Application of High Throughput Genotyping SNP Array for Citrus

We developed two high-density SNP genotyping arrays for citrus using the Axiom™ platform (Affymetrix, Inc.), Citrus15 (1.4M autosomal and 1002 Chloroplast SNPs) and Citrus56 (58K autosomal and 500 Chloroplast SNPs). The arrays, designed from whole genome sequences of 41 diverse Citrus and Citrus relatives, target genes and adjacent sequences and have good genome coverage. 229 diverse accessions of Citrus and closely related genera were genotyped to assess the array performance of Citrus15 and to select validated probe sets to be represented on Citrus56. 1482 accessions from the UCR Citrus Variety Collection (CVC), breeding germplasm, and mapping populations have been successfully genotyped with Citrus56. Genotyping success was above 90% (% PolyHigh Resolution ). Average reproducibilities of Citrus15 and Citrus56 were 99.8% and 99.9% respectively and the arrays were shown to be robust and accurately call SNPs in Citrus and Poncirus. Allele calling was performed with Axiom™ Analysis Suite with default settings. Principal component analysis (PCA) and population structure were analyzed with TASSEL and ADMIXTURE respectively to determine relationships among the accessions in the CVC. Heterozygous markers in selected accessions were also assessed for their application in mapping important traits. For example, Fairchild mandarin was heterozygous for more than 10,000 SNPs. Citrus56 array was also used to genotype whole genome amplifications from 221 single pollen grains from 39 diploid accessions with a success rate of about 71%. In addition, comparison of Citrus15 genotypes of accessions derived by natural mutation identified regions with loss of heterozygosity (putative deletions).