Characterisation of selected Hass avocado (persea americana mill. Var. Hass) genotypes for future creation of an elite, true-to-type germplasm collection

Abstract

This study focused on characterising of Hass avocado (Persea americana. Mill.Var Hass) at National Forestry Resources Research Institute (NAFORRI) mother garden in Uganda addressing the limited genetic diversity that restricts avocado production in the region. The study aimed at developing an elite true-to –type germpalsm collection. The study utilised DArT-Seq, a highthroughput DNA sequencing technology used to identify genetic variations across genomes by identifying Single Nucleotide Polymorphisms (SNP) to examine genetic variation within the Hass Avocado trees at NAFORRI. The aim was to support future development of a genetically diverse, robust Hass avocado population in Uganda by understanding and preserving essential genetic traits. BLASTn analysis was used to trace genetic relationships, comparing sequences from 288 accessions from the mother garden to the reference genome (GCA_002908915.1) of the Hass cultivar, provided by Hainan University, China. Detailed morphological assessments of each Hass avocado tree, examining traits like fruit dimensions (average length and width), growth characteristics (number of branches, crown width and tree height), and productivity (number of fruits per tree) was done. Observed phenotypic variations were attributed to the diverse microclimatic, soil, and management conditions within the NAFORRI mother garden. ANOVA (Analysis of Variance) showed no significant morphological differences between the trees. This indicated that the observed phenotypic similarities suggest a common ancestral origin for the Hass avocado trees. The genetic diversity analysis for the Hass avocado tree samples that could be sequenced, found low levels of observed and expected heterozygosity (Ho = 0.0014, He = 0.0016, and Ht = 0.0016) and a positive inbreeding coefficient (FIS = 0.1342) suggested that the Hass trees were genetically homogeneous. The results from the BLASTn analysis showed a high level of genetic similarity, with 45 accessions displaying 100% match, and were classified as “Exact Matches”. 116 accessions that showed 95-99% identity were classified as “True-to-Type” for Hass avocado. The 51 accessions that demonstrated 85-95% identity were classified as “Related”. Lastly 58 accessions that had less than 70% identity were categorized as “Divergent” indicating divergence from the Hass reference genome. These four categories (Exact matches, True-to-type, Related and Divergent) highlighted varying levels of homogeneity within the mother garden, revealing that while the collection retained high fidelity to the Hass cultivar, it may lack the genetic diversity required for long-term breeding goals. Findings suggest that the current population may not provide the genetic base necessary for sustainable Hass avocado breeding in Uganda. Future research should focus on identifying trees with key traits such as diseases resistance, early maturity and superior fruit quality to serve as parent material for breeding programs for lines that are not only true-to-type but also better suited to Uganda’s unique environmental conditions. By addressing these genetic limitations, the study supports future efforts to develop a resilient and productive Hass avocado industry in Uganda.