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.
Highlights
Castor (Ricinus communis L.) is the only species within the genus, Ricinus in the Euphorbiaceae family, that is both an autogamous and allogamous species with a diploid number of chromosomes (2n = 2x = 20) and a genome of approximately 320 Mb in size[1]
Markers based on single nucleotide polymorphisms (SNPs) hold promise in genetic studies and breeding applications and can assist in linkage map construction, marker-trait association, and marker-assisted selection because of their abundance, high level of polymorphism, high throughput capability, and cost-effectiveness
Paired-end (PE) sequencing libraries were generated using the genomic DNA of all samples
Summary
To increase castor production, elite high-yielding cultivars that display resistance to biotic and abiotic stresses need to be developed Such cultivar development can be accelerated if molecular markers are integrated into current castor breeding programmes, as proven in other crops. Markers based on single nucleotide polymorphisms (SNPs) hold promise in genetic studies and breeding applications and can assist in linkage map construction, marker-trait association, and marker-assisted selection because of their abundance, high level of polymorphism, high throughput capability, and cost-effectiveness. GBS is an NGS protocol employed to simultaneously discover and score segregating markers in populations of interest by sequencing highly multiplexed reduced representation libraries of samples[17]. At present, this technique has certain limitations for crop genotyping. The experimental operation of GBS and data analysis are beyond the capabilities of an average breeding programme; in contrast, ‘genotyping arrays’ can be used to genotype many samples within a short period, and the data analysis is relatively easy[19]
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