Development and validation of an SNP genotyping array and construction of a high-density linkage map in castor

Scientific Reports
S SenthilvelPrashanth G Bagali

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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Citations

May 3, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Javier TelloAgnès Doligez
Feb 11, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Deepa JaganathanRajeev K Varshney
Nov 25, 2021·Genome Génome / Conseil National De Recherches Canada·Ranjan K ShawS Senthilvel

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Methods Mentioned

BETA
genotyping
Chip
electrophoresis
PCR

Software Mentioned

LPmerge
SAMtools
Illumina Assay Design tools ( ADT
RECORD
Joinmap
Trimmomatic
GenomeStudio
Mapfuser
PowerMarker
BWA

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