Move over, Neolithic ancestors: Designer domesticates are here

Somewhere between reading Jared Diamond, joining a lab that studies the evolution of rice, and adding quinoa to my palate, I’ve come to have a very domestication-centric view of the world. Domestication refers to a process through which new populations, species, or subspecies of crops and animals arise from wild progenitors due to conscious or unconscious selection mediated by humans. Neolithic hunter-gatherers first started cultivating, and through selecting for desirable traits, domesticating crops such as wheat and barley more than ten thousand years ago. These innovations, which independently cropped up in a few sites across multiple continents, spread rapidly and led to a global transition from hunting and gathering to sedentary farming. Food surpluses, large populations, complex political economies, and major technological advances like writing directly followed.

Archaeobotanical examinations of crop remains support a slow process of initially unconscious selection of domestication traits after first bringing wild crops into cultivation, often taking place over thousands of years. In addition, domestication often proceeded via episodes of gene flow between multiple regional centers of cultivation. It should not be surprising, then, that it has been difficult for humans to replicate this complex and protracted process, and the ancient domesticates continue to feed the world.

With urbanization and climate change promising to rapidly and significantly reduce the amount of land that can be used to cultivate our current set of crops, there is motivation now to try and diversify our crop repertoire. There is growing interest, for instance, in deploying locally significant but globally underutilized crops such as groundnut and finger millet. Another approach, espoused by the new study that motivated this post, could be to simply edit new domesticates into existence. Decades of molecular research have equipped us with an understanding of the genetic bases of domestication traits in many different crop species, opening up the possibility of genetically manipulating wild crops to introduce these traits. You may rightly be wondering if it wouldn’t be easier to edit existing domesticates to help them grow in different climates, but there’s more than one way to cook your rice.

The study lays out a step-by-step guide to domesticating novel species of wild rice, more specifically allopolyploid wild rice species. Allopolyploid species arise from hybridization between individuals from different species and retention of both sets of chromosomes in the genome of the offspring. While extremely uncommon in animals, allopolyploidy has been frequently observed in plants, with these plants harboring greater genetic diversity and adaptive potential in the face of environmental change. The steps to domestication would be to, 1) select an appropriate wild rice species to start with, 2) create resources such as a sequenced and annotated reference genome, 3) introduce domesticated-related genes using gene-editing tools, and 4) finally push for social acceptance and consumption. If successful, the new allopolyploid species could have advantages over current domesticated rice varieties, which are diploid (having one set or pair of chromosomes).

The authors take us part of the way through step 3 to illustrate the feasibility of their proposed approach. After selecting the species Oryza alta based on how amenable it is to genetic transformation or modification, and assembling a reference genome sequence, they identified genes and their functions based on similarities to known genes in domesticated Asian rice (Oryza sativa). They then employed CRISPR/cas9 gene-editing to edit two genes controlling canonical domestication-related traits: shattering for seed release, and awn length for seed dispersal.

Wild grasses, including Oryza alta, tend to produce seeds that shatter and fall to the nearby ground, and have longer awn lengths to aid in dispersal. Humans, when they harvested grains from grasses using sickles, disproportionately collected seeds that had not shattered and were still on the plant, and over time selected for non-shattering varieties with reduced awn lengths. The authors in this study demonstrated the direct introduction of mutations conferring non-shattering seeds and reduced awn length using gene-editing, showing that it should be possible to similarly incorporate other domestication-related traits and create new domesticated crops.

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