Molecular Breeding

, 36:87 | Cite as

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

  • Andrea Ariani
  • Jorge Carlos Berny Mier y Teran
  • Paul Gepts
Article

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.

Keywords

Common bean Copy number variation (CNV) Genome-wide SNPs calling Genotyping-by-sequencing (GBS) Next-generation sequencing 

Supplementary material

11032_2016_512_MOESM1_ESM.pdf (32 kb)
Supplementary File S1Bean genotypes analyzed in this study with the barcodes used for multiplexed sequencing (PDF 32 kb)
11032_2016_512_MOESM2_ESM.pdf (138 kb)
Supplementary File S2Correlation 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)
11032_2016_512_MOESM3_ESM.pdf (12.4 mb)
Supplementary File S3Distribution of variants and genes with the relative density in 1 Mb non-overlapping bins in the 11 P. vulgaris chromosomes (PDF 12663 kb)
11032_2016_512_MOESM4_ESM.pdf (107 kb)
Supplementary File S4Read coverage in 1 Mb non-overlapping bins across the 11 chromosomes for the G19833 reference genotype (PDF 107 kb)
11032_2016_512_MOESM5_ESM.pdf (75 kb)
Supplementary File S5RRC in the analyzed genotypes (PDF 75 kb)
11032_2016_512_MOESM6_ESM.pdf (35 kb)
Supplementary File S6Regions 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)
11032_2016_512_MOESM7_ESM.pdf (5.6 mb)
Supplementary File S7Significant 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)
11032_2016_512_MOESM8_ESM.pdf (63 kb)
Supplementary File S8Annotation, 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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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Andrea Ariani
    • 1
  • Jorge Carlos Berny Mier y Teran
    • 1
  • Paul Gepts
    • 1
  1. 1.Department of Plant Sciences/MS1University of CaliforniaDavisUSA

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