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Whole-genome resequencing: changing the paradigms of SNP detection, molecular mapping and gene discovery

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Abstract

Next-generation sequencing (NGS) technologies open up a wealth of opportunities for plant breeding and genomic research and change the paradigms of DNA marker detection, genotyping, and gene discovery. Abundant genomic resources have been generated using a whole-genome resequencing (WGR) strategy and utilized in genome-wide association, genome diversity, and evolution studies in many crops with a reference genome such as rice and maize. The WGR-based quantitative trait loci mapping approach developed in soybean combines single nucleotide polymorphism (SNP) discovery, validation and genotyping and has the potential to identify candidate genes and causal SNPs without a time-consuming fine-mapping process. Given that this approach solves issues caused by genome duplications and repetitive sequences, it can be widely utilized in crops with a reference genome. The combination of WGR with bulked segregant analysis provides a rapid way to identify genes or causal mutations. Currently, DNA sequencing technologies are being improved rapidly. Third-generation sequencing platforms can overcome some inherent disadvantages of NGS and are expected to promote the application of WGR-based approaches and revolutionize plant breeding, genomic and genetic research.

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Abbreviations

BSA:

Bulked segregant analysis

CNV:

Copy number variation

GBS:

Genotyping by sequencing

GWA:

Genome-wide association

HMM:

Hidden Markov model

LD:

Linkage disequilibrium

MPR:

Maximum parsimony of recombination

MSG:

Multiplexed shotgun genotyping

NGM:

Next-generation mapping

NGS:

Next-generation sequencing

PAV:

Presence/absence variation

QTL:

Quantitative trait loci

QTN:

Quantitative trait nucleotides

RIL:

Recombinant inbred line

RRS:

Reduced representation sequencing

SMRT™:

Single-molecule real-time sequencing

SNP:

Single nucleotide polymorphism

TGS:

Third-generation sequencing

TILLING:

Targeting induced local lesions in genomes

tsMS™:

True single-molecule sequencing

WGR:

Whole-genome resequencing

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  1. Wheat, Peanut and Other Field Crop Research Unit, USDA-ARS, 1301 N Western Rd, Stillwater, OK, 74075, USA

    Xiangyang Xu

  2. Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506, USA

    Guihua Bai

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Correspondence to Xiangyang Xu.

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Xu, X., Bai, G. Whole-genome resequencing: changing the paradigms of SNP detection, molecular mapping and gene discovery. Mol Breeding 35, 33 (2015). https://doi.org/10.1007/s11032-015-0240-6

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