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Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seqapproaches
BACKGROUND: Maize (Zea mays L.) is one of the main agricultural crops with the largest yield and acreage in the world. However, maize germplasm is very sensitive to low temperatures, mainly during germination, and low temperatures significantly affect plant growth and crop yield. Therefore, the iden...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362524/ https://www.ncbi.nlm.nih.gov/pubmed/32664856 http://dx.doi.org/10.1186/s12870-020-02543-9 |
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author | Zhang, Hong Zhang, Jiayue Xu, Qingyu Wang, Dandan Di, Hong Huang, Jun Yang, Xiuwei Wang, Zhoufei Zhang, Lin Dong, Ling Wang, Zhenhua Zhou, Yu |
author_facet | Zhang, Hong Zhang, Jiayue Xu, Qingyu Wang, Dandan Di, Hong Huang, Jun Yang, Xiuwei Wang, Zhoufei Zhang, Lin Dong, Ling Wang, Zhenhua Zhou, Yu |
author_sort | Zhang, Hong |
collection | PubMed |
description | BACKGROUND: Maize (Zea mays L.) is one of the main agricultural crops with the largest yield and acreage in the world. However, maize germplasm is very sensitive to low temperatures, mainly during germination, and low temperatures significantly affect plant growth and crop yield. Therefore, the identification of genes capable of increasing tolerance to low temperature has become necessary. RESULTS: In this study, fourteen phenotypic traits related to seed germination were used to assess the genetic diversity of maize through genome-wide association study (GWAS). A total of 30 single-nucleotide polymorphisms (SNPs) linked to low-temperature tolerance were detected (−log10(P) > 4), fourteen candidate genes were found to be directly related to the SNPs, further additional 68 genes were identified when the screen was extended to include a linkage disequilibrium (LD) decay distance of r(2) ≥ 0.2 from the SNPs. RNA-sequencing (RNA-seq) analysis was then used to confirm the linkage between the candidate gene and low-temperature tolerance. A total of ten differentially expressed genes (DEGs) (|log(2) fold change (FC)| ≥ 0.585, P < 0.05) were found within the set distance of LD decay (r(2) ≥ 0.2). Among these genes, the expression of six DEGs was verified using qRT-PCR. Zm00001d039219 and Zm00001d034319 were putatively involved in ‘mitogen activated protein kinase (MAPK) signal transduction’ and ‘fatty acid metabolic process’, respectively, based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Thus, these genes appeared to be related to low-temperature signal transduction and cell membrane fluidity. CONCLUSION: Overall, by integrating the results of our GWAS and DEG analysis of low-temperature tolerance during germination in maize, we were able to identify a total of 30 SNPs and 82 related candidate genes, including 10 DEGs, two of which were involved in the response to tolerance to low temperature. Functional analysis will provide valuable information for understanding the genetic mechanism of low-temperature tolerance during germination in maize. |
format | Online Article Text |
id | pubmed-7362524 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-73625242020-07-17 Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seqapproaches Zhang, Hong Zhang, Jiayue Xu, Qingyu Wang, Dandan Di, Hong Huang, Jun Yang, Xiuwei Wang, Zhoufei Zhang, Lin Dong, Ling Wang, Zhenhua Zhou, Yu BMC Plant Biol Research Article BACKGROUND: Maize (Zea mays L.) is one of the main agricultural crops with the largest yield and acreage in the world. However, maize germplasm is very sensitive to low temperatures, mainly during germination, and low temperatures significantly affect plant growth and crop yield. Therefore, the identification of genes capable of increasing tolerance to low temperature has become necessary. RESULTS: In this study, fourteen phenotypic traits related to seed germination were used to assess the genetic diversity of maize through genome-wide association study (GWAS). A total of 30 single-nucleotide polymorphisms (SNPs) linked to low-temperature tolerance were detected (−log10(P) > 4), fourteen candidate genes were found to be directly related to the SNPs, further additional 68 genes were identified when the screen was extended to include a linkage disequilibrium (LD) decay distance of r(2) ≥ 0.2 from the SNPs. RNA-sequencing (RNA-seq) analysis was then used to confirm the linkage between the candidate gene and low-temperature tolerance. A total of ten differentially expressed genes (DEGs) (|log(2) fold change (FC)| ≥ 0.585, P < 0.05) were found within the set distance of LD decay (r(2) ≥ 0.2). Among these genes, the expression of six DEGs was verified using qRT-PCR. Zm00001d039219 and Zm00001d034319 were putatively involved in ‘mitogen activated protein kinase (MAPK) signal transduction’ and ‘fatty acid metabolic process’, respectively, based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Thus, these genes appeared to be related to low-temperature signal transduction and cell membrane fluidity. CONCLUSION: Overall, by integrating the results of our GWAS and DEG analysis of low-temperature tolerance during germination in maize, we were able to identify a total of 30 SNPs and 82 related candidate genes, including 10 DEGs, two of which were involved in the response to tolerance to low temperature. Functional analysis will provide valuable information for understanding the genetic mechanism of low-temperature tolerance during germination in maize. BioMed Central 2020-07-14 /pmc/articles/PMC7362524/ /pubmed/32664856 http://dx.doi.org/10.1186/s12870-020-02543-9 Text en © The Author(s) 2020 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 Zhang, Hong Zhang, Jiayue Xu, Qingyu Wang, Dandan Di, Hong Huang, Jun Yang, Xiuwei Wang, Zhoufei Zhang, Lin Dong, Ling Wang, Zhenhua Zhou, Yu Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seqapproaches |
title | Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seqapproaches |
title_full | Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seqapproaches |
title_fullStr | Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seqapproaches |
title_full_unstemmed | Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seqapproaches |
title_short | Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seqapproaches |
title_sort | identification of candidate tolerance genes to low-temperature during maize germination by gwas and rna-seqapproaches |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362524/ https://www.ncbi.nlm.nih.gov/pubmed/32664856 http://dx.doi.org/10.1186/s12870-020-02543-9 |
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