Genes and pathways underlying maize highland adaptation

Highland maize is cultivated in low-temperature mountainous regions globally as high as 3,600 meters above sea level where it is grown by poor owners of small farms as one of the main sources of calories in their diet. However, grain yield of highland maize is still much lower than tropical lowland and temperate maize and the genetic basis of highland adaptation is still poorly understood. To identify genes and pathways underlying highland adaptation, we used allele-specific expression (ASE) to scan the genome for genes with common cis-regulatory variation in highland landraces and for gene pathways that were differentially activated between highland and lowland landraces. We developed a novel genetic design for ASE analysis by crossing 108 maize landraces from highland and lowland sites of Mexico and South America with a common inbred line B73 to produce F1 hybrids and a novel workflow for directly counting allelic reads at gene level.