Genetic diversity of sugar palm (Arenga pinnata) derived from nine regions in Indonesia based on SSR markers

Rinawati, Dian Yunita; Reflinur, Reflinur; Dinarti, Diny; Sudarsono, Sudarsono

doi:10.13057/biodiv/d220919

Cited by 6 publications

(6 citation statements)

References 27 publications

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“…Pontederia korsakowii and P. vaginalis have the closest genetic distance (0,004), while P. spinescens and L. minor showed the furthest distance (0,164). The kinship relationship between these species can influence genetic distance in species with a large or small value (Rinawati and Dinarti 2021). Pontederia korsakowii and P. vaginalis are related to each other.…”

Section: Discussionmentioning

confidence: 99%

Diversity of aquatic plants in the Rote Dead Sea area, East Nusa Tenggara, Indonesia, based on rbcL marker

LONTHOR

Miftahudin²,

KAYAT³

et al. 2023

Biodiversitas

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Abstract. Lonthor DW, Miftahudin, Kayat, Julzarika A, Subehi L, Iswandono E, Dima AOM, Dianto A, Setiawan F, Nugraha MFI. 2023. Diversity of aquatic plants in the Rote Dead Sea area, East Nusa Tenggara, Indonesia, based on rbcL marker. Biodiversitas 24: 810-818. The Rote Dead Sea area in Rote Islands has two freshwater and 24 saltwater lakes. The saltwater lakes have salinity levels varied between 0-100 ppt. Every lake has specific aquatic plant species. Species identification through morphological analysis only has its limitations; therefore, DNA barcoding is a preference due to an effective, accurate, and faster method for species identification. In this study, we used the rbcL marker to identify and analyze the diversity of the aquatic plant species in lakes Ledulu, Oenduy, Oemasapoka, Oesotimori, and Landu Leko. Plants samples' DNA was amplified using rbcL primers, and the amplicons were sequenced. Species identification was based on morphological study and the rbcL sequence database. Diversity analyses were performed based on pairwise genetic distances, analysis of molecular variance, and genetic relationships based on the Kimura 2 parameter. The results showed that all 20 aquatic plants were correctly identified, and high genetic diversity was discovered. AMOVA analysis showed that genetic variations within the population were higher than among the population. All plant species were grouped into four groups based on the phylogenetic tree and fractional component analyses. The species belonging to the certain family were grouped in the same clade and the closely related plant families. The rbcL marker can be used to discriminate aquatic plant species and analyze their genetic diversity and relationships.

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Section: Discussionmentioning

confidence: 99%

Diversity of aquatic plants in the Rote Dead Sea area, East Nusa Tenggara, Indonesia, based on rbcL marker

LONTHOR

Miftahudin²,

KAYAT³

et al. 2023

Biodiversitas

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“…Genetic diversity analysis DARWin software has also successfully been carried out in oil palm (Nugroho et al 2019), sugar palm (Rinawati et al 2021), and date palm (Huda et al 2019). Clustering using DARwin software was commonly used to evaluate the genetic diversity of the evaluated samples based on dominant and co-dominant data (Saha et al 2019).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis

et al. 2022

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Abstract. Hatta ANNL, Sukma D, Maskromo I, Sudarsono. 2022. Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis. Biodiversitas 23: 5122-5131. The coconut (Cocos nucifera L.) genome sequences were available at the chromosome level in 2019, and they can be used to develop the whole genome SSR markers. This study aimed to conduct in silico analysis of the whole coconut genome to mine SSR sequences, design SSR markers distributed across coconut chromosomes, validate the designed primers to generate SSR markers, and use them for the phylogenetic analysis of coconuts. The SSR loci were mined from publicly available coconut genomes. Targeted primers for amplifying 20 dinucleotide SSR loci were selected and used for phylogenetic analysis of coconuts. The SSR mining identified 543,774 dinucleotide repeat motifs across the coconut genome, and most of the dinucleotide SSRs are AG (46.18%) and AT (40.03%) repeats. Primer pairs targeted to amplify 876 SSR loci and distributed in 16 coconut chromosomes were successfully designed and deposited in a public data repository for public access. The 237 SSR primer loci were novel and could generate new SSR markers. Among 20 selected and tested primers, 18 produced SSR markers, and 15 pairs yielded polymorphic markers when used to evaluate 25 coconut accessions. The analysis showed that the designed SSR primers were informative for evaluating coconut genetic diversity and phylogenetic analysis.

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“…Young leaves were harvested from selected palms and sent to Plant Molecular Biology (PMB) Laboratory, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University. Total DNA was isolated from leaf samples (0.3 g) using standard cetyltrimethylammonium bromide (CTAB) procedures, routinely used for DNA isolation in the palm species (Larekeng et al 2015a, b;Natawijaya et al 2019;Rinawati et al 2021). The isolated DNA was resuspended in 50-100 µL of aqua bidest and checked for its quantity using 0.8% agarose gel electrophoresis.…”

Section: Plant Materials and Dna Isolationmentioning

confidence: 99%

Genetic diversity analysis of Puan Kalianda kopyor coconuts (Cocos nucifera) from South Lampung, Indonesia based on SSR markers

Rahayu

Setiawan²,

Maskromo³

et al. 2021

Biodiversitas

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Abstract. Rahayu MS, Setiawan A, Maskromo I, Purwito A, Sudarsono. 2021. Genetic diversity analysis of Puan Kalianda kopyor coconuts (Cocos nucifera) from South Lampung, Indonesia based on SSR markers. Biodiversitas 23: 205-211. Puan Kalianda kopyor coconut (Cocos nucifera L.) is a newly released tall kopyor coconut from Kalianda, South Lampung, Indonesia. The kopyor coconut is an exotic, highly economic value coconut mutant with an abnormal endosperm. This study aimed to analyze the genetic diversity of Puan Kalianda kopyor coconut from South Lampung, Indonesia using SSR markers. As many as 91 Puan Kalianda kopyor coconut accessions were genotyped using 10 SSR marker loci, and the generated data were used to evaluate their genetic diversity and population structure. The results showed a high degree of SSR marker polymorphism (PIC value = 67%), indicating the SSR marker loci are informative for revealing the genetic diversity within the evaluated Puan Kalianda kopyor coconut population. The Puan Kalianda coconut population showed a 70% expected heterozygosity (He) and 60% observed heterozygosity. The phylogenetic analysis formed two main clusters, and each cluster consisted of three sub-clusters. The Genetic structure analysis showed that the population most probably derived from two ancestral origins (K = 2) and can further be clustered into six sub-clusters (K = 6). Therefore, since genetic diversity within the population is relatively high, the Puan Kalianda tall kopyor coconut population can be considered an essential genetic resource for future kopyor coconut development.

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Genetic diversity of sugar palm (Arenga pinnata) derived from nine regions in Indonesia based on SSR markers

Cited by 6 publications

References 27 publications

Diversity of aquatic plants in the Rote Dead Sea area, East Nusa Tenggara, Indonesia, based on rbcL marker

Diversity of aquatic plants in the Rote Dead Sea area, East Nusa Tenggara, Indonesia, based on rbcL marker

Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis

Genetic diversity analysis of Puan Kalianda kopyor coconuts (Cocos nucifera) from South Lampung, Indonesia based on SSR markers

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