Validação de uma plataforma de genotipagem (Coffee Axiom Chip - 26K) com aplicação em seleção genômica ampla e GWAS, em Coffea canephora

Abstract

Coffee is a perennial, long-cycle species and, therefore, conventional breeding programs of this species are time-consuming (several years) and costly. The generation of superior cultivars via genetic improvement still deals with the challenge of simultaneously aggregating several quantitative characteristics of agronomic relevance and the generation of superior cultivars via genetic improvement still deals with the challenge of simultaneously aggregating several quantitative characteristics of agronomic relevance and beverage quality. Large-scale genotyping platforms, and in particular DNA arrays, have enabled the identification of a high density of SNPs covering the entire genome, and in addition, recent advances in coffee genomics, such as the sequencing of the C. canephora reference genome, provided the necessary resources for the advancement of breeding of the species by genomic selection and gene discovery by GWAS, although Coffea genus studies using high-throughput genotyping methodologies are still few. The development and validation of a C. canephora 26K Axiom SNP array was possible, covering most of the known genetic diversity of the species, including also a large part of the genotypes belonging to the main breeding programs in Brazil. Of a total of 25,456 SNPs present on the array, 25,411 SNPs were successfully converted and more than 85% classified as polymorphic. Joining the high-throughput genotyping data, using the developed array, and the phenotypic data generated for 1,319 C. canephora individuals, cultivated at Embrapa Cerrados (Planaltina-DF), was carried out in this work: (i) genomic wide association study (GWAS) and (ii) genomic selection for several important characteristics in coffee breeding. GWAS has been widely used in the genetic analysis of complex traits and SG has been studied to increase genetic gain and reduce the duration of breeding cycles, especially in the case of perennial plants such as coffee. A large number of associated markers were identified in the GWAS for several characteristics, suggesting the usefulness of SNPs identified on the array as a potential resource for the identification of genomic targets and of higher genotypes that would be sources of genes of interest. GS analyzes were performed by the G-BLUP method and heritabilities and accuracy were estimated. The characteristics evaluated in this study presented high complexity, since they are controlled by several genes, and low heritability. GS is a promising and innovative approach to be applied for C. canephora breeding. In practice, in comparison with traditional phenotypic evaluation, GWAS and SG might now be employed to foster and accelerate the breeding programmes of C. canephora with a very good forecast of success in addition might maintain genetic diversity and increase the gain genetic selection per unit of time.