Creation of BAC genomic resources for cocoa (Theobroma cacao L.) for physical mapping of RGA containing BAC clones

Abstract

We have constructed and validated the first cocoa ( Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp ( palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.

Cocoa Agronomy, Quality, Nutritional, and Health Aspects

“…The identification of QTLs for the aforementioned characters would facilitate the development of superior genotypes for planting and evaluation under specific environmental conditions. Guiltinan (2007) and Clement et al (2004) described the value of the recently constructed cacao bacterial artificial chromosome (BAC) libraries for gene discovery in cacao. Marcano et al (2009) reported on a genome-wide mapping study for yield factors and morphological traits in cacao.…”

Mapping of rhizoctonia root rot resistance genes in sugar beet using pathogen response‐related sequences as molecular markers

“…Interestingly, such R‐loci often exist as clusters of resistance genes (Michelmore and Meyers 1998) as demonstrated by genetic and physical mapping and fluorescence in situ hybridization (Shen et al. 1998, Clement et al. 2004).…”

“…Based on their sequence and structural conservation, cloning and genetic mapping of resistance gene analogues (RGAs) and PRs from different genomes with putative function in pathogen response are possible by using a degenerate primer approach (Leister et al 1996, Pflieger et al 2001. Interestingly, such R-loci often exist as clusters of resistance genes as demonstrated by genetic and physical mapping and fluorescence in situ hybridization (Shen et al 1998, Clement et al 2004. In beet, a number of RGAs have been identified either from expressed sequence tag (EST) databases or by PCR (Tian et al 2004).…”

Moniliophthora perniciosa, the causal agent of witches’ broom disease of cacao: what's new from this old foe?

“…This QTL explained up to 51% of the phenotypic variance for resistance, while a secondary minor QTL was detected on chromosome 1, near a resistance gene analogue locus (Brown et al ., 2005; Faleiro et al ., 2006). A BAC library from ‘Scavina 6’ was constructed (Clement et al ., 2004) for map‐based cloning of this major gene. The major QTL was also reported in another mapping progeny derived from ‘SCA‐6 × ICS‐1’, which explained 35% of the phenotypic resistance to WBD (Queiroz et al ., 2003).…”