Population Genetic Structure of Phytophthora cinnamomi Associated with Avocado in California and the Discovery of a Potentially Recent Introduction of a New Clonal Lineage

Abstract

Phytophthora root rot (PRR) of avocado (Persea americana), caused by Phytophthora cinnamomi, is the most serious disease of avocado worldwide. Previous studies have determined that this pathogen exhibits a primarily clonal reproductive mode but no population level studies have been conducted in the avocado-growing regions of California. Therefore, we used amplified fragment length polymorphism based on 22 polymorphic loci and mating type to investigate pathogen diversity from 138 isolates collected in 2009 to 2010 from 15 groves from the Northern and Southern avocado-growing regions. Additional isolates collected from avocado from 1966 to 2007 as well as isolates from other countries and hosts were also used for comparative purposes. Two distinct clades of A2 mating-type isolates from avocado were found based on neighbor joining analysis; one clade contained both newer and older collections from Northern and Southern California, whereas the other clade only contained isolates collected in 2009 and 2010 from Southern California. A third clade was also found that only contained A1 isolates from various hosts. Within the California population, a total of 16 genotypes were found with only one to four genotypes identified from any one location. The results indicate significant population structure in the California avocado P. cinnamomi population, low genotypic diversity consistent with asexual reproduction, potential evidence for the movement of clonal genotypes between the two growing regions, and a potential introduction of a new clonal lineage into Southern California.

New microsatellite markers for population studies of Phytophthora cinnamomi, an important global pathogen

“…The current knowledge on genetic diversity and movement of P. cinnamomi in natural populations is still very limited. To date, several population studies have been conducted using isozyme analysis 11 , 12 , AFLP 22 , or only three SSR markers 16 . Although the use of isozyme and AFLP have been intensively used in the past and have proven to be useful in assessing diversity and relatedness, the results obtained from these techniques are often difficult to consistently reproduce and hence prohibit the transferability of the data between studies.…”

“…In all of these studies, P. cinnamomi was found to have low genetic variability within and among geographically defined populations. Interestingly, the A1 and A2 mating types can often be distinguished based on the genetic differentiation 19 , 22 .…”

Plant growth-promoting rhizobacteria associated with avocado display antagonistic activity against Phytophthora cinnamomi through volatile emissions

“…In avocado ( Persea americana Mill. ), Phytophthora root rot is caused by the oomycete Phytophthora cinnamomi Rand, a soil-borne pathogen which has been reported to affect more than 3,000 plant species and about 70% of avocado orchards [ 12 ]. Phytophthora cinnamomi attacks the feeder roots of avocado trees, which leads to root rot and consequently to branch-dieback, and is often followed by tree death.…”

Rainfall and temperatures changes have confounding impacts on Phytophthora cinnamomi occurrence risk in the southwestern USA under climate change scenarios

“…Pc occurs in this region (Tidwell et al, 1984;Swiecki et al, 2003;Garbelotto et al, 2006;Chavarriaga et al, 2007;Pagliaccia et al, 2011Pagliaccia et al, , 2013) but its range is poorly delineated. Here, we apply a mechanistic modeling approach to explore how climate change could impact pathogen range and activity.…”

“…To do this we couple two existing models that describe controls on the range of the generalist root pathogen Pc in the state of California and surrounding regions in the states of Oregon, Nevada, and Arizona in the southwest USA. Pc occurs in this region (Tidwell et al, 1984;Swiecki et al, 2003;Garbelotto et al, 2006;Chavarriaga et al, 2007;Pagliaccia et al, 2011Pagliaccia et al, , 2013) but its range is poorly delineated. In other warm climates such as southern Australia and Hawaii, Pc has had a devastating effect on timber production, natural forests and agriculture (Newhook & Podger, 1972;Hwang & Ko, 1978;Weste & Marks, 1987;Balci & Halmschlager, 2003;Harham, 2005;Judelson & Blanco, 2005;Benson et al, 2006;J€ onsson, 2006).…”