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Population structure and phenotypic variation of Sclerotinia sclerotiorum from dry bean in the USA
Version 2 2018-01-16, 22:13
Version 1 2018-01-16, 22:09
poster
posted on 2018-01-16, 22:13 authored by Zhian KamvarZhian Kamvar, B. Sajeewa Amaradasa, Rachana Jhala, Serena McCoy, James R. Steadman, Sydney E. EverhartThis is a poster version of https://peerj.com/articles/4152/ describing the results and computational workflow to produce the results.
CONTENTS
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sclerotinia-initiative-2018-version-2.pdf : pdf version of the poster
sclerotinia-initiative-2018-v2.svg : original inkscape svg file
maps.R : R script to generate maps
ABSTRACT
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The ascomycete pathogen and causal agent of white mold on dry bean, Sclerotinia sclerotiorum, is a necrotrophic pathogen on over 400 known host plants. Currently, there are no known cultivars of dry bean with complete resistance to white mold. For over 20 years, bean breeders have used white mold screening nurseries (WMSN) with natural populations of S. sclerotiorum to screen new cultivars for resistance. It is thus important to know if the genetic diversity in populations of S. sclerotiorum within these nurseries a) reflect the genetic diversity of the populations in the surrounding region and b) are stable over time. Furthermore, previous studies have investigated the correlation between mycelial compatibility groups (MCG) and multilocus haplotypes (MLH), but none have formally tested these patterns. We genotyped 366 isolates of S. sclerotiorum from producer fields and WMSN surveyed over 10 years in 2003–2012 representing 11 states in the United States of America, Australia, France, and Mexico at 11 microsatellite loci resulting in 165 MLHs. Populations were loosely structured over space and time based on analysis of molecular variance and discriminant analysis of principal components, but not by cultivar, aggressiveness, or field source. Our study suggests that breeders should continue to test dry bean lines in several WMSN across the USA to account for both the phenotypic and genotypic variation that exists across regions. All aspects of this project from raw data, R analysis pipeline, and figure generation are publicly available and reproducible online. Thus, this represents a gold standard for open science research and a case study for reproducible research in the Sclerotinia community that is attainable by anyone in our field of work.
CONTENTS
----------------
sclerotinia-initiative-2018-version-2.pdf : pdf version of the poster
sclerotinia-initiative-2018-v2.svg : original inkscape svg file
maps.R : R script to generate maps
ABSTRACT
----------------
The ascomycete pathogen and causal agent of white mold on dry bean, Sclerotinia sclerotiorum, is a necrotrophic pathogen on over 400 known host plants. Currently, there are no known cultivars of dry bean with complete resistance to white mold. For over 20 years, bean breeders have used white mold screening nurseries (WMSN) with natural populations of S. sclerotiorum to screen new cultivars for resistance. It is thus important to know if the genetic diversity in populations of S. sclerotiorum within these nurseries a) reflect the genetic diversity of the populations in the surrounding region and b) are stable over time. Furthermore, previous studies have investigated the correlation between mycelial compatibility groups (MCG) and multilocus haplotypes (MLH), but none have formally tested these patterns. We genotyped 366 isolates of S. sclerotiorum from producer fields and WMSN surveyed over 10 years in 2003–2012 representing 11 states in the United States of America, Australia, France, and Mexico at 11 microsatellite loci resulting in 165 MLHs. Populations were loosely structured over space and time based on analysis of molecular variance and discriminant analysis of principal components, but not by cultivar, aggressiveness, or field source. Our study suggests that breeders should continue to test dry bean lines in several WMSN across the USA to account for both the phenotypic and genotypic variation that exists across regions. All aspects of this project from raw data, R analysis pipeline, and figure generation are publicly available and reproducible online. Thus, this represents a gold standard for open science research and a case study for reproducible research in the Sclerotinia community that is attainable by anyone in our field of work.
