Molecular identification of root-lesion nematodes, Pratylenchus spp. in agricultural crops from Costa Rica
Introduction. The root-lesion nematodes, Pratylenchus spp., have a wide host range and reduce the yield of different crops. Information on the diversity of Pratylenchus species is scarce in Costa Rica. Objective. To identify the Pratylenchus species associated with 12 crops based on the D3 region of the 28S rDNA gene. Materials and methods. During 2013 to 2015, root samples were collected in Alajuela, Cartago, Guanacaste, Heredia, and San José in crops of rice (Oryza sativa), black pepper (Piper nigrum), sugarcane (Saccharum officinarum), aster (Aster sp.), coffee (Coffea arabica), banana (Musa paradisiaca), lily (Lilium sp.), gypsophila (Gypsophila sp.), onion (Allium cepa), potato (Solanum tuberosum), strawberry (Fragaria x ananassa), and leather-leaf fern (Rumohra adiantiformis). The D3 region of the 28S rDNA gene from each population was amplified and sequenced. A GenBank Blast Search was performed for each sequence. The phylogenetic relationships were established by Bayesian Inference. Results. Blast Search indicated the presence of P. pseudocoffeae in aster, P. brachyurus in black pepper, P. crenatus in onion and potato, P. hippeastri and P. gutierrezi in sugarcane and coffee, respectively. Pratylenchus bolivianus in leather-leaf fern and potato, P. penetrans in onion, strawberry, gypsophila, and lily, P. zeae in rice and sugarcane, while P. speijeri in banana. The phylogenetic analysis corroborated the Pratylenchus species identity with exceptions of sequences from 1) banana, grouped to P. coffeae complex group, 2) sugar cane, grouped to P. hippeastri complex group 3) onion and potato were related with P. crenatus, in an independent group, and 4) leather-leaf fern and potato were grouped with P. bolivianus with low resolution. Conclusions. Nine genetic groups of Pratylenchus were found, some of those should be verified with other molecular markers to get a conclusive identification.
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Sandoval-Ruiz, Rebeca Gómez-Alpízar, Luis Humphreys-Pereira, Danny A. Flores-Chaves, Lorena |
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Sandoval-Ruiz, Rebeca Gómez-Alpízar, Luis Humphreys-Pereira, Danny A. Flores-Chaves, Lorena Molecular identification of root-lesion nematodes, Pratylenchus spp. in agricultural crops from Costa Rica |
| author_facet |
Sandoval-Ruiz, Rebeca Gómez-Alpízar, Luis Humphreys-Pereira, Danny A. Flores-Chaves, Lorena |
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Sandoval-Ruiz, Rebeca |
| title |
Molecular identification of root-lesion nematodes, Pratylenchus spp. in agricultural crops from Costa Rica |
| title_short |
Molecular identification of root-lesion nematodes, Pratylenchus spp. in agricultural crops from Costa Rica |
| title_full |
Molecular identification of root-lesion nematodes, Pratylenchus spp. in agricultural crops from Costa Rica |
| title_fullStr |
Molecular identification of root-lesion nematodes, Pratylenchus spp. in agricultural crops from Costa Rica |
| title_full_unstemmed |
Molecular identification of root-lesion nematodes, Pratylenchus spp. in agricultural crops from Costa Rica |
| title_sort |
molecular identification of root-lesion nematodes, pratylenchus spp. in agricultural crops from costa rica |
| description |
Introduction. The root-lesion nematodes, Pratylenchus spp., have a wide host range and reduce the yield of different crops. Information on the diversity of Pratylenchus species is scarce in Costa Rica. Objective. To identify the Pratylenchus species associated with 12 crops based on the D3 region of the 28S rDNA gene. Materials and methods. During 2013 to 2015, root samples were collected in Alajuela, Cartago, Guanacaste, Heredia, and San José in crops of rice (Oryza sativa), black pepper (Piper nigrum), sugarcane (Saccharum officinarum), aster (Aster sp.), coffee (Coffea arabica), banana (Musa paradisiaca), lily (Lilium sp.), gypsophila (Gypsophila sp.), onion (Allium cepa), potato (Solanum tuberosum), strawberry (Fragaria x ananassa), and leather-leaf fern (Rumohra adiantiformis). The D3 region of the 28S rDNA gene from each population was amplified and sequenced. A GenBank Blast Search was performed for each sequence. The phylogenetic relationships were established by Bayesian Inference. Results. Blast Search indicated the presence of P. pseudocoffeae in aster, P. brachyurus in black pepper, P. crenatus in onion and potato, P. hippeastri and P. gutierrezi in sugarcane and coffee, respectively. Pratylenchus bolivianus in leather-leaf fern and potato, P. penetrans in onion, strawberry, gypsophila, and lily, P. zeae in rice and sugarcane, while P. speijeri in banana. The phylogenetic analysis corroborated the Pratylenchus species identity with exceptions of sequences from 1) banana, grouped to P. coffeae complex group, 2) sugar cane, grouped to P. hippeastri complex group 3) onion and potato were related with P. crenatus, in an independent group, and 4) leather-leaf fern and potato were grouped with P. bolivianus with low resolution. Conclusions. Nine genetic groups of Pratylenchus were found, some of those should be verified with other molecular markers to get a conclusive identification. |
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2022 |
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https://revistas.ucr.ac.cr/index.php/agromeso/article/view/49445 |
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AT sandovalruizrebeca molecularidentificationofrootlesionnematodespratylenchussppinagriculturalcropsfromcostarica AT gomezalpizarluis molecularidentificationofrootlesionnematodespratylenchussppinagriculturalcropsfromcostarica AT humphreyspereiradannya molecularidentificationofrootlesionnematodespratylenchussppinagriculturalcropsfromcostarica AT floreschaveslorena molecularidentificationofrootlesionnematodespratylenchussppinagriculturalcropsfromcostarica AT sandovalruizrebeca identificacionmoleculardenematodoslesionadoresderaizpratylenchussppencultivosagricolasdecostarica AT gomezalpizarluis identificacionmoleculardenematodoslesionadoresderaizpratylenchussppencultivosagricolasdecostarica AT humphreyspereiradannya identificacionmoleculardenematodoslesionadoresderaizpratylenchussppencultivosagricolasdecostarica AT floreschaveslorena identificacionmoleculardenematodoslesionadoresderaizpratylenchussppencultivosagricolasdecostarica |
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oai:portal.ucr.ac.cr:article494452023-06-16T13:42:49Z Molecular identification of root-lesion nematodes, Pratylenchus spp. in agricultural crops from Costa Rica Identificación molecular de nematodos lesionadores de raíz, Pratylenchus spp., en cultivos agrícolas de Costa Rica Sandoval-Ruiz, Rebeca Gómez-Alpízar, Luis Humphreys-Pereira, Danny A. Flores-Chaves, Lorena 28S gene robosomal DNA PCR DNA sequence gen 28S ADN ribosomal PCR secuencia de ADN Introduction. The root-lesion nematodes, Pratylenchus spp., have a wide host range and reduce the yield of different crops. Information on the diversity of Pratylenchus species is scarce in Costa Rica. Objective. To identify the Pratylenchus species associated with 12 crops based on the D3 region of the 28S rDNA gene. Materials and methods. During 2013 to 2015, root samples were collected in Alajuela, Cartago, Guanacaste, Heredia, and San José in crops of rice (Oryza sativa), black pepper (Piper nigrum), sugarcane (Saccharum officinarum), aster (Aster sp.), coffee (Coffea arabica), banana (Musa paradisiaca), lily (Lilium sp.), gypsophila (Gypsophila sp.), onion (Allium cepa), potato (Solanum tuberosum), strawberry (Fragaria x ananassa), and leather-leaf fern (Rumohra adiantiformis). The D3 region of the 28S rDNA gene from each population was amplified and sequenced. A GenBank Blast Search was performed for each sequence. The phylogenetic relationships were established by Bayesian Inference. Results. Blast Search indicated the presence of P. pseudocoffeae in aster, P. brachyurus in black pepper, P. crenatus in onion and potato, P. hippeastri and P. gutierrezi in sugarcane and coffee, respectively. Pratylenchus bolivianus in leather-leaf fern and potato, P. penetrans in onion, strawberry, gypsophila, and lily, P. zeae in rice and sugarcane, while P. speijeri in banana. The phylogenetic analysis corroborated the Pratylenchus species identity with exceptions of sequences from 1) banana, grouped to P. coffeae complex group, 2) sugar cane, grouped to P. hippeastri complex group 3) onion and potato were related with P. crenatus, in an independent group, and 4) leather-leaf fern and potato were grouped with P. bolivianus with low resolution. Conclusions. Nine genetic groups of Pratylenchus were found, some of those should be verified with other molecular markers to get a conclusive identification. Introducción. Los nematodos lesionadores, Pratylenchus spp., poseen un amplio rango de hospederos y reducen los rendimientos de diferentes cultivos. La información sobre la diversidad de especies de Pratylenchus en Costa Rica es escasa. Objetivo. Identificar las especies de Pratylenchus asociadas a 12 cultivos con base en la región D3 del gen 28SrDNA. Materiales y métodos. Durante el 2013 al 2015, se recolectaron muestras de raíces en Alajuela, Cartago, Guanacaste, Heredia y San José en cultivos de arroz (Oryza sativa), pimienta negra (Piper nigrum), caña de azúcar (Saccharum officinarum), aster (Aster sp.), café (Coffea arabica), banano (Musa paradisiaca), lirio (Lilium sp.), gysophila (Gypsophila sp.), cebolla (Allium cepa), papa (Solanum tuberosum), fresa (Fragaria x ananassa) y helecho de hoja de cuero (Rumohra adiantiformis). Se amplificó y secuenció la región D3 del gen 28S del ADNr de cada población. Se realizó una búsqueda en el Gen Bank con un “Blast Search” para cada secuencia. Las relaciones filogenéticas se establecieron mediante inferencia bayesiana. Resultados. “Blast Search” indicó la presencia de P. pseudocoffeae en aster, P. brachyurus en pimienta negra, P. crenatus en cebolla y papa, P. hippeastri y P. gutierrezi en caña de azúcar y café, respectivamente. P. bolivianus en helecho hoja de cuero y papa, P. penetrans en cebolla, fresa, gypsophila y lirio, P. zeae en arroz y caña de azúcar, mientras que P. speijeri en banano. El análisis filogenético corroboró la identidad de especies de Pratylenchus con excepciones de secuencias de: 1) banano, agrupada al grupo complejo P. coffeae, 2) caña de azúcar al grupo complejo P. hippeastri 3) cebolla y papa relacionados a P. crenatus, en un grupo independiente y 4) helecho de hoja de cuero y papa se agruparon con P. bolivianus con baja resolución. Conclusiones. Se encontraron nueve grupos genéticos de Pratylenchus, algunos de los cuales deben verificarse con otros marcadores moleculares para lograr una identificación concluyente. Universidad de Costa Rica 2022-12-15 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Article text texto text/xml application/pdf application/epub+zip text/html audio/mpeg audio/mpeg https://revistas.ucr.ac.cr/index.php/agromeso/article/view/49445 10.15517/am.v34i1.49445 Agronomía Mesoamericana; 2023: Agronomía Mesoamericana: Vol. 34, Issue 1 (January-April) ; 49445 Agronomía Mesoamericana; 2023: Agronomía Mesoamericana: Vol. 34, Nº 1 (enero-abril) ; 49445 Agronomía Mesoamericana; 2023: Agronomía Mesoamericana: Vol. 34, Issue 1 (January-April) ; 49445 2215-3608 1021-7444 eng spa https://revistas.ucr.ac.cr/index.php/agromeso/article/view/49445/53934 https://revistas.ucr.ac.cr/index.php/agromeso/article/view/49445/53935 https://revistas.ucr.ac.cr/index.php/agromeso/article/view/49445/53936 https://revistas.ucr.ac.cr/index.php/agromeso/article/view/49445/53937 https://revistas.ucr.ac.cr/index.php/agromeso/article/view/49445/53938 https://revistas.ucr.ac.cr/index.php/agromeso/article/view/49445/53939 Copyright (c) 2022 Rebeca Sandoval-Ruiz, Luis Gómez-Alpízar, Danny A. Humphreys-Pereira, Lorena Flores-Chaves https://creativecommons.org/licenses/by-nc-nd/4.0 |