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Genome Wide Association Identifies Novel Loci Involved in Fungal Communication

Understanding how genomes encode complex cellular and organismal behaviors has become the outstanding challenge of modern genetics. Unlike classical screening methods, analysis of genetic variation that occurs naturally in wild populations can enable rapid, genome-scale mapping of genotype to phenot...

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Autores principales: Palma-Guerrero, Javier, Hall, Charles R., Kowbel, David, Welch, Juliet, Taylor, John W., Brem, Rachel B., Glass, N. Louise
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731230/
https://www.ncbi.nlm.nih.gov/pubmed/23935534
http://dx.doi.org/10.1371/journal.pgen.1003669
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author Palma-Guerrero, Javier
Hall, Charles R.
Kowbel, David
Welch, Juliet
Taylor, John W.
Brem, Rachel B.
Glass, N. Louise
author_facet Palma-Guerrero, Javier
Hall, Charles R.
Kowbel, David
Welch, Juliet
Taylor, John W.
Brem, Rachel B.
Glass, N. Louise
author_sort Palma-Guerrero, Javier
collection PubMed
description Understanding how genomes encode complex cellular and organismal behaviors has become the outstanding challenge of modern genetics. Unlike classical screening methods, analysis of genetic variation that occurs naturally in wild populations can enable rapid, genome-scale mapping of genotype to phenotype with a medium-throughput experimental design. Here we describe the results of the first genome-wide association study (GWAS) used to identify novel loci underlying trait variation in a microbial eukaryote, harnessing wild isolates of the filamentous fungus Neurospora crassa. We genotyped each of a population of wild Louisiana strains at 1 million genetic loci genome-wide, and we used these genotypes to map genetic determinants of microbial communication. In N. crassa, germinated asexual spores (germlings) sense the presence of other germlings, grow toward them in a coordinated fashion, and fuse. We evaluated germlings of each strain for their ability to chemically sense, chemotropically seek, and undergo cell fusion, and we subjected these trait measurements to GWAS. This analysis identified one gene, NCU04379 (cse-1, encoding a homolog of a neuronal calcium sensor), at which inheritance was strongly associated with the efficiency of germling communication. Deletion of cse-1 significantly impaired germling communication and fusion, and two genes encoding predicted interaction partners of CSE1 were also required for the communication trait. Additionally, mining our association results for signaling and secretion genes with a potential role in germling communication, we validated six more previously unknown molecular players, including a secreted protease and two other genes whose deletion conferred a novel phenotype of increased communication and multi-germling fusion. Our results establish protein secretion as a linchpin of germling communication in N. crassa and shed light on the regulation of communication molecules in this fungus. Our study demonstrates the power of population-genetic analyses for the rapid identification of genes contributing to complex traits in microbial species.
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spelling pubmed-37312302013-08-09 Genome Wide Association Identifies Novel Loci Involved in Fungal Communication Palma-Guerrero, Javier Hall, Charles R. Kowbel, David Welch, Juliet Taylor, John W. Brem, Rachel B. Glass, N. Louise PLoS Genet Research Article Understanding how genomes encode complex cellular and organismal behaviors has become the outstanding challenge of modern genetics. Unlike classical screening methods, analysis of genetic variation that occurs naturally in wild populations can enable rapid, genome-scale mapping of genotype to phenotype with a medium-throughput experimental design. Here we describe the results of the first genome-wide association study (GWAS) used to identify novel loci underlying trait variation in a microbial eukaryote, harnessing wild isolates of the filamentous fungus Neurospora crassa. We genotyped each of a population of wild Louisiana strains at 1 million genetic loci genome-wide, and we used these genotypes to map genetic determinants of microbial communication. In N. crassa, germinated asexual spores (germlings) sense the presence of other germlings, grow toward them in a coordinated fashion, and fuse. We evaluated germlings of each strain for their ability to chemically sense, chemotropically seek, and undergo cell fusion, and we subjected these trait measurements to GWAS. This analysis identified one gene, NCU04379 (cse-1, encoding a homolog of a neuronal calcium sensor), at which inheritance was strongly associated with the efficiency of germling communication. Deletion of cse-1 significantly impaired germling communication and fusion, and two genes encoding predicted interaction partners of CSE1 were also required for the communication trait. Additionally, mining our association results for signaling and secretion genes with a potential role in germling communication, we validated six more previously unknown molecular players, including a secreted protease and two other genes whose deletion conferred a novel phenotype of increased communication and multi-germling fusion. Our results establish protein secretion as a linchpin of germling communication in N. crassa and shed light on the regulation of communication molecules in this fungus. Our study demonstrates the power of population-genetic analyses for the rapid identification of genes contributing to complex traits in microbial species. Public Library of Science 2013-08-01 /pmc/articles/PMC3731230/ /pubmed/23935534 http://dx.doi.org/10.1371/journal.pgen.1003669 Text en © 2013 Palma-Guerrero et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Palma-Guerrero, Javier
Hall, Charles R.
Kowbel, David
Welch, Juliet
Taylor, John W.
Brem, Rachel B.
Glass, N. Louise
Genome Wide Association Identifies Novel Loci Involved in Fungal Communication
title Genome Wide Association Identifies Novel Loci Involved in Fungal Communication
title_full Genome Wide Association Identifies Novel Loci Involved in Fungal Communication
title_fullStr Genome Wide Association Identifies Novel Loci Involved in Fungal Communication
title_full_unstemmed Genome Wide Association Identifies Novel Loci Involved in Fungal Communication
title_short Genome Wide Association Identifies Novel Loci Involved in Fungal Communication
title_sort genome wide association identifies novel loci involved in fungal communication
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731230/
https://www.ncbi.nlm.nih.gov/pubmed/23935534
http://dx.doi.org/10.1371/journal.pgen.1003669
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