Keragaman Genetik Kultivar Padi Beras Hitam Lokal Berdasarkan Penanda Mikrosatelit

Abstract

Indonesia has diverse
accessions of local black rice, which are important sources
of germplasm. However, some of the local black rice
cultivars have different names, leading a need to be
identified to determine their genetic diversity using
molecular marker. This study aimed to identify genetic
diversity of eleven cultivars of local black rice, collection of
the Assessment Institute for Agricultural Technology,
Yogyakarta and compared them with two white rice
varieties using four microsatellite markers. Detection of
microsatellite alleles polymorphism was carried out by
visualization of PCR amplicons by electrophoresis on
agarose gel. To estimate their genetic diversity, phylogenetic
tree and principal coordinate analysis were performed using
binary data of SSR alleles. The results revealed that total
markers enabled to differentiate black rice cultivars as
reflected by high value of polymorphic information content
(PIC) mean (0.695). This value was consistent with the high
genetic diversity of black rice (genetic diversity index, h =
0.283) in comparison with white rice cultivars (h = 0.020).
The phylogenetic and main coordinate analyses suggested
that black rice cultivars genetically differed from white rice.
The local black rice cultivars were preferentially grouped
based on their genetic those were distributed in three
coordinates and did not represent their local geographic
origin. Genetic diversity analysis in this study will be useful
as an initial basis for proper identification and selection for
appropriate parents to assist breeding program of black rice
in Indonesia.