title: Loss of heterozygosity drives clonal diversity of Phytophthora capsici in China.
abstract: Phytophthora capsici causes significant loss to pepper (Capsicum annum) in China and our goal was to develop single nucleotide polymorphism (SNP) markers for P. capsici and characterize genetic diversity nationwide. Eighteen isolates of P. capsici from locations worldwide were re-sequenced and candidate nuclear and mitochondrial SNPs identified. From 2006 to 2012, 276 isolates of P. capsici were recovered from 136 locations in 27 provinces and genotyped using 45 nuclear and 2 mitochondrial SNPs. There were two main mitochondrial haplotypes and 95 multi-locus genotypes (MLGs) identified. Genetic diversity was geographically structured with a high level of genotypic diversity in the north and on Hainan Island in the south, suggesting outcrossing contributes to diversity in these areas. The remaining areas of China are dominated by four clonal lineages that share mitochondrial haplotypes, are almost exclusively the A1 or A2 mating type and appear to exhibit extensive diversity based on loss of heterozygosity (LOH). Analysis of SNPs directly from infected peppers confirmed LOH in field populations. One clonal lineage is dominant throughout much of the country. The overall implications for long-lived genetically diverse clonal lineages amidst a widely dispersed sexual population are discussed.
authors.affiliation: Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, China ; Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America.
authors.forename: Jian
authors.initials: J
authors.lastname: Hu
authors.affiliation: Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.
authors.forename: Yongzhao
authors.initials: Y
authors.lastname: Diao
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America.
authors.forename: Yuxin
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Lin
authors.affiliation: Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Bi
authors.affiliation: Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.
authors.forename: Zhili
authors.initials: Z
authors.lastname: Pang
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Trout Fryxell
authors.affiliation: Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.
authors.forename: Xili
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America.
authors.forename: Kurt
authors.initials: K
authors.lastname: Lamour
mesh_terms: D002681:China; D016000:Cluster Analysis; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques; D005843:Geography; D019656:Loss of Heterozygosity; D010838:Phytophthora / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci