Comprehensive population genetics and genome-wide association studies revealed the genetic basis of avocado fruit quality traits

Authors: LI, JIN - Orise Fellow; ELTAHER, SHAMSELDEEN - Orise Fellow; Freeman, Barbara - Barbie; Singh, Sukhwinder; Ali, Gul - Shad

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/22/2024
Publication Date: 8/13/2024
Citation: Li, J., Eltaher, S., Freeman, B.L., Singh, S., Ali, G.S. 2024. Comprehensive population genetics and genome-wide association studies revealed the genetic basis of avocado fruit quality traits. Frontiers in Plant Science. 15. https://doi.org/10.3389/fpls.2024.1433436.
DOI: https://doi.org/10.3389/fpls.2024.1433436

Interpretive Summary: Avocado - popularly know as a superfood - has gained tremendous popularity and an increase in consumption and demand worldwide. With increased demand there is a need for new superior varieties that are adapted to a wider geoclimatic conditions, has desirable fruit quality traits. Avocados breeding is costly and time consuming due to its long juvenile period, large trees sizes and complex genetics. Application of molecular tools that enable predicting mature tree traits, such as fruit quality traits, at the seedling stage would speed up breeding this increasingly important fruit crop. In this report, ARS scientists accomplished identification of molecular markers for several fruit quality traits such as fruit color, taste, shape and skin texture. Application of these markers in breeding are expected to significantly improve and accelerate breeding avocado varieties with desirable fruit quality traits.

Technical Abstract: Avocado (Persea americana) is a highly nutritious fruit gaining popularity worldwide. However, its cultivation is currently reliant on a limited number of cultivars with limited genetic diversity. This situation calls for the development of new avocado cultivars with improved horticultural, fruit quality, and nutritional traits, as well as resistance to diseases and pests, and adaptability to changing climatic conditions. The potential of marker-assisted selection in accelerating the development of new avocado varieties offers a ray of hope for the future of avocado cultivation, promising a brighter and more diverse avocado market. This report investigated the genetic diversity and population structure of a diversity panel of 110 avocado accessions. We also conducted genome-wide association studies (GWAS) targeting nine fruit-quality traits using 4,706 high-quality single nucleotide polymorphisms (SNPs) with two different models: GLM (PCA) and MLM (PCA + K). Our analysis revealed three distinct populations, each corresponding to one of the three avocado ecotypes. Phylogenetic analysis showed a close relationship between the Guatemalan and West Indian races, compared to the Mexican race, supported by population pairwise FST analysis. GWAS identified 12 markers within 11 genomic regions strongly associated with fruit quality traits, including fruit color, shape, taste, and skin texture. These markers collectively explained an average of 25% of the variation in these traits. Annotation analyses of these genomic regions unveiled candidate genes responsible for controlling these traits. These findings provide a better understanding of the genetic composition of avocado germplasm and offer valuable insights into the genes that govern fruit quality traits. These could significantly impact breeding and parent selection efforts to improve avocado cultivars.