Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Recurrent parent genome (RPG) recovery analysis in a marker-assisted backcross breeding based on the genotyping-by-sequencing in tomato (Solanum lycopersicum L.)

토마토 MABC 육종에서 GBS(genotyping-by-sequencing)에 의한 RPG(recurrent parent genome) 회복률 분석

  • Kim, Jong Hee (Department of Horticultural Life Science, Hankyong National University) ;
  • Jung, Yu Jin (Department of Horticultural Life Science, Hankyong National University) ;
  • Seo, Hoon Kyo (Department of Horticultural Life Science, Hankyong National University) ;
  • Kim, Myong-Kwon (Tomato Research Center) ;
  • Nou, Ill-Sup (Department of Horticulture, Sunchon National University) ;
  • Kang, Kwon Kyoo (Department of Horticultural Life Science, Hankyong National University)
  • 김종희 (한경대학교 원예생명과학과) ;
  • 정유진 (한경대학교 원예생명과학과) ;
  • 서훈교 (한경대학교 원예생명과학과) ;
  • 김명권 (주)토마토연구소) ;
  • 노일섭 (순천대학교 원예학과) ;
  • 강권규 (한경대학교 원예생명과학과)
  • Received : 2019.06.07
  • Accepted : 2019.07.08
  • Published : 2019.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

Marker-assisted backcrossing (MABC) is useful for selecting an offspring with a highly recovered genetic background for a recurrent parent at early generation to various crops. Moreover, marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and it accelerates recurrent parent genome (RPG) recovery. In this study, we were employed to incorporate rin gene(s) from the donor parent T13-1084, into the genetic background of HK13-1151, a popular high-yielding tomato elite inbred line that is a pink color fruit, in order to develop a rin HK13-1084 improved line. The recurrent parent genome recovery was analyzed in early generations of backcrossing using SNP markers obtained from genotyping-by-sequencing analysis. From the $BC_1F_1$ and $BC_2F_1$ plants, 3,086 and 4868 polymorphic SNP markers were obtained via GBS analysis, respectively. These markers were present in all twelve chromosomes. The background analysis revealed that the extent of RPG recovery ranged from 56.7% to 84.5% and from 87.8% to 97.8% in $BC_1F_1$ and $BC_2F_1$ generations, respectively. In this study, No 5-1 with 97.8% RPG recovery rate among $BC_2F_1$ plants was similar to HK13-1151 strain in the fruit shape. Therefore, the selected plants were fixed in $BC_2F_2$ generation through selfing. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in the backcross generations. MABC can greatly reduce breeding time as compared to the conventional backcross breeding. For instance, MABC approach greatly shortened breeding time in tomato.

Marker-assisted backcrossing (MABC)은 marker-assisted selection (MAS)와 함께 다양한 작물에서 여교배 초기세대에서 반복친 게놈의 회복률이 높은 개체선발을 위한 분자육종 기술로 매우 유용하게 사용하고 있다. 본 연구에서는 토마토 MABC 육종 프로그램의 일환으로 저장성이 강한 rin유전자를 주)토마토연구소에서 육성한 핑크계 엘리트 토마토계통에 도입하고자 수행하였다. foreground 선발은 RIN SCAR 분자 마커를 이용하여 100개 $BC_1F_1$ 식물체에서 Rr 유전자형 가진 42개체를 선발하였다. 그리고 이를 이용하여 GBS 분석을 이용하여 background 선발을 하였다. 총 3,086개 SNP를 대상으로 반복친 HK13-1151과 게놈 회복률을 조사한 결과, 56.7%에서 84.5%를 보여 평균 70.5%로 나타났다. 이 중 87.2%을 보인 $BC_1F_1$개체를 이용하여 192개 $BC_2F_1$ 식물체를 육성하여 foreground 선발을 하였다. 선발된 102개 중 88개 식물체를 이용하여 GBS 분석을 수행한 결과 4,868개의 다형 SNP 마커를 얻었으며, 이를 이용하여 RPG 회복률을 조사하였다. $BC_2F_1$ 식물체들에서 HK13-1151 반복친 게놈과 87.8%에서 97.8% 유사하였다. 본 연구에서 $BC_2F_1$ 식물 중 RPG 회복률이 97.8%인 5-1 개체는 반복친인 HK13-1151과 과일특성에서 매우 유사하였다. 따라서 선발된 5-1 개체는 $BC_2F_2$ 세대를 육성하여 계통화 하고자 한다. 본 연구를 통해 MABC는 전통 여교배 육종에 비해 육종연한을 획기적으로 줄일 수 있으며, 원하는 육종모델을 완수할 수 있는 첨단육종 기술로 평가 할 수 있다.

Keywords

Acknowledgement

Supported by : 농림식품기술기획평가원, 한국연구재단

References

  1. An SJ, Kwon JK, Yang HB, Choi HJ, Jeong HJ, Kim YJ, Choi GJ, Kang BC (2010) SNP marker development for purity test of oriental melon and melon. Korean J Breed Sci 42(4):397-406
  2. Chagne D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One 7(2):e31745 https://doi.org/10.1371/journal.pone.0031745
  3. Collard BC, Mackill DJ (2008) Marker-assisted selection: An approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B 363:557-5 https://doi.org/10.1098/rstb.2007.2170
  4. Consortium TG (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635-641 https://doi.org/10.1038/nature11119
  5. Cuesta-Marcos A, Szucs P, Close TJ, Filichkin T, Muehlbauer GJ, Smith KP, Hayes PM (2010) Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure. BMC Genomics 11(1):707 https://doi.org/10.1186/1471-2164-11-707
  6. Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 8(1):2-9 https://doi.org/10.1111/j.1467-7652.2009.00459.x
  7. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS ONE 6(5):e19379 https://doi.org/10.1371/journal.pone.0019379
  8. Foolad MR (2007) Genome mapping and molecular breeding of tomato. International Journal of Plant Genomics Article 2007:64358
  9. Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14(7):1457-1467 https://doi.org/10.1105/tpc.010479
  10. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS ONE 28;9(2):e90346
  11. Gupta P, Roy J, Prasad M (2001) Single nucleotide polymorphisms (SNPs): a new paradigm in molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Current Science 80(4):524-535
  12. He J, Zhao X, Laroche A, Lu ZX, Lou H, Li Z (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 30;5:484
  13. Hyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor Corrales M, Cregan PB (2010) High-throughput SNP discovery and assay development in common bean. BMC Genomics 11(1):475 https://doi.org/10.1186/1471-2164-11-475
  14. Kim HJ, Lee HR, Hyun JY, Hong DO, Won DC, Han CH (2013) A SCAR Marker Linked to RIPENING-INHIBITOR in Tomato. Korean J Breed Sci 45(2):104-108 https://doi.org/10.9787/KJBS.2013.45.2.104
  15. Kim S, Misra A (2007) SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng 9:289-320 https://doi.org/10.1146/annurev.bioeng.9.060906.152037
  16. Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zhen, Z, Zhang Z, Lun Y, Li S, Wang X (2014) Genomic analyses provide insights into the history of tomato breeding. Nature Genet 46:1220-1226 https://doi.org/10.1038/ng.3117
  17. Randhawa HS, Mutti JS, Kidwell K, Morris CF, Chen X, Gill KS (2009) Rapid and targeted introgression of genes into popular wheat cultivars using marker-assisted background selection. PLoS One 4:e5752 https://doi.org/10.1371/journal.pone.0005752
  18. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNAsepacer-length polymorphism in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci 81:8014-8019 https://doi.org/10.1073/pnas.81.24.8014
  19. Servin B, Hospital F (2002) Optimal positioning of markers to control genetic background in marker assisted backcrossing. Journal of Heredity 93:214-217 https://doi.org/10.1093/jhered/93.3.214
  20. Shirasawa K, Fukuoka H, Matsunaga H, Kobayashi Y, Kobayashi I, Hirakawa H, Isobe S, Tabata S (2013) Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato DNA. Res 20(6):593-603
  21. Shirasawa K, Isobe S, Hirakawa H, Asamizu E, Fukuoka H, Just D, Rothan C, Sasamoto S, Fujishiro T, Kishida Y (2010) SNP discovery and linkage map construction in cultivated tomato DNA. Res 17(6):381-391 https://doi.org/10.1159/000192076
  22. Thomson MJ (2014) High-Throughput SNP Genotyping to Accelerate Crop Improvement. Plant Breed Biotech 2(3):195-212 https://doi.org/10.9787/PBB.2014.2.3.195
  23. Trebbi D, Maccaferri M de Heer P, Sorensen A, Giuliani S, Salvi S, Sanguineti MC, Massi A van der Vossen EAG, Tuberosa, R (2011) High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf). Theor Appl Genet 123(4):555-569 https://doi.org/10.1007/s00122-011-1607-7
  24. Van Deynze A, Stoffel K, Buell CR, Kozik A, Liu J van der Knaap E, Francis D (2007) Diversity in conserved genes in tomato. BMC Genomics 8(1):465 https://doi.org/10.1186/1471-2164-8-465
  25. Wang DG, Fan J-B, Siao C-J, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280(5366):1077-1082 https://doi.org/10.1126/science.280.5366.1077
  26. Xu J, Ranc N, Munos S, Rolland S, Bouchet JP, Desplat N, Le Paslier MC, Liang Y, Brunel D, Causse M (2013) Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theor Appl Genet 126(3):567-581 https://doi.org/10.1007/s00122-012-2002-8
  27. Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30(1):105-111 https://doi.org/10.1038/nbt.2050