Novel microsatellite markers for the analysis of Phytophthora infestans populations

Abstract

Co-dominant microsatellite molecular markers for Phytophthora infestans were developed and their potential for monitoring the genetic variation in populations was demonstrated in the UK, across Europe and worldwide. Markers were developed according to two strategies. First, several thousand P. infestans expressed sequence tag (EST) and bacterial artificial chromosome (BAC) sequences were screened for the presence of simple sequence repeat (SSR) motifs, and, of these, 100 candidate loci were selected for further investigation. Primer pairs developed to these loci were tested against a panel of 10 P. infestans isolates and approximately 10% were shown to be polymorphic and therefore appropriate for further testing. Secondly, the construction and screening of a partial genomic library resulted in the development of one additional polymorphic marker. The resulting 12 SSR markers were converted to higher-throughput fluorescence-based assays and used in combination with two previously published markers to characterize a wider collection of 90 P. infestans isolates from the UK and six other countries. Several isolates from the closely related species P. mirabilis , P. ipomoea and P. phaseoli collected from around the world were also genotyped using these markers. Amongst the 90 isolates of P. infestans examined, considerable SSR diversity was observed, with 68 different genotypes and an average of 3·9 (range 2-9) alleles per locus. When other Phytophthora species were genotyped, all loci were successfully amplified and the majority were polymorphic, indicating their transferability for the potential study of other closely related taxa.

Epidemiology and Integrated Control of Potato Late Blight in Europe

“…A much greater percentage of the A2 mating type in Great Britain was reported in 2005 . By 2007, the A2 mating type was dominant in Great Britain with genotype 13_A2 accounting for 82% of the population (Lees et al 2008), while in Northern Ireland it increased to over 50% of the population in 2009 (Kildea et al 2010). The role of oospores in initiating infection in the UK is currently under investigation, but to date, there is no evidence that this occurs other than very rarely.…”

Occurrence and Distribution of Potato Pests and Diseases in Kenya

“…Late blight lesions from leaves from four individual plants at each farm were pressed onto FTA ™ cards and sent to the JHI, where DNA was extracted according to the manufacturer's instructions. Each DNA sample was characterized using simple sequence repeat (SSR) markers (Lees et al 2006;Li et al 2013), and the SSR data were scored in GeneMapper 3.7 (Applied Biosystems) and a genotype assigned.…”

Analisis keragaman genetik Phytophthora palmivora dari tanaman kakao di Indonesia menggunakan AFLP Genetic diversity analysis of Phytophthora palmivora from cocoa in Indonesia using AFLP

“…Berbagai metode analisis telah digunakan untuk mempelajari keragaman populasi Phytophthora spp., di antaranya adalah Restriction Fagment Length Polymorphisms (RFLP) (Goodwin et al, 1992), analisis sekuen (Schena et al, 2006), single nucleotide polymorphisms (SNPs) (Kroon et al, 2004;Bilodeau et al, 2007), Random Amplified Polymorphic DNA (RAPD) (Cooke et al, 1996;Abu-El Samen et al, 2003), Amplified Fragment Length Polymorphism (AFLP) (Ivors et al, 2004;Bowers et al, 2007), microsatellites (Dobrowolski et al, 2003;Lees et al, 2006), dan mitochondrial haplotypes (Gavino & Fry, 2002;Martin, 2008). Analisis keragaman genetik P. palmivora memerlukan penanda genetik yang handal dan informatif.…”