Martinez-Ainsworth, N. E. | Search bioRxiv

bioRxiv2022

Capturing the distribution as it shifts: chile pepper (Capsicum annuum L.) domestication gradient meets geography.

AimDomestication is an ongoing well-described process. However, while many have studied the changes domestication causes in the genetic landscape, few have explored the way domestication changes the geographic landscape in which the plants exist. Therefore, the goal of this study was to understand how the domestication status changed the suitable geographic space of chile pepper in its center of origin. MethodsCapsicum annuum is a major crop species globally whose domestication center, Mexico, has been well studied. This provides a unique opportunity to explore the degree to which ranges of different domestication classes diverged and how these ranges might be altered by climate change. To this end, we created ecological niche models for four domestication classes (wild, semiwild, landrace, modern cultivar) based on present climate and future climate scenarios for 2050, 2070, and 2090. ResultsConsidering present environment, we found substantial overlap in the geographic niches of all the domestication gradient categories. Yet, there were also clear unique environmental and geographic aspects to the current ranges. Wild and commercial varieties were at ease in desert conditions as opposed to landraces. With projections into the future, habitat was lost asymmetrically, with wild, semiwild and landraces at far greater risk than modern cultivars. Further, we identified areas where future suitability overlap between landraces and wilds is expected to decouple. Main conclusionsWhile range expansion is widely associated with domestication, there is little support of a constant niche expansion (either in environmental or geographical space) throughout the domestication gradient. However, a shift to higher altitudes with cooler climate was identified for landraces. The clear differences in environmental adaptation, such as higher mean diurnal range and precipitation seasonality along the domestication gradient classes and their future potential range shifts show the need to increase conservation efforts, particularly to preserve landraces and semiwild genotypes.

evolutionary biology↗

bioRxiv2019

Genomic footprints of local adaptation along elevation gradients associate with present phenotypic variation in teosintes

Local adaptation across species range is widespread. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Because elevation gradients display continuous environmental changes at a short geographical scale, they provide an exceptional opportunity to investigate these questions. Here, we used two common gardens to phenotype 1664 plants from 11 populations of annual teosintes. These populations were sampled across two elevation gradients in Mexico. Our results point to a syndrome of adaptation to altitude with the production of offspring that flowered earlier, produced less tillers, and larger, longer and heavier grains with increasing elevation. We genotyped these plants for 178 outlier single nucleotide polymorphisms (SNPs), which had been chosen because they displayed excess of allele differentiation and/or correlation with environmental variables in six populations with contrasted altitudes. A high proportion of outlier SNPs associated with the phenotypic variation of at least one trait. We tested phenotypic pairwise correlations between traits, and found that the higher the correlation, the greater the number of common associated SNPs. In addition, allele frequencies at 87 of the outlier SNPs correlated with an environmental component best summarized by altitudinal variation on a broad sample of 28 populations. Chromosomal inversions were enriched for both phenotypically-associated and environmentally-correlated SNPs. Altogether, our results are consistent with the set-up of an altitudinal syndrome promoted by local adaptation of teosinte populations in the face of gene flow. We showed that pleiotropy is pervasive and potentially has constrained the evolution of traits. Finally, we recovered variants underlying phenotypic variation at adaptive traits. Because elevation mimics climate change through space, these variants may be relevant for future maize breeding. Author summaryAcross their native range, species encounter a diversity of habitats promoting local adaptation of geographically distributed populations. While local adaptation is widespread, much has yet to be discovered about the conditions of its emergence, the targeted traits, their molecular determinants and the underlying ecological drivers. Here we employed a reverse ecology approach, combining phenotypes and genotypes, to mine the determinants of local adaptation of teosinte populations distributed along two steep altitudinal gradients in Mexico. Evaluation of 11 populations in two common gardens located at mid-elevation pointed to the set-up of an altitudinal syndrome, in spite of gene flow. We scanned genomes to identify loci with allele frequencies shifts along elevation. Interestingly, variation at these loci was commonly associated to variation of phenotypes. Because elevation mimics climate change through space, these variants may be relevant for future maize breeding.

evolutionary biology↗