The most comprehensive study of the donkey genome provides new data on its evolutionary history and the influence of selection on coat pigmentation

Crag News

The most comprehensive study of the donkey genome provides new data on its evolutionary history and the influence of selection on coat pigmentation

CRAG researchers M. Amills and A. Noce have participated in this large study led from China
Donkeys with different coat pigmentation (Credit: Melanie van de Sande/Pixabay)
Donkeys with different coat pigmentation (Credit: Melanie van de Sande/Pixabay)

The so far most exhaustive population genetics study on donkey evolution has just been published this week in Nature Communications. The study sheds light on when, where and how donkey domestication occurred, and on the reproductive management effects on the species variability. The study, led by Dr Changfa Wang from the Shandong Academy of Agricultural Sciences and researchers from other Chinese institutions, has counted with the participation of the CRAG researchers Marcel Amills and Antonia Noce, and the researcher from the Autonomous University of Barcelona (UAB) Jordi Jordana.

The study involved the de novo assembly of a high-resolution chromosome-level reference genome of one male donkey and the sequencing of the genomes of 126 domestic donkeys from nine countries encompassing four continents (Africa, Europe, Oceania, and Asia). The study also included resequencing data from seven wild asses (6 African and 1 Asian). Unlike previous work, millions of genetic markers (17 million autosomal polymorphisms) with a uniform distribution throughout the donkey genome have been used for this large population genetics study.

The research published this week confirms the results of a previous study published in 2004 using mitochondrial DNA (inherited only through the mother), which indicated that donkey was domesticated in Northeast Africa 6000 years ago from the African wild ass (Equus africanus), and not from the Asian wild ass (Equus hemionus). The authors of the new study point out that there is not yet enough evidence to state whether the domestication process took place in one or more geographic areas, or whether it involved one or more subspecies, reinforcing the need to sequence a broad collection of ancient and modern African samples from wild asses and domestic donkeys.

Genetic consequences of the selection process

The study reveals that, contrary to what had been previously described, there was a significant reproductive bias in donkey’s evolutionary history, as a result of the selective process that took place during or after domestication. 

“The variability of the donkey Y chromosome is pretty low, much lower than the mitochondrial variability. This suggests that, historically, as has already been shown in the horse, a low number of male donkeys were intensively used as breeders, mating with numerous females”, explains the UAB Associate Professor and CRAG researcher Marcel Amills.

Furthermore, the researchers have also studied the imprint of selection on two clearly differentiated coat pigmentation patterns in donkeys: the Dun pattern, more ancestral, characterized by a strong dilution of pigmentation - individuals are gray or light chestnut-, and the so-called non-Dun, in which this dilution of the coloration does not exist and, therefore, the individuals, essentially domestic donkeys, display non-diluted black or chestnut coat colors.

The research team found that a mutation in the TBX3 gene is responsible for the non-Dun coloration in donkeys. In horses, two different mutations from that observed in donkeys, but located in the same gene, are responsible for the non-Dun coloration. Hence, this work has shown that the biochemical basis of pigmentation dilution is very similar in horses and donkeys, since in both species the TBX3 gene affects the symmetry of the distribution of pigment granules in the hair.

“This result shows that the process of selection of undiluted colorations that took place in horses and donkeys thousands of years ago, possibly at the beginning of domestication, convergently targeted the same gene (TBX3) in both species,” says Marcel Amills. “The reason for selecting coat color is not known. Perhaps on a whim or for practical reasons, such as facilitating the location of animals, or for cultural or religious reasons”, he adds.


Article of Reference: Changfa Wang et al. Donkey genomes provide new insights into domestication and selection for coat color (2020) Nature Communications
A Spanish and Catalan longer version of this news piece can be find at the Universitat Autònoma de Barcelona (UAB) website.