Wednesday, January 4, 2017

Early Chile Domestication

I first discussed Capsicum annuum var. glabriusculum in an earlier post. I've collected wild seeds for this species from a few different sources throughout the desert southwest.

The two views at right are the same plant, grown from seed collected in Phoenix-Az. The comparison of above and side views shows how well the down-hanging fruit of this plant are hidden from above, where birds would be more likely to see them while flying overhead. Since birds are the primary distributors of wild chile seeds, this trait would not encourage dispersal of the seeds and so the trait would not spread.

Early human farmers would have found this trait useful, as it would help reduce crop loss to birds. The majority of non-ornamental chile varieties grown today share this trait.

The lack of any other traits associated with domestication make me think this plant either represents the impact of selection pressure by early farmers, or a much more recent introgression event where all the other modern traits were heavily selected against. The seeds were wild-collected in Arizona (where humans have been living and using chiles for thousands of years) and modern chiles are commonly grown in the area, so either scenario is likely.

An approach which might help clarify the plant's ancestry is to compare its genome to more domesticated types. If it has this trait due to a modern introgression, there will be regions of its genome that match the relatively low diversity found in domesticated chiles. If it has had this trait for far longer, it's genome will be covered in variations not found in domesticated chiles.

Processing out some genomic DNA (gDNA) is a pretty easy thing. The difficulty will come in getting the material sequenced. I do have reasonably simple access to a nanopore DNA sequencer, but the data that comes from that technology has been problematic for some whole genome analyses in my experience (and in the experience of others). Ideally I'd have the gDNA sequenced using Illumina technology. This technology also introduces errors into the resulting data, but at lower levels and in ways that I have already written software to compensate for.

As I continue to build out my lab, this is probably one of the projects I'll be investigating further. Clarifying the ancestry questions for this chile would be personally rewarding, but also might fill in a tiny little detail about how people of the desert southwest lived. This might be very interesting to a large number of people.

I expect the other seed lines I have for C. annuum var. glabriusculum will grow to have upright fruit, but otherwise match the characteristics of these plants. I like the small size and pungency of the fruit, so I'll probably keep growing them even if I can't think of a breeding project to use them in.