Avocado Genome is at the Center of New Study

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Despite the popularity of the avocado, the fruit is dominated by a single variety: Hass. A perennial, subtropical crop grown in both the U.S. and Mexico, the Hass has some breeding challenges. So University of California (UC) researchers turned to “Gwen,” a descendant variety of Hass, in an effort to map a different avocado (Persea americana) genome to further explore the fruit’s evolutionary history.

UC President’s Postdoctoral Fellow at UC Davis, Edwin Solares and his team used Expanse at the San Diego Supercomputer Center (UC San Diego) and Bridges and Bridges-2 at the Pittsburgh Supercomputing Center (Carnegie Mellon) to run genome assembly, alignment and simulations for the study, conducted while Solares was a postdoctoral researcher at UC Irvine’s Department of Ecology and Evolutionary Biology. Results of the study were recently published in an article entitled, Insights into the domestication of avocado and potential genetic contributors to heterodichogamy in the Genes, Genomes, Genetics journal.

Solares explained that the Hass avocado accounts for approximately 90 percent of avocado cultivation worldwide, thus dominating the market. Yet avocados are very genetically diverse mainly because there are three botanically domesticated groups: Lowland (also known as West Indian), Mexican and Guatemalan.   

“Due to the different morphologies of the avocados between the groups and genetic data, it is suggested that they have been domesticated separately,” Solares said. “Because of this, the groups likely have varying alleles and therefore different genes of interest for crop improvement.” 

According to the scientist, this is important because avocado breeding currently remains challenging due to the fruit’s slow maturity, reproductive system and heterodichogamy nature — trees exhibit both male and female traits but at different times of the day. 

“Because the Hass genome is the only variety of avocados that has been deciphered, we chose to map the genome of ‘Gwen,’ a different variety of avocado, to use it for evolutionary analysis of the avocado,” Solares said. “The Gwen avocado is largely unexplored, so we examined the domestication history and chromosomal regions of potential agronomic interest using evolutionary genomic tools with a focus on genomic diversity in the context of interesting traits, like A vs B flowering types.”

The Gwen variety contains similar characteristics of the Hass but produces higher yields and presents better fruit storage on the avocado tree. It has been subjected to intensive breeding efforts for the past three decades, partly motivating researchers to create a Gwen reference, such as the one that Solares developed in his work.

“We utilized a whole-genome resequencing data set including 34 avocado accessions and produced a genome of 1,456 Mb with 5,122 contigs,” Solares said. “Our analyses implied that three independent domestication events occurred due to the presence of genetic mutations unique to each of the three groups, with Mexican avocados being the most genetically distant.”