A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers

Abstract

A linkage map of cacao based on codominant markers has been constructed by integrating 201 new simple sequence repeats (SSR) developed in this study with a number of isoenzymes, restriction fragment length polymorphisms (RFLP), microsatellite markers and resistance and defence gene analogs (Rgenes-RFLP) previously mapped in cacao. A genomic library enriched for (GA)(n) and (CA)(n) was constructed, and 201 new microsatellite loci were mapped on 135 individuals from the same mapping population used to establish the first reference maps. This progeny resulted from a cross between two heterozygous cacao clones: an Upper-Amazon Forastero (UPA 402) and a Trinitario (UF 676). The new map contains 465 markers (268 SSRs, 176 RFLPs, five isoenzymes and 16 Rgenes-RFLP) arranged in ten linkage groups corresponding to the haploid chromosome number of cacao. Its length is 782.8 cM, with an average interval distance between markers of 1.7 cM. The new microsatellite markers were distributed throughout all linkage groups of the map, but their distribution was not random. The length of the map established with only SSRs was 769.6 cM, representing 94.8% of the total map. The current level of genome coverage is approximately one microsatellite every 3 cM. This new reference map provides a set of useful markers that is transferable across different mapping populations and will allow the identification and comparison of the most important regions involved in the variation of the traits of interest and the development of marker-assisted selection strategies.

Pathogenic variability of Moniliophthora perniciosa in three agroecological zones of the cacao region of Bahia, Brazil

“…The identification of QTL (Quantitative Trait Loci) reinforces this argument (Lanaud et al 1995, Crouzillat et al 1996, Motilal et al 2002, Pugh et al 2004. This is the reason that progenies of Scavina clones crossed with other resistance sources maintain a resistant performance in the field .…”

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping

“…The microsatellite molecular markers themselves, shown in Fig. 1, are well-established, still in use, and detailed in previous studies Lanaud et al 1999;Pugh et al 2004;Schnell et al 2005). While some of the microsatellite loci used were characterized by a single repeated di-or tri-nucleotide element, most contained nonrepeat units or multiple repeating units.…”

Genetic mapping of Theobroma cacao (Malvaceae) seedlings of the Parinari series, carriers of the lethal gene Luteus-Pa

“…In the mapping analysis, we did not observe linkage of the three genomic microsatellite loci with the lethal gene 'Luteus-Pa'. These markers map in distinct linkage groups: mTcCIR 15 in group 1, mTcCIR25 in group 6 and mTcCIR 45 in group 8 (Risterucci et al, 2000;Pugh et al, 2004). This demonstrates that 'Luteus-Pa' is not in these genomic regions.…”

“…The availability of highly polymorphic neutral markers, allied to modern statistical procedures, allows the construction of linkage maps for most plant species, even perennials, such as forest and fruit trees (Carneiro and Vieira, 2002). In the case of T. cacao, genetic mapping has been done with molecular markers, comparing segregating populations (Pugh et al, 2004;Faleiro et al, 2006).…”