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Molecular Breeding

, 39:161 | Cite as

Genotyping-by-sequencing approaches using optimized two-enzyme combinations in Asian pears (Pyrus spp.)

  • Kidong Hwang
  • Sewon Oh
  • Keumsun Kim
  • Hyeondae Han
  • Youngjae Oh
  • Hyeonkyu Lim
  • Yoon-Kyeong Kim
  • Daeil KimEmail author
Article
  • 59 Downloads

Abstract

In genotyping-by-sequencing (GBS) library construction, restriction enzyme (RE) can influence the size and number of DNA fragments. The objective of the present study was to improve GBS efficiency in pears (Pyrus spp.) by selecting optimized RE combination. To prove GBS efficiency of selected RE combination, population structure and genetic diversity results of Asian pears were compared in two single nucleotide polymorphisms (SNP) sets derived from different GBS libraries. After in silico digestion, ApeKI, ApeKI/TfiI, and ApeKI/MseI were selected to construct GBS libraries and the number of SNPs obtained from ApeKI/TfiI library were about six times more than that from the ApeKI library. In addition, the SNPs of ApeKI/TfiI library showed high accuracy in classification of Asian pear accessions. Thus, ApeKI/TfiI combination is recommended for construction of GBS library in pears because such RE combination could provide genome-wide and numerous informative SNPs for pear genetic studies.

Keywords

ApeKI Next generation sequencing Pyrus Single nucleotide polymorphism Tfi

Notes

Acknowledgements

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

Supplementary material

11032_2019_1071_MOESM1_ESM.tif (3.2 mb)
DNA fragments of ApeKI, ApeKI/TfiI, and ApeKI/MseI libraries before and after purification. M, 100 bp of ladder marker. Black triangles indicate DNA band size of 500 and 1,000 bp (TIF 3226 kb)
11032_2019_1071_Fig7_ESM.png (292 kb)
ESM 2

(PNG 292 kb)

11032_2019_1071_MOESM2_ESM.tif (3.5 mb)
Estimated delta K values for determining optimal population numbers of 26 pear accessions. a, ApeKI library; b, ApeKI/TfiI library (TIF 3611 kb)
11032_2019_1071_Fig8_ESM.png (181 kb)
ESM 4

(PNG 181 kb)

11032_2019_1071_MOESM3_ESM.tif (2 mb)
The number of raw SNPs distribtuted in the pseudo-chromsome of pear (TIF 2070 kb)
11032_2019_1071_Fig9_ESM.png (197 kb)
ESM 6

(PNG 197 kb)

11032_2019_1071_MOESM4_ESM.docx (12 kb)
ESM 7 (DOCX 12 kb)
11032_2019_1071_MOESM5_ESM.docx (33 kb)
ESM 8 (DOCX 32 kb)
11032_2019_1071_MOESM6_ESM.docx (33 kb)
ESM 9 (DOCX 33 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of HorticultureChungbuk National UniversityCheongjuSouth Korea
  2. 2.Department of Horticultural Science, IFAS Gulf Coast Research and Education CenterUniversity of FloridaWimuamaUSA
  3. 3.Pear Research station, National Institute of Horticultural and Herbal ScienceRural Development AdministrationNajuSouth Korea

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