Expression and Variation of the Genes Involved in Rhizobium Nodulation in Red Clover
Red clover (<i>Trifolium pratense</i> L.) is an important forage crop and serves as a major contributor of nitrogen input in pasture settings because of its ability to fix atmospheric nitrogen. During the legume-rhizobial symbiosis, the host plant undergoes a large number of gene express...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/21/2888 |
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| author | Randy D. Dinkins Julie A. Hancock Derek M. Bickhart Michael L. Sullivan Hongyan Zhu |
| author_facet | Randy D. Dinkins Julie A. Hancock Derek M. Bickhart Michael L. Sullivan Hongyan Zhu |
| author_sort | Randy D. Dinkins |
| collection | DOAJ |
| description | Red clover (<i>Trifolium pratense</i> L.) is an important forage crop and serves as a major contributor of nitrogen input in pasture settings because of its ability to fix atmospheric nitrogen. During the legume-rhizobial symbiosis, the host plant undergoes a large number of gene expression changes, leading to development of root nodules that house the rhizobium bacteria as they are converted into nitrogen-fixing bacteroids. Many of the genes involved in symbiosis are conserved across legume species, while others are species-specific with little or no homology across species and likely regulate the specific plant genotype/symbiont strain interactions. Red clover has not been widely used for studying symbiotic nitrogen fixation, primarily due to its outcrossing nature, making genetic analysis rather complicated. With the addition of recent annotated genomic resources and use of RNA-seq tools, we annotated and characterized a number of genes that are expressed only in nodule forming roots. These genes include those encoding nodule-specific cysteine rich peptides (NCRs) and nodule-specific Polycystin-1, Lipoxygenase, Alpha toxic (PLAT) domain proteins (NPDs). Our results show that red clover encodes one of the highest number of NCRs and ATS3-like/NPDs, which are postulated to increase nitrogen fixation efficiency, in the Inverted-Repeat Lacking Clade (IRLC) of legumes. Knowledge of the variation and expression of these genes in red clover will provide more insights into the function of these genes in regulating legume-rhizobial symbiosis and aid in breeding of red clover genotypes with increased nitrogen fixation efficiency. |
| first_indexed | 2024-03-09T18:43:48Z |
| format | Article |
| id | doaj.art-2406dae073d941f78d573eedefbf6214 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T18:43:48Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-2406dae073d941f78d573eedefbf62142023-11-24T06:24:40ZengMDPI AGPlants2223-77472022-10-011121288810.3390/plants11212888Expression and Variation of the Genes Involved in Rhizobium Nodulation in Red CloverRandy D. Dinkins0Julie A. Hancock1Derek M. Bickhart2Michael L. Sullivan3Hongyan Zhu4Forage-Animal Production Research Unit, USDA-ARS, Lexington, KY 40506, USACollege of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40508, USAUS Dairy Forage Research Center, USDA-ARS, Madison, WI 53706, USAUS Dairy Forage Research Center, USDA-ARS, Madison, WI 53706, USADepartment of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USARed clover (<i>Trifolium pratense</i> L.) is an important forage crop and serves as a major contributor of nitrogen input in pasture settings because of its ability to fix atmospheric nitrogen. During the legume-rhizobial symbiosis, the host plant undergoes a large number of gene expression changes, leading to development of root nodules that house the rhizobium bacteria as they are converted into nitrogen-fixing bacteroids. Many of the genes involved in symbiosis are conserved across legume species, while others are species-specific with little or no homology across species and likely regulate the specific plant genotype/symbiont strain interactions. Red clover has not been widely used for studying symbiotic nitrogen fixation, primarily due to its outcrossing nature, making genetic analysis rather complicated. With the addition of recent annotated genomic resources and use of RNA-seq tools, we annotated and characterized a number of genes that are expressed only in nodule forming roots. These genes include those encoding nodule-specific cysteine rich peptides (NCRs) and nodule-specific Polycystin-1, Lipoxygenase, Alpha toxic (PLAT) domain proteins (NPDs). Our results show that red clover encodes one of the highest number of NCRs and ATS3-like/NPDs, which are postulated to increase nitrogen fixation efficiency, in the Inverted-Repeat Lacking Clade (IRLC) of legumes. Knowledge of the variation and expression of these genes in red clover will provide more insights into the function of these genes in regulating legume-rhizobial symbiosis and aid in breeding of red clover genotypes with increased nitrogen fixation efficiency.https://www.mdpi.com/2223-7747/11/21/2888forage legumesnitrogen fixationgene expressionnodulationnodule-specific cysteine rich peptides |
| spellingShingle | Randy D. Dinkins Julie A. Hancock Derek M. Bickhart Michael L. Sullivan Hongyan Zhu Expression and Variation of the Genes Involved in Rhizobium Nodulation in Red Clover Plants forage legumes nitrogen fixation gene expression nodulation nodule-specific cysteine rich peptides |
| title | Expression and Variation of the Genes Involved in Rhizobium Nodulation in Red Clover |
| title_full | Expression and Variation of the Genes Involved in Rhizobium Nodulation in Red Clover |
| title_fullStr | Expression and Variation of the Genes Involved in Rhizobium Nodulation in Red Clover |
| title_full_unstemmed | Expression and Variation of the Genes Involved in Rhizobium Nodulation in Red Clover |
| title_short | Expression and Variation of the Genes Involved in Rhizobium Nodulation in Red Clover |
| title_sort | expression and variation of the genes involved in rhizobium nodulation in red clover |
| topic | forage legumes nitrogen fixation gene expression nodulation nodule-specific cysteine rich peptides |
| url | https://www.mdpi.com/2223-7747/11/21/2888 |
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