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Genetic Variation and Phylogenetic Analysis of Strawberry ( Fragaria spp.) on Yogyakarta and Central Java, Indonesia, Based on rbc L DNA Barcoding.

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Název: Genetic Variation and Phylogenetic Analysis of Strawberry ( Fragaria spp.) on Yogyakarta and Central Java, Indonesia, Based on rbc L DNA Barcoding.
Autoři: Aristya GR, Budiman MS, Kasiamdari RS, Widiastuti A, Arif MF
Zdroj: Pakistan journal of biological sciences : PJBS [Pak J Biol Sci] 2025 Feb; Vol. 28 (3), pp. 121-130.
Způsob vydávání: Journal Article
Jazyk: English
Informace o časopise: Publisher: Asian Network for Scientific Information Country of Publication: Pakistan NLM ID: 101247723 Publication Model: Print Cited Medium: Internet ISSN: 1812-5735 (Electronic) Linking ISSN: 10288880 NLM ISO Abbreviation: Pak J Biol Sci Subsets: MEDLINE
Imprint Name(s): Original Publication: Faisalabad : Asian Network for Scientific Information
Výrazy ze slovníku MeSH: Phylogeny* , Genetic Variation*/genetics , Fragaria*/genetics , Fragaria*/classification , DNA Barcoding, Taxonomic*/methods , DNA, Plant*/genetics, Indonesia ; Haplotypes ; Fruit/genetics
Abstrakt: <b>Background and Objective:</b> Strawberry (<i>Fragaria</i> spp.) is known for producing fruit with high economic value and significant nutritional content. Recently, the growing diversity of cultivated strawberries in Indonesia has made it challenging to distinguish the original characteristics of early ancestors and identify superior traits. The DNA barcoding, mainly through the chloroplast gene <i>rbc</i>L, offers a precise and detailed method for this identification. This research aims to reconstruct a phylogenetic tree, analyze genetic variation and determine the haplotype distribution of six strawberry cultivars from Java, particularly Yogyakarta and Central Java, based on the <i>rbc</i>L gene. <b>Materials and Methods:</b> The <i>rbc</i>L gene was amplified using DNA amplification techniques with <i>rbc</i>L-F and <i>rbc</i>L-R primers. The resulting data were analyzed to construct a phylogenetic tree using ML via IQtree software and BI using MrBayes software. The alignment results were used to determine genetic distances and identify polymorphic sites. This study assessed intraspecific genetic variation by examining h, identifying polymorphic sites, generating a haplotype network using PopART v1.7 and conducting PCoA with GenAIEx 6.503. <b>Results:</b> The results showed that the <i>rbc</i>L gene was successfully amplified with a length of 1,221 bp after alignment with the GenBank database. Phylogenetic analysis using ML revealed that the six cultivars formed a single clade with a bootstrap value of 97. BI similarly indicated the formation of one clade with a posterior probability value of 1. Haplotype analysis showed that the cultivars 'Californica', 'Knia', 'Mencir', 'Moha' and 'Geolhyang' belonged to the same haplotype group, while the 'Bali×Jumbo' cultivar was placed in a different group. <b>Conclusion:</b> Haplotype network analysis and PCoA further indicated that the genetic variation of Indonesian strawberries, as assessed through the <i>rbc</i>L gene, is similar to strawberries from the United States and China.
Contributed Indexing: Keywords: Bayesian inference; DNA barcoding; genetic distance; maximum-likelihood; rbcL
Substance Nomenclature: 0 (DNA, Plant)
Entry Date(s): Date Created: 20250625 Date Completed: 20250625 Latest Revision: 20250625
Update Code: 20250625
DOI: 10.3923/pjbs.2025.121.130
PMID: 40556097
Databáze: MEDLINE
Popis
Abstrakt:&lt;b&gt;Background and Objective:&lt;/b&gt; Strawberry (&lt;i&gt;Fragaria&lt;/i&gt; spp.) is known for producing fruit with high economic value and significant nutritional content. Recently, the growing diversity of cultivated strawberries in Indonesia has made it challenging to distinguish the original characteristics of early ancestors and identify superior traits. The DNA barcoding, mainly through the chloroplast gene &lt;i&gt;rbc&lt;/i&gt;L, offers a precise and detailed method for this identification. This research aims to reconstruct a phylogenetic tree, analyze genetic variation and determine the haplotype distribution of six strawberry cultivars from Java, particularly Yogyakarta and Central Java, based on the &lt;i&gt;rbc&lt;/i&gt;L gene. &lt;b&gt;Materials and Methods:&lt;/b&gt; The &lt;i&gt;rbc&lt;/i&gt;L gene was amplified using DNA amplification techniques with &lt;i&gt;rbc&lt;/i&gt;L-F and &lt;i&gt;rbc&lt;/i&gt;L-R primers. The resulting data were analyzed to construct a phylogenetic tree using ML via IQtree software and BI using MrBayes software. The alignment results were used to determine genetic distances and identify polymorphic sites. This study assessed intraspecific genetic variation by examining h, identifying polymorphic sites, generating a haplotype network using PopART v1.7 and conducting PCoA with GenAIEx 6.503. &lt;b&gt;Results:&lt;/b&gt; The results showed that the &lt;i&gt;rbc&lt;/i&gt;L gene was successfully amplified with a length of 1,221 bp after alignment with the GenBank database. Phylogenetic analysis using ML revealed that the six cultivars formed a single clade with a bootstrap value of 97. BI similarly indicated the formation of one clade with a posterior probability value of 1. Haplotype analysis showed that the cultivars 'Californica', 'Knia', 'Mencir', 'Moha' and 'Geolhyang' belonged to the same haplotype group, while the 'Bali×Jumbo' cultivar was placed in a different group. &lt;b&gt;Conclusion:&lt;/b&gt; Haplotype network analysis and PCoA further indicated that the genetic variation of Indonesian strawberries, as assessed through the &lt;i&gt;rbc&lt;/i&gt;L gene, is similar to strawberries from the United States and China.
ISSN:1812-5735
DOI:10.3923/pjbs.2025.121.130