Transcriptome Analysis of Hybrid Progeny of Caucasian Clover and White Clover in the Early Stages of Rhizobia Infection
The hybrid progeny (1-1) resulting from the cross between Caucasian clover and white clover initially demonstrated an inability to fix nitrogen naturally via spontaneous nodulation. However, following inoculation with specific rhizobia strains derived from the Trifolium genus, successful nodulation...
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MDPI AG
2025-02-01
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| Series: | Nitrogen |
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| author | Peizhi Zhu Sijing Wang Kefan Cao |
| author_facet | Peizhi Zhu Sijing Wang Kefan Cao |
| author_sort | Peizhi Zhu |
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| description | The hybrid progeny (1-1) resulting from the cross between Caucasian clover and white clover initially demonstrated an inability to fix nitrogen naturally via spontaneous nodulation. However, following inoculation with specific rhizobia strains derived from the Trifolium genus, successful nodulation and nitrogen fixation were observed in the 1-1 progeny, resulting in enhanced biomass production and adaptability. To explore in greater depth the mechanisms driving nitrogen fixation in these hybrid progeny, the inoculation was carried out using the dominant rhizobia strain (No. 5), isolated from Mengnong Clover No. 1. Root samples were collected at 3, 6, and 9 days post inoculation for RNA sequencing. A total of 1755 differentially expressed unigenes were identified between the control and treatment groups. KEGG pathway analysis highlighted key pathways associated with nodule nitrogen fixation. In combination with Weighted Gene Co-expression Network Analysis (WGCNA) and Gene Set Enrichment Analysis (GSEA), several differentially expressed genes were identified, suggesting their potential contribution to nitrogen fixation. Noteworthy among these, the gene <i>TRINITY_DN7551_c0_g1</i> in the Phenylpropanoid biosynthesis pathway (MAP00940) emerged as a key candidate. This study offers valuable RNA-seq data, contributing significantly to the understanding of the molecular regulatory mechanisms underpinning nodule nitrogen fixation in legumes, thereby laying a solid foundation for future investigations into the hybrid progeny of Caucasian and white clover crosses. |
| format | Article |
| id | doaj-art-ea5c81a550b04bf699bbfe144cd1c61d |
| institution | DOAJ |
| issn | 2504-3129 |
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| publishDate | 2025-02-01 |
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| spelling | doaj-art-ea5c81a550b04bf699bbfe144cd1c61d2025-08-20T02:42:23ZengMDPI AGNitrogen2504-31292025-02-01611110.3390/nitrogen6010011Transcriptome Analysis of Hybrid Progeny of Caucasian Clover and White Clover in the Early Stages of Rhizobia InfectionPeizhi Zhu0Sijing Wang1Kefan Cao2College of Grassland Science/Key Laboratory of Grassland Resources of Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, ChinaYinshanbeilu Grassland Eco-Hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing 100038, ChinaCollege of Grassland Science/Key Laboratory of Grassland Resources of Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, ChinaThe hybrid progeny (1-1) resulting from the cross between Caucasian clover and white clover initially demonstrated an inability to fix nitrogen naturally via spontaneous nodulation. However, following inoculation with specific rhizobia strains derived from the Trifolium genus, successful nodulation and nitrogen fixation were observed in the 1-1 progeny, resulting in enhanced biomass production and adaptability. To explore in greater depth the mechanisms driving nitrogen fixation in these hybrid progeny, the inoculation was carried out using the dominant rhizobia strain (No. 5), isolated from Mengnong Clover No. 1. Root samples were collected at 3, 6, and 9 days post inoculation for RNA sequencing. A total of 1755 differentially expressed unigenes were identified between the control and treatment groups. KEGG pathway analysis highlighted key pathways associated with nodule nitrogen fixation. In combination with Weighted Gene Co-expression Network Analysis (WGCNA) and Gene Set Enrichment Analysis (GSEA), several differentially expressed genes were identified, suggesting their potential contribution to nitrogen fixation. Noteworthy among these, the gene <i>TRINITY_DN7551_c0_g1</i> in the Phenylpropanoid biosynthesis pathway (MAP00940) emerged as a key candidate. This study offers valuable RNA-seq data, contributing significantly to the understanding of the molecular regulatory mechanisms underpinning nodule nitrogen fixation in legumes, thereby laying a solid foundation for future investigations into the hybrid progeny of Caucasian and white clover crosses.https://www.mdpi.com/2504-3129/6/1/11Caucasian clovertranscriptomedifferentially expressed genesnodular nitrogenrhizobia |
| spellingShingle | Peizhi Zhu Sijing Wang Kefan Cao Transcriptome Analysis of Hybrid Progeny of Caucasian Clover and White Clover in the Early Stages of Rhizobia Infection Nitrogen Caucasian clover transcriptome differentially expressed genes nodular nitrogen rhizobia |
| title | Transcriptome Analysis of Hybrid Progeny of Caucasian Clover and White Clover in the Early Stages of Rhizobia Infection |
| title_full | Transcriptome Analysis of Hybrid Progeny of Caucasian Clover and White Clover in the Early Stages of Rhizobia Infection |
| title_fullStr | Transcriptome Analysis of Hybrid Progeny of Caucasian Clover and White Clover in the Early Stages of Rhizobia Infection |
| title_full_unstemmed | Transcriptome Analysis of Hybrid Progeny of Caucasian Clover and White Clover in the Early Stages of Rhizobia Infection |
| title_short | Transcriptome Analysis of Hybrid Progeny of Caucasian Clover and White Clover in the Early Stages of Rhizobia Infection |
| title_sort | transcriptome analysis of hybrid progeny of caucasian clover and white clover in the early stages of rhizobia infection |
| topic | Caucasian clover transcriptome differentially expressed genes nodular nitrogen rhizobia |
| url | https://www.mdpi.com/2504-3129/6/1/11 |
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