyuan
Zheng, Rongqi
Liu, Meng
Zeng, Ruizhen
Wang, Shaokui
Zhu, Haitao
Ye, Heng
Zhao, Guangmiao
Cao, Wei
Liu, Guifu
Zhang, Guiquan
Zhou, Yuliang
author_facet Pan, Zhaoyuan
Tan, Bin
Cao, Guiyuan
Zheng, Rongqi
Liu, Meng
Zeng, Ruizhen
Wang, Shaokui
Zhu, Haitao
Ye, Heng
Zhao, Guangmiao
Cao, Wei
Liu, Guifu
Zhang, Guiquan
Zhou, Yuliang
author_sort Pan, Zhaoyuan
collection PubMed
description Low-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment substitution lines (SSSLs) was used to conduct a genetic dissection for LTG across four cropping seasons. LTG was a typical quantitative trait with a high combined broad-sense heritability of 0.71. By comparison with the recipient parent, Huajingxian74, 24 SSSLs were identified as carrying LTG QTLs, which were further merged into integrated QTLs with shorter genetic distances by substitution mapping. Finally, 14 LTG QTLs were mapped on ten chromosomes, including seven positive-effect and seven negative-effect QTLs, with additive effect contributions ranging from 19.2 to 39.9%. qLTG3a, a main-effect and novel QTL, was confirmed by bulk segregant analysis using an F(2) segregating population, and five key recombinants were selected to develop F(3) populations for progeny testing. Marker-trait association analysis fine mapped qLTG3a to a 332.7-kb physical region between markers M6026 and M6341. Within this interval, 40 annotated genes were revealed, and three genes (Os03g0213300, Os03g0214400, and Os03g0214600) were considered as pivotal candidate genes for qLTG3a based on their sequence variations and expression patterns. Besides low temperature, qLTG3a can also enhance seed germination under standard temperature and osmotic stress. In summary, this study identified some genetic factors regulating LTG and opened a new window for breeding elite direct-seeded rice varieties. It will help reduce the climate risk in the production process of rice, which is of great significance to ensuring food security. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12284-021-00544-2.
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spelling pubmed-86744022021-12-17 Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice Pan, Zhaoyuan Tan, Bin Cao, Guiyuan Zheng, Rongqi Liu, Meng Zeng, Ruizhen Wang, Shaokui Zhu, Haitao Ye, Heng Zhao, Guangmiao Cao, Wei Liu, Guifu Zhang, Guiquan Zhou, Yuliang Rice (N Y) Original Article Low-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment substitution lines (SSSLs) was used to conduct a genetic dissection for LTG across four cropping seasons. LTG was a typical quantitative trait with a high combined broad-sense heritability of 0.71. By comparison with the recipient parent, Huajingxian74, 24 SSSLs were identified as carrying LTG QTLs, which were further merged into integrated QTLs with shorter genetic distances by substitution mapping. Finally, 14 LTG QTLs were mapped on ten chromosomes, including seven positive-effect and seven negative-effect QTLs, with additive effect contributions ranging from 19.2 to 39.9%. qLTG3a, a main-effect and novel QTL, was confirmed by bulk segregant analysis using an F(2) segregating population, and five key recombinants were selected to develop F(3) populations for progeny testing. Marker-trait association analysis fine mapped qLTG3a to a 332.7-kb physical region between markers M6026 and M6341. Within this interval, 40 annotated genes were revealed, and three genes (Os03g0213300, Os03g0214400, and Os03g0214600) were considered as pivotal candidate genes for qLTG3a based on their sequence variations and expression patterns. Besides low temperature, qLTG3a can also enhance seed germination under standard temperature and osmotic stress. In summary, this study identified some genetic factors regulating LTG and opened a new window for breeding elite direct-seeded rice varieties. It will help reduce the climate risk in the production process of rice, which is of great significance to ensuring food security. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12284-021-00544-2. Springer US 2021-12-15 /pmc/articles/PMC8674402/ /pubmed/34910270 http://dx.doi.org/10.1186/s12284-021-00544-2 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Original Article
Pan, Zhaoyuan
Tan, Bin
Cao, Guiyuan
Zheng, Rongqi
Liu, Meng
Zeng, Ruizhen
Wang, Shaokui
Zhu, Haitao
Ye, Heng
Zhao, Guangmiao
Cao, Wei
Liu, Guifu
Zhang, Guiquan
Zhou, Yuliang
Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice
title Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice
title_full Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice
title_fullStr Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice
title_full_unstemmed Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice
title_short Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice
title_sort integrative qtl identification, fine mapping and candidate gene analysis of a major locus qltg3a for seed low-temperature germinability in rice
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8674402/
https://www.ncbi.nlm.nih.gov/pubmed/34910270
http://dx.doi.org/10.1186/s12284-021-00544-2
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