Association analysis for pomological traits in mango (Mangifera indica L.) by genic-SSR markers

A set of five genic-SSR markers ( p < 0.1) are significantly associated ( r (2) = 19.92%) with six critical pomological traits. This information will facilitate marker-assisted genetic enhancement in mango. India is considered the home of mango cultivation and is the highest contributor to the global mango production. However, India has low productivity because of the lack of understanding of the genomic complexity of regular bearing habit, fruit quality, and yield-related traits. In the present investigation, 17 critical pomological traits in mango were mapped through genome-wide association mapping using the generalized linear model (GLM) and mixed linear model (MLM) approaches. Significant phenotypic variability in the selected traits was observed in 60 mango varieties, which indicated the suitability of these varieties for association studies. Genotyping of the varieties was performed using 87 polymorphic genic-simple sequence repeats (SSR) markers. Population structure analysis performed using the genotyping data revealed three distinct sub-populations that corroborated with the geographical origin of the varieties. Subsequently, the association analysis performed using the GLM identified 23 genic-SSR markers associated with 13 different pomological traits. However, only five genic-SSR markers were associated with six different pomological traits in MLM approach. The A and C alleles of the MSSR 190 locus were significantly associated with fruit diameter, pulp: stone ratio and fruit weight with significant phenotypic variance, and the B allele of the MSSR 146 locus was associated with fruit length and fruit width in both the GLM and MLM approaches with a high amount of phenotypic variance. The ranges of phenotypic variation explained by the associated loci were 13.18-42.39 and 13.31-27.34% in the GLM and MLM approaches, respectively. Extensive phenotypic and genotypic characterization of mango varieties, population structure, and markers associated with critical traits provided in this study will facilitate marker-assisted improvement programs in mango.