Mapping of SSRs derived from ESTs of T. cacao tissues infected by M. perniciosa

What is it about?

We report on the detection and analysis of SSR markers derived of cacao–Moniliophthora perniciosa expressed sequence tags (ESTs) in relation to cacao resistance to witches’ broom disease (WBD), and we compare the polymorphism of those ESTs (EST-simple sequence repeat (SSR)) with classical neutral SSR markers. A total of 3,487 ESTs was used in this investigation. SSRs were identified in 430 sequences: 277 from TSH 1188 (resistant genotype) and 153 from Catongo (susceptible genotype), totalizing 505 EST-SSRs with three types of motifs: dinucleotides (72.1%), trinucleotides (27.3%), and tetranucleotides (0.6%). EST-SSRs were classified into 16 main categories; most of the EST-SSRs belonged to “Unknown function” and “No homology” categories (45.82%). A high frequency of SSRs was found in the 5’UTR and in the ORF (about 27%) and a low frequency was observed in the 3’UTR (about 8%). Forty-nine EST-SSR primers were designed and evaluated in 21 cacao accessions, 12 revealed polymorphism, having 47 alleles in total, with an average of 3.92 alleles per locus. On the other hand, the 11 genomic SSR markers revealed a total of 47 alleles, with an average of 5.22 alleles per locus. The association of EST-SSR with the genomic SSR enhanced the analysis of genetic distance among the genotypes. Among the 12 polymorphic EST-SSR markers, two were mapped on the F2 Sca 6 × ICS 1 population reference for WBD resistance.

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Why is it important?

The cacao production is threatened by many pathogens such as Moniliophthora (Crinipellis) perniciosa, the causal agent of the witches’ broom disease (WBD) which has spread throughout Brazil, destroying cacao plantations and leading to important economical and social changes in affected areas. The main strategy for WBD control is the use of resistant varieties, and the major source of resistance is the Peruvian clones Scavinas. However, the fungus is adapting to this source. Therefore, the selection of new sources of resistance and accumulation of genes (pyramiding) in varieties became the priority of cacao breeding programs in producing countries. Molecular markers significantly increases the power of selective breeding and enable to save breeding cycles, which is a critical issue in the case of trees.

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