Towards GWAS and genomic prediction in coffee: development and validation of a 26K SNP chip for Coffea canephora. [W173]

Genome-wide SNP genotyping platforms aiming at high-throughput and high-precision genotyping constitute an essential tool to advance breeding by genomic prediction and gene discovery by GWAS. Recent advances in coffee genomics with the sequencing of the Coffea canephora reference genome, has provided the coffee scientific community the necessary resource to develop a SNPs toolbox for genome-wide genotyping. C. canephora, an allogamous diploid species, and one of the parents of the allotetraploid C. arabica, has been an important source of genetic variability for breeding programs of both cultivated species. Highly heterozygous genomes such as C. canephora require a much higher sequence depth to reach acceptable marker call rates and genotype accuracy, when using sequence-based genotyping methods such that their cost effectiveness may not be realized. Here we describe the development and validation of a 26K Axiom SNP array (Affymetrix) whose genome-wide distributed SNP content was discovered from pooled whole-genome resequencing of C. canephora accessions covering most of its known genetic diversity. Besides facilitating low cost, high marker density, polymorphism and speed of data generation, the platform displays high genotype call accuracy and reproducibility. Genotyping validation resulted in 24,073 SNPs (94.6%) successfully converted out of the 25,456 SNPs on the array. 20,982 markers(87.1%) were scored as providing high-resolution genotypic data in a set of 800 individuals of a breeding population in which 19,586 (81.4%) were polymorphic and 1,396 (5.8%) were monomorphic. The remaining set of 3,091 (12.8%) successfully converted markers were of lower accuracy in the studied sample and may require additional cluster analysis to proper biological interpretation, i.e. targeting CNVs. This large validated SNP collection provides a powerful tool for molecular breeding and population genetics investigation within coffee species. Some preliminary results of a GWAS using this genotyping platform will be presented. (Résumé d'auteur

Assessment of SNPs for linkage mapping in Eucalyptus: construction of a consensus SNP/microsatellite map from two unrelated pedigrees

Financial support. Brazilian Ministry of Science and Technology (CNPq Grant 577047-2008-6), FAP-DF NEXTREE Grant 193.000.570/2009 and EMBRAPA Macroprogram 2 project grant 02.07.01.004

Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome

Diversity Arrays Technology (DArT) provides a robust, high throughput, cost effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization

Desenvolvimento e validação de uma plataforma de genotipagem em larga escala para Coffea canephora

O cultivo de espécies de café como Coffea canephora e C. arabica, são muito importantes em regiões tropicais de todo o mundo e possuem grande valor econômico e cultural. As plataformas de genotipagem de SNPs oferecem ensaios altamente multiplexados a um custo relativamente baixo e podem ser uma ferramenta válida para a identificação dos marcadores associados a características de interesse. Neste trabalho é proposto o desenvolvimento e a validação de uma plataforma de genotipagem Affymetrix Axiom (®) para C. canephora (Coffee Axiom chip – 26K) com SNPs identificados a partir de dados de resequenciamento de pools de C. canephora, cobrindo a maior parte da diversidade genética conhecida para a espécie, e distribuídos ao longo de todo o genoma. Mais de 1.500 indivíduos de C. canephora foram genotipados com o chip para se avaliar a eficácia do mesmo. A grande maioria dos SNPs (20.920 ou 82%) pertence à classe de polimorfismos de alta resolução. O chip Coffee Axiom - 26K- se constitui uma ferramenta de referência para a pesquisa de genética molecular e genética de populações em espécies de café

Genomic characterization, high-density mapping and anchoring of DArT markers to the reference genome of Eucalyptus

Genetic linkage maps have been essential tools to examine the inheritance of qualitative and quantitative traits, to carry out comparative mapping and to provide markers for molecular breeding applications. Linkage maps for species of Eucalyptus have been reported for several pedigrees using different molecular marker technologies [1]. However improved marker density, throughput and transferability across species are necessary to increase resolution of current maps for a variety of genomic applications. We report the development of a high density linkage map for Eucalyptus based on microsatellites and DArT (Diversity Arrays Technology) markers generated by a standardized genotyping microarray [2]. DNA probes that constitute the DArT microarray were sequenced and positioned on the reference Eucalyptus genome providing information about their sequence content, their distribution relative to annotated genes as well as the relationship between physical and recombination distance in the Eucalyptus genome. [Poster Presentation