Plant Breeding and Biotechnology

  • 제6권4호
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  • Pages.434-443
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  • 2018
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  • 2287-9358(pISSN)
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  • 2287-9366(eISSN)
한국육종학회 (The Korean Society of Breeding Science)
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DOI QR코드

DOI QR Code

Development of an Apple F1 Segregating Population Genetic Linkage Map Using Genotyping-By-Sequencing

  • Ban, Seung Hyun (College of Agriculture and Life Science, Kyungpook National University) ;
  • Choi, Cheol (College of Agriculture and Life Science, Kyungpook National University)
  • 투고 : 2018.10.26
  • 심사 : 2018.11.15
  • 발행 : 2018.12.01
⟨ 이전 논문 다음 논문 ⟩

초록

Genotyping-by-sequencing (GBS) has been used as a viable single nucleotide polymorphism (SNP) validation method that provides reduced representation sequencing by using restriction endonucleases. Although GBS makes it possible to perform marker discovery and genotyping simultaneously with reasonable costs and a simple molecular biology workflow, the standard TASSEL-GBS pipeline was designed for homozygous groups, and genotyping of heterozygous groups is more complicated. To addresses this problem, we developed a GBS pipeline for heterozygous groups that called KNU-GBS pipeline, specifically for apple (Malus domestica). Using KNU-GBS pipeline, we constructed a genetic linkage map consisting of 1,053 SNP markers distributed over 17 linkage groups encompassing a total of 1350.1 cM. The novel GBS pipeline for heterozygous groups will be useful for marker-assisted breeding programs, and diverse heterozygous genome analyses.

키워드

과제정보

연구 과제 주관 기관 : Rural Development Administration

참고문헌

  1. Barba P, Cadle-Davidson L, Harriman J, Glaubitz JC, Brooks S, Hyma K, et al. 2014. Grapevine powdery mildew resistance and susceptibility loci identified on a highresolution SNP map. Theor. Appl. Genet. 127: 73-84. https://doi.org/10.1007/s00122-013-2202-x
  2. Cox MP, Peterson DA, Biggs PJ. 2010. SolexaQA: At-a-glance quality assessment of Illumina secondgeneration sequencing data. BMC Bioinformatics 11: 485. https://doi.org/10.1186/1471-2105-11-485
  3. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. 2011. A Robust, Simple Genotypingby- Sequencing (GBS) Approach for High Diversity Species. PLoS One 6: e19379. https://doi.org/10.1371/journal.pone.0019379
  4. Gardner KM, Brown P, Cooke TF, Cann S, Costa F, Bustamante C, et al. 2014. Fast and cost-effective genetic mapping in apple using next-generation sequencing. G3. 4: 1681-1687.
  5. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, et al. 2014. TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One 9: e90346. https://doi.org/10.1371/journal.pone.0090346
  6. Grattapaglia D, Sederoff R. 1994. Genetic-linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137: 1121-1137.
  7. He J, Zhao X, Laroche A, Lu ZX, Liu H, Li Z. 2014. Genotyping-by-sequencing (GBS), an ultimate markerassisted selection (MAS) tool to accelerate plant breeding. Front. Plant Sci. 5: 484.
  8. Kenis K, Keulemans J. 2005. Genetic linkage maps of two apple cultivars (Malus $\times$ domestica Borkh.) based on AFLP and microsatellite markers. Mol. Breed. 15: 205-219. https://doi.org/10.1007/s11032-004-5592-2
  9. Kenis K, Keulemans J. 2007. Study of tree architecture of apple (Malus $\times$ domestica Borkh.) by QTL analysis of growth traits. Mol. Breed. 19: 193-208. https://doi.org/10.1007/s11032-006-9022-5
  10. Kim JE, Oh SK, Lee JH, Lee BM, Jo SH. 2014. Genome-wide SNP calling using next generation sequencing data in tomato. Mol. Cells 37: 36-42. https://doi.org/10.14348/molcells.2014.2241
  11. Kosambi DD. 1943. The estimation of map distances from recombination values. Ann. Hum. Genet. 12: 172-175.
  12. 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
  13. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
  14. Li X, Wei Y, Acharya A, Jiang Q, Kang J, Brummer EC. 2014. A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotypingby- sequencing is highly syntenous with the Medicago truncatula genome. G3. 4: 1971-1979.
  15. Liebhard R, Kellerhals M, Pfammatter W, Jertmini M, Gessler C. 2003a. Mapping quantitative physiological traits in apple (Malus $\times$ domestica Borkh.). Plant Mol. Biol. 52: 511-526. https://doi.org/10.1023/A:1024886500979
  16. Liebhard R, Koller B, Gianfranceschi L, Gessler C. 2003b. Creating a saturated reference map for the apple (Malus $\times$ domestica Borkh.) genome. Theor. Appl. Genet. 106: 1497-1508. https://doi.org/10.1007/s00122-003-1209-0
  17. Liebhard R, Koller B, Patocchi A, Kellerhals M, Pfammatter W, Jermini M, et al. 2003c. Mapping quantitative field resistance against apple scab in a 'Fiesta' x 'Discovery' progeny. Phytopathology 93: 493-501. https://doi.org/10.1094/PHYTO.2003.93.4.493
  18. Ma XF, Jensen E, Alexandrov N, Troukhan M, Zhang LP, Thomas-Jones S, et al. 2012. High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis. PLoS One 7: e33821. https://doi.org/10.1371/journal.pone.0033821
  19. Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17: 10-12.
  20. Poland JA, Brown PJ, Sorrells ME, Jannink JL. 2012. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7: e32253. https://doi.org/10.1371/journal.pone.0032253
  21. Russell J, Hackett C, Hedley P, Liu H, Milne L, Bayer M, et al. 2014. The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences. Mol. Breed. 33: 835-849. https://doi.org/10.1007/s11032-013-9996-8
  22. Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, et al. 2013. Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor. Appl. Genet. 126: 2699-2716. https://doi.org/10.1007/s00122-013-2166-x
  23. Van Ooijen JW. 2006. Join Map 4.0, Software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V. Wageningen, Netherlands.
  24. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, et al. 2010. The genome of the domesticated apple (Malus x domestica Borkh.). Nat. Genet. 42: 833-839. https://doi.org/10.1038/ng.654
  25. Ward JA, Bhangoo J, Fernandez-Fernandez F, Moore P, Swanson JD, Viola R, 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
  26. Weeden NF, Hemmat M, Lawson DM, Lodhi M, Bell RL, Manganaris AG, et al. 1994. Development and application of molecular marker linkage maps in woody fruit crops. Euphytica 77: 71-75. https://doi.org/10.1007/BF02551464
  27. Wu J, Li L, Li M, Khan M, Li X, Chen H, et al. 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