Design of efficient simplified genomic DNA and bisulfite sequencing in large plant populations

Abstract

The next generation sequencing enables generation of high resolution and high throughput data for structure sequence of any genome at a fast declining cost. This opens opportunity for population based genetic and genomic analyses. In many applications, whole genome sequencing or re-sequencing is unnecessary or prohibited by budget limits. The Reduced Representation Genome Sequencing (RRGS), which sequences only a small proportion of the genome of interest, has been proposed to deal with the situations. Several forms of RRGS are proposed and implemented in the literature. When applied to plant or crop species, the current RRGS protocols shared a key drawback that a significantly high proportion (up to 60%) of sequence reads to be generated may be of non-genomic origin but attributed to chloroplast DNA or rRNA genes, leaving an exceptional low efficiency of the sequencing experiment. We recommended and discussed here the design of optimized simplified genomic DNA and bisulfite sequencing strategies, which may greatly improves efficiency of the sequencing experiments by bringing down the presentation of the undesirable sequencing reads to less than 10% in the whole sequence reads. The optimized RAD-seq and RRBS-seq methods are potentially useful for sequence variant screening and genotyping in large plant/crop populations.

Graphical abstract

Keywords

plant/crop genomes / next generation sequencing / genotyping / restriction-enzyme sites associated DNA (RAD) / DNA methylation / reduced representation bisulfite sequencing

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SUPPLEMENTARY MATERIALS

The supplementary materials can be found online with this article at DOI 10.1007/s40484-016-0079-9.

ACKNOWLEDGEMENTS

This study is supported by the National Basic Research Program of China (No. 2012CB316505).

COMPLIANCE WITH ETHICS GUIDELINES

The authors Jinhua Wu, Zewei Luo and Ning Jiang declare that they have no conflict of interests.ƒThis article does not contain any studies with human or animal subjects performed by any of the authors.

Funding

RIGHTS & PERMISSIONS

2016 Higher Education Press and Springer-Verlag Berlin Heidelberg