Genetic Variation Analysis of Four Local Varieties of Indonesian Black Rice (Oryza sativa L.) Based on Partially rbcL cpDNA Gene Sequence
DOI:
https://doi.org/10.21776/ub.jels.2021.011.01.01Abstract
Black rice (Oryza sativa L.) varieties i.e. Toraja (South Sulawesi), Cempo Ireng (Yogyakarta), Wojalaka (East Nusa Tenggara), and Manggarai (East Nusa Tenggara) are four local black rice varieties in Indonesia whose character has not been widely studied, especially the character of genetic variation. Research aimed to determine the variation of the rbcL gene in the four local black rice varieties. The sample for testing the variation of the rbcL gene sequence in the form of black rice leaves six weeks after planting. Dendogram was carried out using the UPGMA method with the Kimura 2-parameter algorithmic calculation model using the MEGA5 version 5.2.2 program. The results showed that partially the rbcL gene sequence was successfully amplified on four black rice varieties with a sequence length of 487 bp. The partial rbcL sequence of black rice consisted of 26.58% tyrosine, 21.38% cytosine, 28.86% adenine, and 23.18% guanine. The value of G + C content was 0.446, with the frequency of invariable sites of 97.13%. The frequency of informative parsimony sites was 1.43% with a nucleotide diversity (Pi) value of 42-10, the number of haplotypes was 5, and the total number of mutations and polymorphic sites was 14. The ratio between transition and transversion (ts/tv ratio k) for purine bases was 1.741 and pyrimidine was 3.571, with the estimated overall ratio between transition and transversion (R) of 1.31. Based on the dendogram, the farthest genetic distance was found in Wojalaka and Manggarai varieties, which were 0.019 respectively.
Keywords: black rice, genetic variation, local varieties, rbcL genDownloads
Published
Issue
Section
License
Authors who publish with this journal agree to the following terms:- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).