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DNA Analysis Study Reveals Origins of Maize in Southwestern US

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NEW YORK (GenomeWeb) – The specific details about how maize made its way from Mexico, where it was initially domesticated, to throughout the Americas have long been unclear.

Now, a newly published analysis of the DNA from ancient samples of the plant suggests that it was first introduced to the US by way of the Sierra Madre Mountains about 4,000 years ago, and then cross bred with maize from the Pacific coast region thousands of years later.

The findings not only shed new light on the evolution of one of North America's most important crops, but help demonstrate the potential of paleogenomics to provide a detailed understanding of the process of domestication.

It is known that maize was domesticated from the wild grass teosinte in southern Mexico and diffused throughout the Americas beginning with its introduction to the Southwest US about 4,000 years ago. However, there has been a longstanding debate among archeologists about the specific course of that introduction, with some in the field arguing for a highland route and others supporting a lowland, Pacific coast route.

"Maize is such an important crop today because it grows in a wide range of environments," Thomas Gilbert, a researcher at the University of Copenhagen and senior author of the study, told GenomeWeb.

But this versatility leaves a fundamental question of how a plant that originated in the warm and moist environment of Western Mexico evolved the traits necessary to survive in much colder and drier climates such as those found in the American Midwest, he said. There was also a question of whether maize domestication occurred through the selection of traits in a single teosinte lineage or involved cross breeding.

To answer these questions, Gilbert and his international team of collaborators sampled DNA from archaeological maize samples from the Southwest dating to around 4000 to 3000 and 750 cal BP, as well as four ancient Mexican samples dating to circa 5910, 5280, and 1410 cal BP. Cal BP, or calibrated years before the present, is a term used in archaeology to refer to years before the year 1950, with measurements calibrated to account for variations in radiocarbon dating. They also examined a single modern highland Mexican maize variety.

Sequence data from ancient samples was generated using a hybridization target-capture approach that was enriched for the exons of 348 genes, while the modern sample was sequenced using a whole-genome shotgun approach.

Sequence data from ancient samples was generated using a hybridization target-capture approach that was enriched for the exons of 348 genes, while the modern sample was sequenced using a whole-genome shotgun approach.

"To these data we added published sequence data from an additional ancient sample from Mexico and modern samples of teosinte subspecies … as well as Southwest and Mexican maize," the scientists wrote in their report, which appeared in Nature Plants.

One of the first observations made by the investigators was that the earliest maize samples showed signs of repression of zagl1, a gene that corresponds to a MADS-box transcription factor associated with ear shattering — a key domestication feature strongly selected for by human harvesting.

"When plants are domesticated, one of the key things to do is turn off the shattering ability [so] that when the fruits are ripe, they don't get banged and send their seeds all over the place," Gilbert explained.

They also found evidence of selective pressure around genes involved in drought tolerance, he said, which fits the theory that maize initially diffused north from Mexico by way of a dry, highland route.

Indeed, a comparison of shared derived alleles between the ancient Southwest samples and the modern samples pointed strongly to a highland origin of the earliest Southwest maize, which was consistent with low-density single nucleotide polymorphism data from a sample of more than 2,000 modern maize landraces and teosinte, the team wrote in their paper.

Evidence of teosinte admixture in all ancient Southwest maize was also observed. Given that there is no history of teosinte in the Southwest, this finding further points to the highland origin of maize. Yet the research group also saw indications of gene flow from a lowland, coastal maize approximately 2,000 years ago.

Taken together, the data argue for "a complex origin of Southwest maize, originally entering the United States via a highland route by 4000 BP and subsequently receiving gene flow from lowland maize via the Pacific coastal corridor starting around 2000 BP," according to the Nature Plants report.

In addition to this broader finding, Gilbert and his colleagues were also able to track maize's adaptation from its earliest to its modern forms. While genes associated with drought tolerance were some of the most highly selected, they also found major genetic changes affecting the starch biosynthesis pathway, which resulted in changes to cob size and kernel texture, as well as sugar content.

Overall, the findings help resolve the key archaeological question surrounding maize's origin. But they also show how paleogenomics can further the study of domestication when combined with well-documented temporal sequences of archaeological assemblages, the study's authors wrote.

"It is now possible to move beyond a simple distinction of 'wild' versus 'domesticated' and track sequence changes in a wide range of genes over the course of thousands of years," they concluded.

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