Study of the genetic diversity and structure of a natural population of Nectandra megapotamica (Spreng.) Mez. using RAPD markers

Abstract

ABSTRACT. Nectandra megapotamica (Spreng.) Mez. is a tree species that naturally occurs in the Atlantic Forest, Brazil. The aim of this study was to evaluate the genetic diversity and structure of a natural population of 12 N. megapotamica individuals using random amplified polymorphic DNA markers. Eleven primers were used in this study, producing 81 bands, of which 98.99% were polymorphic. Analysis using STRUCTURE defined three different clusters (K = 3), results that were consistent with those of principal coordinates analysis. Both Nei's genetic diversity (h = 0.33) and Shannon's diversity index (I = 0.49) were relatively high. Analysis of molecular variance indicated that 24.89% of the genetic variability was among clusters, while the remaining 75.11% was within clusters. The Mantel test showed a weak correlation between genetic and geographic distances (r = 0.25, P = 0.105). Overall, the results revealed high levels of genetic diversity within clusters and high genetic differentiation among clusters without any spatial pattern of genetic variability. In addition, gene flow was independent of the geographical distribution and was compatible with the hierarchical island model.

Research Article Diversity and genetic structure of the native Brazil nut tree (Bertholletia excelsa Bonpl.) population.

“…Such genetic structure pattern meets the studies in the literature: tropical tree species reproducing through allogamy maintain greater genetic variability proportion within populations than between populations (Zucchi et al, 2005). Costa et al (2015) studied the genetic structure of a Nectandra megapotamica population and found greater diversity within groups (75.11%) than among groups (24.89%). Soares (2016) observed the same effect when he studied the genetic diversity of a native Hancornia speciosa population; the greatest genetic variation occurred within groups (83.39%), rather than between groups (16.61%).…”

Molecular analysis of genetic diversity among vine accessions using DNA markers

“…Random amplified polymorphic DNA (RAPD) markers are one of the most widespread markers applied to the breeding of several crops, due to their ease of use, speed, and low cost. They are used to estimate genetic distance between populations, and to characterize germplasm banks or collections (Han et al, 2014;Mendes et al, 2014;Asad et al, 2015;Costa et al, 2015;Santos et al, 2015;Sharaf-Eldin et al, 2015). This is also true for vine crops, and RAPD markers have been used in diversity studies, marker-assisted selection, in the distinction of varieties confirming and/or rejecting hypotheses of synonymy, determining distribution and relationships with geographic areas and other variables, and also for the study of natural processes of evolution, migration, and selection (Moreno et al, 1995;Lahogue et al, 1998;Vidal et al, 1999Vidal et al, , 2000Tamhankar et al, 2001;Ulanovsky et al, 2002a;Schneider et al, 2015).…”

HUBUNGAN KEKERABATAN Shorea gysbertsiana DENGAN TIGA JENIS SHOREA PENGHASIL TENGKAWANG LAINNYA BERDASARKAN PENANDA RAPD

“…Penanda ini berdasarkan pada teknik PCR (Polymerase Chain Reaction) yang menggunakan DNA dalam jumlah yang kecil sehingga metode ini sesuai jika diterapkan pada materi genetik sedikit atau spesies yang terancam punah dengan materi genetik terbatas. Beberapa jenis tanaman hutan yang baru-baru ini dikarakterisasi menggunakan penanda RAPD diantaranya adalah Caesalpinia pulcherrima (L.) Sw. (Rodrigues, Mazzini, Pivetta, Alves, & Desidério, 2012), Poincianella pyramidalis (Mendes, Araujo Neto, Nascimento, & Lima, 2014), Calophyllum brasiliense (Schühli, Oliveira, Oliveira, & Fowler, 2013), Hancornia speciosa Gomes (Da Silva, Rabbani, De Sena-Filho, Almeida, & Feitosa, 2012), dan Nectandra megapotamica (Costa, Reiniger, Heinzmann, Amaral, & Serrote, 2015 Pemilihan penanda RAPD dilakukan menggunakan 49 penanda RAPD (Operon Technologies) dari 13 set penanda yaitu set penanda A, B, C, D, E, G, N, O, Q, R, X, Y, dan Z (Sulistyawati, data tidak dipublikasikan). Proses seleksi penanda didasarkan pada pemilihan penanda yang mempunyai jumlah pola pita DNA polimorfik paling banyak, variasi fragmen, tingkat reprodusibilitas dan kejelasan pita DNA yang teramplifikasi.…”