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Updated: Jan 28, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Development and validation of an SNP genotyping array and construction of a high-density linkage map in castor
S Senthilvel1, Arpita Ghosh2, Mobeen Shaik3
1ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030, India. senthilvel.senapathy@icar.gov.in.
Abstract:
Castor is a commercially important oilseed crop that provides raw materials for several industries. Currently, the availability of genomic resources for castor is very limited. In this study, genome-wide SNPs were discovered in castor via whole-genome sequencing of 14 diverse lines to an average of 34X coverage. A total of 2,179,759 putative SNPs were detected, and a genotyping array was designed with 6,000 high-quality SNPs representing 2,492 scaffolds of the draft castor genome (87.5% genome coverage). The array was validated by genotyping a panel of 314 inbred castor lines, which resulted in 5,025 scorable SNPs with a high call rate (98%) and reproducibility (100%). Using this array, a consensus linkage map consisting of 1,978 SNP loci was constructed with an average inter-marker distance of 0.55 cM. The genome-wide SNP data, the genotyping array and the dense linkage map are valuable genomic tools for promoting high-throughput genomic research and molecular breeding in castor.
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