Identification of Single Nucleotide Polymorphisms Associated with Fruit Sweetness in Dragon Fruit (Hylocereus spp.): An Integrated Bioinformatics and Multi-Omics Analysis

DOI

10.2991/978-94-6239-821-4_11How to use a DOI?

Keywords

Dragon fruit (Hylocereus spp.); Single Nucleotide Polymorphism (SNP); fruit sweetness; whole-genome sequencing; bioinformatics pipeline; variant calling; RNA-seq; metabolomics; marker-assisted selection

Abstract

Dragon fruit (Hylocereus spp.) has grown into a tropical crop of real commercial importance, valued for its nutrition, antioxidant content, and expanding market demand worldwide. Sweetness is arguably the trait consumers notice first, and it isn’t controlled by a single gene but by an interlinked set of genetic and metabolic pathways. Mapping the genomic variation behind sweetness could give breeders a genuine head start when applying marker-assisted selection. With that in mind, this study set out to identify single nucleotide polymorphisms (SNPs) linked to fruit sweetness in dragon fruit, using publicly available next-generation sequencing (NGS) datasets alongside an integrated bioinformatics pipeline.

Whole-genome sequencing data from sweet and less-sweet cultivars formed the starting point. We first ran quality checks (FastQC, MultiQC) and trimmed adapters, then aligned the reads to the chromosome-level pitaya reference genome using BWA-MEM. Variants were called with GATK and the resulting SNPs filtered against standard quality thresholds. SnpEff annotation against the pitaya GFF3 gene models placed each SNP in its genomic context and predicted its likely biological effect, with special attention given to SNPs located in genes tied to sugar metabolism, carbohydrate transport, and ripening — namely the SWEET, SUT, SPS, SUS, and invertase families.

Genotype data alone only tells part of the story, so RNA-seq expression profiles and metabolomics measurements of soluble sugar accumulation were layered onto the SNP calls. Population structure, principal component, correlation, and SNP–trait association analyses, run in PLINK, TASSEL, and R, then narrowed the field down to variants significantly associated with sweetness. What emerged is a set of high-confidence SNP markers tied to sweetness-related traits, along with a clearer picture of the genetic architecture driving sugar accumulation in dragon fruit. These resources are meant to support functional genomics, quantitative trait analysis, and marker-assisted breeding aimed at sweeter, higher-quality cultivars.

Copyright

© 2026 The Author(s)

Open Access

Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

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TY  - CONF
AU  - Vedaanshi Verma
AU  - Preenon Bagchi
PY  - 2026
DA  - 2026/10/31
TI  - Identification of Single Nucleotide Polymorphisms Associated with Fruit Sweetness in Dragon Fruit (Hylocereus spp.): An Integrated Bioinformatics and Multi-Omics Analysis
BT  - Proceedings of the International Conference on Information Systems Design And Intelligent Applications (ICISDA 2026)
PB  - Atlantis Press
SP  - 113
EP  - 131
SN  - 1951-6851
UR  - https://doi.org/10.2991/978-94-6239-821-4_11
DO  - 10.2991/978-94-6239-821-4_11
ID  - Verma2026
ER  -