Landraces (traditional varieties) of domesticated species preserve useful genetic variation, yet they remain untapped due to the genetic linkage between the few useful alleles and hundreds of undesirable alleles. We integrated two approaches to characterize the diversity of 4,471 maize landraces. First, we mapped genomic regions controlling latitudinal and altitudinal adaptation and identified 1,498 genes. Second, we used F-one association mapping (FOAM) to map the genes that control flowering time, across 22 environments, and identified 1,005 genes. In total, we found that 61.4% of the single-nucleotide polymorphisms (SNPs) associated with altitude were also associated with flowering time. More than half of the SNPs associated with altitude were within large structural variants (inversions, centromeres and pericentromeric regions). The combined mapping results indicate that although floral regulatory network genes contribute substantially to field variation, over 90% of the contributing genes probably have indirect effects. Our dual strategy can be used to harness the landrace diversity of plants and animals.

Threats to crop production due to climate change are one of the greatest challenges facing plant breeders today. While considerable adaptive variation exists in traditional landraces, natural populations of crop wild relatives, and ex situ germplasm collections, separating adaptive alleles from linked deleterious variants that impact agronomic traits is challenging and has limited the utility of these diverse germplasm resources. Modern genome editing techniques such as CRISPR offer a potential solution by targeting specific alleles for transfer to new backgrounds, but such methods require a higher degree of precision than traditional mapping approaches can achieve. Here we present a high-resolution genome-wide association analysis to identify loci exhibiting adaptive patterns in a large panel of more than 4500 traditional maize landraces representing the breadth of genetic diversity of maize in Mexico. We evaluate associations between genotype and plant performance in 13 common gardens across a range of environments, identifying hundreds of candidate genes underlying genotype by environment interaction. We further identify genetic associations with environment across Mexico and show that such loci are associated with variation in yield and flowering time in our field trials and predict performance in independent drought trials. Our results indicate that the variation necessary to adapt crops to changing climate exists in traditional landraces that have been subject to ongoing environmental adaptation and can be identified by both phenotypic and environmental association.

ern corn borer resistance. Few plant breeders have access to insect rearing facilities, which are necessary to Southwestern corn borer (Diatraea grandiosella Dyar) and fall maximize selection efficiency. Negative traits tend to armyworm [Spodoptera frugiperda (J.E. Smith)] damage ratings were measured on an F2-derived maize (Zea mays L.) population segregat-mask genetic gains in resistance at early generations of ing for leaf feeding resistance following artificial infestation with neo-backcrossing, and levels of resistance tend to be modernates. Damage ratings for each insect were recorded in replicated ate. Quantitative trait mapping can be used to overcome trials at three locations and used in conjunction with a genetic linkage some of these problems and facilitate manipulation of map to identify quantitative trait loci (QTL) associated with resistance. genetic resistance. Significant QTL and their interactions were estimated by multiple Through a series of separate studies, researchers have interval mapping analysis. Resistance to southwestern corn borer leaf identified QTL associated with southwestern corn borer feeding was fit to a model containing eight QTL and two interactions resistance in inbreds developed from Antigua Group 2 explaining 20% of the phenotypic variation. A model containing sevenand Dominican Republic Group 1 germplasm. Resistance QTL and one interaction best fit resistance to fall armyworm leaf feed-QTL ranging in number from five to nine were identified ing damage, and it explained approximately 14% of the phenotypic variation. Three QTL located on chromosomes 6, 9, and 10 affect in tropical growing conditions accounting for between leaf feeding damage ratings of both insects with similar effects and 32 and 52% of phenotypic variation in three mapping Abbreviations: CIM, composite interval mapping; LOD, log10-likelihood ratio; QTL, quantitative trait locus or loci; SSR, simple sequence

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