Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in the wild relatives of maize. Here, we characterize a high-density genomic variation map from ~700 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 65 million single nucleotide polymorphisms (SNPs), 8 million Insertion/Deletion (InDel) polymorphisms, and over one thousand novel inversions. The variation map reveals evidence of selection within taxa displaying novel adaptations such as perenniality and regrowth. We focus in detail on evidence of convergent adaptation in highland teosinte and temperate maize. This study not only indicates the key role of hormone related pathways in highland adaptation and flowering time related pathways in high latitude adaptation, but also identifies significant overlap in the genes underlying adaptations to both environments. To show how this data can identify useful genetic variants, we generated and characterized novel mutant alleles for two flowering time candidate genes. This work provides the most extensive sampling to date of the genetic diversity inherent in the genus Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

Introductory paragraphMuch of biology is associated with convergent traits, and it is challenging to determine the extent to which underlying molecular mechanisms are shared across phylogeny. By analyzing plants representing eighteen independent origins of C4 photosynthesis, we quantified the extent to which this convergent trait utilises identical molecular mechanisms. We demonstrate that biochemical changes that characterise C4 species are recovered by this process, and expand the paradigm by four metabolic pathways not previously associated with C4 photosynthesis. Furthermore, we show that expression of many genes that distinguish C3 and C4 species respond to low CO2, providing molecular evidence that reduction in atmospheric CO2 was a driver for C4 evolution. Thus the origin and architecture of complex traits can be derived from transcriptome comparisons across natural diversity.

Nitrogen (N) is essential for growth, development and defense but, how low N affects defense and the role of Trichoderma in enhancing defense under low nitrate is not known. Low nitrate fed Arabidopsis plants displayed reduced growth and compromised local and systemic acquired resistance responses when infected with both avirulent and virulent Pseudomonas syringae DC3000. These responses were enhanced in the presence of Trichoderma. The mechanism of increased local and systemic acquired resistance mediated by Trichoderma involved increased N uptake and enhanced protein levels via modulation of nitrate transporter genes. The nrt2.1 mutant is compromised in local and systemic acquired resistance responses suggesting a link between enhanced N transport and defense. Enhanced N uptake was mediated by Trichoderma elicited nitric oxide (NO). Low NO producing nia1,2 mutant and nsHb+ over expressing lines were unable to induce nitrate transporters and thereby compromised defense in the presence of Trichoderma under low N suggesting a signaling role of Trichoderma elicited NO. Trichoderma also induced SA and defense gene expression under low N. The SA deficient NahG transgenic line and the npr1 mutant were also compromised in Trichoderma-mediated local and systemic acquired resistance responses. Collectively our results indicated that the mechanism of enhanced plant defense under low N mediated by Trichoderma involves NO, ROS, SA production as well as the induction of NRT and marker genes for systemic acquired resistance.One-sentence summaryTrichoderma enhances local and systemic acquired resistance under low nitrate nutrition

Aluminium is a limiting factor for crop productivity in acidic soils (pH ≤ 5.5). Since acid soil distribution on Earth cannot adequately explain the differential Al tolerance across the plant kingdom, we investigated photoperiod effects on plant Al tolerance. We observed that with increasing distance from the equator, Al tolerance disappears, suggesting a relationship with the photoperiod. Long-day (LD) species are generally more Al-sensitive than short-day (SD) species, whereas genetic conversion of tomato for SD growth boosts Al tolerance. Reduced Al tolerance correlates with DNA-checkpoint activation under LD. DNA-checkpoint-related genes are under positive selection in Arabidopsis accessions from regions with shorter days, suggesting photoperiod acts as a selective barrier for Al tolerance. Our findings revealed that diel regulation and genetic diversity affect Al tolerance, suggesting that day-length orchestrates Al tolerance.