First Microsatellite Markers Developed From Cupuassu Ests: Application In Diversity Analysis And Cross-species Transferability To Cacao

The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit's pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta-And trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively. The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit's pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta-And trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively. © 2016 Ferraz dos Santos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.11

Diversidade genética entre acessos de cacau de fazendas e de banco de germoplasma na Bahia Genetic diversity among farm and germplasm bank accessions of cacao in Bahia, Brazil

O objetivo deste trabalho foi avaliar a diversidade genética de acessos de cacau, selecionados previamente como produtivos e resistentes à vassoura-de-bruxa na Bahia, e estudar suas inter-relações com genótipos no banco de germoplasma. Amostras de DNA de folhas dos 120 acessos, coletados em 17 fazendas de sete municípios do Sul da Bahia, foram amplificadas pela técnica de RAPD ("random amplified polymorphic DNA"). Os coeficientes de dissimilaridade genética, calculados pelo método de Jaccard a partir das bandas RAPD, permitiram evidenciar, pela análise de agrupamento, que a maioria das seleções das fazendas (89,2%) agrupou-se com acessos do banco de germoplasma considerados representativos da diversidade de cacau (híbridos, trinitários, Scavinas, amazônicos e cacau-comum). As demais seleções distribuíram-se em outros sete grupos distintos. Há elevada diversidade genética entre as seleções das fazendas, e algumas delas devem ter-se originado de genitores não incluídos nesta análise. Esses materiais apresentam potencial para seleção de clones com maior diversidade para novos cruzamentos ou uso pelos agricultores.<br>The objective of this work was to assess genetic diversity of farm cacao accessions, previously selected as productive and resistant to witch broom in Bahia, Brazil, and to study their interrelationship with reference genotypes on germplasm bank. DNA samples from 120 cacao accessions, collected on 17 farms in seven counties in Southern Bahia, were amplified by RAPD technique (random amplified polymorphic DNA). The coefficients of genetic dissimilarity, calculated from the RAPD bands by Jaccard method, allowed to show by cluster analysis that most farm selections (89.2%) grouped with accessions from germplasm bank considered representatives of the cacao genetic diversity (hybrids, Trinitarian, Scavina, Amazon and common cacao). The other selections were distributed in seven distinct groups. There is high genetic diversity among farm selections, and some of them may have originated from other progenitors not included in this analysis. These materials present potential for clone selection with higher diversity for new crossings or direct use by agriculturists