Genetic diversity in the germplasm of black pepper determined by EST-SSR markers

Abstract

ABSTRACT. This study aimed to assess genetic diversity in the germplasm of black pepper from around the world using SSR markers from EST. In total, 13 markers were selected and successfully amplified the target loci across the black pepper germplasm. All the EST-SSR markers showed high levels of polymorphisms with an average polymorphism information content of 0.93. The genetic similarity coefficients among all accessions ranged from 0.724 to 1.000, with an average of 0.867. These results indicated that black pepper germplasms possess a complex genetic background and high genetic diversity. Based on a cluster analysis, 148 black pepper germplasms were grouped in two major clades: the Neotropics and the Asian tropics. Peperomia pellucida was grouped separately and distantly from all other accessions. These results generally agreed with the genetic and geographic distances. However, the Asian tropics clade did not cluster according to their geographic origins. In addition, compared with the American accessions, the Asian wild accessions and cultivated accessions grouped together, indicating a close genetic relationship. This verified the

Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications

“…In another study, the molecular characterization carried out using SSR markers could demarcate Indian and exotic Piper species [54]. Genetic diversity assessed using 13 EST SSR markers detected high genetic diversity among 148 black pepper germplasm [13]. These reports are in congruence with the present study in black pepper where a high genetic diversity is observed among the 30 landraces of black pepper at 50 identified SSR loci.…”

“…Western Ghats, especially the Kerala state of India harbours the maximum genetic diversity of black pepper [8]. However, there have been a very few studies on genetic diversity using molecular markers [9–13] primarily due to limitations in genetic resources availability. Therefore black pepper remained largely untouched from genomic interventions.…”

“…In black pepper there have been only a few reports of generation of SSRs [13, 22]. Lately, transcriptome based approaches have been employed for generation of SSRs in black pepper [23–24].…”

Karakterisasi Keragaman Genetik 27 Genotipe Cabai Berdasarkan Marka SSR (Simple Sequence Repeat)

“…SSR merupakan sekuen pendek (2 -4 nukleotida) berulang yang keberadaannya melimpah dalam genom organisme eukariotik (Ting et al, 2010), bersifat kodominan (Chiang et al, 2012;Surapaneni et al, 2013), serta mudah dalam aplikasinya (Prasetiyono dan Tasliah, 2004). Di luar negeri, marka SSR telah banyak digunakan untuk mengidentifikasi keragaman genetik plasma nutfah cabai (Kwon et al, 2005;Hanáček et al, 2009;Nicholai et al, 2013;Dhaliwal et al, 2014;Carvalho et al, 2015;Jiaowen et al, 2016;Wu et al, 2016;Pachecolvera et al, 2012). Penelitian mengenai analisis keragaman genetik cabai telah dilakukan sebelumnya di Indonesia oleh Rosyadi (2007), tetapi marka yang digunakan masih terbatas hanya pada marka morfologi dan biokimia serta genotipe yang digunakan merupakan genotipe koleksi IPB.…”

“…Nilai PIC pada penelitian ini berkisar antara 0,598 (CaSSRBio3.1) hingga 0,920 (CaSSRBio2.1) dengan rerata sebesar 0,758. Kisaran nilai PIC pada penelitian ini lebih tinggi dibandingkan hasil penelitian Oh et al (2012) dengan kisaran 0,061-0,63; Tilahun et al (2013) dengan kisaran 0,00-0,75; dan Chamikara et al (2015) dengan kisaran 0,65-0,88, namun lebih rendah dari hasil penelitian Wu et al (2016) dengan kisaran nilai PIC 0,91-0,96; dan Aguilar et al (2016) dengan kisaran 0,14-1,00. Seluruh marka SSR yang digunakan dalam penelitian ini memiliki nilai PIC >0,5, sehingga berdasarkan kriteria Botstein et al (1980) keseluruhan marka SSR tersebut dikategorikan sebagai marka sangat informatif yang bermanfaat untuk karakterisasi genotipe-genotipe cabai kedepannya (Tabel 2).…”