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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MDPI AG
2023-10-01
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| author | Lei Du Xin Peng Hao Zhang Wangsen Xin Kejun Ma Yongzhong Liu Guangcan Hu |
| author_facet | Lei Du Xin Peng Hao Zhang Wangsen Xin Kejun Ma Yongzhong Liu Guangcan Hu |
| author_sort | Lei Du |
| collection | DOAJ |
| 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 (<i>Zm00001d031951</i>, <i>Zm00001d031953</i>) related to glutathione metabolism and one hub gene (<i>Zm00001d031617</i>) 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. |
| first_indexed | 2024-03-11T10:15:08Z |
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| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T10:15:08Z |
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| spelling | doaj.art-c678e3364b064113b8ec397acecc48d32023-11-16T10:29:47ZengMDPI AGGenes2073-44252023-10-011410191710.3390/genes14101917Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in MaizeLei Du0Xin Peng1Hao Zhang2Wangsen Xin3Kejun Ma4Yongzhong Liu5Guangcan Hu6Hubei Hongshan Laboratory, Wuhan 430070, ChinaCollege of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaCollege of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaCollege of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaCollege of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaHubei Hongshan Laboratory, Wuhan 430070, ChinaInstitute of Upland Food Crops, YiChang Academy of Agricultural Science, Yichang 443011, ChinaLow-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 (<i>Zm00001d031951</i>, <i>Zm00001d031953</i>) related to glutathione metabolism and one hub gene (<i>Zm00001d031617</i>) 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.https://www.mdpi.com/2073-4425/14/10/1917low-temperature germination abilitytranscriptome analysisWGCNAquantitative trait locusdoubled haploidcandidate gene |
| spellingShingle | Lei Du Xin Peng Hao Zhang Wangsen Xin Kejun Ma Yongzhong Liu Guangcan Hu Transcriptome Analysis and QTL Mapping Identify Candidate Genes and Regulatory Mechanisms Related to Low-Temperature Germination Ability in Maize Genes low-temperature germination ability transcriptome analysis WGCNA quantitative trait locus doubled haploid candidate gene |
| 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 | low-temperature germination ability transcriptome analysis WGCNA quantitative trait locus doubled haploid candidate gene |
| url | https://www.mdpi.com/2073-4425/14/10/1917 |
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