Abstract
Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate.
Original language | English |
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Article number | 1103969 |
Journal | Frontiers in Genetics |
Volume | 14 |
DOIs | |
State | Published - 2023 |
Bibliographical note
Publisher Copyright:Copyright © 2023 Ortiz, Chang, Sang, Jacobs, Malvick, Baird, Mathew, Estévez de Jensen, Wise, Mosquera and Chilvers.
Funding
This work was supported in part by the United Soybean Board, Michigan Soybean Committee, North Central Soybean Research Program, Colombian Department of Science, Technology and Innovation (COLCIENCIAS), and Project GREEEN.
Funders | Funder number |
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Guangdong Provincial Department of Science and Technology and Guangzhou Science Technology and Innovation Commission | |
Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS) | |
United Soybean Board |
Keywords
- charcoal rot
- climate change
- genotype–environment associations
- landscape genetics
- pathogen adaptation
- phylogenomics
- redundancy analysis
ASJC Scopus subject areas
- Molecular Medicine
- Genetics
- Genetics(clinical)