Data from: Genome-wide diversity in lowland and highland maize landraces from southern South America: Population genetics insights to assist conservation

Maize (Zea mays ssp. mays L.) landraces are traditional American crops
with high genetic variability that conform a source of original alleles
for conventional maize breeding. Northern Argentina, one the southernmost
regions of traditional maize cultivation in the Americas, harbours around
57 races traditionally grown in two regions with contrasting environmental
conditions, namely the Andean mountains in the Northwest and the tropical
grasslands and Atlantic Forest in the Northeast. These races encounter
diverse threats to their genetic diversity and persistence in their
regions of origin, with climate change standing out as one of the major
challenges. In this work, we use genome-wide SNPs derived from ddRADseq to
study the genetic diversity of individuals representing the five groups
previously described for this area. This allowed us to distinguish two
clearly differentiated gene pools, the Highland Northwestern maize (HNWA)
and the Floury Northeastern maize (FNEA). Subsequently, we employed
Essential Biodiversity Variables at the genetic level, as proposed by the
Group on Earth Observations Biodiversity Observation Network (GEO BON), to
evaluate the conservation status of these two groups.  This
assessment encompassed genetic diversity (Pi), inbreeding coefficient (F),
and effective population size (Ne). FNEA showed low Ne values and high F
values, while HNWA showed low Ne values and low Pi values, indicating that
further genetic erosion is imminent for these landraces. Outlier detection
methods allowed identification of putative adaptive genomic regions,
consistent with previously reported flowering-time loci and chromosomal
regions displaying introgression from the teosinte Zea mays ssp. mexicana.
Finally, species distribution models were obtained for two future climate
scenarios, showing a notable reduction in the potential planting area of
HNWA and a shift in the cultivation areas of FNEA. These results suggest
that maize landraces from Northern Argentina may be unable to cope with
climate change. Therefore, active conservation policies are advisable.