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The history of two beans, the history of all beans

Text by Agustín Ávila Casanueva

Illustration by Santiago da Silva y Daniela Correa Field



In Mexico, legend has it that there is a god in the shape of a snake but covered in feathers that goes by the name of Quetzalcóatl, who created our world and created us. Quetzalcóatl also purveyed us with food, which is why he turned into a black ant, to go behind a red ant and get the corn that would give us strength. But corn wasn’t enough, Quetzalcóatl wanted to get the black corn, the white corn, the bean, chia and all the foods found in the hill of subsistence, for which he called upon Nanáhuatl to destroy the hill with his lightening bolt and the gods of rain to snatch the food found there. Science now tells us that at least two of these hills must have existed.

The bean had a single origin as a wild legume more than 168,000 years ago somewhere in America. In its coming and going through the American woods and jungles, the Mesoamerican bean gave way to a different variety, that of the Andes, some 165,000 years ago. By that time, the two sub-species had small seeds and although there was a greater variety among wild Mesoamerican beans, it didn’t compare to the variety that we know today.

Domestication generated the great diversity of beans we know as well as enlarged the side of its seed and the quantity of seeds per pod, as well as the quantity of pods per plant. This amazing process through which corn, pumpkin and chili also went through – the rest of their peers in the field- not only took place in Mexico, but also in South America.

To reach this conclusion, it is not enough to simply add more water to the beans, a group of researchers from different institutions and universities in the United States and France, lead by Jeremy Schmutz obtained a draft of the unfathomable genome of the wild bean, Phaseolus vulgaris. And with 80% of the total genome sequence, they were able to tell large part of its history.

The domestication left indelible marks on the genes. When we compare the genes of wild beans with those of domesticated beans, we can see that those that played an important role in the domestication have one or multiple changes in their sequence, but with an important characteristic: they’re always the same and they’re always there. They’re fixed.

Things weren’t easy for Jeremy and his team. They were trying to find two versions of these fixed variations, two ways to convert a wild bean into one worthy of being cooked; they found the story of two beans.

When they saw in greater detail the different varieties of the bean they had sequenced – aside from the genome of the wild bean, Jeremy and his colleagues sequenced 160 varieties of bean cultivated throughout America -, they found that there were certain adaptations for different zones. A greater resistance to altitude and cold weather in the Andean varieties, for example. Thus, there were two adaptations, two stories within the genomes.

There’s more to mutations than adaptations and physiological changes, there are also changes in the gene sequence that do not greatly alter the capacities or qualities of the plant. They are called neutral mutations, mutations that do not benefit nor damage the individual, but create a change in its genome. The rhythm with which these mutations occur is almost constant, like the needles of a clock, and when counted, the passage of time can be calibrated, a molecular clock can be calculated. For these two beans, their clock tells us that both domestications occurred – in Mexico and somewhere in South America -, some 8,000 years ago.

The researchers of this study were able to “cook the beans to perfection” solely using their DNA sequences and their point of origin. Not bad for researchers that, like the rest of us, are made of corn.

Walter Krickeberg. Mitos y leyendas de los aztecas, incas, mayas y muiscas, Mexico: Fondo de Cultura Económica, 1971.

Brandon S. Gaut. “The complex domestication history of the common bean”, Nature Genetics46, 663–664 (2014) doi:10.1038/ng.3017, 26 June 2014.


Jeremy Schmutz et al. “A reference genome for common bean and genome-wide analysis of dual domestications”, Nature Genetics46, 707–713 (2014) doi: 10.1038/ng.3008, 08 June 2014.

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