Advertisement

Integrated genetic linkage maps for Korean pears (Pyrus hybrid) using GBS-based SNPs and SSRs

  • Hyeondae Han
  • Youngjae Oh
  • Keumsun Kim
  • Sewon Oh
  • Sunheum Cho
  • Yoon-Kyeong Kim
  • Daeil KimEmail author
Research Report
  • 8 Downloads

Abstract

Integrated linkage maps are a valuable tool for comparative mapping between and within genus and species. Novel single-nucleotide polymorphism (SNP) linkage maps integrated with simple sequence repeats (SSRs) based on pseudo-chromosomes of the Chinese pear reference genome of ‘Dangshansuli’ (Pyrus bretschneideri) were constructed. In total, 4801 qualified SNP markers were obtained using a customized pipeline. The consensus map for ‘Whangkeumbae’ and ‘Minibae’ contained 321 SNP and 30 SSR markers spanning 1511.1 cM with an average genetic distance of 4.3 cM. A total of 30 SSR markers made it possible to compare our consensus map to other pear and apple maps. SSR markers originating from pear and apple maps showed high co-linearity. SNPs coordinated with pseudo-chromosomes, provide information on physical length coverage for 17 corresponding linkage groups, and enable easier genome annotation for genomic regions detected by quantitative trait loci analysis. Genotyping-by-sequencing-based SNP maps integrated with SSRs in the interspecific mapping population illustrate the genomic structure of Korean pear resources and will be used as our reference maps for tribe Maleae.

Keywords

Genotyping-by-sequencing Maleae ‘Minibae’ Reference map Synteny ‘Whangkeumbae’ 

Notes

Acknowledgements

This work was supported by a Grant from the Next-Generation BioGreen 21 Program (No. PJ01311501), Rural Development Administration, Republic of Korea.

Author’s contribution

HH performed the overall data analysis including SNP calling and compared the linkage map with published pear and apple maps. YO constructed the linkage map using SNP and SSR markers. HH and YO drafted the manuscript together. KK, SO, and SC contributed SSR marker analysis including sample preparation and marker detection. YK generated and maintained the plant materials. DK designed and managed whole experiments and finalized the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

13580_2019_171_MOESM1_ESM.docx (22 kb)
Supplementary file1 (DOCX 22 kb)

References

  1. Ahn YH (2001) Distribution and characteristics of plant resources of native Pyrus sp. Plant Res 4:157–160Google Scholar
  2. Bielenberg DG, Rauh B, Fan S, Gasic K, Abbott AG, Reighard GL, Okie WR, Wells CE (2015) Genotyping by sequencing for SNP-based linkage map construction and QTL analysis of chilling requirement and bloom date in peach [Prunus persica (L.) Batsch]. PLoS ONE 10:e0139406.  https://doi.org/10.1371/journal.pone.0139406 CrossRefGoogle Scholar
  3. Cao Y, Tian L, Gao Y, Liu F (2012) Genetic diversity of cultivated and wild Ussurian Pear (Pyrus ussuriensis Maxim.) in China evaluated with M13-tailed SSR markers. Genet Resour Crop Evol 59:9–17.  https://doi.org/10.1007/s10722-011-9661-1 CrossRefGoogle Scholar
  4. Celton JM, Tustin DS, Chagné D, Gardiner SE (2009) Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences. Tree Genet Genomes 5:93–107.  https://doi.org/10.1007/s11295-008-0171-z CrossRefGoogle Scholar
  5. Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, et al (2014) The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). PLoS ONE 9:e92644.  https://doi.org/10.1371/journal.pone.0092644 CrossRefGoogle Scholar
  6. Chen H, Song Y, Li LT, Awais Khan M, Li XG, Korban SS, Wu J, Zhang SL (2015) Construction of a high-density simple sequence repeat consensus genetic map for pear (Pyrus spp.). Plant Mol Biol Rep 33:316–325.  https://doi.org/10.1007/s11105-014-0745-x CrossRefGoogle Scholar
  7. Cho HM, Cho KS, Kang SS, Koh GC, Hong KH, Kim WC, Kim KY (2002) Breeding of early summer pear cultivar ‘Minibae’. Kor J Hortic Sci Technol 20:238–241Google Scholar
  8. Choi JK, Na DY, Kim D, Shin IS, Kim MY, Lee HJ (2010) Genetic linkage mapping using interspecific hybrid population between Korean wild pear (Pyrus ussuriensis) and Japanese pear (P. pyrifolia). Hortic Environ Biotechnol 51:319–325Google Scholar
  9. Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11:485.  https://doi.org/10.1186/1471-2105-11-485 CrossRefGoogle Scholar
  10. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158.  https://doi.org/10.1093/bioinformatics/btr330 CrossRefGoogle Scholar
  11. Elshire RJ, Glaubitz JC, Poland JA, Kawamoto K, Buckler ES (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379.  https://doi.org/10.1371/journal.pone.0019379 CrossRefGoogle Scholar
  12. Gabay G, Dahan Y, Izhaki Y, Faigenboim A, Ben-Ari G, Elkind Y, Flaishman MA (2018) High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time. BMC Plant Biol 18:175.  https://doi.org/10.1186/s12870-018-1386-2 CrossRefGoogle Scholar
  13. Gardner KM, Brown P, Cooke TF, Cann S, Costa F, Bustamante C, Velasco R, Troggio M, Myles S (2014) Fast and cost-effective genetic mapping in apple using next-generation sequencing. G3 Genes Genomes Genet 4:1681–1687.  https://doi.org/10.1534/g3.114.011023 Google Scholar
  14. Guajardo V, Simón S, Sagredo B, Gainza F, Carlos M, Gasic K, Hinrichsen P (2015) Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS). PLoS ONE 10:e0127750.  https://doi.org/10.1371/journal.pone.0127750 CrossRefGoogle Scholar
  15. He J, Zhao X, Laroche A, Lu ZX, Liu H, Li Z (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5:484.  https://doi.org/10.3389/fpls.2014.00484 CrossRefGoogle Scholar
  16. Hong J, Shim E, Kwon Y (2017) Construction of a microsatellite DNA profile database for pear cultivars and germplasm. Hortic Sci Technol 35:98–107.  https://doi.org/10.12972/kjhst.20170011 Google Scholar
  17. Hummer KE, Janick J (2009) Rosaceae: taxonomy, economic importance, genomics. In: Gardiner SE, Folta KM (eds) Genetics and genomics of Rosaceae, vol 6. Springer, New York, pp 1–17Google Scholar
  18. Joobeur T, Viruel MA, de Vicente MC, Juregui B, Ballester J, Dettori MT, Verde I, Truco MJ, Batlle RI et al (1998) Construction of a saturated linkage map for Prunus using an almond×peach F2 progeny. Theor Appl Genet 97:1034–1041CrossRefGoogle Scholar
  19. Khan MA, Han Y, Zhao YF, Troggio M, Korban SS (2012) A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome. PLoS ONE 7:e47864.  https://doi.org/10.1371/journal.pone.0047864 CrossRefGoogle Scholar
  20. Kim YS, Kim WC, Hong KH, Kim JB, Kim UJ, Hong SB, Kim JH, Kim YK, Moon JY et al (1985) A new mid-season pear cultivar, ‘Whangkeumbae’ with high soluble solids content and beautiful appearance. Res Rpt RDA Hortic 27:103–106Google Scholar
  21. Kim HJ, Lee JN, Cho KS, Won HS, Suh JT (2019) Genetic diversity and population structure analysis of ever-bearing and June-bearing strawberry cultivars using SSR markers. Hortic Sci Technol 37:108–118.  https://doi.org/10.12972/kjhst.20190010 Google Scholar
  22. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760.  https://doi.org/10.1093/bioinformatics/btp324 CrossRefGoogle Scholar
  23. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079.  https://doi.org/10.1093/bioinformatics/btp352 CrossRefGoogle Scholar
  24. Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van De Weg E, Gessler C (2002) Development and characterization of 140 new microsatellites in apple (Malus × domestica Borkh.). Mol Breed 4:217–241.  https://doi.org/10.1023/A:1020525906332 CrossRefGoogle Scholar
  25. Liebhard R, Kellerhals M, Pfammater W, Jertmini M, Gessler C (2003) Mapping quantitative physiological traits in apple (Malus × domestica Borkh.). Plant Mol Biol 52:511–526.  https://doi.org/10.1023/A:1024886500979 CrossRefGoogle Scholar
  26. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12.  https://doi.org/10.14806/ej.17.1.200 CrossRefGoogle Scholar
  27. Martínez-García PJ, Parfitt DE, Ogundiwin EA, Fass J, Chan HM, Ahmad R, Lurie S, Dandekar A, Gradziel TM et al (2013) High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.). Tree Genet Genomes 9:19–36.  https://doi.org/10.1007/s11295-012-0522-7 CrossRefGoogle Scholar
  28. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303.  https://doi.org/10.1101/gr.107524.110 CrossRefGoogle Scholar
  29. Nguyen TK, Yu J, Choi HW, In BC, Lim JH (2018) Optimization of genotyping-by-sequencing (GBS) in Chrysanthemums: selecting proper restriction enzymes for GBS library construction. Hortic Sci Technol 36:108–114.  https://doi.org/10.12972/kjhst.20180012 Google Scholar
  30. Sabre-barcode-demultiplexing. Available via https://github.com/najoshi/sabre. Accessed 27 Sept 2013
  31. Semagn K, Bjørnstad Å, Ndjiondjop MN (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 5:2540–2568. http://www.academicjournals.org/AJB
  32. Silfverberg-Dilworth E, Matasci CL, Van de Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE et al (2006) Microsatellite markers spanning the apple (Malus × domestica Borkh.) genome. Tree Genet Genomes 2:202–224.  https://doi.org/10.1007/s11295-006-0045-1 CrossRefGoogle Scholar
  33. Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Nat Biotechnol 7:257–264.  https://doi.org/10.1038/nbt0389-257 CrossRefGoogle Scholar
  34. Terakami S, Kimura T, Nishitani C, Sawamura Y, Saito T, Hirabayashi T, Yamamoto T (2009) Genetic linkage map of the Japanese pear ‘Housui’ identifying three homozygous genomic regions. J Jpn Soc Hortic Sci 78:417–424.  https://doi.org/10.2503/jjshs1.78.417 CrossRefGoogle Scholar
  35. Terakami S, Nishitani C, Kunihisa M, Shirasawa K, Sato S, Tabata S, Kurita K, Kanamori H, Katayose Y et al (2014) Transcriptome-based single nucleotide polymorphism markers for genome mapping in Japanese pear (Pyrus pyrifolia Nakai). Tree Genet Genomes 10:853–863.  https://doi.org/10.1007/s11295-014-0726-0 CrossRefGoogle Scholar
  36. Tokamaneh D, Laroche J, Bastien M, Abed A, Belzile F (2017) Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping by-sequencing data. BMC Bioinformatics 18:5.  https://doi.org/10.1186/s12859-016-1431-9 CrossRefGoogle Scholar
  37. Van Ooijen JW (2006) JoinMap 4. Software for the calculation of genetic linkage maps in experimental populations, Kyazma BV, WageningenGoogle Scholar
  38. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78CrossRefGoogle Scholar
  39. Ward JA, Bhangoo J, Fernández-Fernández F, Moore P, Swanson JD, Viola R, Velasco R, Bassil N, Weber CA et al (2013) Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 14:2.  https://doi.org/10.1186/1471-2164-14-2 CrossRefGoogle Scholar
  40. Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS et al (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23:396–408.  https://doi.org/10.1101/gr.144311.112 CrossRefGoogle Scholar
  41. Wu J, Li LT, Li M, Khan MA, Li XG, Chen H, Yin H, Zhang SL (2014) High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers. J Exp Bot 65:5771–5781.  https://doi.org/10.1093/jxb/eru311 CrossRefGoogle Scholar
  42. Yamamoto T, Terakami S (2016) Genomics of pear and other Rosaceae fruit trees. Breed Sci 66:149–159.  https://doi.org/10.1270/jsbbs.66.148 Google Scholar
  43. Yamamoto T, Kimura T, Shoda M, Ban Y, Hayashi T, Matsuta N (2002) Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai). Mol Ecol Notes 2:14–16.  https://doi.org/10.1046/j.1471-8286.2002.00128.x CrossRefGoogle Scholar
  44. Yang Z, Yoder AD (1999) Estimation of the transition/transversion rate bias and species sampling. J Mol Evol 48:274–283.  https://doi.org/10.1007/PL00006470 CrossRefGoogle Scholar
  45. Zhang S, Chen W, Xin L, Gao Z, Hou Y, Yu X, Zhang Z, Qu S (2014) Genomic variants of genes associated with three horticultural traits in apple revealed by genome re-sequencing. Hortic Res 1:14045.  https://doi.org/10.1038/hortres.2014.45 CrossRefGoogle Scholar

Copyright information

© Korean Society for Horticultural Science 2019

Authors and Affiliations

  1. 1.Department of HorticultureChungbuk National UniversityCheongjuKorea
  2. 2.IFAS, GCRECUniversity of FloridaWimaumaUSA
  3. 3.Pear Research Station, National Institute of Horticultural & Herbal ScienceRural Development AdministrationNajuKorea

Personalised recommendations