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Title: Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality

Author
item ALI, SHAHIN - Foreign Agricultural Service (FAS, USDA)
item Shao, Jonathan
item Strem, Mary
item PHILLIPS-MORA, WILBERTH - Catie Tropical Agricultural Research
item Zhang, Dapeng
item Meinhardt, Lyndel
item Bailey, Bryan

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/4/2015
Publication Date: 8/27/2015
Citation: Ali, S., Shao, J.Y., Strem, M.D., Phillips-Mora, W., Zhang, D., Meinhardt, L.W., Bailey, B.A. 2015. Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality. Frontiers in Microbiology. doi: 10.3389/fmicb.2015.00850.

Interpretive Summary: Chocolate is produced from the seeds of the cacao tree. The fungus Moniliophthora roreri causes frosty pod rot of cacao, a disease that can completely destroy cacao yields. Understanding the genetic diversity associated with the pathogens population in the field is critical to developing sustainable disease management strategies for frosty pod rot and this includes breeding for resistance to disease. New genetic markers based on single nucleotide polymorphisms, were developed and used to identify the center of genetic diversity for the pathogen causing frosty pod rot. The largest amount of genetic diversity among Moniliophthora roreri isolates was found in the upper Magdalena Valley of Colombia, identifying it as the center of origin for the pathogen. It was also determined that the genetic diversity of the pathogen in locations outside the center of origin was narrow. The Magdalena Valley was identified as an important location for further studies of the pathogens evolution and as a potential site for breeders to use when screening for resistance to the disease in cacao. It was also clear that careful quarantine continues to be required even in areas where the pathogen already exist to prevent the introduction of additional pathogen genetic diversity which would complicate disease management efforts by farmers. By understanding the pathogens genetic diversity should aid in limiting its spread to the benefit of cacao farmers, the cacao industry, and ultimately consumers of chocolate.

Technical 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 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 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 primarily through homothallism. 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.