Identifying key genes controlling flesh colour in mangoes using genome-wide association studies (GWAS)

Abstract

Mango flesh colour when fully ripe can range from pale-yellow to dark orange, largely depending on the cultivar. The consumer preference of this pulp colour can vary depending on the geographical region and culture, leading to a need for breeders to efficiently produce cultivars of desired colours. This study utilised a genome-wide association study (GWAS) to identify candidate genes and potential molecular markers for flesh colour. The GWAS consisted of using genomic single nucleotide polymorphism (SNP) data and corresponding flesh colours across 201 cultivars of mangoes. After pruning of the SNP data set, the GWAS utilised 871,835 SNPs resulting in a total of 87 associated genes using the top 0.01% of -log10(P) values. A gene ontology (GO) enrichment analysis indicated an association with the category for ‘biotic stress response’ for biological processes, however further investigation is required to understand the direct or indirect effect of each of the 87 associated genes on flesh colour.