A Five-Species 50K Axiom SNP Microarray Allows High Quality Genotyping of Coffee, Cashew, Cassava, Brazilian Pine and Eucalyptus

The identification of new sources of genetic variation is a key component of any long-term breeding strategy to increase the productivity, resilience and sustainability of crop varieties. Over six million crop accessions are currently being conserved worldwide in still largely untapped genebanks. High throughput, low cost and robust SNP genotyping technologies are necessary to unlock this wealth of diversity and release the data in an organized fashion to allow user friendly adoption by germplasm curators and breeders. Although more targeted and robust GbS methods have been developed, fixed content SNP-arrays indisputably provide the gold standard for user friendly, interchangeable and fast turnaround SNP data. To defray the upfront cost of developing a SNP microarray we have built and validated a multispecies 50K Axiom SNP microarray. The array real estate was shared among five species according to the marker density needed, in turn determined by the foreseen genetic application that included high-density linkage mapping, genomic selection, pedigree reconstruction and germplasm characterization. From a total of 1,918 samples distributed across the five species, 1,817 (94.7%) were successfully genotyped showing that the Axiom technology is robust across variable DNA sources. The SNP content was distributed as follows: 26,546 SNPs for Coffee, 16,504 for Cashew, 3,417 for Cassava, 3,400 for Araucaria (Brazilian Pine) and 2,000 for Eucalyptus. All SNPs were newly developed from whole-genome (Cashew, Coffee, Cassava) or RAD and RNAseq (Araucaria) data while previously validated SNPs were used for Eucalyptus as control. SNP conversion rates were 84% for Cashew, 94% for Cassava, 93% for Coffee and a lower 74% for Araucaria likely due to the very complex and huge 23Gbp genome and limited RAD and RNAseq data used for SNP discovery. For Eucalyptus, 92% of the SNPs were successfully converted from an Illumina Infinium chip. This microarray has enabled a number of powerful genetic studies in breeding and conservation and represents the successful demonstration needed to build a larger array to accommodate SNPs for twelve species toward comprehensive large scale genebanks genotyping at EMBRAPA.