Whole Genome Resequencing of 205 Avocado Trees Unveils the Genomic Patterns of Racial Divergence in the Americas

Avocado (<i>Persea americana</i> Mill.) is one of the most widely consumed fruits worldwide. The tree species is traditionally classified into three botanical races: Mexican, Guatemalan, and West Indian (with a potentially distinct Colombian genepool). However, previous studies using molecular markers, such as AFLPs, microsatellites (SSRs), and GBS-derived SNP markers, have only partially resolved this racial divergence, especially in the hyper agrobiodiverse region of northwest South America. Therefore, in order to confirm genetic identity and origin of "criollo" avocado cultivars in the region, as well as to improve their traceability as rootstocks for the Hass variety, we performed low-coverage whole genome resequencing (lcWGS) on 205 ex situ conserved tree samples, comprising 42 commercial varieties and 163 "criollo" trees from various provinces in Colombia. This characterization yielded a total of 64,310,961 SNPs at an average coverage of 4.69×. Population structure analysis using principal component analysis (PCA) and ADMIXTURE retrieved at least five genetic clusters (<i>K</i> = 5), partly confirmed by Bayesian phylogenetic inference. Three clusters matched the recognized Mesoamerican botanical races (Mexican, Guatemalan, and West Indian), and two clusters reinforced the distinctness of two novel Andean and Caribbean Colombian genetic groups. Finally, in order to retrieve high-quality SNP markers for racial screening, a second genomic dataset was filtered, consisting of 68 avocado tree samples exhibiting more than 80% ancestry to a given racial cluster, and 9826 SNPs with a minimum allele frequency (<i>maf</i>) of 5%, a minimum sequencing depth (SD) of 10× per position, and missing data per variant not exceeding 20% (i.e., variants with genotypes present in at least 80% of the samples). This racially segregating high-quality subset was analyzed against the racial substructure using linear mixed models (LMMs), enabling the identification of 254 SNP markers associated with the five avocado genetic races. The previous candidate SNPs may be leveraged by nurseries and producers through a high-throughput SNP screening system for the racial traceability of seedling donor trees, saplings, and rootstocks. These genomic resources will support the selection of regionally adapted elite rootstocks and represent a landmark in Colombian horticulture as the first large-scale lcWGS-based characterization of a local avocado germplasm collection.