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. 2012;19(1):23-35.
doi: 10.1093/dnares/dsr039. Epub 2011 Dec 30.

Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L

Mathilde Allegre  1 , Xavier Argout, Michel Boccara, Olivier Fouet, Yolande Roguet, Aurélie Bérard, Jean Marc Thévenin, Aurélie Chauveau, Ronan Rivallan, Didier Clement, Brigitte Courtois, Karina Gramacho, Anne Boland-Augé, Mathias Tahi, Pathmanathan Umaharan, Dominique Brunel, Claire Lanaud
Affiliations

Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L

Mathilde Allegre et al. DNA Res. 2012.

Abstract

Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr.

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Figures

Figure 1.
Figure 1.
Genetic map constructed from an F1 progeny of 264 individuals (located in CNRA, Côte d'Ivoire) belonging to the UPA402 × UF676 cross. This map consists of 1043 markers of a known DNA sequence (461 SNPs, 524 SSRs, and 58 RFLPs), spanning 752 cM. The average distance between two markers is 0.7 cM. The new markers added to this map are printed in red.
Figure 2.
Figure 2.
Genetic map constructed from an F2 progeny of 132 individuals (located at CEPLAC, Brazil) obtained by selfing of a single (Scavina 6 × ICS1) selected hybrid. This map consists of 531 SNP markers, spanning 754 cM. The average distance between two markers is 1.4 cM.
Figure 3.
Figure 3.
Consensus map of (UPA402 × UF676) and F2 progenies. Markers segregating in both progenies are indicated in black, those segregating only in (UPA402 × UF676) are printed in green (previously mapped markers) and blue (newly mapped markers). Markers segregating only in the F2 progeny are printed in pink. This consensus map consists of 1262 markers of a known DNA sequence, and it has a length of 734 cM. The average distance between two markers is 0.6 cM. Among the 1262 markers, 810 correspond to markers defined in expressed genes. Significant skewed segregations are indicated by asterisks (*P< 0.05, **P< 0.01) or dots (F2 population).
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References

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