Evolution of an Experimental Population of Phytophthora capsici in the Field

Abstract

Populations of the vegetable pathogen Phytophthora capsici are often highly diverse, with limited gene flow between fields. To investigate the structure of a newly established, experimental population, an uninfested research field was inoculated with two single-zoospore isolates of P. capsici in September 2008. From 2009 through 2012, ≈50 isolates of P. capsici were collected from the field each year and genotyped using five microsatellite loci. The same two isolates were also crossed in the lab. High levels of diversity were detected in the research field, with 26 to 37 unique multilocus genotypes detected each year. Through 2012, genotypic diversity did not decline and no evidence of genetic drift was observed. However, during the 2011 and 2012 growing seasons, four new alleles not present in either parental isolate were observed in the field. Selfing (but not apomixis) was observed at low frequency among in vitro progeny. In addition, evidence for loss of heterozygosity was observed in half of the in vitro progeny. These results suggest that recombination, mutation, and loss of heterozygosity can affect the genetic structure observed in P. capsici populations.

Temporal Genetic Dynamics of an Experimental, Biparental Field Population of Phytophthora capsici

“…These in vitro isolates served as a reference for the field isolates, for which generation was a priori unknown. Three of the in vitro progeny were identified as putative selfs by Dunn et al (2014), which was confirmed by our analysis (see ‘Selfing in the lab and field’), and are hereafter referred to as in vitro selfs to distinguish them from the in vitro F 1 progeny. The A1 (isolate: 0664-1) and A2 (isolate: 06180-4) founding parents were genotyped 14 and 11 times, respectively, to estimate laboratory and genotyping errors (Supplementary Table S2).…”

“…Exposure to mating type specific hormones (α1 and α2) stimulates production of the gametangia, subsequent outcrossing, and formation of recombinant oospores (Ko, 1988). However, both mating types produce both male and female gametangia, and thus are capable of self-fertilization (Shattock, 1986; Ko, 1988), which is thought to occur at a lower rate relative to outcrossing in P. capsici (Uchida and Aragaki, 1980; Dunn et al, 2014). …”

“…In a preliminary study, we tracked the allele and genotypic frequencies of five microsatellite markers in the field population from 2009–2012 (Dunn et al, 2014). We demonstrated that sexual reproduction resulted in high genotypic diversity, a function of the proportion of unique isolates (Grünwald et al, 2003), in 2009–2011, with a reduction in genotypic diversity in 2012.…”

New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations

“…oryzicola [25]). Studies investigating population structure on a small geographical scale have seldom been realized for plant-associated bacteria or for plant-associated oomycetes and fungi (22,(26)(27)(28).…”

Best Practices for Population Genetic Analyses

“…Markers with high mutation rates such as microsatellites (also known as simple sequence repeats or SSRs) provide insights into recent divergence (Atallah et al 2010;Baumgartner et al 2010;Berbegal et al 2013;Dunn et al 2014;Dutech et al 2010;Goss et al 2009b), whereas mitochondrial, nuclear or other sequence loci provide inferences about the more distant evolutionary history given the slower mutation rates Goss et al 2009a;Malvarez et al 2007;Schoebel et al 2014;Stukenbrock et al 2007).…”