Abstract
Moniliophthora roreri is the fungal pathogen that causes frosty pod rot (FPR) disease of Theobroma cacao L., the source of chocolate. FPR occurs in most of the cacao producing countries in the Western Hemisphere, causing yield losses up to 80%. Genetic diversity within the FPR pathogen population may allow the population to adapt to changing environmental conditions and adapt to enhanced resistance in the host plant. The present study developed single nucleotide polymorphism (SNP) markers from RNASeq results for 13 M. roreri isolates and validated the markers for their ability to reveal genetic diversity in an international M. roreri collection. The SNP resources reported herein represent the first study of RNA sequencing (RNASeq)-derived SNP validation in M. roreri and demonstrates the utility of RNASeq as an approach for de novo SNP identification in M. roreri. A total of 88 polymorphic SNPs were used to evaluate the genetic diversity of 172 M. roreri cacao isolates resulting in 37 distinct genotypes (including 14 synonymous groups). Absence of heterozygosity for the 88 SNP markers indicates reproduction in M. roreri is clonal and likely due to a homothallic life style. The upper Magdalena Valley of Colombia showed the highest levels of genetic diversity with 20 distinct genotypes of which 13 were limited to this region, and indicates this region as the possible center of origin for M. roreri.
Highlights
IntroductionC. Evans, Stalpers, Samson, and Benny is the causal agent of frosty pod rot (FPR) of Theobroma cacao L
We identify and characterized 88 single nucleotide polymorphism (SNP) markers in M. roreri and use them to assess the genetic diversity of M. roreri across its geographic range
Among the 25 randomly selected homozygous and heterozygous SNPs tested, none of the homozygous SNPs containing flanking regions showed more than one hit (E > 2e– 50) within the M. roreri genome while all but one heterozygous SNP containing flanking regions showed two or more hits (E > 2e–50) with the exception being SNP 485_1_1286 (See Supplementary Excel file S3)
Summary
C. Evans, Stalpers, Samson, and Benny is the causal agent of frosty pod rot (FPR) of Theobroma cacao L. FPR occurs in most major cacao producing countries in the Western Hemisphere, other than Brazil (Phillips-Mora et al, 2007a), causing yield losses up to 80% (Hidalgo et al, 2003). During the biotrophic phase the fungus slowly colonizes the Development of SNP markers for Moniliophthora roreri fruit causing malformations and positions itself to exploit the nutritive resources released when necrosis is triggered. A major shift in M. roreri gene expression occurs between the biotrophic and necrotrophic phases, and pod metabolites are rapidly metabolized by the pathogen during the necrotrophic phase and sporulation occurs (Bailey et al, 2013). Dikaryotization of the fungal mycelia from a haploid state is thought to occur in association with the shift to the necrotrophic phase
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