Identification of simple sequence repeat markers using restriction site-associated DNA sequencing (RADSeq) of Garcinia prainiana


Citation

Siti Nadrah Abd Hisham, . and Muhammad Fairuz Mohd Yusof, . and Azuan Amron, . and Khairun Hisam Nasir, . and Siti Norsaidah Ibrahim, . Identification of simple sequence repeat markers using restriction site-associated DNA sequencing (RADSeq) of Garcinia prainiana. pp. 174-185. ISSN 2462-1757

Abstract

Garcinia prainiana (cerapu) is an underutilized fruit and native to Malaysia. A restriction site-associated DNA sequencing (RADSeq) of G. prainiana DNA using restriction enzyme EcoR1combined with Illumina paired-end sequencing generated a clean data of 910.3 Mbp reads. Data assemblies produced 245 721 scaffolds with 38.05 guanine-cytosine (GC-content). These sequences were mined for simple sequence repeats (SSRs) and a total of 5 086 SSRs were identified which consisted of mono- (33.21) di- (19.94) tri- (13.43) tetra- (1.91) penta- (0.59) and hexanucleotide (0.11) repeats. From the 100 SSRs selected for fragment analysis of cerapu accessions 11 polymorphic SSRs were identified and a phylogenetic tree was generated which consisted of two main groups.


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Abstract

Garcinia prainiana (cerapu) is an underutilized fruit and native to Malaysia. A restriction site-associated DNA sequencing (RADSeq) of G. prainiana DNA using restriction enzyme EcoR1combined with Illumina paired-end sequencing generated a clean data of 910.3 Mbp reads. Data assemblies produced 245 721 scaffolds with 38.05 guanine-cytosine (GC-content). These sequences were mined for simple sequence repeats (SSRs) and a total of 5 086 SSRs were identified which consisted of mono- (33.21) di- (19.94) tri- (13.43) tetra- (1.91) penta- (0.59) and hexanucleotide (0.11) repeats. From the 100 SSRs selected for fragment analysis of cerapu accessions 11 polymorphic SSRs were identified and a phylogenetic tree was generated which consisted of two main groups.

Additional Metadata

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Item Type: Article
AGROVOC Term: Genetic markers
AGROVOC Term: Molecular markers
AGROVOC Term: Sampling
AGROVOC Term: Data analysis
AGROVOC Term: Genetic diversity within species
Depositing User: Mr. AFANDI ABDUL MALEK
Last Modified: 24 Apr 2025 00:55
URI: http://webagris.upm.edu.my/id/eprint/10537

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