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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences BIOTROPIA - The Southeast Asian Journal of Tropical Biology Agrovigor: Jurnal Agroekoteknologi Biotropika Jurnal Teknologi Pertanian AGRIVITA, Journal of Agricultural Science Buletin Kebun Raya JURNAL BIOLOGI INDONESIA Jurnal Ilmiah Pertanian BIOLINK (Jurnal Biologi Lingkungan, Industri, Kesehatan) Jurnal Biologi Tropis Jurnal Biotek
Lia Hapsari
Purwodadi Botanic Garden
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Computer Science & IT Education Environmental Science Immunology & microbiology Veterinary

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Journal : Biotropika

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Identification and Genetic Diversity of Pineapple Local Accessions from Kediri and Closely Related Species (Bromeliaceae) Based on matK Gene Rasyadan Taufiq Probojati; Hadiyanti, Nugraheni; Hapsari, Lia
Biotropika: Journal of Tropical Biology Vol. 12 No. 3 (2024)
Publisher : Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2024.012.03.01

Abstract

Ananas comosus L. belongs to the Bromeliaceae family and has around eight subfamilies. Accessions of local pineapple have spread widely in several areas, one of which is in Kediri. However, some accessions and closely related species (Bromeliaceae) likely remain poorly understood relationships. The highly diverse morphological characters and low levels of sequence divergence in Bromeliaceae have been problematic in resolving the reconstruction of phylogenetic relationships. This study aimed to evaluate the efficiency of the matK gene as a DNA barcode to determine genetic diversity and reconstruct a phylogenetic tree in local pineapple and closely related species (Bromeliaceae). A total of 15 specimens were used in this research, of which 7 were local pineapple accessions from Kediri and eight were closely related species from the Bromeliaceae family. Whole genome DNA was isolated using a Tiangen kit and amplified using the polymerase chain reaction (PCR) technique using a specific primer. The results showed that matK was easily amplified with a DNA fragment length of 750-800 bp. The average composition value of each base was 36.9% T (U) bases, 30.1% in A bases, 15.9% in G bases, and 17.1% in C. BLAST analysis of the sequences showed that all samples were confirmed and identified according to the species names spread across local pineapple production areas (with query cover of 96-98%). However, the species names registered in the PBG database were confirmed to be different species but still in the same genus, i.e., samples B9-B14. The phylogenetic relationship analysis distinguished each accession into two large clades according to sub-families, i.e., Bromelioideae and Pitcairnioideae. This research shows that the matK gene is suitable and recommended as a DNA barcode for local pineapple and closely related species.
Phenotypic Variation and RAPD Polymorphism of Pisang Kepok Local Cultivars (Musa acuminata x Musa balbisiana, ABB, Saba Subgroup) Wahyudi, Didik; Ilmi, Zahrobatul Lil; Hapsari, Lia
Biotropika: Journal of Tropical Biology Vol. 10 No. 3 (2022)
Publisher : Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2022.010.03.03

Abstract

Pisang Kepok is a major local banana cultivar in Indonesia with high economic, social and cultural value. Particularly on the island of Java, there are several variations of Pisang Kepok recognised with their own local names, which makes difficulties in taxonomic identification and grouping. Morphological features are used in conventional banana cultivar classification, but they are deemed less precise due to their subjectivity, thus, it is supposed to be complemented with a molecular approach. This study aims to identify the phenotypic variation of Pisang Kepok local cultivars also their genetic polymorphism using Random Amplified Polymorphic DNA marker. Phenotypic variation was observed using 35 morphological characters. Six RAPD primers were used, i.e. OPA2, OPA3, OPA4, OPA11, OPA12, and OPA18. Clustering analysis, both phenotypic and genetic were performed using PAST v4.02. The morphological characterisation identified four variants of Pisang Kepok i.e. Kepok Abang, Kepok Putih, Kepok Manurun, and Kepok Australi; which all confirmed as ABB genome group. Phenotypic clustering showed that Pisang Kepok cultivars were separated into 3 clusters based on their local name, with a high similarity value of >90%. PCA biplot showed that the fruit flesh colour was the most important character contributed to the cultivar variation. RAPD marker also showed that each specimen was grouped according to its local name and source, with a similarity value of >80%. Both morphology and molecular (RAPD) markers resulted in the branching of Pisang Kepok which was closer to Pisang Klutuk than Pisang Barlin.
Co-Authors Abdul Basith Abywijaya, Ilham Kurnia Ade Meylisa Crystel Rohie Ahmad Masrum Catur Retnaningdyah Devina Cinantya Anindita Dewi Ayu Lestari Didik Wahyudi Edy Kustiani Gusmiati, Lutfiana Hasanah Hari Rusdwi Novitasiah Ilmi, Zahrobatul Lil Maic Audo Lin Sihombing Mas'udah, Shofiyatul Mudinillah, Adam Munawaroh, Putri Syepty SriJanatul Nareswari, Aptika Hana Prastiwi Nugraheni Hadiyanti Ramadhan, Riski Jefri Rasyadan Taufiq Probojati Ridesti Rindyastuti Santoso, Yusuf Saputra, Yudha Setyawan Agung Danarto Siti Nurfadilah Supandji, Supandji Trimanto Trimanto Widya Dwi Rukmi Putri