Could Colombian avocado trees hold overlooked genetic diversity useful for breeding future varieties?

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Genomic characterization of ex situ plant collections—collections maintained outside their natural habitats—can improve the use of genetic resources by identifying redundant accessions, revealing hidden variation, establishing reference collections, and supporting pre-breeding and breeding efforts.

However, evolutionary genomic analyses are often missing from studies of biodiversity within crop gene pools. This is also the case for avocado, Persea americana Mill., an iconic fruit tree crop of the Americas whose nutritional properties have driven unprecedented worldwide expansion. With commercial production relying on a very restricted number of clones, avocado plantations are becoming more vulnerable to diseases and climate change. This makes it important to explore sources of evolutionary novelty and genetic diversity beyond commercial varieties derived from traditional gene pools in Mexico and Central America.

The researchers aimed to characterize the genomic diversity of Colombian avocado trees. In this observational genomic study, they constructed reduced representation genomic libraries and used genotyping by sequencing on 144 accessions from the Colombian National genebank and 240 materials from local commercial orchards in the Colombian northwest Andes. They combined the resulting sequencing reads with available sequences of reference genotypes from the three known avocado groups, also called races—Mexican, Guatemalan, and West Indian—and identified 4931 single-nucleotide polymorphisms (SNPs). They then analyzed population structure and phylogenetic diversity and reconstructed evolutionary scenarios that might have led to new genetic groups in Colombian germplasm.

They detected demographic stratification despite evidence of gene flow between groups. Beyond the three classical avocado groups, they identified a distinct Colombian group, with possible genetic substructure related to Andean and Caribbean geographical origins. Phylogenetic analyses and ABC demographic modeling suggested that the Colombian group evolved in the Pleistocene, before human agriculture began, and that its closest relative among the three recognized races would be the West Indian group.

The researchers conclude that northwest South America offers a hidden source of novel alleles that could strengthen avocado pre-breeding strategies, helping select rootstock candidates well adapted to specific eco-geographical regions in Colombia and abroad.