Domestication and lowland adaptation of coastal preceramic maize from Paredones, Peru

Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating ~6700-5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by ~6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.

Mining alleles for tar spot complex resistance from CIMMYT's maize Germplasm Bank

The tar spot complex (TSC) is a devastating disease of maize (Zea mays L.), occurring in 17 countries throughout Central, South, and North America and the Caribbean, and can cause grain yield losses of up to 80%. As yield losses from the disease continue to intensify in Central America, Phyllachora maydis, one of the causal pathogens of TSC, was first detected in the United States in 2015, and in 2020 in Ontario, Canada. Both the distribution and yield losses due to TSC are increasing, and there is a critical need to identify the genetic resources for TSC resistance. The Seeds of Discovery Initiative at CIMMYT has sought to combine next-generation sequencing technologies and phenotypic characterization to identify valuable alleles held in the CIMMYT Germplasm Bank for use in germplasm improvement programs. Individual landrace accessions of the “Breeders' Core Collection” were crossed to CIMMYT hybrids to form 918 unique accessions topcrosses (F1 families) which were evaluated during 2011 and 2012 for TSC disease reaction. A total of 16 associated SNP variants were identified for TSC foliar leaf damage resistance and increased grain yield. These variants were confirmed by evaluating the TSC reaction of previously untested selections of the larger F1 testcross population (4,471 accessions) based on the presence of identified favorable SNPs. We demonstrated the usefulness of mining for donor alleles in Germplasm Bank accessions for newly emerging diseases using genomic variation in landraces.

Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays

While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.

Genome size in plants can vary by orders of magnitude, but this variation has long been considered to be of little functional consequence. Studying three independent adaptations to high altitude in Zea mays, we find that genome size experiences parallel pressures from natural selection, causing a reduction in genome size with increasing altitude. Though reductions in overall repetitive content are responsible for the genome size change, we find that only those individual loci contributing most to the variation in genome size are individually targeted by selection. To identify the phenotype influenced by genome size, we study how variation in genome size within a single wild population impacts leaf growth and cell division. We find that genome size variation correlates negatively with the rate of cell division, suggesting that individuals with larger genomes require longer to complete a mitotic cycle. Finally, we reanalyze data from maize inbreds to show that faster cell division is correlated with earlier flowering, connecting observed variation in genome size to an important adaptive phenotype.

Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays

While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.