Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in <i>Saccharum</i> spp. and <i>Tripidium</i> spp.
Due to complex polyploid, sugarcane whole genome sequencing and characterization lag far behind other crops. PCR-based DNA markers are a viable low-cost option to evaluate genetic diversity and verify genotypes. In this study, the 5S ribosomal RNA-intergenic spacer (ITS) of 171 accessions of <i&g...
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MDPI AG
2023-10-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/13/11/2728 |
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| author | Yong-Bao Pan James R. Todd Lionel Lomax Paul M. White Sheron A. Simpson Brian E. Scheffler |
| author_facet | Yong-Bao Pan James R. Todd Lionel Lomax Paul M. White Sheron A. Simpson Brian E. Scheffler |
| author_sort | Yong-Bao Pan |
| collection | DOAJ |
| description | Due to complex polyploid, sugarcane whole genome sequencing and characterization lag far behind other crops. PCR-based DNA markers are a viable low-cost option to evaluate genetic diversity and verify genotypes. In this study, the 5S ribosomal RNA-intergenic spacer (ITS) of 171 accessions of <i>Saccharum</i> spp. and <i>Tripidium</i> spp. was dissected, including 30 accessions of <i>S. officinarum</i>, 71 of <i>S. spontaneum</i>, 17 of <i>S. robustum</i>, 25 of <i>S. barberi</i>, 13 of <i>S. sinense</i>, 2 of <i>S. edule</i>, 5 sugarcane cultivars (<i>Saccharum</i> spp. hybrids), 6 of <i>Tripidium</i> spp. (formally <i>Erianthus</i> spp.), and 2 of unknown species. The ITS spacers were amplified from 10 ng of the leaf DNA of each accession with the universal PCR primers PI and PII. The PCR-amplified spacers (amplicons) were analyzed by both agarose gel and capillary electrophoresis (CE). While agarose gel electrophoresis revealed five banding patterns, a total of 42 polymorphic amplicons, ranging from 60 to 506 bp, were detected by CE. Three amplicons, 234-, 235-, and 236-bp in size, were amplified from all accessions of six <i>Saccharum</i> species, except for three <i>S. robustum</i> accessions (Molokai 5573, NG 57-054, and NG 77-235) that lacked the 236-bp amplicon. The 234-, 235-, 236-bp banding pattern found in <i>S. spontaneum</i> was less consistent than other <i>Saccharum</i> species, sometimes missing a few but not all the bands in this region. An amplicon of 61-bp was amplified only from the sugarcane hybrid varieties. The PI/PII patterns indicated diversity and subpopulations within <i>Saccharum</i>, which could potentially be used in Breeding. Moreover, all <i>Saccharum</i>-specific amplicons were mostly absent in <i>Tripidium</i> spp. accessions, which produced 405-bp and 406-bp amplicons, and any pattern of the exceptions indicated misidentification. The <i>T. bengalense</i> accession Kalimpong had a unique CE-banding pattern that was different from all other accessions. Although the clustering pattern of the 42 amplicons only discriminated at the genus level, these amplicons helped identify nine misclassified accessions. This study further demonstrates that these PI/PII amplicons could be particularly useful markers for breeders at sugarcane field stations to quickly confirm and discriminate among the accessions of germplasm collections. |
| first_indexed | 2024-03-09T17:06:36Z |
| format | Article |
| id | doaj.art-9d963a614a9843fab14a9dcdeb444ace |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-09T17:06:36Z |
| publishDate | 2023-10-01 |
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| series | Agronomy |
| spelling | doaj.art-9d963a614a9843fab14a9dcdeb444ace2023-11-24T14:23:46ZengMDPI AGAgronomy2073-43952023-10-011311272810.3390/agronomy13112728Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in <i>Saccharum</i> spp. and <i>Tripidium</i> spp.Yong-Bao Pan0James R. Todd1Lionel Lomax2Paul M. White3Sheron A. Simpson4Brian E. Scheffler5Sugarcane Research Unit, USDA-ARS, Houma, LA 70360, USASugarcane Research Unit, USDA-ARS, Houma, LA 70360, USASugarcane Research Unit, USDA-ARS, Houma, LA 70360, USASugarcane Research Unit, USDA-ARS, Houma, LA 70360, USAGenomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, USAGenomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, USADue to complex polyploid, sugarcane whole genome sequencing and characterization lag far behind other crops. PCR-based DNA markers are a viable low-cost option to evaluate genetic diversity and verify genotypes. In this study, the 5S ribosomal RNA-intergenic spacer (ITS) of 171 accessions of <i>Saccharum</i> spp. and <i>Tripidium</i> spp. was dissected, including 30 accessions of <i>S. officinarum</i>, 71 of <i>S. spontaneum</i>, 17 of <i>S. robustum</i>, 25 of <i>S. barberi</i>, 13 of <i>S. sinense</i>, 2 of <i>S. edule</i>, 5 sugarcane cultivars (<i>Saccharum</i> spp. hybrids), 6 of <i>Tripidium</i> spp. (formally <i>Erianthus</i> spp.), and 2 of unknown species. The ITS spacers were amplified from 10 ng of the leaf DNA of each accession with the universal PCR primers PI and PII. The PCR-amplified spacers (amplicons) were analyzed by both agarose gel and capillary electrophoresis (CE). While agarose gel electrophoresis revealed five banding patterns, a total of 42 polymorphic amplicons, ranging from 60 to 506 bp, were detected by CE. Three amplicons, 234-, 235-, and 236-bp in size, were amplified from all accessions of six <i>Saccharum</i> species, except for three <i>S. robustum</i> accessions (Molokai 5573, NG 57-054, and NG 77-235) that lacked the 236-bp amplicon. The 234-, 235-, 236-bp banding pattern found in <i>S. spontaneum</i> was less consistent than other <i>Saccharum</i> species, sometimes missing a few but not all the bands in this region. An amplicon of 61-bp was amplified only from the sugarcane hybrid varieties. The PI/PII patterns indicated diversity and subpopulations within <i>Saccharum</i>, which could potentially be used in Breeding. Moreover, all <i>Saccharum</i>-specific amplicons were mostly absent in <i>Tripidium</i> spp. accessions, which produced 405-bp and 406-bp amplicons, and any pattern of the exceptions indicated misidentification. The <i>T. bengalense</i> accession Kalimpong had a unique CE-banding pattern that was different from all other accessions. Although the clustering pattern of the 42 amplicons only discriminated at the genus level, these amplicons helped identify nine misclassified accessions. This study further demonstrates that these PI/PII amplicons could be particularly useful markers for breeders at sugarcane field stations to quickly confirm and discriminate among the accessions of germplasm collections.https://www.mdpi.com/2073-4395/13/11/27285S rRNA-ITScapillary electrophoresisgermplasmsugarcane<i>Saccharum</i> spp.<i>Tripidium</i> spp. |
| spellingShingle | Yong-Bao Pan James R. Todd Lionel Lomax Paul M. White Sheron A. Simpson Brian E. Scheffler Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in <i>Saccharum</i> spp. and <i>Tripidium</i> spp. Agronomy 5S rRNA-ITS capillary electrophoresis germplasm sugarcane <i>Saccharum</i> spp. <i>Tripidium</i> spp. |
| title | Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in <i>Saccharum</i> spp. and <i>Tripidium</i> spp. |
| title_full | Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in <i>Saccharum</i> spp. and <i>Tripidium</i> spp. |
| title_fullStr | Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in <i>Saccharum</i> spp. and <i>Tripidium</i> spp. |
| title_full_unstemmed | Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in <i>Saccharum</i> spp. and <i>Tripidium</i> spp. |
| title_short | Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in <i>Saccharum</i> spp. and <i>Tripidium</i> spp. |
| title_sort | molecular dissection of the 5s ribosomal rna intergenic transcribed spacers in i saccharum i spp and i tripidium i spp |
| topic | 5S rRNA-ITS capillary electrophoresis germplasm sugarcane <i>Saccharum</i> spp. <i>Tripidium</i> spp. |
| url | https://www.mdpi.com/2073-4395/13/11/2728 |
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