Natural variation in the pattern-triggered immunity response in plants: Investigations, implications and applications.

The pattern-triggered immunity (PTI) response is triggered at the plant cell surface by the recognition of microbe-derived molecules known as microbe- or pathogen-associated molecular patterns or molecules derived from compromised host cells called damage-associated molecular patterns. Membrane-localized receptor proteins, known as pattern recognition receptors, are responsible for this recognition. Although much of the machinery of PTI is conserved, natural variation for the PTI response exists within and across species with respect to the components responsible for pattern recognition, activation of the response, and the strength of the response induced.

Thermal sensitivity and seasonal change in the gut microbiome of a desert ant, Cephalotes rohweri.

Microorganisms within ectotherms must withstand the variable body temperatures of their hosts. Shifts in host body temperature resulting from climate change have the potential to shape ectotherm microbiome composition. Microbiome compositional changes occurring in response to temperature in nature have not been frequently examined, restricting our ability to predict microbe-mediated ectotherm responses to climate change.

Analysis of genotype-by-environment interactions in a maize mapping population.

Genotype-by-environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype-by-environment interactions in a maize multiparent advanced generation intercross population grown across 5 environments. We found that genotype-by-environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits.

Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci.

The search for quantitative trait loci that explain complex traits such as yield and drought tolerance has been ongoing in all crops. Methods such as biparental quantitative trait loci mapping and genome-wide association studies each have their own advantages and limitations. Multiparent advanced generation intercross populations contain more recombination events and genetic diversity than biparental mapping populations and are better able to estimate effect sizes of rare alleles than association mapping populations.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day.