Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.–Moniliophthora perniciosa interaction ESTs

Abstract

In this study, we report results of 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 the resistant genotype TSH 1188 and 153 from the susceptible one Catongo, 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 Communicated by J. DavisElectronic supplementary material The online version of this article (

Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki

“…These markers provide a functional insight into gene-based diversity analysis. Expressed sequence tags (ESTs) have been effectively utilized for the development of these markers and have been subsequently used in the characterization of germplasm (Lima et al, 2010;Kumar Yadav et al, 2011). Simple sequence repeats (SSRs), also called microsatellites, are repetitive stretches of DNA varying from 1-6 bp in length, whereas targeted region amplified polymorphism (TRAP), uses the anchored and arbitrary primers to target the functional gene regions (Hu and Vick, 2003).…”

Structural characterization and mapping of functional EST-SSR markers in Theobroma cacao

“…These markers were identified in the first ESTs (6581 sequences) from leaf and bean cDNA libraries (Jones et al 2002), and from suppressive subtractive hybridization (SSH) from leaves treated with inducers of the defense response (Verica et al 2004), and shoot tips inoculated with witches' broom caused by Moniliophthora perniciosa (Leal et al 2007). More recently, Lima et al (2010) identified 49 EST-SSRs from full length and SSH libraries constructed from shoots and pods elicited with M. perniciosa.…”

First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao

“…Here, the highest proportions of EST-SSRs identified were hepta- and trinucleotides (29.3% and 25.4%, respectively; Fig 2A ). Trinucleotides were generally considered as the most abundant class of SSRs in plant ESTs [ 27 , 55 – 57 ] but other works also indicated dinucleotides [ 33 , 58 ]. Since the addition or deletion of three nucleotides within translated regions usually does not affect the ORFs, it is not uncommon to detect a high abundance of these repeat motifs in EST-SSRs [ 59 , 60 ], as we observed in our results ( Fig 4B ).…”