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.
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.
CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France.
Mathilde
M
Allegre
Xavier
X
Argout
Michel
M
Boccara
Olivier
O
Fouet
Yolande
Y
Roguet
Aurélie
A
Bérard
Jean Marc
JM
Thévenin
Aurélie
A
Chauveau
Ronan
R
Rivallan
Didier
D
Clement
Brigitte
B
Courtois
Karina
K
Gramacho
Anne
A
Boland-Augé
Mathias
M
Tahi
Pathmanathan
P
Umaharan
Dominique
D
Brunel
Claire
C
Lanaud
D001947:Breeding; D002099:Cacao / Q000235:genetics*; D002874:Chromosome Mapping; D020224:Expressed Sequence Tags; D008040:Genetic Linkage; D005838:Genotype; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA