, Volume 192, Issue 1, pp 107–115 | Cite as

High resolution genotyping by restriction enzyme-phased sequencing of advanced backcross lines of rice exhibiting differential cold stress recovery

  • Sang-Ic Kim
  • Thomas H. Tai


Advanced backcross rice lines MIb 4853-9 and 6885-2 harbor major seedling cold tolerance QTL qCTS4 and qCTS12 from the temperate japonica M202 in the genetic background of the indica IR50. Previous studies have shown that these lines exhibit the same tolerance, based on visual ratings, under constant and intermittent exposure to cold stress. However, some differences between the MIb lines with regard to physiological stress indicators are observed under constant exposure and a clear difference is detected using a cold stress recovery assay. Genotyping with over 120 SSR markers did not detect any polymorphisms. Here we report using a reduced representation sequencing method called Restriction Enzyme Site Comparative Analysis to identify M202 introgressions unique to each MIb line as candidate loci for the cold stress recovery trait.


Rice Oryza sativa Reduced representation sequencing Seedling Cold tolerance Recovery 



This work was supported by USDA-ARS CRIS Project 5306-21000-017-00D (T.H.T.) and California Rice Research Board Project RB-3 (T.H.T.). The authors gratefully acknowledge the technical support of P. Colowit. Thanks to Dr. V. C. Andaya and Dr. S. N. Ahn for comments on improving this manuscript.


  1. Andaya VC, Mackill DJ (2003) Mapping of QTLs associated with cold tolerance during the vegetative stage in rice. J Exp Bot 54:2579–2585PubMedCrossRefGoogle Scholar
  2. Andaya VC, Tai TH (2006) Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theor Appl Genet 113:467–475PubMedCrossRefGoogle Scholar
  3. Andaya VC, Tai TH (2007) Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Breed 20:349–358CrossRefGoogle Scholar
  4. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510PubMedCrossRefGoogle Scholar
  5. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076PubMedCrossRefGoogle Scholar
  6. Jiang GH, He YQ, Xu CG, Li XH, Zhang Q (2004) The genetic basis of stay-green in rice analyzed in a population of doubled haploid lines derived from an indica by japonica cross. Theor Appl Genet 108:688–698PubMedCrossRefGoogle Scholar
  7. Kim S, Kim D, Tai TH (2012) Evaluation of rice seedling cold tolerance to constant and intermittent low temperature stress. Rice Sci 19:295–308CrossRefGoogle Scholar
  8. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25:1754–1760PubMedCrossRefGoogle Scholar
  9. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (1000) Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079CrossRefGoogle Scholar
  10. Monson-Miller J, Sanchez-Mendez D, Fass J, Henry I, Tai TH, Comai L (2012) Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. BMC Genom 13:72CrossRefGoogle Scholar
  11. Tai T, Tanksley S (1990) A rapid and inexpensive method for isolation of total DNA from dehydrated plant tissue. Plant Mol Biol Rep 8:297–303CrossRefGoogle Scholar
  12. van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan G, Caromel B, Ghareeb B, Isidore E, De Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort J, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser R, Bkker J, van Eck H (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173:1075–1087PubMedCrossRefGoogle Scholar
  13. Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530PubMedCrossRefGoogle Scholar
  14. Xie W, Feng Q, Yu H, Huang X, Zhao Q, Xing Y, Yu S, Han B, Zhang Q (2010) Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci USA 107:10578–10583PubMedCrossRefGoogle Scholar
  15. Yu H, Xie W, Wang J, Xing Y, Xu C, Li X, Xiao J, Zhang Q (2011) Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS ONE 6:e17595PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht (outside the USA) 2013

Authors and Affiliations

  1. 1.USDA-ARS Crops Pathology and Genetics Research Unit, Department of Plant SciencesUniversity of CaliforniaDavisUSA

Personalised recommendations