Genetically Diverse Long-Lived Clonal Lineages ofPhytophthora capsicifrom Pepper in Gansu, China

Abstract

Phytophthora capsici causes significant loss to pepper production in China, and our objective was to investigate the population structure in Gansu province. Between 2007 and 2011, 279 isolates were collected from pepper at 24 locations. Isolates (or subsets) were assessed for simple sequence repeat (SSR) genotype, metalaxyl resistance, mating type, and physiological race using cultivars from the World Vegetable Center (AVRDC) and New Mexico recombinant inbred lines (NMRILs). The A1 and A2 mating types were recovered from nine locations and metalaxyl-resistant isolates from three locations. A total of 104 isolates tested on the AVRDC panel resolved five physiological races. None of 42 isolates tested on the NMRIL panel caused visible infection. SSR genotyping of 127 isolates revealed 59 unique genotypes, with 42 present as singletons and 17 having 2 to 13 isolates. Isolates with identical genotypes were recovered from multiple sites across multiple years and, in many cases, had different race types or metalaxyl sensitivities. Isolates clustered into three groups with each group having almost exclusively the A1 or A2 mating type. Overall it appears long-lived genetically diverse clonal lineages are dispersed across Gansu, outcrossing is rare, and functionally important variation exists within a clonal framework.

Loss of Heterozygosity Drives Clonal Diversity of Phytophthora capsici in China

“…The SNP analysis of the 28 isolates previously reported from Gansu province corroborates the recent findings based on SSR markers – identifying the same three clonal lineages [18]. Furthermore, these clonal lineages are dispersed over wide areas of the country.…”

“…In the South American countries of Peru and Argentina, the situation is markedly different and long-lived clonal lineages persist for years and there is little evidence to suggest sexual recombination is active [19]. A recent study of 279 P. capsici isolates recovered from pepper in Gansu province using SSR markers revealed three long-lived clonal lineages dominate the population structure and one of our goals was to determine if the epidemiology of P. capsici across the whole of China may be similar to S. America [18]. Because loss of heterozygosity (LOH) can occur once an isolate is brought into axenic culture [33], infected tissue samples were also genotyped to determine if LOH is primarily an artifact due to growing isolates in laboratory culture on agar plates or if LOH occurs during asexual clonal reproduction in vivo , in the field setting.…”

“…This study includes isolates from 34 provinces of China and includes 28 of the 279 isolates analyzed previously from Gansu province [18]. Overall, the genetic diversity is highly structured with clonal reproduction and clonal lineages causing disease across the entire country.…”

“…The situation is different in the South American countries of Peru and Argentina where country-specific clonal lineages survive multiple years and are spread widely [17,19]. Similarly, a recent study of P. capsici from Gansu province, China indicates three long-lived genetically diverse clonal lineages are widely distributed [18]. …”

“…The mechanism(s) underlying LOH in P. capsici are unknown but LOH was associated with a mating type switch (A2 to A1) and altered virulence and pathogencity in some isolates [33]. The extent or impact of LOH in natural populations is unknown although it is increasingly clear the P. capsici genome is highly plastic during in vitro asexual growth and that mating type is an unstable character [18,33]. …”