Biology subjects

Kantar, M.

Publications and source records attributed to Kantar, M..

5 recordsLinked to original sources

bioRxiv2023

Genomic signatures of adaptation to abiotic stress from a geographically diverse collection of chile peppers (Capsicum spp.) from Mexico

Extreme environmental variability requires the identification of genetic diversity that can help crops withstand difficult abiotic conditions. Understanding the genetic basis of adaptation to abiotic stress can provide tools for adapting agriculture to changing climates. Crop landraces and their wild ancestors from centers of domestication have often evolved across diverse environmental conditions and provide a unique opportunity to locate loci harboring alleles that could contribute to abiotic stress tolerance, among other traits. We collected chile peppers (Capsicum spp.) from farmers in southern Mexico along environmental transects crossing temperature, precipitation, and elevational gradients. Using 32,623 filtered SNPs generated from genotyping-by-sequencing (GBS), we conducted an environmental association analysis (EAA) combined with two outlier analyses, FST and spatial ancestry analyses to detect priority candidate loci associated with climate and soil phenotypes relevant to drought tolerance. Even though cultivated species may be shielded from some environmental selection by management practices (e.g., irrigation), we found fifteen priority loci whose genetic variation covaried with environmental variation in our EAA and were also allele frequency outliers (i.e., Fst and/or SPA). Thirty-three percent of the priority loci were validated with phenotype in response to water deficit. The haplotype blocks associated with these loci identify unique genetic variants worthy of conservation and harbor genes with abiotic stress-related functions. This work provides valuable information to explore quantitative trait loci (QTLs) underlying abiotic stress tolerance in chile pepper and is a new resource for improving plant breeding around the world. Article SummaryThe extreme environmental variability faced by crops requires the identification of potentially adaptive loci for abiotic stressors. We conducted an environmental association analysis (EAA) environments using chile peppers collected in southern Mexico along environmental transects crossing temperature, precipitation, and elevational gradients. We combined EAA with outlier analyses FST and spatial ancestry analysis to detect priority candidate loci associated with climate and soil phenotypes relevant to drought tolerance that may putatively contribute to abiotic stress adaptation.

genetics↗

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↗

bioRxiv2022

Phylogenetic resolution of the Cannabis genus reveals extensive admixture

Population structure of Cannabis sativa L. was explored across nine independent collections that each contained a unique sampling of varieties. Hierarchical Clustering of Principal Components (HCPC) identified a range of three to seven genetic clusters across datasets with inconsistent structure based on use type indicating the importance of sampling particularly when there is limited passport data. There was broader genetic diversity in modern cultivars relative to landraces. Further, in a subset of geo-referenced landrace accessions, population structure was observed based on geography. The inconsistent structure across different collections shows the complexity within Cannabis, and the importance of understanding any particular collection which could then be leveraged in breeding programs for future crop improvement.

genomics↗

bioRxiv2021

Environment of origin and domestication affect morphological, physiological, and agronomic response to water deficit in chile pepper (Capsicum sp.)

Global climate change is having a significant effect on agriculture by causing greater precipitation variability and an increased risk of drought. To mitigate these effects, it is important to identify specific traits, adaptations, and germplasm that improve tolerance to soil water deficit. Local varieties, known as landraces, have undergone generations of farmer-mediated selection and can serve as sources of variation, specifically for tolerance to abiotic stress. Landraces can possess local adaptations, where accessions adapted to a particular environment will outperform others grown under the same conditions. We explore adaptations to water deficit in chile pepper landraces from across an environmental gradient in Mexico, a center of crop domestication and diversity, as well in improved varieties bred for the US. In the present study, we evaluated 25 US and Mexico accessions in a greenhouse experiment under well-watered and water deficit conditions and measured morphological, physiological, and agronomic traits. Accession and irrigation regime influenced biomass and height, while branching, CO2 assimilation, and fruit weight were all influenced by an interaction between accession and irrigation. A priori group contrasts revealed possible adaptations to water deficit for primary branching, CO2 assimilation, and plant height associated with geographic origin, domestication level, and pepper species. Additionally, within the Mexican landraces, the number of primary branches had a strong relationship with precipitation from the environment of origin. This work provides insight into chile pepper response to water deficit and adaptation to drought and identifies possibly tolerant germplasm.

plant biology↗

bioRxiv2020

The hidden land use cost of widespread cover cropping

Cover cropping is considered a cornerstone practice in sustainable agriculture; however, little attention has been paid to the cover crop production supply chain. In this Perspective, we estimate land use requirements to supply the United States maize production area with cover crop seed, finding that across 18 cover crops, on average 3.8% (median 2.0%) of current production area would be required, with the popular cover crops rye and hairy vetch requiring as much as 4.5% and 11.9%, respectively. The latter land requirement is comparable to the annual amount of maize grain lost to disease in the U.S. We highlight avenues for reducing these high land use costs.

ecology↗