A genome-wide association study identifed SNP markers and candidate genes associated with morphometric fruit quality traits in mangoes

Authors: SHAMSELDEEN, ELTAHER - Oak Ridge Institute For Science And Education (ORISE); LI, JIN - Oak Ridge Institute For Science And Education (ORISE); Freeman, Barbara; Singh, Sukhwinder; Ali, Gul

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/22/2025
Publication Date: 2/7/2025
Citation: Shamseldeen, E., Li, J., Freeman, B.L., Singh, S., Ali, G.S. 2025. A genome-wide association study identifed SNP markers and candidate genes associated with morphometric fruit quality traits in mangoes. Horticulture Research. https://doi.org/10.1186/s12864-025-11278-6.
DOI: https://doi.org/10.1186/s12864-025-11278-6

Interpretive Summary: Mango, considered as the king of fruit is a popular fruit around the world and has seen increased popularity in the United States lately. The genetic basis of currently grown culitvars is narrow, which make them prone to diseases and pests and also does not capture the wide variety of flavors and nutritional benefits that are available in different mango cultivars and crop wild relatives. There is a need for breeding new superior varieties with a wider genetic basis that are adapted to a wider geoclimatic conditions, has desirable fruit quality traits and nutritional profiles. However, due to its long juvenile period, large trees sizes and complex genetics makes breeding mango difficult, time consuming and costly. Application of marker-assisted selection strategies and genomic selection approaches that allow selection of fruit quality and nutritional traits as well as tree canopy structure at the seedling stage would speed up breeding new mango cultivars. In this report, ARS scientists identified molecular markers for desirable fruit quality traits. In addition, based on genetic diversity and allele variation, a new approach crosses is suggested, which identified approximately two dozen mango accession as the most promising parents for crossing to produce novel hybrid mangoes. Application of this strategy as well as these markers along with additional markers in conjunction with genomic selection tools are expected to improve the genetics of germplasm by introgressing desirable alleles from distantly related accessions including crop wild relatives.

Technical Abstract: Mangos (Mangifera indica L.) are a widely grown fruit tree crop across the world, but breeding new varieties can take several years due to the long juvenile period and high heterozygosity. Marker-assisted selection can accelerate breeding new mango cultivars for desirable traits for fruit quality, storage, horticulture, pest and disease resistance, and nutrition. To achieve this, a genome-wide association study (GWAS) was conducted to discover molecular markers for fourteen morphometric and economically important fruit traits of 192 mango accessions with diverse genetic backgrounds. These traits included pulp and brix; fruit weight, length, thickness, and width; stone weight, length, thickness, and width; and seed weight, length, thickness, and width. In this report, we employed the fixed and random model circulating probability unification (FarmCPU) model for conducting GWAS using 135,079 high-quality SNP markers. These analyses revealed 159 SNPs that were significantly associated with these traits. Of these markers, twenty-six were commonly associated with different traits, while 133 markers were uniquely associated with specific traits. To select the most promising mango accessions for future breeding crossing and for closing genetic gaps among the accessions and increasing genetic diversity, a new approach is suggested based on phenotypic traits such as high-yielding mango fruit cultivars, number of reference alleles, and genetic distance among the selected parents. Based on these criteria, twenty accessions were considered the most promising parents for crossing to produce high mango yield. Gene annotation of the significant markers revealed candidate genes coding for important proteins, enzymes, and transcription factors associated with fruit development traits.