Introduction
⌅Cenchrus purpureus (Schumach.) Morrone, formerly Pennisetum purpureum, is one of the most important forage grasses in tropical livestock systems and its use in ruminants feeding through cutting or grazing is notable. In addition, other uses are reported as an ornamental and medicinal plant, in the industry its fiber is used for paper manufacturing and as biofuel (Nguyen et al. 2021Nguyen, B.T., Le, L.B., Pham, L.P., Nguyen, H.T., Tran, T.D. & Van Thai, N. 2021. The effects of biochar on the biomass yield of elephant grass (Pennisetum purpureum Schumach) and properties of acidic soils. Industrial Crops and Products, 161: 113224, ISSN: 1872-633X. https://doi.org/10.1016/j.indcrop.2020.113224. , Tan et al. 2022Tan, F., He, L., Zhu, Q., Wang, Y., Chen, C. & He, M. 2022. Pennisetum hydridum: a potential energy crop with multiple functions and the current status in China. BioEnergy Research, 15: 850-862, ISSN: 1939-1242. https://doi.org/10.1007/s12155-021-10263-7., Wessapak et al. 2023Wessapak, P., Ngernsaengsaruay, C. & Duangjai, S. 2023. A taxonomic revision of Cenchrus L. (Poaceae) in Thailand, with lectotypification of Pennisetum macrostachyum Benth. PhytoKeys, 234: 1-33, ISSN: 1314-2003. https://doi.org/10.3897/phytokeys.234.106486. and POWO 2025POWO. 2025. Plants of the World Online. Kew Royal Botanic Gardens. Available at: https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:77106033-1. [Consulted: January 03, 2025].).
At the Instituto de Ciencia Animal (ICA) of the Republic of Cuba, accessions of C. purpureus developed through the genetic improvement program of this genus aimed at increasing biomass production, nutritional quality and tolerance to abiotic stresses such as salinity and drought are conserved (Herrera 2022Herrera, R.S. 2022. Evaluation of Cenchrus purpureus varieties tolerant to drought in the western region of Cuba. Cuban Journal of Agricultural Science, 56(2): 135-143, ISSN: 2079-3480. https://cjascience.com/index.php/CJAS/article/view/1049. , Fortes et al. 2023Fortes, D., Herrera, R.S. & Herrera, M. 2023. Morphoagronomic performance of Cenchrus purpureus new clones. Cuban Journal of Agricultural Science, 57: 8, ISSN: 2079-3480. https://cjascience.com/index.php/CJAS/article/view/1105. and Álvarez et al. 2024Álvarez, Y., Herrera, R.S., Ramírez, J.L., Verdecia, D.M., Benítez, D. & López, S. 2024. Performance of Cenchrus purpureus varieties tolerant to salinity under the edaphoclimatic conditions of Granma province, Cuba. Cuban Journal of Agricultural Science, 58: e01, ISSN: 2079-3480. https://cu-id.com/1996/v58e01. ). This collection was evaluated for forage production and response to grazing using morphological and quality indicators (Herrera et al. 2019Herrera, R., García, M. & Cruz, A.M. 2019. Study of morphoagronomic indicators of Cenchrus purpureus clones for biomass production. Cuban Journal of Agricultural Science, 53(2): 189-196, ISSN: 2079-3480. https://cjascience.com/index.php/CJAS/article/view/886. ) and molecular markers such as isozymes, Simple Sequence Repeat (SSR) and regions between simple sequence repeat (ISSR) (Cruz et al. 1993Cruz, R., Sosa, A., Herrera, R.S. & Martínez, R.O. 1993. Identificación electroforética de Pennisetum purpureum cv. King grass. Revista Cubana de Ciencia Agrícola, 27(2): 219-223, ISSN: 2079-3480. https://cjascience.com/index.php/CJAS. , González and Martínez 2019González, C. & Martínez, R.O. 2019. Genetic characterization of clones and varieties of Cenchrus purpureus with microsatellite markers. Cuban Journal of Agricultural Science, 53(3): 307-318, ISSN: 2079-3480. https://cjascience.com/index.php/CJAS/article/view/914. and Álvarez 2021Álvarez Báez, Y. 2021. Comportamiento productivo de nuevas variedades de Cenchrus purpureus en el Valle del Cauto, Cuba. Tesis de Doctorado. Universidad de Granma. Cuba. p. 99.).
Molecular markers are fundamental tools for characterizing genetic diversity, optimizing germplasm conservation, and designing assisted selection strategies (Özbek 2024Özbek, Ö. 2024. Molecular Markers Used to Reveal Genetic Diversity and Phylogenetic Relationships in Crop Plants. OBM Genetics, 8(4): 1-25, ISSN: 2577-5790. https://doi.org/10.21926/obm.genet.2404274.). Currently, specific primers exist for studying genetic diversity in plants, such as the plant DNA barcode markers rbcL and matK, which are used in phylogenetic studies of flowering plants and conifers (de Vere et al. 2012de Vere. N., Rich, T.C.G., Ford, C.R., Trinder, S.A., Long, C., Moore, C.W., Satterthwaite, D., Davies, H., Allainguillaume, J., Ronca, S., Tatarinova, T. Garbett, H., Walker, K. & Wilkinson, M.J. 2012. DNA Barcoding the Native Flowering Plants and Conifers of Wales. PLoS ONE, 7(6): e37945, ISSN: 1932-6203. https://doi.org/10.1371/journal.pone.0037945. and Jones et al. 2021Jones, L., Twyford, A.D., Ford, C.R., Rich, T.C., Davies, H., Forrest, L.L., Hart, M.L., McHaffie, H., Brown, M.R., Hollingsworth, P.M. & De Vere, N. 2021. Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom. Molecular Ecology Resources, 21(6): 2050-2062. ISSN: 1755-0998. https://doi.org/10.1111/1755-0998.13388. ). However, other markers derived from the ITS (Internal Transcribed Spacer) region of the nuclear ribosomal DNA are notable for their utility in identifying different evolutionary levels such as fungi, bacteria, and plants; in the latter, their use stands out in phylogenetic studies at the genus and species level due to their high nucleotide substitution rate and wide availability in databases (Alaklabi 2021Alaklabi, A. 2021. Ficus Species Genetic Diversity Based on Internal Transcribed Spacer (ITS) Region Analysis. Egyptian Academic Journal of Biological Sciences, H. Botany, 12(1): 21-27, ISSN: 2090-3820. https://doi.org/10.21608/eajbsh.2021.148134. ).
In Poaceae, this region has clarified taxonomic relation in genera such as Sorghum (Sun et al. 1994Sun, Y., Skinner, D.Z., Liang, G.H. & Hulbert, S.H. 1994. Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA. Theoretical and Applied Genetics, 89: 26-32, ISSN: 1432-2242. https://doi.org/10.1007/BF00226978.), Urochloa (González and Morton 2005González, A.T. & Morton, C.M. 2005. Molecular and morphological phylogenetic analysis of Brachiaria and Urochloa (Poaceae). Molecular Phylogenetics and Evolution, 37(1): 36-44, ISSN: 1095-9513. https://doi:10.1016/j.ympev.2005.06.003. ), Chloris (Liao et al. 2020Liao, H.C., Ming-Hui, C. & Chih-Hui, C. 2020. Barcode of nuclear ribosomal internal transcribed spacer regions (ITS) as a useful tool to recognize a newly naturalized and potentially invasive weed, Chloris pilosa Schumach. (Poaceae), in Taiwan. Taiwania, 65(2): 129, ISSN: 0372-333X. https://doi.org/10.6165/tai.2020.65.129. ), Phalaris (Al Rahbawi et al. 2021Al Rahbawi, S.M., Al-Edhari, A.H. & Sardar, A.S. 2021. Phylogenetic Study of the Genus Phalaris L. (Poaceae) based on Nuclear Internal Transcript Region (ITS) in Iraq. Annals of the Romanian Society for Cell Biology, 25(3): 8278-8281, ISSN: 2067-8282. http://annalsofrscb.ro/index.php/journal/article/view/2368. ) and the species Cenchrus americanus (L.) Morrone (Almutairi 2021Almutairi, Z.M. 2021. Molecular identification and phylogenetics of local pearl millet cultivars using internal-transcribed spacers of nuclear ribosomal DNA. Plant Genetic Resources: Characterization and Utilization, 19(4): 339-346, ISSN: 1479-2621. https://doi.org/10.1017/S1479262121000393. ). However, there is a not study reported in the literature where ITS primers are used in C. purpureus, which limits its genomic information, which in turn restricts its application in phylogenetic and intraspecific diversity studies, and its management in genetic improvement programs.
In Cuba, studies using molecular markers in C. purpureus are scarce and have focused on traditional markers, limiting the understanding of its genomic diversity. Therefore, the objective of this study was to identify a fragment of the ITS region using the universal primers ITS1/ITS4 in C. purpureus and contribute to the molecular genetics knowledge for future phylogenetic and assisted selection analyses.
Materials and Methods
⌅This research was conducted in the DNA Laboratory, belonging to Semillas del Futuro building, at the Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Valle del Cauca, Colombia.
Plant material: the samples under study were obtained from 62 accessions of C. purpureus, with similar regrowth age and cultivation conditions, preserved in the germplasm bank of grasses and forages, belonging to the Experimental Center of Grasses and Forages Miguel Sistachs Naya from Instituto de Ciencia Animal, San José de las Lajas, Mayabeque, Cuba, located at 22º 53 NL and 82º 02 WL at 80 m.o.s.l. Additionally, two samples of Urochloa decumbens (Stapf) R. D. Webster - CIAT 606 and Urochloa ruziziensis (R. Germ. & C. M. Evrard) Crins - CIAT 6713 were included from the Genetic Resources Program of the Alliance of Bioversity International and the International Center for Tropical Agriculture, Colombia.
DNA extraction and amplification: for the extraction of genomic DNA, the modified MATAB method was used (Risterucci et al. 2000Risterucci, A., Grivet, L., N’Goran, Pieretti, J., Flament, M. & Lanaud, C. 2000. A high-density linkage map of Theobroma cacao L. Theoretical and Applied Genetics, 101: 948-955, ISSN: 0040-5752. https://doi.org/10.1007/s001220051566.). The DNA amplification was performed by polymerase chain reaction (PCR), using the ITS1/ITS4 direct and reverse primer combination described by White et al. 1990White, T. J., Bruns, T., Lee, S.J.W.T. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: a guide tomethods and applications. M. Innis, D. Gelfand, J. Sninsky & T. White (eds.). Academic Press, INC. San Diego California. pp. 315-322. ISBN: 0-12-372181-4. (table 1).
| Primer | Direction | Sequence 5'---- 3' | Source |
|---|---|---|---|
| ITS1 | Direct | 5'TCCGTAGGTGAACCTGCGG3' | (White et al. 1990White, T. J., Bruns, T., Lee, S.J.W.T. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: a guide tomethods and applications. M. Innis, D. Gelfand, J. Sninsky & T. White (eds.). Academic Press, INC. San Diego California. pp. 315-322. ISBN: 0-12-372181-4.) |
| ITS4 | Reverse | 3'TCCTCCGCTTATTGATATGC5' |
The PCR mixture was performed in a final volume of 12 μL, using 4 μL of 2X Promega buffer (GoTaq® Green Master Mix), 0.2 μL of ITS1 and ITS4, with a final concentration of 0.2 μM in each primer and 6.6 μL of ultrapure water (UltraPure™ DNase/RNase-Free Distilled Water, Catalog number: 10977015-Invitrogen) and 1 μL of genomic DNA with a concentration of 10 ng.
Amplification was performed in an Eppendorf Mastercycler Nexus Gradient Thermal Cyclers Cole-Parmer® USA. The PCR reaction was carried out following a program lasting approximately 2 hours. The thermal profile consisted of an initial denaturation at 95 °C for 2 minutes, followed by 35 cycles consisting of: denaturation at 95 °C for 30 seconds, hybridization at 55 °C for 1 minute, and extension at 72 °C for 45 seconds. Finally, a final extension was performed at 72 °C for 10 minutes to complete the synthesis of the amplified fragments.
Separation of PCR products: the amplified products were analyzed by electrophoresis on a 1.5 % agarose gel prepared with GelRed™ (Biotium) as an intercalating agent. The run was performed in 0.5X TBE buffer at 100 V for approximately 2 hours. The 1Kb DNA Ladder molecular weight markers, INVITROGEN®, was used.
Visualization of PCR products: visualization and analysis of the amplified DNA fragments was performed by photography, using the BIO-RAD ChemiDoc MP Imaging System Universal Hood III Photodocumenter, USA.
Results and Discussion
⌅The DNA from the 62 C. purpureus accessions and the controls U. decumbens and U. ruziziensis were amplified with the ITS1/ITS4 primers. The amplification products revealed, in most samples, a clear polymorphic band in the gels. However, in some cases amplification of double bands could be observed in accessions 6, 28, 31, 42, 47, 49, 51, 52, 59 and 61 as well as weak bands in accessions 29, 30, 46, 50 and 53 or diffuse bands in accessions 5, 17, 32, 40, 47 and 49. The amplified fragments had an approximate size of 850 bp in Urochloa spp and 1000 bp in the C. purpureus accessions (figure 1).
The molecular differences, between species and genera, found in this study are in agreement with Ghosh et al. (2017)Ghosh, J. S., Bhattacharya, S. & Pal, A. 2017. Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure. Genetica, 145(3): 319-333, ISSN: 1573-6857. https://doi.org/10.1007/s10709-017-9967-9. , who state that ITS are considered a useful source of characters for the identification of different groups of Angiosperm plants, since they generate important polymorphisms within the same taxonomic entity, particularly for genus and species. Also, the ITS region does not encode amino acids and therefore are subject to high variability due to its ubiquitous nature, rapid evolution, high representation in the genome, and the ability to be amplified with minimal amounts of DNA.
The amplification of 1000 and 850 bp ITS primers in C. purpureus and Urochloa spp. respectively, differ from those reported by Baldwin et al. (1995)Baldwin, B.G., Sanderson, M.J., Porter, J.M., Wojciechowski, M.F., Campbell, C.S. & Donoghue, M.J. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden, 82(2): 247-277, ISSN: 2162-4372. https://www.jstor.org/stable/2399880. who stated that the ITS region is small and uniform in flowering plants and its total length is between 600 and 700 bp. In contrast, Liston et al. (1996)Liston, A., Robinson, W.A., Oliphant, J.M. & Álvarez-Buylla, E.R. 1996. Length variation in the nuclear ribosomal DNA internal transcribed spacers of non-flowering seed plants. Systematic Botany, 21(2): 109-120, ISSN: 1548-2324. https://doi.org/10.2307/2419742. describe shorter lengths of this region for Angiosperms, ranging from 565 to 700 bp; in contrast, the ITS region of gymnosperms is considerably longer and has a greater range of variation, from 750 to 3125 bp.
Studies of the ITS region in the species C. purpureus, U. decumbens and U. ruziziensis are scarce. However, Chen et al. (2010)Chen, Z.T., Huang, Q.L., Pan, W.B. & Huang, Y.B. 2010. Sequence analysis of the rDNA ITS region of Pennisetum species (Poaceae). Acta Prataculturae Sinica, 19(4): 135, ISSN: 1004-5759. http://cyxb.magtech.com.cn/EN/Y2010/V19/I4/135. in a research on 15 species of the Cenchrus genus from areas such as Fujian, Jiangsu and Hainan in China, reported amplification of 573 to 586 bp for C. purpureus x C. americanus hybrids. In addition, in the species C. americanus 2n=2x=14 chromosomes and AA genome, genetically homologous to C. purpureus 2n=4x=28 chromosomes and A'A'BB genome, Almutairi (2021)Almutairi, Z.M. 2021. Molecular identification and phylogenetics of local pearl millet cultivars using internal-transcribed spacers of nuclear ribosomal DNA. Plant Genetic Resources: Characterization and Utilization, 19(4): 339-346, ISSN: 1479-2621. https://doi.org/10.1017/S1479262121000393. found a length of 772 to 774 bp for the amplification of the ITS region, in a study of six local cultivars of pearl millet from Saudi Arabia and their similarity to 31 accessions from India and France.
On the other hand, in a molecular phylogenetic study in 22 species from Urochloa genus it was determined that the amplification of the ITS region varied from 582 bp in U. decumbens, to 587 bp in Urochloa eruciformis (Sm.) Nelson & Fern. Casas, Urochloa xantholeuca (Hack. ex Schinz) H. Scholz, U. ruziziensis, and Urochloa mosambicensis (Hack.) Dandy (González and Morton 2005González, A.T. & Morton, C.M. 2005. Molecular and morphological phylogenetic analysis of Brachiaria and Urochloa (Poaceae). Molecular Phylogenetics and Evolution, 37(1): 36-44, ISSN: 1095-9513. https://doi:10.1016/j.ympev.2005.06.003. ).
The results regarding base pair number in C. purpureus and Urochloa spp. can be explained according to those reported by Baldwin et al. (1995)Baldwin, B.G., Sanderson, M.J., Porter, J.M., Wojciechowski, M.F., Campbell, C.S. & Donoghue, M.J. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden, 82(2): 247-277, ISSN: 2162-4372. https://www.jstor.org/stable/2399880. , who stated that approximately 300 bp is estimated for each ITS spacer, but depending on the plant family, ITS 1 may be larger or smaller and potentially more informative. Thus, Bult and Zimmer (1993)Bult, C. & Zimmer, E. 1993. Nuclear ribosomal RNA seguences for inferring tribal relationships within Onagraceae. Systematic Botany, 18(1): 48-63, ISSN: 1548-2324. https://www.jstor.org/stable/2419787. indicated that ITS spacers are more variable compared to the coding regions that are conserved in the genome.
The variability in the amplification of the ITS region in Angiosperms, compared to the results obtained in C. purpureus and Urochloa spp., can be observed in other species of Poaceae such as the study carried out by Hsiao et al. (1995)Hsiao, C., Chatterton, N. J., Asay, K. H. & Jensen, K. B. 1995. Molecular phylogeny of the Pooideae (Poaceae) based on nuclear rDNA (ITS) sequences. Theoretical and Applied Genetics, 90: 389-398, ISSN: 1432-2242. https://doi.org/10.1007/BF00221981. in 26 species of grasses. In the research, the authors found that the ITS region ranged from 585 to 602 bp among the tribes Oryzeae, Aveneae, Brachypodieae, Bromeae, Meliceae, Poeae, Stipeae, and Triticeae.
Also, Hsiao et al. (1998)Hsiao, C., Jacobs, S.W.L., Chatterton, N.J. & Asay, K.H. 1998. A molecular phylogeny of the grass family (Poaceae) based on the sequences of nuclear ribosomal DNA (ITS). Australian Systematic Botany, 11(6): 667-688, ISSN: 1446-5701. https://doi.org/10.1071/SB97012. continued the study and expanded the sample to 200 grass species. The results of the study revealed variations ranging from 584 to 633 bp for the ITS region in six subfamilies: Bambusoideae, Pooideae, Arundinoideae, Centothecoideae, Chloridoideae, and Panicoideae. Both researchers showed differences in this region in Poaceae and confirmed its ubiquitous nature in the plant genome.
The ITS markers have bi-paternal inheritance, allowing to reveal cases of hybridization and polyploidy in genera and species of Poaceae (Wang et al. 2022Wang, J., Yan, Z., Zhong, P., Shen, Z., Yang, G. & Ma, L. 2022. Screening of universal DNA barcodes for identifying grass species of Gramineae. Frontiers in Plant Science, 13: 998863, ISSN: 1664-462X. https://doi.org/10.3389/fpls.2022.998863.). However, in C. purpureus and Urochloa spp the ITS1/ITS4 primers did not has polymorphic bands, which did not allow a clear determination of the genetic diversity between accessions of the same taxonomic entity. Furthermore, there were not differences in the C. purpureus x C. americanus hybrids that are in the germplasm under study. These results may be due to the need to include other primer pairs that complement those used or to genome sequencing, as indicated by Hsiao et al. (1998)Hsiao, C., Jacobs, S.W.L., Chatterton, N.J. & Asay, K.H. 1998. A molecular phylogeny of the grass family (Poaceae) based on the sequences of nuclear ribosomal DNA (ITS). Australian Systematic Botany, 11(6): 667-688, ISSN: 1446-5701. https://doi.org/10.1071/SB97012. , who observed that the use of different primer combinations (ITS1/ITS4, ITS1/ITS2 and ITS3/ITS4) allowed determining the variability of nuclear ribosomal DNA among Poaceae species.
This contradicts what referred by Ahmadi et al. (2022)Ahmadi, H., Solouki, M., Fazeli-Nasab, B., Heidari, F. & Sayyed, R.Z. 2022. Internal transcribed spacer (ITS) regions: A powerful tool for analysis of the diversity of wheat genotypes. Indian Journal of Experimental Biology, 60(2): 137-143, ISSN: 0975-1009. http://op.niscair.res.in/index.php/IJEB/article/view/34886. , who stated that ITS markers can be used as a more appropriate assessment tool to analyze interspecific and intraspecific relations when distinguishing different genotypes, since nucleotide changes decrease as evolution progresses, so that only a few nucleotide changes occur. In this sense, the results obtained in this study show that the ITS are more effective in identifying variability between species of different genera and are not efficient in determining genetic differences between accessions of the same species.
The amplification products of C. purpureus revealed, in some cases, the presence of double, weak or diffuse bands. González (2002)González, A.C. 2002. Detección del polimorfismo genético mediante marcadores bioquímicos en plantas. En: Marcadores moleculares: nuevos horizontes en la genética y la selección de las plantas. Cornide, M. T. (Coord.). Ed. Félix Varela, La Habana, Cuba. pp. 36-63. ISBN: 959-258-351-X. and Nadeem et al. (2018)Nadeem, M.A., Nawaz, M.A., Shahid, M.Q., Doğan, Y., Comertpay, G., Yıldız, M., Hatipoğlu, R., Ahmad, F., Alsaleh, A., Labhane, N., Özkan, H., Chung, G. & Baloch, F.S. 2018. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment, 32(2): 261-285, ISSN: 1310-2818. https://doi.org/10.1080/13102818.2017.1400401. report that these characteristics in the amplification of the band patterns could be due to the composition of the gel and the buffer, as well as the voltage and current intensity conditions. In addition, some of the primers used may have more than one hybridization region in the genomic DNA of the studied samples, the presence of introns in the rDNA subunits, and the amplification technique or amplification of DNA from external contamination. So, it is necessary to check the influence of these factors on the amplification of ITS primers in subsequent assays.
Conclusions
⌅It is concluded that the ITS1/ITS4 primers are effective in amplifying DNA from C. purpureus and Urochloa spp. accessions, demonstrating their usefulness as a tool for evaluating the quality of the extracted DNA and its amplification capacity by PCR. However, these primers do not have sufficient resolution to distinguish genetic differences between accessions of both species within the fragment of the ITS region analyzed.
Although ITS markers can be used to verify the amplification of C. purpureus samples and for general differentiation between species of the genus in the Poaceae family, it is recommended to complement these analyses with sequencing techniques to achieve a more precise genetic characterization.
The information generated in this study expands the genetic-molecular knowledge of C. purpureus and creates the initial conditions for future phylogenetic studies in the genus Cenchrus, as well as for the application of assisted selection strategies in improvement and conservation programs for its germplasm.