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Molecular Breeding

, 39:6 | Cite as

Molecular marker development and primary physical map construction for the tuber shape Ro gene locus in diploid potato (Solanum tuberosum L.)

  • Na Chen
  • Wenwen Zhu
  • Jianfei Xu
  • Shaoguang Duan
  • Chunsong Bian
  • Jun Hu
  • Wanxing Wang
  • Guangcun LiEmail author
  • Liping JinEmail author
Article
  • 85 Downloads

Abstract

Potato (Solanum tuberosum L.) is an important crop worldwide that is consumed fresh and processed in many different ways. The tuber shape is a critical trait in potato breeding, because it directly affects processing quality. Previous studies have demonstrated that the Ro locus on chromosome X is the major locus controlling tuber shape, and the round shape allele, Ro, is dominant over the long shape allele, ro. However, no reports on the cloning or physical mapping of this locus have been published. In this study, whole genome sequencing and bacterial artificial chromosome (BAC) library construction were applied to develop molecular markers and construct a physical map of Ro. Eight round-tuber genotypes were used to construct the BAC library, which contains about 40,000 clones with an average insert size of 85 kb and represents approximately four haploid potato genomes. A total of 66 individuals with extreme round or long tubers were selected to construct a round-tuber shape DNA bulk and a long-tuber shape DNA bulk for WGS. Single-nucleotide polymorphisms (SNPs) identified from WGS data were used to develop nine polymorphic markers linked to Ro. These markers were used to screen the BAC library, and eight positive BAC clones were ultimately identified and then analyzed by restriction enzyme digestion and BAC end sequencing and used to develop markers and identify new positive BAC clones. Finally, a primary physical map of Ro was constructed using a chromosome walking strategy. This map provides an important reference for cloning the potato tuber shape gene and studying tuber shape variation.

Keywords

Potato Bacterial artificial chromosome library Tuber shape Physical map 

Notes

Acknowledgements

This research was supported by the National Natural Science Fund of China (31561143006, 31801421), National Key R&D Program of China (2017YFD0101905), and the China Agriculture Research System (CARS-9). We thank Prof. De Jong (Department of Plant Genetics and Breeding, Cornell University, USA) for kindly providing the potato parent materials.

References

  1. Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30(2):174–178CrossRefGoogle Scholar
  2. Baig MN, Yu A, Guo W, Deng X (2009) Construction and characterization of two Citrus BAC libraries and identification of clones containing the phytoene synthase gene. Genome 52(5): 484–489Google Scholar
  3. Bradshaw JE, Makay GR (1994) Potato genetics. CAB International, WallingfordGoogle Scholar
  4. Chen LL, Zhang J, Peng CY, Liao DF, Li HJ, Gao HL, Li K (2005) Novel mechanism of 3′ exonuclease of polymerase in maintenance of DNA replication fidelity and its application in SNP assay. Hereditas 27(2):279–283PubMedGoogle Scholar
  5. Choi S, Creelman RA, Mullet JE, Wing RA (1995) Construction and characterization of a bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol Biol Rep 13(2): 124–128Google Scholar
  6. Custers J (2015) Identifying the gene involved in the shape of potato tubers. Master thesis, Wageningen UniversityGoogle Scholar
  7. D’hoop BB, Paulo MJ, Mank RA, van Eck HJ, Eeuwijk FAV (2008) Association mapping of quality traits in potato (Solanum tuberosum L.). Euphytica 161(1):47–60CrossRefGoogle Scholar
  8. De Jong H, Burns VJ (1993) Inheritance of tuber shape in cultivated diploid potatoes. Am Potato J 70(3):267–284CrossRefGoogle Scholar
  9. Gao XM, Chen YL, Liu GS, Li FX, Wang WF, Ren YY, Sun YH (2012) BAC library construction of villi tobacco Nicotiana tomentosiformis. Chin Tob Sci 33(3): 68–71Google Scholar
  10. Guo X, Yang XH, Yang Y, Mao ZC, Liu F, Ma WQ, Xie BY, Li GC (2016) Bacterial artificial chromosome library construction of root-knot nematode resistant pepper genotype HDA149 and identification of clones linked to Me3 resistant locus. J Integr Agric 15(0):60345–60347Google Scholar
  11. Hu Y, Lu YM, Ma D, Guo WZ, Zhang TZ (2011) Construction and Characterization of a Bacterial Artificial Chromosome Library for the A-Genome of Cotton (G. arboreum L.). J Biomed Biotechnol 2011: 457137Google Scholar
  12. Huang SW, Vleeshouwers VG, Werij JS, Hutten RC, van Eck HJ, Visser RG, Jacobsen E (2004) The R3 resistance to Phytophthora infestans in potato is conferred by two closely linked R genes with distinct specificities. Mol Plant-Microbe Interact 17(4):428–435CrossRefGoogle Scholar
  13. Jo K-R, Arens M, Kim T-Y, Jongsma MA, Visser RGF, Jacobsen E, Vossen JH (2011) Mapping of the S. demissum late blight resistance gene R8 to a new locus on chromosome IX. Theor Appl Genet 123:1331–1340CrossRefGoogle Scholar
  14. Li GC, Huang SW, Guo X, Li Y, Yang Y, Guo Z, Kuang HH, Rietman H, Bergervoet M, Vleeshouwers V, van der Vossen E, Qu DY, Visser R, Jacobsen E, Vossen J (2011) Cloning and characterization of R3b; Members of the R3 super family of late blight resistance genes show sequence and functional divergence. Mol Plant-Microbe Interact 24(10):1132–1142CrossRefGoogle Scholar
  15. Li MJ, Yang Y, Gao XN, Guo X, He MQ, Shi ZL, Guo JK (2014) Construction and characterization of BAC library from common wheat Shimai 15. J Triticeae Crops 34(2): 164–168Google Scholar
  16. Lindqvist-Kreuze H, Khan A, Salas E, Meiyalaghan S, Thomson S, Gomez R, Bonierbale M (2015) Tuber shape and eye depth variation in a diploid family of Andean potatoes. BMC Genet 16(1):57CrossRefGoogle Scholar
  17. Lokossou AA, Park TH, van Arkel G, Arens M, Ruyter-Spira C, Morales J, Whisson SC, Birch PR, Visser RG, Jacobsen E, van der Vossen EA (2009) Exploiting knowledge of R/Avr genes to rapidly clone a new LZ-NBS-LRR family of late blight resistance genes from potato linkage group IV. Mol Plant-Microbe Interact 22(6):630–641CrossRefGoogle Scholar
  18. Masson MF (1985) Mapping, combining abilities, heritabilities and heterosis with 4X x 2X crosses in potato. PhD thesis, Wisconsin UniversityGoogle Scholar
  19. Mu CH, Zhang FJ, Yang Y, Li WC, Lu SP, Sun Q, Yu YL, Meng ZD, Zhang XQ, Li GC (2013) Construction and characterization of a bacterial artificial chromosome library of maize (Zea mays L.) inbred line Qi319. J Agric Biotechnol 21(11):1389–1395Google Scholar
  20. Prashar A, Hornyik C, Young V, McLean K, Sharma SK, Dale MF, Bryan GJ (2014) Construction of a dense SNP map of a highly heterozygous diploid potato population and QTL analysis of tuber shape and eye depth. Theor Appl Genet 127(10):2159–2171CrossRefGoogle Scholar
  21. Sambrook J, Fritsch EF (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New YorkGoogle Scholar
  22. Sliwka J, Wasilewicz-Flis I, Jakuczun H, Gebhardt C (2008) Tagging quantitative trait loci for dormancy, tuber shape, regularity of tuber shape, eye depth and flesh color in diploid potato originated from six Solanum species. Plant Breed 127(1):49–55CrossRefGoogle Scholar
  23. Song JQ, Dong FG, Jiang JM(2000) Construction of a bacterial artificial chromosome (BAC) library for potato molecular cytogenetics research. Genome 43: 199–204Google Scholar
  24. Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74(1):174–183CrossRefGoogle Scholar
  25. Tao QZ, Chang YL, Wang J, Chen H, Islam-Faridi MN, Scheuring C, Wang B, Stelly DM, Zhang HB (2001) Bacterial Artificial Chromosome-Based Physical Map of the Rice Genome Constructed by Restriction Fingerprint Analysis. Genetics 158(4):1711–1724Google Scholar
  26. The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195CrossRefGoogle Scholar
  27. van der Vossen E, Sikkema A, Hekkert B, Gros J, Stevens P, Muskens M, Wouters D, Pereira A, Stiekema W, Allefs S (2003) An ancient R gene from the wild potato species Solanum bulbocastanum confers broad-spectrum resistance to Phytophthora infestans in cultivated potato and tomato. Plant J 36(6):867–882CrossRefGoogle Scholar
  28. van der Vossen E, Gros J, Sikkema A, Muskens M, Wouters D, Wolters P, Pereira A, Allefs S (2005) The Rpi-bib2 gene from Solanum bulbocastanum is an Mi-1 gene homolog conferring broad-spectrum late blight resistance in potato. Plant J 44(2):208–222CrossRefGoogle Scholar
  29. van Eck HJ, Jacobs JM, Stam P, Ton J, Stiekema WJ, Jacobsen E (1994) Multiple alleles for tuber shape in diploid potato detected by qualitative and quantitative genetic analysis using RFLPs. Genetics 137(1):303–309PubMedGoogle Scholar
  30. Vreugdenhil D, Bradshaw J, Gebhardt C, Govers F, Taylor MA, MacKerron DK, Ross HA (2011) Potato biology and biotechnology: advances and perspectives: advances and perspectives. Elsevier, Amsterdam, pp 211–213Google Scholar
  31. Zhu WW (2015) Genetic mapping and molecular markers development of tuber shape gene in potato. Master thesis, Chinese Academy of Agricultural SciencesGoogle Scholar

Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Na Chen
    • 1
  • Wenwen Zhu
    • 1
  • Jianfei Xu
    • 1
  • Shaoguang Duan
    • 1
  • Chunsong Bian
    • 1
  • Jun Hu
    • 1
  • Wanxing Wang
    • 1
  • Guangcun Li
    • 1
    Email author
  • Liping Jin
    • 1
    Email author
  1. 1.Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences / Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropMinistry of AgricultureBeijingChina

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