Assessment on Genetic Diversity and Relationship of 19 Bird Pepper Genotypes Based on Morphological and SSR Markers

Rustikawati Rustikawati, Catur Herison, Mimi Sutrawati, Wuri Prameswari

Abstract


A comprehensive assessment of genetic diversity offers invaluable insights to breeders. This study aims to analyze the genetic diversity of 19 cayenne pepper genotypes using morphological and SSR markers.  Morphological markers are essential for evaluating visible traits while SSR markers provide deeper insights into genetic variation. Using both morphological and SSR markers provides a more robust, multidimensional approach to understanding genetic diversity. Morphological characterization was conducted on 19 bird pepper genotypes using 30 distinct traits, further divided into 95 sub-traits, to evaluate vegetative and generative growths. Molecular profiling was carried out using 10 SSR primers. The SSR analysis yielded 80 scorable bands, of which 72 were polymorphic. The high polymorphic information content suggests that these markers were effective in differentiating the genotypes.   The genetic diversity within the population was substantially high, providing valuable genetic material for breeding programs. Genetic similarity analysis divided the population into six distinct groups. Among them, Group I (genotype A05 Taiwan) and Group VI (genotype A02, Bengkulu Indonesia) formed unique, solitary groups, distinguishing them from other clusters. This information is highly beneficial for bird pepper cultivar development, emphasizing the importance of incorporating additional traits to align with the cultivar development of high yielding and saline-stress tolerance.


Keywords


Capsicum; Genetic similarity; Molecular marker; Polymorphic Information Content; Principal Component Analysis

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References


Arrufitasari, P. N., Sutjahjo, S. H., & Wirnas, D. (2022). Performance of tomato M7 mutant lines and their similarities to the parents based on SSR markers. Biodiversitas Journal of Biological Diversity, 23(3), 1239-1245. DOI

Avval, S. E. (2017). Assessing polymorphism information content (PIC) using SSR molecular markers on local species of Citrullus colocynthis. Case study: Iran, Sistan-Balouchestan province. Journal of Molecular Biology Research, 7(1), 42-49. DOI

Baba, V. Y., Rocha, K. R., Gomes, G. P., De Fátima Ruas, C., Ruas, P. M., Rodrigues, R., & Gonçalves, L. S. A. (2016). Genetic diversity of Capsicum chinense accessions based on fruit morphological characterization and AFLP markers. Genetic Resources and Crop Evolution, 63(8), 1371–1381. DOI

Badan Pusat Statistik. 2023. Produk-Tabel Statistik Pertanian, Kehutanan, Perikanan. Badan Pusat Statistik (BPS). website

Bhandari, H. R., Bhanu, A. N., Srivastava, K., Singh, M. N. & Shreya, H.A. (2017). Assessment of genetic diversity in crop plants - an overview. Advances in Plants & Agriculture Research, 7(3), 279‒286. DOI

Castillo-Aguilar, C. C., Castilla, L. L., Pacheco, N., Cuevas-Bernardino, J. C., Garruña, R., & Andueza-Noh, R. H. (2021). Phenotypic diversity and capsaicinoid content of chilli pepper landraces (Capsicum spp.) from the Yucatan Peninsula. Plant Genetic Resources, 19(2), 159-166. DOI

Colney, L., Tyagi, W. & Rai, M. (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. DOI

Deviona, Syukur, M., Zuhry, E., Armaini, Yunandra & Riska, F. (2023). Principal component and cluster analyses of 20 genotypes of chilli (Capsicum sp.) planted on peatlands. IOP Conference Series: Earth and Environmental Science, 1228(1), 012003. DOI

Dos S. Pessoa, A. M., Rêgo, E. R., Barroso, P. A., & Rêgo, M. M. (2015). Genetic diversity and importance of morpho-agronomic traits in a segregating f2 population of ornamental pepper. Acta Horticulturae, 1087, 195–200. DOI

Fu, Y.B. (2015). Understanding crop genetic diversity under modern plant breeding. Theoretical and Applied Genetics, 128(11), 2131–2142. DOI

Gurung, T., Sitaula, B. K., Penjor, T. & Tshomo, D. (2020). Genetic diversity of chili pepper (Capsicum spp.) genotypes grown in Bhutan based on morphological characters. SABRAO Journal of Breeding and Genetics, 52(4), 446–464. PDF

Herison, C., Handajaningsih, M., Fahrurrozi, & Rustikawati. (2017). Wet season trials on growth and yield of six newly developed chili pepper hybrids at three different locations. International Journal on Advanced Science, Engineering and Information Technology, 7(5), 1913-1919. DOI

Herison, C., Rustikawati, Meita R., & Hasanudin. (2020). Analisis cluster dan seleksi primer SSR (Simple Sequence Repeats) untuk sifat toleran aluminium pada cabai. Jurnal Hortikultura Indonesia (JHI), 11(1), 61-71. DOI

Herison, C., Surmaini, E., Rustikawati, R., & Yulian, Y. (2018a). Morphological characterization of 10 hot pepper genotipes in low altitude location. Akta Agrosia, 21(2), 47–54. DOI

Herison, C., Sutjahjo, S.H., Sulastrini, I., Rustikawati & Marwiyah, S. (2018b). Genetic diversity analysis in 27 tomato accessions using morphological and molecular markers. AGRIVITA, Journal of Agricultural Science, 40(1), 36-44. DOI

Herison, C., Winarsih, S., Handayaningsih, M., & Rustikawati. (2012). DNA marker-assisted and morphological selection on BC3 genotypes shortcut the introgression of CMV tolerance genes on chili pepper. AGRIVITA Journal of Agricultural Science, 34(3), 215-224. DOI

Idrees, M, & Irshad, M. (2014). Molecular markers in plants for analysis of genetic diversity: A review European Academic Research, 2(1), 1513-1540

IPGRI, AVRDC and CATIE. (1995). Descriptors for Capsicum (Capsicum spp.). International Plant Genetic Resources Institute. Asian Vegetable Research and Development Center, Taipei, Taiwan

Jindal, S.K., Dhaliwal M.S., Vikal Y. & Meena, O.P. (2021). Species diversity of genus Capsicum using agromorphological descriptors and simple sequence repeat markers. Indian Journal of Experimental Biology, 59, 906-915. DOI

Karim, K. M. R., Rafii, M. Y., Misran, A., Ismail, M. F., Harun, A. R., Ridzuan, R., Chowdhury, M. F. N., Hosen, M., Yusuff, O. & Haque, M. A. (2022). Genetic diversity analysis among Capsicum annuum mutants based on morpho-physiological and yield traits. Agronomy, 12, 2436. DOI

Korir, N.K., Diao, W., Tao, R., Li, X., Kayesh, E., Li, A., Zhen, W. & Wang, S. (2014). Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers. Genetics and Molecular Research, 13(1), 43-53. DOI

Legendre, P. & Legendre, L. (2012). Numerical Ecology. Third Edition. Elsevier. Amsterdam. 990p

Loseñara, J. M. M., & Ylanan, L. (2019). Morphological variability of the chili, Capsicum annuum (L.) grown within Cebu Province. Journal of Agriculture and Technology Management (JATM), 22(2), 13-18

Nascimento, K.S., Rêgo, M.M., Nascimento, A.M.M. & Rêgo, E.R. (2015) Ethyl methanesulfonate in the generation of genetic variability in Capsicum. Acta Horticulturae, 1087, 357–363. DOI

Peñuela, M., Arias, L.L., Viáfara-Vega, R., Franco, N.R. & Cardenas, H. (2021). Morphological and molecular description of three commercial Capsicum varieties: a look at the correlation of traits and genetic distancing. Genetic Resources and Crop Evolution, 68, 261–277. DOI

Poudyal, D, Joshi, B. K., Singh, K. P., Shakya, S. M., Ottosen, C. & Dahal, K. C. (2023). A review of the diversity, distribution, and uses of Akabare chili landraces (Capsicum spp.) in Nepal, Scientia Horticulturae, 311, 111799. DOI

Rahevar, P. M., Patel, J. N., Axatjoshi, Sushilkumar, & Gediya, L. N. (2021). Genetic diversity study in chilli (Capsicum annuum L.) using multivariate approaches. Electronic Journal of Plant Breeding, 12(2), 314-324. DOI

Ramalho Do Rêgo, E., & Monteiro Do Rêgo, M. (2016). Genetics and breeding of chili pepper Capsicum spp. In E. Ramalho Do Rêgo, M. Monteiro Do Rêgo, & F. L. Finger, Production and Breeding of Chilli Peppers (Capsicum spp.) (pp. 57–80). Springer International Publishing. DOI

Rohlf, F.J. (2000). NTSYSpc numerical taxonomy and multivariate analysis system (Version 2.1): User guide.

Rustikawati, Herison, C., Sutrawati, M., & Umroh, D. (2023). Assessment of salinity tolerance on chili pepper genotypes. E3S Web of Conferences, 373, 03023. DOI

Sarmah, P., Sarma, D., & Gogoi, S. (2018). Genetic diversity, phylogenetic tree and principal component analysis based on morpho-metric traits of Assam chilli. Journal of Plant Genetics and Crop Research, 1(1), 47–61. DOI

Sharifova, S.S., Mehdiyeva, S.P. & Abbasov, M.A. (2017) Analysis of genetic diversity among different tomato genotypes using ISSR DNA marker. Genetika, 49(1), 31-42. DOI

Silva, W.C., de Carvalho, S.I.C., & Duarte, J.B. (2013). Identification of minimum descriptors for characterization of Capsicum spp. germplasm. Horticultura Brasileira, 31(2), 190-202. DOI

Virga, G., Licata, M., Consentino, B.B., Tuttolomondo, T., Sabatino, L., Leto, C. & La Bella, S. (2020) Agro-morphological characterization of sicilian chili pepper accessions for ornamental purposes. Plants, 9, 1400. DOI




DOI: http://doi.org/10.17503/agrivita.v47i1.4447

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