Abstract
Cacao (Theobroma cacao L.) is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13,530 SNPs identified within a small diversity panel of cacao. Of these SNPs, 12,643 derive from variation within annotated cacao genes. The genotypes of 3,072 trees were obtained, including two mapping populations from Ecuador. High-density linkage maps for these two populations were generated and compared to the cacao genome assembly. Phenotypic data from these populations were combined with the linkage maps to identify the QTLs for yield and disease resistance.
Highlights
With a preferred growing range between 10◦N and 10◦S of the equator, Theobroma cacao L. is a diploid understory tree crop with 10 chromosomes (2n = 2x = 20)
Due to the dense genotype data provided by this Single Nucleotide Polymorphisms (SNPs) array and the relatively large population size of one of the mapping populations, our analyses identified new QTLs for agronomically important traits, and further allowed us to insert orphan sequence contigs into the cacao genome assembly
Of the 13,530 SNPs selected for the Cacao15kSNP array, 12,643 gene models (27.10% of all identified gene models) were each represented by a single SNP, in contrast is less than 1 Mbp, found on the linkage group 10
Summary
(cacao) is a diploid understory tree crop with 10 chromosomes (2n = 2x = 20). Cacao remains an important cash crop in the tropics of Central and South America, Asia, and Africa (Cuatrecasas, 1964; Hunter, 1990; Motamayor et al, 2002). Due to increases in the demand for cocoa products, which have been exacerbated by increased disease pressure in its growing regions and the fact that it is mainly grown on smallholder farms, the importance of cacao germplasm improvement is more essential than ever (Lattre-Gasquet et al, 1998; ICCO Production Values, 2012). Efforts to make cacao production more sustainable are of great importance, and building on the assembled cacao genomes to assist traditional breeding methods by developing molecular tools holds the promise of accelerating germplasm improvement toward this goal
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