Genomic-Wide Association Studies For Resistance to Anthracnose in a Pseudo-F2 Mango Population

Goal: This study aimed to apply genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with resistance to mango anthracnose. Theoretical Framework: The statistical methods of GWAS aim to identify associations among genotypes with phenotypes for marker-assisted selection (MAS) or genome dissection of important traits. Method: Ninety-four plants of a ‘Haden’ × ‘Tommy Atkins’ pseudo-F2 population were genotyped with 705 SNPs and phenotyped for resistance to Colletotrichum siamense, anthracnose causal agent, by spraying young leaves, three times at different periods, with 103 conidia/mL. Qualitative GWAS, with Plink Fisher’s exact test and Cochran-Armitage trend genotypic test, and quantitative GWAS, with Tassel general (GLM) and mixed linear models (MLM) were applied. F2 plants with symptoms mean absence >75% were considered moderately resistant to the fungus. Results and discussion: Qualitative and quantitative GWAS methods combined enable the identification of two consensus SNP loci controlling 24.76% of total variance to mango anthracnose resistance. Other four SNPs, identified, exclusively in quantitative or qualitative analysis, explained 28.55% of total variance to mango anthracnose. These SNPs loci are promising candidate for further PCR primers design in order to apply MAS in mango. Research implications: This study facilitates the identification of consensus chromosomal regions associated with mango anthracnose resistance. The application of MAS in mango breeding will accelerate the development of new cultivars. Originality/Value: To our knowledge, this a pioneering GWAS study applied to anthracnose, which is the most significant and widespread fungal disease affecting mango fruit globally.