Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript...

Area of Science:

• Genomics
• Crop Science
• Molecular Biology

Background:

• Next-generation sequencing enables target enrichment sequencing (TES) for identifying genomic variations.
• Peanut, an allotetraploid crop, presents challenges for variant analysis due to its large genome size.

Purpose of the Study:

• To assess the feasibility of designing probes from transcript sequences for TES in peanut.
• To identify sequence variants in peanut using TES.

Main Methods:

• In-solution hybridization was used to enrich DNA sequences from seven peanut genotypes.
• Probes were designed from peanut transcript sequences for target enrichment.

Main Results:

• TES is feasible in polyploid peanut using transcript-derived probes, targeting 5131 and 7521 genes in A and B genomes, respectively.
• High-depth coverage of target regions was achieved, with an average on-target rate of 42.47%.
• TES demonstrated superior target region coverage compared to whole genome sequencing, RNA sequencing, and genotyping by sequencing.

Conclusions:

• TES using transcript-derived probes is a successful strategy for SNP identification in peanut.
• This approach provides valuable markers for peanut genotyping and offers a model for non-model species lacking genome references.