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Almond Genome Sequenced

The domesticated almond tree (Prunus amygdalus) has been feeding humans for millennia. Derivation from the wild, bitter, and toxic almond required loss of the cyanogenic diglucoside amygdalin. A team of European scientists has sequenced the almond genome and analyzed the genomic region responsible for this shift.

Almond kernels.

Almond kernels.

The almond is the main tree nut species worldwide, with a cultivated area of about 1.9 million ha and an annual in-shell production exceeding 2.2 million tons.

It’s thought that its initial domestication occurred in the Near East sometime during the first half of the Holocene, a hypothesis supported by early archaeological evidence of the nut in both ancient Egypt and Greece.

Kernels (seeds) of wild almond species are bitter and highly toxic to humans and predators because they accumulate a toxic compound called amygdalin.

Previous studies have suggested that the domestication was enabled by the selection of sweet, edible kernel genotypes, which originated within the inedible wild genotypes.

Despite the distribution and economic importance of the almond, however, a detailed understanding of its genome has lagged behind that other species in the Rosaceae family of plants, and the nature of the gene that allowed for edible, sweet kernel nuts has remained elusive.

Now Dr. Raquel Sánchez-Pérez from the Unviersities of Espinardo and Copenhagen, Dr. Stefano Pavan from Italy’s Institute of Biomedical Technologies and the University of Bari and their colleagues have assembled the draft genome of the sweet almond cultivar Lauranne.

What’s more, the researchers used the sequence to reveal the genetic differences between toxic, bitter almonds and their sweet counterparts.

“We discovered a cluster of five basic helix-loop-helix transcription factors, bHLH1 to bHLH5, associated with sweet kernel genotypes,” they said.

Among these, bHLH2 was revealed to be involved with the regulation of the biosynthetic pathway for the production of amygdalin.

A mutation in bHLH2 prevents amygdalin production, resulting in the sweet almond genotype, which was actively selected for during domestication.

“Our results provide insights into almond domestication history, as well as a sequence inventory for studies of other almond agronomic traits such as flowering time, drought tolerance, and resistance to disease,” the scientists said.

The findings were published in the journal Science.


R. Sánchez-Pérez et al. 2019. Mutation of a bHLH transcription factor allowed almond domestication. Science 364 (6445): 1095-1098; doi: 10.1126/science.aav8197

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