Molecular comparison of chili populations (Capsicum spp.) from Tabasco and Chiapas, Mexico
Keywords:
C. annuun, C. frutescens, genetic diversity, molecular analysis, molecular markers, populations structureAbstract
Based on the importance of chile in the Southeast of Mexico, the objectives of this research were to characterize molecularly, and estimate the polymorphism and genetic structure of 21 populations of Capsicum spp. of Tabasco and Chiapas States, Mexico. After 40 days of germination of the seeds collected, two young leaves of each population were cut per each of 10 plants. The 20 leaves were mixed and three samples of 0,5 g were taken to extract the DNA. Four microsatellite markers (SSR) to determine the genetic diversity. A total of 229 alleles were detected, and 70 were polymorphics. The marker Hpms1-106 detected 38.8 % polymorphism, and HpmsCaSIG-19 the lowest polymorphism (20,55 %). The AMOVA explained 13,0 % of the variability among populations, and individuals within populations explained the remaining 87,0 %. The statistics FST = 0.176, showed a large differentiation between populations. The FIS = -0,448 showed an excess of heterozygous in populations, and the FIT = -0,193 showed that individuals in each population have moderate non-random mating effect between them. Cluster analysis grouped all evaluated chili populations into six clusters. The cluster I grouped 13 populations, some of these such as Amashito Cerro Blanco and Colmillo de Lagarto El Porvenir showed to be the most genetically similar. In the cluster VI, Pico de Paloma Miahuatlán showed to be different from the rest of populations. Microsatellite markers were useful to analyze the genetic diversity of these chili populations.
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References
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25. Kwon, Y.S., J.Y. Moon, S.I. Yi, K.M. Bae, E.H. Soh, I.H. Cho y B.D. Kim. 2007. Comparative analysis of pepper (Capsicum annuum L.) varieties using morphological characters, AFLP and SSR markers. Korean Journal of Genetics 29(1): 11-20.
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31. Massot, P.H.K. y R.L. Barbieri. 2016. Plant breeding of chili peppers (Capsicum, Solanaceae) – A review. Australian Journal of Basic and Applied Sciences 10(15): 148-154.
32. Nei, M. y W.H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences 76(10): 5269-5273.
33. Nicolaï, M., M. Cantet, V. Lefebvre, A.M. Sage-Palloix y A. Palloix. 2013. Genotyping a large collection of pepper (Capsicum spp.) with SSR loci brings new evidence for the wild origin of cultivated C. annuum and the structuring of genetic diversity by human selection of cultivar types. Genetic Resources and Crop Evolution 60(8): 2375-2390.
34. Pacheco-Olvera, A., S. Hernández-Verdugo, V. Rocha-Ramírez, A. González-Rodríguez y K. Oyama. 2012. Genetic diversity and structure of pepper (Capsicum annuum L.) from Northwestern Mexico analyzed by microsatellite markers. Crop Science 52(1): 231-241.
35. Patel, A.S., N. Sasidharan y A.G. Vala. 2011. Research article genetic relation in Capcicum annum L. cultivars through microsatellite markers: SSR and ISSR. Electronic Journal of Plant Breeding. 2(1): 67-76.
36. Peakall, R. y P.E. Smouse. 2012. GenAlEx 6,5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28: 2537-2539.
37. Rahevar, P. M., Patel, J. N., Kumar, S., & Acharya, R. R. 2019. Morphological, biochemical and molecular characterization for genetic variability analysis of Capsicum annuum. Vegetos 32(2): 131-141.
38. Rivera, A., A.B. Monteagudo, E. Igartuac, A. Taboada, A. García-Ulloa, F. Pomar, M. Riveiro-Leira y C. Silvar. 2016. Assessing genetic and phenotypic diversity in pepper (Capsicum annuum L.) landraces from North-West Spain. Scientia Horticulturae 203: 1–11.
39. Sambrook, J., E. Fritsch y T. Maniatis. 1989. Molecular cloning: a laboratory manual. 2ed. New York: Cold Spring Harbor Laboratory Press.
40. Sharmin, A., M.E. Hoque, M.M. Haque y F. Khatun. 2018. Molecular Diversity Analysis of Some Chilli (Capsicum spp.) Genotypes Using SSR Markers. American Journal of Plant Sciences 9(3): 368-379.
41. Shiferaw, A.A., A. Destaw M., y G. Samuel A. 2018. Genetic diversity study of Ethiopian hot pepper cultivars (Capsicum spp.) using Inter Simple Sequence Repeat (ISSR) marker. J Plant Mol Breed. 5(2): 27-37.
42. Stavêlíková, H., P. Hanáĉek y T. Vyhnánek. 2010. The morphological description and DNA tools analysis: for detection of duplicitions in the Czech germplasm collection of pepper (Capsicum annuum L.). Acta univ. agric. et silvic. Mendel. Brun. LVIII (1): 191–198.
43. Thul, S.T., M.P. Darokar, A.K. Shasany y S.P. Khanuja. 2012. Molecular profiling for genetic variability in Capsicum species based on ISSR and RAPD markers. Molecular Bio-technology 51(2): 137-147.
44. Toledo-Aguilar, R., H. López-Sánchez, A. Santacruz-Varela, E. Valadez-Moctezuma, P. Antonio-López, V.H. Aguilar-Rincón, V.A. González-Hernández y H. Vaquera-Huerta. 2016. Characterization of genetic diversity of native 'Ancho' chili populations of Mexico using microsatellite markers. Chilean Journal of Agricultural Research 76(1): 18-26.
45. Ulhoa, A.B., T.N. Pereira, R.N. Silva, C.F. Ragassi, R. Rodrigues, M.G. Pereira y F.J. Reifschneider. 2014. Caracterização molecular de linhagens de pimenta do tipo Jalapeño amarelo. Horticultura Brasileira 32(1): 35-40.
46. Xiao-min, Z., Z. Zheng-hai, G. Xiao-zhen, M. Sheng-li, L. Xi-xiang, J. Chadœuf, A. Palloix, W. Li-hao y Z. Bao-xi. 2016. Genetic diversity of pepper (Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution. Journal of Integrative Agriculture 15(9): 1991-2001.
2. Baltazar, B. 1997. Diversidad genética del cultivo de chile (Capsicum spp.) determinada por isoenzimas y RFLPs tipos: serrano, jalapeño, manzano y silvestres en su área de distribución. CONABIO proyecto No. G026. http://www.conabio.gob.mx/institucion/cgi-bin /datos.cgi?Letras=G&Numero=26 (consulta de mayo 16, 2019).
3. Bobadilla-Larios, V., E. Esparza-Ibarra, L. Delgadillo-Ruiz, P. Gallegos-Flores y J. L. Ayala-Lujan. 2017. Variedades de chile (Capsicum annuum L.) identificadas mediante marcadores RAPD. Tropical and Subtropical Agroecosystems, 20: 465-473.
4. Brody, J.R. y S.E. Kern. 2004. Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis. Biotechniques 36(2): 214-216.
5. Carvalho, S.I.C., L.B. Bianchetti, C.F. Ragassi, C.S.C. Ribeiro, F.J.B. Reifschneider, G.S.C. Buso y F.G. Faleiro. 2017. Genetic variability of a Brazilian Capsicum frutescens germplasm collection using morphological characteristics and SSR markers. Genetics Molecular Research 16(3): 1-18.
6. Castellón-Martínez, E., J.L. Chávez-Servia, J.C. Carrillo-Rodríguez y A.M. Vera-Guzmán. 2012. Preferencias de consumo de chiles (Capsicum annuum L.) nativos en los valles centrales de Oaxaca, México. Revista fitotecnia mexicana 35(5): 27-35.
7. Chamikara, M.D.M., R.V. Lelwala, M. Ishan, S.S. Karunadasa, M.K.D.I. Perera, P.I. Rajapaksha, V.D.W. Kasthuriarachchi, D.T. Jeyakumar, C.K. Weebadde y S.D.S.S. Sooriyapathirana. 2015. Morphological and Microsatellite Marker Analysis of Fruit Size and Shape in Selected Accessions and Commercial Cultivars of Capsicum Species in Sri Lanka. International Journal of Multidisciplinary Studies (IJMS) 2(1): 29-50.
8. Colney, L., W. Tyagi y M. Rai. 2018. Morphological and molecular characterization of two distinct chilli cultivars from North Eastern India with special reference to pungency related genes. Scientia Horticulturae 240: 1-10.
9. Contreras-Toledo, A.R., H. López-Sánchez, A. Santacruz-Varela, E. Valadez-Moctezuma, V.H. Aguilar-Rincón, T. Corona-Torres y P. Antonio-López. 2011. Diversidad Genética en México de variedades nativas de chile 'poblano' mediante microsatélites. Revista Fitotecnia Mexicana 34(4): 225-232.
10. Dellaporta, S.L., J. Wood y J.B. Hicks. 1983. Una minipreparación de ADN vegetal: versión II. Reporte de Biología Molecular de Plantas 1(4): 19-21.
11. De Vicente, M.C. y T. Fulton. 2003. Using molecular marker technology in studies on plant genetic diversity. https://www.bioversity international.org/fileadmin/user_upload/online_library/publications/pdfs/Molecular_Markers_Volume_1_en.pdf. (consulta de enero 12, 2020).
12. Dhaliwal, M.S., A.Yadav y S.K. Jindal. 2014. Molecular characterization and diversity analysis in chilli pepper using simple sequence repeats (SSR) markers. African Journal of Biotechnology. 13(31): 3137-3143.
13. González, I., Y. Arias, M. Quiñones, I. Miranda, Y. Rodríguez y B. Peteira. 2011. Variabilidad molecular de genotipos de pimiento (Capsicum annuum L.) del programa de mejoramiento genético para la resistencia a PVY. Revista de Protección Vegetal. 26(2): 69-73.
14. González-Jara, P., A. Moreno-Letelier, A. Fraile, D. Piñero y F. García-Arenal. 2011. Impact of Human Management on the Genetic Variation of Wild Pepper, Capsicum annuum var. glabriusculum. PLoS One 6(12): e28715.
15. González-Pérez, S., A. Garcés-Claver, C. Mallor, L.E. Sáenz de Miera, O. Fayos, F. Pomar, F. Merino y C. Silvar. 2014. New insights into Capsicum spp relatedness and the diversification process of Capsicum annuum in Spain. PloS One 9(12): e116276.
16. Guzmán, F. A., M.C. De Vicente, S. Moore y M.M. Jahn. 2020. Microsatellites to enhance characterization, conservation and breeding value of Capsicum germplasm. Gen. Res. and Crop Evol. 67(3): 569-585.
17. Hanáček, P., T. Vyhnánek, M. Rohrer, J. Cieslarová y H. Stavělíková. 2009. DNA polymorphism in genetic resources of red pepper using microsatellite markers. Hort. Sci. (Prague) 36(4): 127-132.
18. Haralayya, B. y I.S. Asha. 2017. Molecular Marker Application in Capsicum spp: A Supplement to Conventional Plant Breeding. Int. J. Curr. Microbiol. App. Sci. 6(11): 3840-3855.
19. Hernández-Verdugo, S., A. González-Rodríguez, P. Sánchez-Peña, A. Casas y K. Oyama. 2006. Estructura y diferenciación genética de poblaciones silvestres y domesticadas de chile del Noroeste de México analizada con isoenzimas y RAPDs. Revista Fitotecnia Mexicana. 29(Es2): 25-29.
20. Hernández-Verdugo, S., R. Luna-Reyes y K. Oyama. 2001. Genetic structure and differentiation of wild and domesticated populations of Capsicum annuum (Solanaceae) from Mexico. Plant Systematics and evolution. 226(3-4): 129-142.
21. Huan-huan, H., Z. Zhang-hua, Z. Zheng-hai, M. Sheng-li, W. Li-hao y Z. Bao-xi. 2011. Analysis of SSRs information in Capsicum spp. from EST database. Agricultural Sciences in China 10(10): 1532-1536.
22. Islam, M.A., P. Sinha, S.S. Sharma, M.S. Negi, B. Neog y S.B. Tripathi. 2016. Analysis of genetic diversity and population structure in Capsicum landraces from North Eastern India using TE-AFLP markers. Plant Molecular Biology Reporter. 34(4): 869-875.
23. Johnson, D. E. 2000. Métodos multivariados aplicados al análisis de datos (No. 519.5 J6). Editorial Paraninfo. 566 p.
24. Konishi, A., N. Furutani, Y. Minamiyama y A. Ohyama. 2019. Detection of quantitative trait loci for capsanthin content in pepper (Capsicum annuum L.) at different fruit ripening stages. Breeding Science 69(1): 30-39.
25. Kwon, Y.S., J.Y. Moon, S.I. Yi, K.M. Bae, E.H. Soh, I.H. Cho y B.D. Kim. 2007. Comparative analysis of pepper (Capsicum annuum L.) varieties using morphological characters, AFLP and SSR markers. Korean Journal of Genetics 29(1): 11-20.
26. Kwon, Y.S, J.M. Lee, G.B. Yi, S.I. Yi, K.M. Kim, E.H. Soh, K.M. Bae, E.K. Park, E.K. Song y B.D. Kim. 2005. Use of SSR markers to complement tests of distinctiveness, uniformity and stability (DUS) of pepper (Capsicum annuum L.) varieties. Molecules & Cells 19(3): 428-435.
27. Latournerie, L., J.L. Chávez, M. Pérez, G. Castañón, S.A. Rodríguez, L.M. Arias y P. Ramírez. 2002. Valoración in situ de la diversidad morfológica de chiles (Capsicum annuum L. y Capsicum chinense Jacq.) en Yaxcabá, Yucatán. Revista Fitotecnia Mexicana. 25(1): 25-33.
28. López Castilla, L. D. C., Garruña Hernández, R., Castillo Aguilar, C. D. L. C., Martínez-Hernández, A., Ortiz-García, M. M., & Andueza-Noh, R. H. 2019. Structure and Genetic Diversity of Nine Important Landraces of Capsicum Species Cultivated in the Yucatan Peninsula, Mexico. Agronomy 9(7): 376.
29. MacNeish, R.S. 1964. Ancient mesoamerican civilization. Science, 143(3606): 531-537.
30. Martínez-Sánchez, D., M. Pérez-Grajales, J.E. Rodríguez-Pérez y E. del C. Moreno-Pérez. 2010. Colecta y caracterización morfológica de 'chile de agua' (Capsicum annuum L.) en Oaxaca, México. Revista Chapingo. Serie Horticultura 16(3): 169-176.
31. Massot, P.H.K. y R.L. Barbieri. 2016. Plant breeding of chili peppers (Capsicum, Solanaceae) – A review. Australian Journal of Basic and Applied Sciences 10(15): 148-154.
32. Nei, M. y W.H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences 76(10): 5269-5273.
33. Nicolaï, M., M. Cantet, V. Lefebvre, A.M. Sage-Palloix y A. Palloix. 2013. Genotyping a large collection of pepper (Capsicum spp.) with SSR loci brings new evidence for the wild origin of cultivated C. annuum and the structuring of genetic diversity by human selection of cultivar types. Genetic Resources and Crop Evolution 60(8): 2375-2390.
34. Pacheco-Olvera, A., S. Hernández-Verdugo, V. Rocha-Ramírez, A. González-Rodríguez y K. Oyama. 2012. Genetic diversity and structure of pepper (Capsicum annuum L.) from Northwestern Mexico analyzed by microsatellite markers. Crop Science 52(1): 231-241.
35. Patel, A.S., N. Sasidharan y A.G. Vala. 2011. Research article genetic relation in Capcicum annum L. cultivars through microsatellite markers: SSR and ISSR. Electronic Journal of Plant Breeding. 2(1): 67-76.
36. Peakall, R. y P.E. Smouse. 2012. GenAlEx 6,5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28: 2537-2539.
37. Rahevar, P. M., Patel, J. N., Kumar, S., & Acharya, R. R. 2019. Morphological, biochemical and molecular characterization for genetic variability analysis of Capsicum annuum. Vegetos 32(2): 131-141.
38. Rivera, A., A.B. Monteagudo, E. Igartuac, A. Taboada, A. García-Ulloa, F. Pomar, M. Riveiro-Leira y C. Silvar. 2016. Assessing genetic and phenotypic diversity in pepper (Capsicum annuum L.) landraces from North-West Spain. Scientia Horticulturae 203: 1–11.
39. Sambrook, J., E. Fritsch y T. Maniatis. 1989. Molecular cloning: a laboratory manual. 2ed. New York: Cold Spring Harbor Laboratory Press.
40. Sharmin, A., M.E. Hoque, M.M. Haque y F. Khatun. 2018. Molecular Diversity Analysis of Some Chilli (Capsicum spp.) Genotypes Using SSR Markers. American Journal of Plant Sciences 9(3): 368-379.
41. Shiferaw, A.A., A. Destaw M., y G. Samuel A. 2018. Genetic diversity study of Ethiopian hot pepper cultivars (Capsicum spp.) using Inter Simple Sequence Repeat (ISSR) marker. J Plant Mol Breed. 5(2): 27-37.
42. Stavêlíková, H., P. Hanáĉek y T. Vyhnánek. 2010. The morphological description and DNA tools analysis: for detection of duplicitions in the Czech germplasm collection of pepper (Capsicum annuum L.). Acta univ. agric. et silvic. Mendel. Brun. LVIII (1): 191–198.
43. Thul, S.T., M.P. Darokar, A.K. Shasany y S.P. Khanuja. 2012. Molecular profiling for genetic variability in Capsicum species based on ISSR and RAPD markers. Molecular Bio-technology 51(2): 137-147.
44. Toledo-Aguilar, R., H. López-Sánchez, A. Santacruz-Varela, E. Valadez-Moctezuma, P. Antonio-López, V.H. Aguilar-Rincón, V.A. González-Hernández y H. Vaquera-Huerta. 2016. Characterization of genetic diversity of native 'Ancho' chili populations of Mexico using microsatellite markers. Chilean Journal of Agricultural Research 76(1): 18-26.
45. Ulhoa, A.B., T.N. Pereira, R.N. Silva, C.F. Ragassi, R. Rodrigues, M.G. Pereira y F.J. Reifschneider. 2014. Caracterização molecular de linhagens de pimenta do tipo Jalapeño amarelo. Horticultura Brasileira 32(1): 35-40.
46. Xiao-min, Z., Z. Zheng-hai, G. Xiao-zhen, M. Sheng-li, L. Xi-xiang, J. Chadœuf, A. Palloix, W. Li-hao y Z. Bao-xi. 2016. Genetic diversity of pepper (Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution. Journal of Integrative Agriculture 15(9): 1991-2001.
Published
2020-12-21
How to Cite
Gálvez Muñoz, Y. A., Cea, M. E., Lesher Gordillo, J. M., Latournerie-Moreno, L., Martínez-Moreno, E., Martínez-Sánchez, J. L., & Castañón-Nájera, G. (2020). Molecular comparison of chili populations (Capsicum spp.) from Tabasco and Chiapas, Mexico. Bioagro, 33(1), 3-12. Retrieved from https://revistas.uclave.org/index.php/bioagro/article/view/3017
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