Construction of high-resolution genetic linkage map in pear pseudo-BC1 ((Pyrus pyrifolia × P. communis) × P. pyrifolia) using GBS-SNPs and SSRs

Abstract

Genetic linkage map of pear ((Pyrus pyrifolia × P. communis) × P. pyrifolia) was constructed to validate the effectiveness of the two-enzyme approach in GBS library preparation. In addition, allele inheritance was analyzed to investigate the usefulness of the pear pseudo-BC1 in genetic analysis. A total of 905 GBS-SNPs and 69 SSRs were anchored in 17 linkage groups with total genetic distance of 1760.1 cM and average marker distance of 1.88 cM. The genetic linkage map represents 80.5% of pear genome. GBS two-enzyme approach improved marker density and genome coverage compared to the single-enzyme approach. In addition, the inheritance analysis of SSR alleles demonstrated that pseudo-BC could allow genetic dissection of donor parent specific trait segregating in the F2. The high-resolution genetic linkage map of pear pseudo-BC1 will be used for candidate gene identification. Moreover, genetic analysis of donor parent specific traits segregating in the pseudo-BC1 hybrids will promote marker development for molecular breeding in pear.

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Acknowledgements

This work was supported by a grant from the Next-generation BioGreen21 Program (No. PJ01311501), Rural Development Administration, Republic of Korea.

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SO performed the overall the experiment and data analysis. SO and YO wrote the manuscript together. KK and HH contributed SNP calling and data analysis. YK contributed SSR marker analysis. KW generated and maintained the plant materials. DK designed and managed whole experiments and finalized the manuscript.

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Correspondence to Daeil Kim.

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Communicated by Ali Sarkhosh.

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Supplementary Table 1

Description of SSR markers used for polymorphism test in the pseudo-BC1 ((Pyrus pyrifolia × P. communis) × P. pyrifolia) and the progenitors (P. pyrifolia cv. Whangkeumbae and P. communis cv. Bartlett) (DOCX 16 kb)

Supplementary Table 2

Summary of genotyping-by-sequencing including the number of reads, mapping rate, and depth of mapped region (DOCX 15 kb)

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Oh, S., Oh, Y., Kim, K. et al. Construction of high-resolution genetic linkage map in pear pseudo-BC1 ((Pyrus pyrifolia × P. communis) × P. pyrifolia) using GBS-SNPs and SSRs. Hortic. Environ. Biotechnol. (2020). https://doi.org/10.1007/s13580-020-00261-7

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Keywords

  • Asian pear
  • European pear
  • Interspecific hybrid
  • Pseudo-backcross
  • Pseudo-testcross
  • Reduced representation library