Sequence information on single nucleotide polymorphism (SNP) through genome sequencing analysis of Carica papaya variety Eksotika and Sekaki

Norzihan Abdullah, . and Norliza Abu Bakar, . and Umi Kalsom Abu Bakar, . and Rabiatul Adawiah Zainal Abidin, . and Muhammad Fairuz Yusof, . Sequence information on single nucleotide polymorphism (SNP) through genome sequencing analysis of Carica papaya variety Eksotika and Sekaki. pp. 219-228. ISSN 1394-9829

Carica papaya L. is a tropical fruit and an important crop grown for export and local consumption. In this study three papaya varieties (Solo Eksotika and Sekaki) genome were sequenced using next generation sequencing platform for single nucleotide polymorphism (SNP) identification and selection. The assembly of Solo sequence reads and Sun Up papaya draft genome were used as reference sequences to align the two papaya genomes (Eksotika and Sekaki). The assembly of Solo sequence reads and Sun Up contigs have generated 23 318 scaffolds with the length of scaffolds above 200 bp. The papaya SNP discovery yielded 934 and 7 959 putative SNPs in Eksotika and Sekaki respectively. Our study demonstrated the utilisation of next generation sequencing technology coupled with bioinformatics approach for the selection of putative SNP markers that will be valuable for the development of papaya SNP markers. The SNPs identified will enable high throughput genotyping of papaya germplasm as well as a tool for marker assisted selection in papaya breeding program.

Full text available from: Official URL: http://jtafs.mardi.gov.my/jtafs/44-2/SNP.pdf

Abstract

Carica papaya L. is a tropical fruit and an important crop grown for export and local consumption. In this study three papaya varieties (Solo Eksotika and Sekaki) genome were sequenced using next generation sequencing platform for single nucleotide polymorphism (SNP) identification and selection. The assembly of Solo sequence reads and Sun Up papaya draft genome were used as reference sequences to align the two papaya genomes (Eksotika and Sekaki). The assembly of Solo sequence reads and Sun Up contigs have generated 23 318 scaffolds with the length of scaffolds above 200 bp. The papaya SNP discovery yielded 934 and 7 959 putative SNPs in Eksotika and Sekaki respectively. Our study demonstrated the utilisation of next generation sequencing technology coupled with bioinformatics approach for the selection of putative SNP markers that will be valuable for the development of papaya SNP markers. The SNPs identified will enable high throughput genotyping of papaya germplasm as well as a tool for marker assisted selection in papaya breeding program.

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Item Type:	Article
AGROVOC Term:	Carica papaya
AGROVOC Term:	Nucleotides
AGROVOC Term:	Polymorphism
AGROVOC Term:	Genomes
AGROVOC Term:	Gene sequence
AGROVOC Term:	Fruit crops
AGROVOC Term:	Identification
AGROVOC Term:	Selection
AGROVOC Term:	Bioinformatics
AGROVOC Term:	Genotypes
Depositing User:	Ms. Suzila Mohamad Kasim
Last Modified:	24 Apr 2025 06:28
URI:	http://webagris.upm.edu.my/id/eprint/24398

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