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Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in Maize

Low-temperature germination ability (LTGA) is an important characteristic for spring sowing maize. However, few maize genes related to LTGA were confirmed, and the regulatory mechanism is less clear. Here, maize-inbred lines Ye478 and Q1 with different LTGA were used to perform transcriptome analysi...

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Autores principales: Du, Lei, Peng, Xin, Zhang, Hao, Xin, Wangsen, Ma, Kejun, Liu, Yongzhong, Hu, Guangcan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10606144/
https://www.ncbi.nlm.nih.gov/pubmed/37895266
http://dx.doi.org/10.3390/genes14101917
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author Du, Lei
Peng, Xin
Zhang, Hao
Xin, Wangsen
Ma, Kejun
Liu, Yongzhong
Hu, Guangcan
author_facet Du, Lei
Peng, Xin
Zhang, Hao
Xin, Wangsen
Ma, Kejun
Liu, Yongzhong
Hu, Guangcan
author_sort Du, Lei
collection PubMed
description Low-temperature germination ability (LTGA) is an important characteristic for spring sowing maize. However, few maize genes related to LTGA were confirmed, and the regulatory mechanism is less clear. Here, maize-inbred lines Ye478 and Q1 with different LTGA were used to perform transcriptome analysis at multiple low-temperature germination stages, and a co-expression network was constructed by weighted gene co-expression network analysis (WGCNA). Data analysis showed that 7964 up- and 5010 down-regulated differentially expressed genes (DEGs) of Ye478 were identified at low-temperature germination stages, while 6060 up- and 2653 down-regulated DEGs of Q1 were identified. Gene ontology (GO) enrichment analysis revealed that ribosome synthesis and hydrogen peroxide metabolism were enhanced and mRNA metabolism was weakened under low-temperature stress for Ye478, while hydrogen peroxide metabolism was enhanced and mRNA metabolism was weakened for Q1. DEGs pairwise comparisons between the two genotypes found that Ye478 performed more ribosome synthesis at low temperatures compared with Q1. WGCNA analysis based on 24 transcriptomes identified 16 co-expressed modules. Of these, the MEbrown module was highly correlated with Ye478 at low-temperature stages and catalase and superoxide dismutase activity, and the MEred, MEgreen, and MEblack modules were highly correlated with Ye478 across low-temperature stages, which revealed a significant association between LTGA and these modules. GO enrichment analysis showed the MEbrown and MEred modules mainly functioned in ribosome synthesis and cell cycle, respectively. In addition, we conducted quantitative trait loci (QTL) analysis based on a doubled haploid (DH) population constructed by Ye478 and Q1 and identified a major QTL explanting 20.6% of phenotype variance on chromosome 1. In this QTL interval, we found three, four, and three hub genes in the MEbrown, MEred, and MEgreen modules, of which two hub genes (Zm00001d031951, Zm00001d031953) related to glutathione metabolism and one hub gene (Zm00001d031617) related to oxidoreductase activity could be the candidate genes for LTGA. These biological functions and candidate genes will be helpful in understanding the regulatory mechanism of LTGA and the directional improvement of maize varieties for LTGA.
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spelling pubmed-106061442023-10-28 Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in Maize Du, Lei Peng, Xin Zhang, Hao Xin, Wangsen Ma, Kejun Liu, Yongzhong Hu, Guangcan Genes (Basel) Article Low-temperature germination ability (LTGA) is an important characteristic for spring sowing maize. However, few maize genes related to LTGA were confirmed, and the regulatory mechanism is less clear. Here, maize-inbred lines Ye478 and Q1 with different LTGA were used to perform transcriptome analysis at multiple low-temperature germination stages, and a co-expression network was constructed by weighted gene co-expression network analysis (WGCNA). Data analysis showed that 7964 up- and 5010 down-regulated differentially expressed genes (DEGs) of Ye478 were identified at low-temperature germination stages, while 6060 up- and 2653 down-regulated DEGs of Q1 were identified. Gene ontology (GO) enrichment analysis revealed that ribosome synthesis and hydrogen peroxide metabolism were enhanced and mRNA metabolism was weakened under low-temperature stress for Ye478, while hydrogen peroxide metabolism was enhanced and mRNA metabolism was weakened for Q1. DEGs pairwise comparisons between the two genotypes found that Ye478 performed more ribosome synthesis at low temperatures compared with Q1. WGCNA analysis based on 24 transcriptomes identified 16 co-expressed modules. Of these, the MEbrown module was highly correlated with Ye478 at low-temperature stages and catalase and superoxide dismutase activity, and the MEred, MEgreen, and MEblack modules were highly correlated with Ye478 across low-temperature stages, which revealed a significant association between LTGA and these modules. GO enrichment analysis showed the MEbrown and MEred modules mainly functioned in ribosome synthesis and cell cycle, respectively. In addition, we conducted quantitative trait loci (QTL) analysis based on a doubled haploid (DH) population constructed by Ye478 and Q1 and identified a major QTL explanting 20.6% of phenotype variance on chromosome 1. In this QTL interval, we found three, four, and three hub genes in the MEbrown, MEred, and MEgreen modules, of which two hub genes (Zm00001d031951, Zm00001d031953) related to glutathione metabolism and one hub gene (Zm00001d031617) related to oxidoreductase activity could be the candidate genes for LTGA. These biological functions and candidate genes will be helpful in understanding the regulatory mechanism of LTGA and the directional improvement of maize varieties for LTGA. MDPI 2023-10-08 /pmc/articles/PMC10606144/ /pubmed/37895266 http://dx.doi.org/10.3390/genes14101917 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Du, Lei
Peng, Xin
Zhang, Hao
Xin, Wangsen
Ma, Kejun
Liu, Yongzhong
Hu, Guangcan
Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in Maize
title Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in Maize
title_full Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in Maize
title_fullStr Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in Maize
title_full_unstemmed Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in Maize
title_short Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in Maize
title_sort transcriptome analysis and qtl mapping identify candidate genes and regulatory mechanisms related to low-temperature germination ability in maize
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10606144/
https://www.ncbi.nlm.nih.gov/pubmed/37895266
http://dx.doi.org/10.3390/genes14101917
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