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Development of SNP markers present in expressed genes of the plant-pathogen interaction: Theobroma cacao - Moniliophtora perniciosa

Lemos L.S.L., Gramacho K.P., Pires J.L., Ferreira Santos R.M., Ganem R.S., Costa M.G.C., Micheli F.. 2017. AgroTropica, 29 (2) : p. 111-118.

DOI: 10.21757/0103-3816.2017v29n2p111-118

We report the detection, validation and analysis of SNPs in the plant-pathogen interaction between cacao and Moniliophthora perniciosa ESTs using resequencing. This analysis in 73 EST sequences allowed the identification of 185 SNPs, 57% of them corresponding to transversion, 29% to transition and 14% to indels. The ESTs containing SNPs were classified into 14 main functional categories. After validation, 91 SNPs were confirmed, categorized and the parameters of nucleotide diversity and haplotype were calculated. Haplotype-based gene diversity and polymorphic information content (PIC) ranged from 0.559 to 0.56 and 0.115 to 0.12; respectively. Also, it was the advantage when considering haplotypes structure for each locus in place of single SNPs. Most of the gene fragments had a major haplotype combined to a series of low frequency haplotypes. Thus, the re-sequencing approach proved to be a valuable resource to identify useful SNPs for wide genetic applications. Furthermore, the cacao genome sequence availability allow a positional selection of DNA fragments to be re-sequenced enhancing the usefulness of the discovered SNPs. These results indicate the potential use of SNPs markers to identify allelic status of cacao resistance genes through marker-assisted selection to support the development of promising genotypes with high resistance to witch's broom disease.

Mots-clés : theobroma cacao; moniliophthora; relation hôte pathogène; interactions biologiques; polymorphisme génétique; résistance génétique; résistance aux maladies; séquence nucléotidique; gène; identification; bahia; moniliophthora perniciosa; séquencage

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