Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in Soybean
Ammonium transporters (AMTs) are responsible for ammonium absorption and utilization in plants. As a high-nitrogen-demand crop and a legume, soybean can also obtain ammonium from symbiotic root nodules in which nitrogen-fixing rhizobia convert atmospheric nitrogen (N<sub>2</sub>) into am...
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MDPI AG
2023-02-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/4/3991 |
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| author | Wei Yang Xiaoxu Dong Zhanxin Yuan Yan Zhang Xia Li Youning Wang |
| author_facet | Wei Yang Xiaoxu Dong Zhanxin Yuan Yan Zhang Xia Li Youning Wang |
| author_sort | Wei Yang |
| collection | DOAJ |
| description | Ammonium transporters (AMTs) are responsible for ammonium absorption and utilization in plants. As a high-nitrogen-demand crop and a legume, soybean can also obtain ammonium from symbiotic root nodules in which nitrogen-fixing rhizobia convert atmospheric nitrogen (N<sub>2</sub>) into ammonium. Although increasing evidence implicates vital roles of ammonium transport in soybean, no systematic analyses of AMTs in soybean (named GmAMTs) or functional analyses of GmAMTs are available. In this study, we aimed to identify all GmAMT family genes and gain a better understanding of the characteristics of <i>GmAMT</i> genes in soybean. Here, due to the improved genome assembly and annotation of soybean, we tried to generate a phylogenetic tree of 16 <i>GmAMTs</i> based on new information. Consistent with reported data, GmAMT family members can be divided into two subfamilies of <i>GmAMT1</i> (6 genes) and <i>GmAMT2</i> (10 genes). Interestingly, unlike <i>Arabidopsis</i>, which has only one <i>AMT2</i>, soybean has substantially increased the number of <i>GmAMT2s</i>, suggesting enhanced demand for ammonium transport. These genes were distributed on nine chromosomes, of which <i>GmAMT1.3, GmAMT1.4</i>, and <i>GmAMT1.5</i> were three tandem repeat genes. The gene structures and conserved protein motifs of the GmAMT1 and GmAMT2 subfamilies were different. All the GmAMTs were membrane proteins with varying numbers of transmembrane domains ranging from 4 to 11. Promoter analysis found that these <i>GmAMT</i> genes have phytohormone-, circadian control-, and organ expression-related <i>cis</i>-elements in their promoters, and notably, there were nodulation-specific and nitrogen-responsive elements in the promoters of the <i>GmAMT1</i> and <i>GmAMT2</i> genes. Further expression data showed that these GmAMT family genes exhibited different spatiotemporal expression patterns across tissues and organs. In addition, <i>GmAMT1.1, GmAMT1.2, GmAMT2.2</i>, and <i>GmAMT2.3</i> were responsive to nitrogen treatment, while <i>GmAMT1.2</i>, <i>GmAMT1.3</i>, <i>GmAMT1.4</i>, <i>GmAMT1.5</i>, <i>GmAMT1.6</i>, <i>GmAMT2.1</i>, <i>GmAMT2.2</i>, <i>GmAMT2.3</i>, <i>GmAMT3.1</i>, and <i>GmAMT4.6</i> showed circadian rhythms in transcription. RT-qPCR validated the expression patterns of <i>GmAMTs</i> in response to different forms of nitrogen and exogenous ABA treatments. Gene expression analysis also confirmed that <i>GmAMTs</i> are regulated by key nodulation gene <i>GmNINa</i>, indicating a role of <i>GmAMTs</i> in symbiosis. Together, these data indicate that GmAMTs may differentially and/or redundantly regulate ammonium transport during plant development and in response to environmental factors. These findings provide a basis for future research on the functions of GmAMTs and the mechanisms through which GmAMTs regulate ammonium metabolism and nodulation in soybean. |
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| language | English |
| last_indexed | 2024-03-11T08:42:10Z |
| publishDate | 2023-02-01 |
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| spelling | doaj.art-ae4dfaab50304a86b408a191b0d19e462023-11-16T21:07:56ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-02-01244399110.3390/ijms24043991Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in SoybeanWei Yang0Xiaoxu Dong1Zhanxin Yuan2Yan Zhang3Xia Li4Youning Wang5National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, ChinaAmmonium transporters (AMTs) are responsible for ammonium absorption and utilization in plants. As a high-nitrogen-demand crop and a legume, soybean can also obtain ammonium from symbiotic root nodules in which nitrogen-fixing rhizobia convert atmospheric nitrogen (N<sub>2</sub>) into ammonium. Although increasing evidence implicates vital roles of ammonium transport in soybean, no systematic analyses of AMTs in soybean (named GmAMTs) or functional analyses of GmAMTs are available. In this study, we aimed to identify all GmAMT family genes and gain a better understanding of the characteristics of <i>GmAMT</i> genes in soybean. Here, due to the improved genome assembly and annotation of soybean, we tried to generate a phylogenetic tree of 16 <i>GmAMTs</i> based on new information. Consistent with reported data, GmAMT family members can be divided into two subfamilies of <i>GmAMT1</i> (6 genes) and <i>GmAMT2</i> (10 genes). Interestingly, unlike <i>Arabidopsis</i>, which has only one <i>AMT2</i>, soybean has substantially increased the number of <i>GmAMT2s</i>, suggesting enhanced demand for ammonium transport. These genes were distributed on nine chromosomes, of which <i>GmAMT1.3, GmAMT1.4</i>, and <i>GmAMT1.5</i> were three tandem repeat genes. The gene structures and conserved protein motifs of the GmAMT1 and GmAMT2 subfamilies were different. All the GmAMTs were membrane proteins with varying numbers of transmembrane domains ranging from 4 to 11. Promoter analysis found that these <i>GmAMT</i> genes have phytohormone-, circadian control-, and organ expression-related <i>cis</i>-elements in their promoters, and notably, there were nodulation-specific and nitrogen-responsive elements in the promoters of the <i>GmAMT1</i> and <i>GmAMT2</i> genes. Further expression data showed that these GmAMT family genes exhibited different spatiotemporal expression patterns across tissues and organs. In addition, <i>GmAMT1.1, GmAMT1.2, GmAMT2.2</i>, and <i>GmAMT2.3</i> were responsive to nitrogen treatment, while <i>GmAMT1.2</i>, <i>GmAMT1.3</i>, <i>GmAMT1.4</i>, <i>GmAMT1.5</i>, <i>GmAMT1.6</i>, <i>GmAMT2.1</i>, <i>GmAMT2.2</i>, <i>GmAMT2.3</i>, <i>GmAMT3.1</i>, and <i>GmAMT4.6</i> showed circadian rhythms in transcription. RT-qPCR validated the expression patterns of <i>GmAMTs</i> in response to different forms of nitrogen and exogenous ABA treatments. Gene expression analysis also confirmed that <i>GmAMTs</i> are regulated by key nodulation gene <i>GmNINa</i>, indicating a role of <i>GmAMTs</i> in symbiosis. Together, these data indicate that GmAMTs may differentially and/or redundantly regulate ammonium transport during plant development and in response to environmental factors. These findings provide a basis for future research on the functions of GmAMTs and the mechanisms through which GmAMTs regulate ammonium metabolism and nodulation in soybean.https://www.mdpi.com/1422-0067/24/4/3991soybeannitrogenammonium transporter (AMT)gene expression |
| spellingShingle | Wei Yang Xiaoxu Dong Zhanxin Yuan Yan Zhang Xia Li Youning Wang Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in Soybean International Journal of Molecular Sciences soybean nitrogen ammonium transporter (AMT) gene expression |
| title | Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in Soybean |
| title_full | Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in Soybean |
| title_fullStr | Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in Soybean |
| title_full_unstemmed | Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in Soybean |
| title_short | Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in Soybean |
| title_sort | genome wide identification and expression analysis of the ammonium transporter family genes in soybean |
| topic | soybean nitrogen ammonium transporter (AMT) gene expression |
| url | https://www.mdpi.com/1422-0067/24/4/3991 |
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