Genetic differences and population structure of Capsicum spp. populations with simple sequences repets markers (SSRs)




Capsicum spp., chili populations, genetic diversity, phylogenetic relations, SSR markers


In the Solanaceae family, Capsicum spp. is a worldwide important vegetable genus, and widely cultivated in Mexico. The objective of this research was to know the genetic relation, genetic diversity, and genetic structure of fourteen populations of Capsicum spp. (six from Tabasco, five from Tamaulipas, Mexico, and three from Cuba) the four oligonucleotides identified 202 alleles, 38 of them were polymorphics. The majority of alleles (65) were amplified by oligo HpmsCaSIG19 and Hpms1-274 detected a small amount of alleles (35), the average of alleles was 50,5. The genetic structure of the population was estimated with the F fixation indices. The value of the diversity between regions (PhiRT) was 0,264, this means that the populations presented 73,6% of variation between them. High diversity was found between subpopulations and inside regions (PhiPR=0,412). The PhiPT (analog of FST)=0,567, can be interpreted as high differentiation in the genics frequency of the populations that were evaluated. The cluster analysis classified the fourteen populations at a distance of 11 in five groups, the clusters I and III were formed by four populations on each one, while, two populations per cluster were observed in the clusters II, IV, and V. In this analysis, the population Cachucha of Cuba was not related with the backcrosses Habanero x Amashito (RCHaAm) and Garbanzo x Habanero (RCGaHa), also was not related with the Habanero population of Tabasco Mexico.


Download data is not yet available.


Alayachew, A.S., D.M. Atnafu, y S.A. Gedefa. 2017. 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.

Annupama, D.A., N. Brajendra, y M. Dinachandra. 2018. Genetic diversity analysis in chilli (Capsicum annuum L.) found in Manipur using RAPD Markers. Int. J. Curr. Microbiol. App. Sci. 7(10): 257-262.

Aranguren-Méndez, J.A., R. Román-Bravo, W. Isea, Y. Villasmil, y J. Jordana. 2005. Los microsatélites (STR´s), marcadores moleculares de ADN por excelencia para programas de conservación: una revisión. Arch. Latinoam. Prod. Anim. 13(1): 1-6.

Balzarini, M., C. Bruno, A. Peña, I. Teich, y J. Di Rienzo. 2010. Estadística en Biotecnología. Aplicaciones en Info-Gen. Encuentro Grupo Editor. Editorial Brujas 1ª Edición. Córdoba, Argentina. 223 p.

Bobadilla-Larios, V., E. Esparza-Ibarra, L. Delgadillo-Ruiz, P. Gallegos-Flores, y J. Ayala-Lujan. 2017. Variedades de chile (Capsicum annuum L.) identificadas mediante marcadores RAPD. Tropical and Subtropical Agroecosystems 20(3): 465-473.

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.

Campos, A.L., T.N. Marostega, N.S.S. Cabral, K.L. Araújo, M.E. Serafim, S. Seabra-Júnior et al. 2015. Morphoagronomic and molecular profiling of Capsicum spp. from southwest Mato Grosso, Brazil. Genetics and Molecular Research 15(3): 1-12.

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. Faleir. 2017. Genetic variability of a Brazilian Capsicum frutescens germplasm collection using morphological characteristics and SSR markers. Genetics and Molecular Research. 16 (3): 1-18.

Castañón-Nájera, G., M. Ramírez-Meraz, N. Mayek-Pérez, A.C. García, y R. Ruíz-Salazar. 2014. Molecular comparison of wild and commercial chilies from Tamaulipas and Tabasco, Mexico. Pak. J. Bot. 46(6): 2101-2106.

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.

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.

Dellaporta, S.L., J. Wood, y J.B. Hicks. 1983. Una minipreparación de ADN vegetal: versión II. Reporte de biología molecular de plantas. 1(14): 19-21.

De Jesus, R., G.N. Santos, A.S. Piccin, T.W.A. Balsalobre, F.C. Sala, y M.S. Carnerio. 2019. Characterization of pepper accessions using molecular markers linked to pungency and SSR. Horticultura Brasileira 37: 152-160.

Earl Dent, A., y M. vonHoldt Bridgett. 2012. Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conservation Genetics Resources. 4(2): 359-361.

Gálvez, Y.A., M.E. Cea, J.M. Lesher, L. Latournerie-Moreno, E. Martínez-Moreno, J.L. Martínez, y G. Castañón-Nájera. 2021. Comparación molecular de poblaciones de chile (Capsicum spp.) de Tabasco y Chiapas, México. Bioagro 33(1): 3-12.

González-Pérez, S., A. Garcés-Claver, C. Mayor, L.E. Sáenz de Miera, O. Fayos, F. Pomar et al. 2014. New Insights into Capsicum spp. Relatedness and the Diversification Process of Capsicum annuum in Spain. Plos One 9(12): 1-23.

Gu, X.Z., Y.C. Cao, Z.H. Zhang, B.X. Zhang, X.M. Zhang, H.P. Wang, y L.H. Wang, 2019. Genetic diversity and population structure analysis of Capsicum germplasm accessions. Journal of Integrative Agriculture 18(6): 1312-1320.

Guzmán, F.A., S. Moore, M.C de Vicente, y M.M Jahn. 2020. Microsatellites to enhance characterization, conservation and breeding value of Capsicum germplasm. Genet Resour Crop Evol 67: 569-585.

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.

Hussein, I.A., y S.S. Mahdi. 2016. SSR-PCR technique for detecting the genetic diversity of Capsicum annuum L. in local and imported samples in Iraq. Ibn Al-Haitham J. for Pure & Appl. Sci. 22: 25-52.

Ibarra-Torres, P., E. Valadez-Moctezuma, M. Pérez-Grajales, J. Rodríguez-Campos, y M.E. Jaramillo-Flores. 2015. Inter and intraspecific differentiation of Capsicum annuum and Capsicum pubescens using ISSR and SSR Markers. Scientia Horticulturae. 181: 137-146.

Igwe, D.O., C.A. Afiukwa, G. Acquaah, y G.N. Ude. 2019. Genetic diversity and structure of Capsicum annuum as revealed by start codon targeted and directed amplified minisatellite DNA markers. Hereditas 156(32): 1-13.

Islam, Md.A., P. Sinha, S. Sundar, N.M. Singh, B. Neog, y T.S. Bhushan. 2016. Analysis of genetic diversity and population structure in Capsicum landraces from North Eastern India using TE-AFLP markers. Plant Mol. Biol. Rep. 34: 869-875.

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: 30-39.

Kraft, K.H., C.H. Brown, G.P. Nabhan, E. Luedeling, J.deJ. Luna R., G.C. d’Eeckenbrugge et al. 2014. Multiple lines of evidence for the origin of domesticated chili pepper, Capsicum annuum, in Mexico. PNAS 111: 6165-6170.

Kuria, M.W., V.W. Ngumi, P.K. Njenga, L.N. Wangai, y M. Esther. 2018. Assessing Genetic diversity of an endangered medicinal plant, Strychnos henningsii (Gilg.) in Nine Populations in Kenyan counties as revealed by ISSR Markers. International Journal of Innovative Research and Knowledge 3(12): 81-94.

Lee, H.Y., S. Moon, H.S. Ro, W.C. Chung, y H. Ryu. 2020. Analysis of genetic diversity and population structure of wild strains and cultivars using genomic SSR markers in Lentinula edodes. Mycobiology 48(2): 115-121.

Lee, H.Y., N.Y. Ro, H.J. Jeong, J.K. Kwon, J. Jo, Y. Ha et al. 2016. Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm. BMC Genetics 17: 142-154.

Leite, P.S., R. Rodrigues, R.N.O. Silva, S. Pimenta, A.M. Medeiros, C.S. Bento, y L.S.A. Gonçalves. 2016. Molecular and agronomic analysis of intraspecific variability in Capsicum baccatum var. pendulum accessions. Genetics and Molecular Research 15(4): 1-16.

Nicolaї, 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. Genet Resour Crop Evol 60: 2375-2390.

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 Sci. 52(1): 231-241.

Patel, A.S., N. Sasidharan, y A.G. Vala. 2011. Research article genetic relation in Capsicum annum L. cultivars through microsatellite markers: SSR and ISSR. Elec J Plant Breed. 2(1): 67-76.

Peakall, R., y P.E. Smouse. 2012. GenAlEx 6.501: genetic analysis in Excel. Population genetic software for teaching and research - an update. Bioinformatics. 28: 2537-2539.

Pérez-Castañeda, L.M., G. Castañon-Nájera, M. Ramírez-Meraz, y N. Mayek-Pérez. 2015. Avances y perspectivas sobre el estudio del origen y la diversidad genética de Capsicum spp. Filogenia y Diversidad en Capsicum 2(4): 117-128.

Pritchard, J.K., X. Wen, y D. Falush. 2012. Documentation for structure software: Version 2.3.4. University of Chicago, Chicago. structure.html

Ruíz-Álvarez, O., R. Arteaga-Ramírez, M.A. Vázquez-Peña, R.E. Ontiveros-Capurata, y R. López-López. 2012. Balance hídrico y clasificación climática del estado de Tabasco, México. Universidad y Ciencia. 28(1): 1-14.

Sharmin, A., H.Md. Ekramul, H.Md. Masudul, y F. Khatun. 2018. Molecular diversity analysis of some chilli (Capsicum spp.) genotypes using SSR Markers. American Journal of Plant Sciences 9: 368-379.

Singh, N., D.R. Choudhury, A.K. Singh, S. Kumar, K. Srinivasan, R.K. Tyagi, et al. 2013. Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties. PLoSONE 8(12): 1-14.

SNICS (Servicio Nacional de Inspección y Certificación de Semillas). 2017. Chile (Capsicum spp.). Generalidades de la Red Chile. (consulta de noviembre, 2023).

Taranto, F., N. D’Agostino, B. Greco, T. Cardi, y P. Tripodi. 2016. Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing. BMC Genomics 17: 943-955.

Tizar, T.R., N.N.D. Ayu, K. Nugroho, D. Saptadi, H. Kurniawan, y P.D. Lestari. 2020. Analisis Keragaman Genetik dan Pengembangan Profil Sidik Jari DNA 20 Varietas Cabai Lokal Indonesia Berdasarkan Marka SSR. J. AgroBiogen 16(2): 45-58.

Toledo-Aguilar, R., H. López-Sánchez, A. Santacruz-Varela, E. Valadez-Moctezuma, P. Antonio-López, V.H. Aguilar-Rincón et al. 2016. Characterization of genetic diversity of native ‘Ancho’ chili populations of Mexico using microsatellite markers. Chilean J. of Agricultural Research 76(1): 18-26.

Wright, S. 1965. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19: 395-420.

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. J. of Integ Agric. 15(9): 1991-2001.



How to Cite

Gálvez-Muñoz, Y. A., Cea-Migenes, M. E., Ruíz Salazar, R., Castañón-Nájera, G., Latournerie-Moreno, L., & Ramírez-Meraz, M. (2024). Genetic differences and population structure of Capsicum spp. populations with simple sequences repets markers (SSRs). Bioagro, 36(1), 27-36.