• A genome-wide association study identified a 220.93 kb region on the avocado chromosome CM056810.1 containing 69 significant variants associated with avocado fruit skin color. • Five MYB transcription factors, including strong candidates PAP1 and PAP2, were discovered within this region, supported by gene ontology enrichment for anthocyanin biosynthesis pathways. • Phylogenetic and comparative genomics analyses revealed conservation and tandem duplication of PAP1 homologs, suggesting functional redundancy in regulating anthocyanin production. • Network analysis identified PAP1 as a central regulatory hub interacting with bHLH, WD40, and light-responsive elements, forming the MBW complex known to modulate anthocyanin biosynthesis. • Competitive allele-specific PCR markers developed from top SNPs were validated across diverse avocado varieties across two different locations, providing practical tools for accelerating marker-assisted breeding for fruit skin color. 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 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 of this region 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 regulators of anthocyanin biosynthesis across diverse crop species. Comparative genomics revealed tandem duplication and conservation of PAP1 homologs, suggesting 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 markers were developed for the most significant SNPs and validated in avocado varieties with purple and green skin across two different locations.
Khan et al. (Sun,) studied this question.