Genome wide association study and molecular marker development of an anthocyanin-related locus underlying the avocado (Persea americana) skin color

Authors: KHAN, ADLI - Oak Ridge Institute For Science And Education (ORISE); SHAMSELDEEN, EL-TAHER - Oak Ridge Institute For Science And Education (ORISE); Freeman, Barbara; Matsumoto Brower, Tracie; Domingo, Ryan; Ali, Gul

Submitted to: Horticulture Scientia
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/10/2026
Publication Date: 4/16/2026
Citation: Khan, A., Shamseldeen, E., Freeman, B.L., Matsumoto Brower, T.K., Domingo, R., Ali, G.S. 2026. Genome wide association study and molecular marker development of an anthocyanin-related locus underlying the avocado (Persea americana) skin color. Horticulture Scientia. https://doi.org/10.1016/j.scienta.2026.114813.
DOI: https://doi.org/10.1016/j.scienta.2026.114813

Interpretive Summary: Avocado consumption and demand in the United States have increased steadily. Currently, the U.S. imports about 90% of the avocados it consumes, highlighting large gap between domestic production and imports. To reduce reliance on imports, new varieties with expanded cultivation areas as well as consumer's preferred fruit quality traits including fruit skin color are needed. Avocado skin color is an important economic trait because it shapes consumer preference, affects marketability, and even helps determine harvest timing for some varieties. However, the genetics behind this trait are still poorly understood, and breeders currently lack molecular markers to predict skin color early in the breeding cycle. To address this gap, we combined high-density genetic data with skin-color evaluations at two locations and identified a single genomic region containing genes known to regulate anthocyanin production, the pigments responsible for purple coloration. To translate these findings into practical tools for breeding, we developed and validated molecular markers for the most significant genetic variants, successfully distinguishing purple- and green-skinned varieties across both study locations. These accomplishments help solve the original problem by revealing the genetic basis of avocado skin color and providing breeders with reliable DNA markers that enable early selection, ultimately speeding the development of new varieties suited to expanding avocado production in the United States.

Technical Abstract: Skin color of avocado fruit is an economically important trait that influences consumer preference, marketability, and serves as an indicator of harvest timing in some cultivars. Despite its significance, the genetic basis of skin color remains poorly understood, and no molecular markers have yet been developed. Understanding the underlying genetics will pave the way for the development of molecular markers, which could accelerate breeding efforts by enabling early selection of fruit skin color at the seedling stage. In the present study, a high-density genotyping dataset together with a highly reliable avocado skin color phenotype datasets collected at two different locations was used to perform a GWAS using a mixed linear model that accounts for population structure and kinship. We identified a single 220.93 kb region on chromosome CM056810.1 harboring 69 significant variants including 40 SNPs and 29 indels. This region contains 13 annotated genes, including five MYB transcription factors – most notably PAP1 and PAP2, known regulators of anthocyanin biosynthesis. Gene ontology enrichment analysis confirmed strong overrepresentation of anthocyanin-related pathways. Phylogenetic analysis revealed that MYB genes found in this region belong to subgroup 6 of the MYB family, which are known to contain positive regulators of anthocyanin biosynthesis across diverse crop species. Comparative genomics revealed tandem duplication and conservation of PAP1 homologs, suggesting evolutionary significance and potential functional redundancy. Furthermore, network analysis highlighted PAP1 as a central regulatory hub interacting with bHLH and WD40 partner, and light responsive elements, forming the MBW complex that modulates anthocyanin biosynthesis in response to environmental and developmental cues. These findings identify PaPAP1 as a strong candidate gene underlying avocado fruit skin color. For application in marker-assisted breeding, PCR allele competitive extension (PAmarkers were developed for the most significant SNPs and validated across in avocado varieties with purple and green skin across two different locations.