Abstract

Advances in next generation sequencing have facilitated a large-scale single nucleotide polymorphism (SNP) discovery in many crop species. Genotyping-by-sequencing (GBS) approach couples next generation sequencing with genome complexity reduction techniques to simultaneously identify and genotype SNPs. Choice of enzymes used in GBS library preparation depends on several factors including the number of markers required, the desired level of multiplexing, and whether the enrichment of genic SNP is preferred. We evaluated various combinations of methylation-sensitive (AatII, PstI, MspI) and methylation-insensitive (SphI, MseI) enzymes for their effectiveness in genome complexity reduction and enrichment of genic SNPs. We discovered that the use of two methylation-sensitive enzymes effectively reduced genome complexity and did not require a size selection step. On the contrary, the genome coverage of libraries constructed with methylation-insensitive enzymes was quite high, and the additional size selection step may be required to increase the overall read depth. We also demonstrated the effectiveness of methylation-sensitive enzymes in enriching for SNPs located in genic regions. When two methylation-insensitive enzymes were used, only 16% of SNPs identified were located in genes and 18% in the vicinity (± 5 kb) of the genic regions, while most SNPs resided in the intergenic regions. In contrast, a remarkable degree of enrichment was observed when two methylation-sensitive enzymes were employed. Almost two thirds of the SNPs were located either inside (32–36%) or in the vicinity (28–31%) of the genic regions. These results provide useful information to help researchers choose appropriate GBS enzymes in oil palm and other crop species.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-016-0572-x) contains supplementary material, which is available to authorized users.

Highlights

  • SHORT COMMUNICATIONEffects of methylation-sensitive enzymes on the enrichment of genic single nucleotide polymorphism (SNP) and the degree of genome complexity reduction in a two-enzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm (Elaeis guineensis)

  • Advances in generation sequencing have facilitated a large-scale single nucleotide polymorphism (SNP) discovery in many crop species

  • Despite a drastic reduction in the cost associated with next-generation sequencing, it is still prohibitively expensive to employ whole genome sequencing for SNP discovery and genotyping of multiple individuals in a target population, especially for organisms with large genomes

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Summary

SHORT COMMUNICATION

Effects of methylation-sensitive enzymes on the enrichment of genic SNPs and the degree of genome complexity reduction in a two-enzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm (Elaeis guineensis). Wirulda Pootakham & Chutima Sonthirod & Chaiwat Naktang & Nukoon Jomchai & Duangjai Sangsrakru & Sithichoke Tangphatsornruang. Received: 20 April 2016 / Accepted: 20 October 2016 / Published online: 10 November 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com

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