High-throughput genotyping in citrus accessions using an SNP genotyping array

• Published in: Tree genetics & genomes Vol. 9; no. 1; pp. 145 - 153
• Main Authors: Fujii, Hiroshi, Shimada, Takehiko, Nonaka, Keisuke, Kita, Masayuki, Kuniga, Takeshi, Endo, Tomoko, Ikoma, Yoshinori, Omura, Mitsuo
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.02.2013; Springer Nature B.V
• Subjects: Barley; Biomedical and Life Sciences; Biotechnology; chromosome mapping; Citrus; Cultivars; Deoxyribonucleic acid; DNA; Flowers & plants; Forestry; Fruits; Genetic diversity; Genetic testing; genetic variation; Genomes; genomics; genotype; Genotypes; Genotyping; Harvest; Hybrids; Life Sciences; marker-assisted selection; Nucleotide sequence; Original Paper; parentage; Plant breeding; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Plant species; Progeny; Research centers; Rice; sequence analysis; Single-nucleotide polymorphism; Software; Tree Biology; Trees; Vocalization behavior; Japan; High throughput; Citrus; SNP; Genotyping; Parentage
• ISSN: 1614-2942; 1614-2950
• DOI: 10.1007/s11295-012-0542-3

We developed a 384 multiplexed SNP array, named CitSGA-1, for the genotyping of Citrus cultivars, and evaluated the performance and reliability of the genotyping. SNPs were surveyed by direct sequence comparison of the sequence tagged site (STS) fragment amplified from genomic DNA of cultivars representing the genetic diversity of citrus breeding in Japan. Among 1497 SNPs candidates, 384 SNPs for a high-throughput genotyping array were selected based on physical parameters of Illumina’s bead array criteria. The assay using CitSGA-1 was applied to a hybrid population of 88 progeny and 103 citrus accessions for breeding in Japan, which resulted in 73,726 SNP calls. A total of 351 SNPs (91 %) could call different genotypes among the DNA samples, resulting in a success rate for the assay comparable to previously reported rates for other plant species. To confirm the reliability of SNP genotype calls, parentage analysis was applied, and it indicated that the number of reliable SNPs and corresponding STSs were 276 and 213, respectively. The multiplexed SNP genotyping array reported here will be useful for the efficient construction of linkage map, for the detection of markers for marker-assisted breeding, and for the identification of cultivars.