Genetic diversity in common wheat lines revealed by fluorescence in situ hybridization

Abstract

Molecular markers and phenotyping have been widely used to evaluate wheat germplasm diversity. However, the feasibility of using chromosome fluorescence in situ hybridization (FISH) to evaluate wheat genetic diversity has not been well investigated. In this study, seventy-six representative Chinese wheat lines in main wheat production area were selected and investigated with multicolour FISH using Oligo-pTa535, Oligo-pSc119.2 and Oligo-(GAA)8 probes. The results indicated that wheat chromosomes can be clearly recognized by FISH. For wheat A, B and D genomes, the number of FISH types ranged from 2 to 7, 2 to 6 and 1 to 5, respectively. The average number of FISH types in the A and B genomes was higher than that in the genome D. The rye-derived 1RS chromosome in wheat background could also be clearly detected by these probes. The frequency of 1RS in Chinese wheat lines investigated was 48.7%, and most (94.6%) of them belonged to 1BL.1RS. The genetic relationships among the seventy-six Chinese wheat lines subjected to FISH were divided into three clusters, e.g., CL1, CL2 and CL3. Those wheat lines derived from Shandong and Henan Provinces were mainly located in clusters CL1 and CL3, respectively, which may suggest that the FISH type is associated with the adaptation of wheat. These results also indicated that multicolour FISH using a combination of three different oligo-probes generates sufficiently diverse hybridization patterns among wheat lines to evaluate the genetic diversity of wheat.

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References

  1. Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S, Uszynski G, Mohler V, Lehmensiek A, Kuchel H, Hayden MJ, Howes N, Sharp P, Vaughan P, Rathmell B, Huttner E, Kilian A (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420. https://doi.org/10.1007/s00122-006-0365-4

    CAS  PubMed  Article  Google Scholar 

  2. Anugrahwati DR, Shepherd KW, Verlin DC, Zhang P, Mirzaqhaderi G, Walker E, Francki MG, Dundas IS (2008) Isolation of wheat-rye 1RS recombinants that break the linkage between the stem rust resistance gene SrR and secalin. Genome 51:341–349. https://doi.org/10.1139/G08-019

    CAS  PubMed  Article  Google Scholar 

  3. Autrique E, Nachit M, Monneveux P, Tanksley SD, Sorrells ME (1996) Genetic diversity in durum wheat based on RFLPs, morphophysiological traits, and coefficient of parentage. Crop Sci 36:735–742. https://doi.org/10.2135/cropsci1996.0011183X003600030036x

    Article  Google Scholar 

  4. Baum M, Appels R (1991) The cytogenetic and molecular architecture of chromosome 1R-one of the most widely utilized sources of alien chromatin in wheat varieties. Chromosoma 101:1–10. https://doi.org/10.1007/BF00360680

    CAS  PubMed  Article  Google Scholar 

  5. Bilgin O, Guzmán C, Başer İ, Crossa J, Korkut KZ, Balkan A (2015) Evaluation of Grain yield and quality traits of bread wheat genotypes cultivated in northwest Turkey. Crop Sci 56:139–141. https://doi.org/10.2135/cropsci2015.03.0148

    CAS  Article  Google Scholar 

  6. Braun HJ, Atlin G, Payne T, Reynolds MP (2010) Multi-location testing as a tool to identify plant response to global climate change. Eur J Neurosci 23:1129–1141

    Google Scholar 

  7. Chai JF, Liu X, Jia JZ (2005) Homoeologous cloning of omega-secalin gene family in a wheat 1BL/1RS translocation. Cell Res 15:658–664. https://doi.org/10.1038/sj.cr.7290335

    CAS  PubMed  Article  Google Scholar 

  8. Chao S, Rouse MN, Acevedo M, Szabohever A, Bockelman H, Bonman JM, Elias E, Klindworth D, Xu S (2017) Evaluation of genetic diversity and host resistance to stem rust in USDA NSGC Durum Wheat Accessions. Pl Genome 10:1–13

    CAS  Google Scholar 

  9. Chen Q, Conner RL, Laroche A, Thomas JB (1998) Genome analysis of Thinopyrum intermedium and Thinopyrum ponticum using genomic in situ hybridization. Genome 41:580–586. https://doi.org/10.1139/g98-055

    CAS  PubMed  Article  Google Scholar 

  10. Chen J, Ren Z, Gao L, Jia J (2005) Developing new SSR markers from EST of wheat. Acta Agron Sin 31:154–158

    Google Scholar 

  11. Cook JP, Blake NK, Heo HY, Martin JM, Weaver DK, Talbert LE (2017) Phenotypic and haplotype diversity among tetraploid and hexaploid wheat accessions with potentially novel insect resistance genes for wheat stem sawfly. Pl Genome 10(1):1–10

    CAS  Google Scholar 

  12. Danilova TV, Friebe B, Gill BS (2012) Single-copy gene fluorescence in situ hybridization and genome analysis: acc-2 loci mark evolutionary chromosomal rearrangements in wheat. Chromosoma 121:597–611

    CAS  Article  Google Scholar 

  13. Danilova TV, Friebe B, Gill BS (2014) Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. Theor Appl Genet 127:715–730. https://doi.org/10.1007/s00412-012-0384-7

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  14. Danilova TV, Akhunova AR, AkhunovT ED, Friebe B, Gill BS (2017) Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae). Plant J 92:317–330. https://doi.org/10.1111/tpj.13657

    CAS  PubMed  Article  Google Scholar 

  15. Godfray H, Beddington J, Crute I, Haddad L, Lawrence D et al (2010) Food security: the challenge of feeding 9 billion people. Science 327:812–818. https://doi.org/10.1126/science.1185383

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  16. Gong WP, Li GR, Zhou JP, Li GY, Liu C, Huang CY, Zhao ZD, Yang ZJ (2014) Cytogenetic and molecular markers for detecting Aegilops uniaristata chromosomes in a wheat background. Genome 57:489–497. https://doi.org/10.1139/gen-2014-0111

    CAS  PubMed  Article  Google Scholar 

  17. Gong WP, Han R, Li HS, Song JM, Yan HF, Li GY, Liu AF, Cao XY, Guo J, Zhai SN, Cheng DG, Zhao ZD, Liu C, Liu JJ (2017) Agronomic traits and molecular marker identification of wheat-Aegilops caudata addition lines. Frontiers Pl Sci 8:1743. https://doi.org/10.3389/fpls.2017.01743

    PubMed  PubMed Central  Article  Google Scholar 

  18. Graybosch RA (2001) Uneasy unions: quality effects of rye chromatin transfers to wheat. J Cereal Sci 33:3–16

    CAS  Article  Google Scholar 

  19. Guo J, He F, Cai J, Wang H, Li A, Wang H, Kong L (2015a) Molecular and cytological comparisons of chromosomes 7el1, 7el2, 7Ee, and 7Ei derived from Thinopyrum. Cytogenet Genome Res 145:68–74. https://doi.org/10.1159/000381838

    PubMed  Article  Google Scholar 

  20. Guo J, Zhang X, Hou Y, Cai J, Shen X, Zhou T, Xu H, Ohm HW, Wang H, Li A (2015b) High-density mapping of the major FHB resistance gene Fhb7 derived from Thinopyrum ponticum and its pyramiding with Fhb1 by marker-assisted selection. Theor Appl Genet 128:2301–2316. https://doi.org/10.1007/s00122-015-2586-x

    CAS  PubMed  Article  Google Scholar 

  21. Guo J, Xu W, Yu X, Shen H, Li H, Cheng D, Liu A, Liu J, Liu C, Zhao S (2016a) Cuticular wax accumulation is associated with drought tolerance in wheat near-isogenic lines. Frontiers Pl Sci 7:1809. https://doi.org/10.3389/fpls.2016.01809

    PubMed  PubMed Central  Article  Google Scholar 

  22. Guo J, Yu X, Yin H, Liu G, Li A, Wang H, Kong L (2016b) Phylogenetic relationships of Thinopyrum and Triticum species revealed by SCoT and CDDP markers. Pl Syst Evol 302:1–9. https://doi.org/10.1007/s00606-016-1332-4

    Article  Google Scholar 

  23. Gupta K, Balyan S, Edwards J, Isaac P, Korzun V, Röder M, Gautier MF, Joudrier P, Schlatter R, Dubcovsky J (2002) Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor Appl Genet 105:413–422. https://doi.org/10.1007/s00122-002-0865-9

    CAS  PubMed  Article  Google Scholar 

  24. Han F, Gao Z, Birchler JA (2009) Reactivation of an inactive centromere reveals epigenetic and structural components for centromere specification in maize. Pl Cell 21:1929–1939. https://doi.org/10.1105/tpc.109.066662

    CAS  Article  Google Scholar 

  25. Howell T, Hale I, Jankuloski L, Bonafede M, Gilbert M, Dubcovsky J (2014) Mapping a region within the 1RS.1BL translocation in common wheat affecting grain yield and canopy water status. Theor Appl Genet 127:2695–2709. https://doi.org/10.1007/s00122-014-2408-6

    PubMed  PubMed Central  Article  Google Scholar 

  26. International Wheat Genome Sequencing Consortium (IWGSC) (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science 345:1250092. https://doi.org/10.1126/science.1250092

    CAS  Article  Google Scholar 

  27. Jiang M, Xaio ZQ, Fu SL, Tang ZX (2017) FISH karyotype of 85 common wheat cultivars/lines displayed by ND-FISH using oligonucleotide probes. Cereal Res Commun 45:549–563. https://doi.org/10.1556/0806.45.2017.049

    CAS  Article  Google Scholar 

  28. Kashi Y, King DG (2006) Simple sequence repeats as advantageous mutators in evolution. Trends Genet 22:253–259. https://doi.org/10.1016/j.tig.2006.03.005

    CAS  PubMed  Article  Google Scholar 

  29. Kato A, Lamb JC, Birchler JA (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci USA 101:13554–13559. https://doi.org/10.1073/pnas.0403659101

    CAS  Article  PubMed  Google Scholar 

  30. Landjeva S, Ganeva G, Korzun V, Palejev D, Chebotar S, Kudrjavtsev A (2015) Genetic diversity of old bread wheat germplasm from the Black Sea region evaluated by microsatellites and agronomic traits. Pl Genet Resources 13:119–130. https://doi.org/10.1017/S1479262114000781

    Article  Google Scholar 

  31. Lee JH, Graybosch RA, Peterson CJ (1995) Quality and biochemical effects of a IBL/IRS wheat-rye translocation in wheat. Theor Appl Genet 90:105–112. https://doi.org/10.1007/BF00221002

    CAS  PubMed  Article  Google Scholar 

  32. Li YC, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Molec Ecol 11:2453–2465. https://doi.org/10.1046/j.1365-294X.2002.01643.x

    CAS  Article  Google Scholar 

  33. Liu JJ, Zhong-Hu HE, Peña JR, Zhao ZD (2004) Effect of 1BL/1RS translocation on grain quality and noodle quality in bread wheat. Acta Agron Sin 30:149–153

    CAS  Google Scholar 

  34. Liu C, Yang ZJ, Li GR, Zeng ZX, Zhang Y, Zhou JP, Liu ZH, Ren ZL (2008) Isolation of a new repetitive DNA sequence from Secale africanum enables targeting of Secale chromatin in wheat background. Euphytica 159:249–258. https://doi.org/10.1007/s10681-007-9484-5

    CAS  Article  Google Scholar 

  35. Liu C, Li GR, Gong WP, Li GY, Han R, Li HS, Song JM, Liu AF, Cao XY, Chu XS, Yang ZJ, Huang CY, Zhao ZD, Liu JJ (2015) Molecular and cytogenetic characterization of a powdery mildew-resistant wheat-Aegilops mutica partial amphiploid and addition line. Cytogenet Genome Res 147:186–194. https://doi.org/10.1159/000443625

    CAS  PubMed  Article  Google Scholar 

  36. Mago R, Spielmeyer W, Lawrence J, Lagudah S, Ellis G, Pryor A (2002) Identification and mapping of molecular markers linked to rust resistance genes located on chromosome 1RS of rye using wheat-rye translocation lines. Theor Appl Genet 104:1317–1324. https://doi.org/10.1007/s00122-002-0879-3

    CAS  PubMed  Article  Google Scholar 

  37. Mukai Y, Nakahara Y, Yamamoto M (1993) Simultaneous discrimination of the three genomes in hexaploid wheat by multicolor fluorescence in situ hybridization using total genomic and highly repeated DNA probes. Genome 36:489–494. https://doi.org/10.1139/g93-067

    CAS  Article  PubMed  Google Scholar 

  38. Payne PI, Nightingale MA, Krattiger AF, Holt LM (1987) The relationship between HMW glutenin subunit composition and the bread-making quality of British-grown wheat varieties. J Sci Food Agric 40:51–65

    CAS  Article  Google Scholar 

  39. Pedersen C, Langridge P (1997) Identification of the entire chromosome complement of bread wheat by two-colour FISH. Genome 40:589–593. https://doi.org/10.1139/g97-077

    CAS  PubMed  Article  Google Scholar 

  40. Qi Z, Liu D, Chen P, Li Q (2001) Molecular cytogenetic analysis of winter wheat germplasm aimengniu. Acta Bot Sin 43:469–474

    Google Scholar 

  41. Quraishi UM, Abrouk M, Bolot S, Pont C, Throude M, Guilhot N, Confolent C, Bortolini F, Praud S, Murigneux A (2009) Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection. Funct Integr Genomics 9:473–484. https://doi.org/10.1007/s10142-009-0129-8

    CAS  PubMed  Article  Google Scholar 

  42. Rabinovich SV (1998) Importance of wheat-rye translocations for breeding modern cultivar of Triticum aestivum L. Euphytica 100:323–340. https://doi.org/10.1023/A:1018361819215

    Article  Google Scholar 

  43. Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z (2017) Crop breeding chips and genotyping platforms: progress, challenges and perspectives. Molec Pl 10:1047–1064. https://doi.org/10.1016/j.molp.2017.06.008

    CAS  Article  Google Scholar 

  44. Reynolds MP, Balota M, Delgado M, Amani I, Fischer RA (1994) Physiological and morphological traits associated with spring wheat yield under hot, irrigated conditions. Funct Pl Biol 21:717–730. https://doi.org/10.1071/pp9940717

    Article  Google Scholar 

  45. Roder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Singh NK, Shepherd KW, Mcintosh RA (1990) Linkage mapping of genes for resistance to leaf, stem and stripe rusts and ω-secalins on the short arm of rye chromosome 1R. Theor Appl Genet 80:609–616. https://doi.org/10.1007/BF00224219

    CAS  PubMed  Article  Google Scholar 

  47. Somers D, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1105–1114. https://doi.org/10.1007/s00122-004-1740-7

    CAS  PubMed  Article  Google Scholar 

  48. Tang Z, Yang Z, Fu S (2014) Oligonucleotides replacing the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 for FISH analysis. J Appl Genet 55:313–318

    CAS  Article  Google Scholar 

  49. Villareal RL, Edel T, Mujeebkazi A, Rajaram S (1995) The 1BL/1RS chromosome translocation effect on yield characteristics in a Triticum aestivum L. cross. Pl Breed 114:497–500. https://doi.org/10.1111/j.1439-0523.1995.tb00843.x

    Article  Google Scholar 

  50. Wang LX, Li HB, Gu TC, Liu LH, Pang BS, Qiu J, Zhao CP (2014) Assessment of wheat variety stability using SSR markers. Euphytica 195:435–452

    CAS  Article  Google Scholar 

  51. Wu W, Li C, Ma B, Shah F, Liu Y, Liao Y (2014) Genetic progress in wheat yield and associated traits in China since 1945 and future prospects. Euphytica 196:155–168

    Article  Google Scholar 

  52. Xue S, Zhang Z, Lin F, Kong Z, Cao Y, Li C, Yi H, Mei M, Zhu H, Wu J (2008) A high-density intervarietal map of the wheat genome enriched with markers derived from expressed sequence tags. Theor Appl Genet 117:181–189. https://doi.org/10.1007/s00122-008-0764-9

    CAS  PubMed  Article  Google Scholar 

  53. Yan BJ, Zhang HQ, Ren ZL (2005) Molecular cytogenetic identification of a new 1RS/1BL translocation line with Secalin absence. Hereditas (Beijing) 27:513–517

    CAS  Google Scholar 

  54. Yu JK, La RM, Kantety RV, Sorrells ME (2004) EST derived SSR markers for comparative mapping in wheat and rice. Molec Genet Genomics 271:742–751. https://doi.org/10.1007/s00438-004-1027-3

    CAS  Article  Google Scholar 

  55. Zhang P, Li W, Fellers J, Friebe B, Gill BS (2004) BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements. Chromosoma 112:288–299. https://doi.org/10.1007/s00412-004-0273-9

    CAS  Article  PubMed  Google Scholar 

  56. Zhang P, He Z, Chen D, Zhang Y, Larroque OR, Xia X (2007) Contribution of common wheat protein fractions to dough properties and quality of northern-style Chinese steamed bread. J Cereal Sci 46:1–10. https://doi.org/10.1016/j.jcs.2006.10.007

    CAS  Article  Google Scholar 

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Acknowledgements

This research was funded by National Key Research and Development Program (2017YFD0100600 and 2016YFD0102000), Natural Science Foundation of Shandong Province (ZR2017MC004), the Modern Agricultural Industry Technology System and Agricultural scientific and technological innovation project of Shandong Academy of Agricultural Sciences (CXGC2018E01).

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C. Liu and Z. Yang conceived and designed the experiments. G. Dan, W. Gong, G. Li and J. Li performed the experiments. J. Guo, W. Gong, C. Liu and Z. Yang analysed the data. W. Gong, H. Li, J. Song, J. Guo and J. Liu contributed reagents/materials/analysis tools. J. Guo and C. Liu wrote the paper.

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Correspondence to Zujun Yang or Cheng Liu.

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Online Resource 1. Wheat lines used in this study.

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Guo, J., Gao, D., Gong, W. et al. Genetic diversity in common wheat lines revealed by fluorescence in situ hybridization. Plant Syst Evol 305, 247–254 (2019). https://doi.org/10.1007/s00606-019-1567-y

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Keywords

  • Fluorescence in situ hybridization (FISH)
  • Genetic analysis
  • Triticum aestivum