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Genome-wide identification of SNPs and copy number variation in common bean (Phaseolus vulgaris L.) using genotyping-by-sequencing (GBS)

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Abstract

Next-generation sequencing technologies have increased markedly the throughput of genetic studies, allowing the identification of several thousands of SNPs within a single experiment. Even though sequencing cost is rapidly decreasing, the price for whole-genome re-sequencing of a large number of individuals is still costly, especially in plants with a large and highly redundant genome. In recent years, several reduced representation library approaches have been developed for reducing the sequencing cost per individual. Among them, genotyping-by-sequencing (GBS) represents a simple, cost-effective, and highly multiplexed alternative for species with or without an available reference genome. However, this technology requires specific optimization for each species, especially for the restriction enzyme (RE) used. Here we report on the application of GBS in a test experiment with 18 genotypes of wild and domesticated Phaseolus vulgaris. After an in silico digestion with different RE of the P. vulgaris genome reference sequence, we selected CviAII as the most suitable RE for GBS in common bean based on the high frequency and even distribution of restriction sites. A total of 44,875 SNPs, 1940 deletions, and 1693 insertions were identified, with 50 % of the variants located in genic sequences and tagging 11,027 genes. SNP and InDel distributions were positively correlated with gene density across the genome. In addition, we were able to also identify putative copy number variations of genomic segments between different genotypes. In conclusion, GBS with the CviAII enzyme results in thousands of evenly spaced markers and provides a reliable, high-throughput, and cost-effective approach for genotyping both wild and domesticated common beans.

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Acknowledgments

This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303. This project was supported by Agriculture and Food Research Initiative (AFRI) Competitive Grant No. 2013-67013-21224 from the USDA National Institute of Food and Agriculture.

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Authors and Affiliations

  1. Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA

    Andrea Ariani, Jorge Carlos Berny Mier y Teran & Paul Gepts

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  1. Andrea Ariani
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  2. Jorge Carlos Berny Mier y Teran
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  3. Paul Gepts
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Correspondence to Andrea Ariani.

Electronic supplementary material

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Supplementary File S1

Bean genotypes analyzed in this study with the barcodes used for multiplexed sequencing (PDF 32 kb)

Supplementary File S2

Correlation between SNP distribution (Total SNPs) and density on a 1 Mb non-overlapping bin (SNPs/Mb) with chromosome length. Regression lines and Pearson regression coefficient (r) are shown (PDF 138 kb)

Supplementary File S3

Distribution of variants and genes with the relative density in 1 Mb non-overlapping bins in the 11 P. vulgaris chromosomes (PDF 12663 kb)

Supplementary File S4

Read coverage in 1 Mb non-overlapping bins across the 11 chromosomes for the G19833 reference genotype (PDF 107 kb)

Supplementary File S5

RRC in the analyzed genotypes (PDF 75 kb)

Supplementary File S6

Regions harboring putative CNVs in the different genotypes. The coordinates of the genomic bins in the different chromosomes are reported in BED format (PDF 35 kb)

Supplementary File S7

Significant GO terms (FDR < 0.05) enriched in the genes located in putative CNVs. Test Set is the set of the up-regulated genes, Reference Set is the background of the P. vulgaris GO terms mapping (PDF 5762 kb)

Supplementary File S8

Annotation, together with the best Arabidopsis hit, of the genes located in putative CNVs. When available the best Arabidopsis hit common name was used (PDF 62 kb)

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Ariani, A., Berny Mier y Teran, J.C. & Gepts, P. Genome-wide identification of SNPs and copy number variation in common bean (Phaseolus vulgaris L.) using genotyping-by-sequencing (GBS). Mol Breeding 36, 87 (2016). https://doi.org/10.1007/s11032-016-0512-9

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