Genetic Resources and Crop Evolution

, Volume 64, Issue 3, pp 531–544 | Cite as

Into the vault of the Vavilov wheats: old diversity for new alleles

  • Adnan Riaz
  • Adrian Hathorn
  • Eric Dinglasan
  • Laura Ziems
  • Cecile Richard
  • Dharmendra Singh
  • Olga Mitrofanova
  • Olga Afanasenko
  • Elizabeth Aitken
  • Ian Godwin
  • Lee Hickey
Research Article

Abstract

Intensive selection in wheat (Triticum aestivum L.) breeding programs over the past 100 years has led to a genetic bottleneck in modern bread wheat. Novel allelic variation is needed to break the yield plateau, particularly in the face of climate change and rapidly evolving pests and pathogens. Landraces preserved in seed banks likely harbour valuable sources of untapped genetic diversity because they were cultivated for thousands of years under diverse eco-geographical conditions prior to modern breeding. We performed the first genetic characterisation of bread wheat accessions sourced from the N. I. Vavilov Institute of Plant Genetic Resources (VIR) in St Petersburg, Russia. A panel comprising 295 accessions, including landraces, breeding lines and cultivars was subject to single seed descent (SSD) and genotyped using the genotyping-by-sequencing Diversity Arrays Technology platform (DArT-seq); returning a total of 34,311 polymorphic markers (14,228 mapped and 20,083 unmapped). Cluster analysis identified two distinct groups; one comprising mostly breeding lines and cultivars, and the other comprising landraces. Diversity was benchmarked in comparison to a set of standards, which revealed a high degree of genetic similarity among breeding material from Australia and the International Maize and Wheat Improvement Center (CIMMYT). Further, 11,025 markers (1888 mapped and 9137 unmapped) were polymorphic in the diversity panel only, thus representing allelic diversity potentially not present in Australian or CIMMYT germplasm. Open-access to DArT-seq markers and seed for SSD lines will empower researchers, pre-breeders and breeders to rediscover genetic diversity in the VIR collection and accelerate utilisation of novel alleles to improve wheat.

Keywords

Genetic diversity Genotyping-by-sequencing Landraces Seed bank Triticum Wheat breeding 

Supplementary material

10722_2016_380_MOESM1_ESM.docx (107 kb)
Supplementary material 1 (DOCX 107 kb)

References

  1. Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S, Uszynski G, Mohler V, Lehmensiek A, Kuchel H, Hayden M, 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 113:1409–1420CrossRefPubMedGoogle Scholar
  2. Allen AM, Barker GLA, Berry ST, Coghill JA, Gwilliam R, Kirby S, Robinson P, Brenchley RC, D’Amore R, McKenzie N, Waite D, Hall A, Bevan M, Hall N, Edwards KJ (2011) Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol J 9:1086–1099CrossRefPubMedGoogle Scholar
  3. Arief VN, DeLacy IH, Dieters MJ, Basford KE (2014) Application of marker-trait association profiles in simulating plant breeding strategies. In: 15th Australasian plant breeding conference, St KildaGoogle Scholar
  4. Baenziger PS, DePauw RM (2009) Wheat breeding: procedures and strategies. In: Carver BF (ed) Wheat: Science and trade. Wiley-Blackwell Publishing, Ames, pp 275–308Google Scholar
  5. Bansal UK, Forrest KL, Hayden MJ, Miah H, Singh D, Bariana HS (2011) Characterisation of a new stripe rust resistance gene Yr47 and its genetic association with the leaf rust resistance gene Lr52. Theor Appl Genet 122:1461–1466CrossRefPubMedGoogle Scholar
  6. Bansal U, Arief V, DeLacy I, Bariana H (2013) Exploring wheat landraces for rust resistance using a single marker scan. Euphytica 194:219–233CrossRefGoogle Scholar
  7. Bhullar NK, Street K, Mackay M, Yahiaoui N, Keller B (2009) Unlocking wheat genetic resources for the molecular identification of previously undescribed functional alleles at the Pm3 resistance locus. Proc Natl Acad Sci USA 106:9519–9524CrossRefPubMedPubMedCentralGoogle Scholar
  8. Brenchley R, Spannagl M, Pfeifer M, Barker GLA, D’Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo M-C, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KFX, Edwards KJ, Bevan MW, Hall N (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491:705–710CrossRefPubMedPubMedCentralGoogle Scholar
  9. Brennan JP, Quade KJ (2006) Evolving usage of materials from CIMMYT in developing Australian wheat varieties. Aust J Agric Res 57:947–952CrossRefGoogle Scholar
  10. Cavanagh CR, Chao S, Wang S, Huang BE, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira GL, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Reynolds M, da Silva ML, Bockelman H, Talbert L, Anderson JA, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell PL, Dubcovsky J, Morell MK, Sorrells ME, Hayden MJ, Akhunov E (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci USA 110:8057–8062CrossRefPubMedPubMedCentralGoogle Scholar
  11. Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321CrossRefPubMedGoogle Scholar
  12. Dorofeev VF, Filatenko AA, Migushova EF, Udaczin RA, Jakubziner MM (1979) Wheat. In: Dorofeev VF, Korovina ON (eds) Flora of cultivated plants, vol 1. Kolos, Leningrad (St. Petersburg), p 346 (In Russian)Google Scholar
  13. Dyck PL, Samborski DJ (1979) Adult-plant leaf rust resistance in PI 250413, an introduction of common wheat. Can J Plant Sci 59:329–332CrossRefGoogle Scholar
  14. Ellis MH, Bonnett DG, Rebetzke GJ (2007) A 192 bp allele at the Xgwm261 locus is not always associated with the Rht8 dwarfing gene in wheat (Triticum aestivum L.). Euphytica 157:209–214CrossRefGoogle Scholar
  15. 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:e19379. doi:10.1371/journal.pone.0019379 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Fischer R (2009) Farming systems of Australia: exploiting the synergy between genetic improvement and agronomy. In: Sadras VO, Calderini D (eds) Crop physiology: applications for genetic improvement and agronomy. Elsevier, Amsterdam, pp 23–54Google Scholar
  17. Fischer RA, Byerlee D, Edmeades GO (2014) Crop yields and global food security: will yield increase continue to feed the world? ACIAR Monograph No. 158 (Australian Centre for International Agricultural Research: Canberra, ACT), pp 92–100Google Scholar
  18. Grassini P, Eskridge KM, Cassman KG (2013) Distinguishing between yield advances and yield plateaus in historical crop production trends. Nat Commun. doi:10.1038/ncomms3918 PubMedPubMedCentralGoogle Scholar
  19. Hennig C (2014) fpc: Flexible procedures for clustering. R package version 2.1-9. http://CRAN.R-project.org/package=fpc
  20. Henry RJ, Nevo E (2014) Exploring natural selection to guide breeding for agriculture. Plant Biotechnol J 12:655–662CrossRefPubMedGoogle Scholar
  21. Herrera-Foessel SA, Lagudah ES, Huerta-Espino J, Hayden MJ, Bariana HS, Singh D, Singh RP (2011) New slow-rusting leaf rust and stripe rust resistance genes Lr67 and Yr46 in wheat are pleiotropic or closely linked. Theor Appl Genet 122:239–249CrossRefPubMedGoogle Scholar
  22. Hickey LT, Dieters MJ, DeLacy IH, Kravchuk OY, Mares DJ, Banks PM (2009) Grain dormancy in fixed lines of white-grained wheat (Triticum aestivum L.) grown under controlled environmental conditions. Euphytica 168:303–310CrossRefGoogle Scholar
  23. Hickey LT, Wilkinson PM, Knight CR, Godwin ID, Kravchuk OY, Aitken EAB, Bansal UK, Bariana HS, Delacy IH, Dieters MJ (2012) Rapid phenotyping for adult-plant resistance to stripe rust in wheat. Plant Breed 131:54–61CrossRefGoogle Scholar
  24. Hiebert CW, Thomas JB, McCallum BD, Humphreys GD, DePauw RM, Hayden MJ, Mago R, Schnipenkoetter W, Hayden M (2010) An introgression on wheat chromosome 4DL in RL6077 (Thatcher*6/PI 250413) confers adult plant resistance to stripe rust and leaf rust (Lr67). Theor Appl Genet 121:1083–1091CrossRefPubMedGoogle Scholar
  25. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang Q-F, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967CrossRefPubMedGoogle Scholar
  26. Ignjatović-Micić D, Ristić D, Babić V, Anđelković V, Marković K, Vančetović J (2013) Genetic assessment of maize landraces from former Yugoslavia. Genetika 45:405–417CrossRefGoogle Scholar
  27. Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270Google Scholar
  28. Jaradat AA (2013) Wheat landraces: a mini review. Emir J Food Agric 25(1):20–29Google Scholar
  29. Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X, Jing R, Zhang C, Ma Y, Gao L, Gao C, Spannagl M, Mayer KFX, Li D, Pan S, Zheng F, Hu Q, Xia X, Li J, Liang Q, Chen J, Wicker T, Gou C, Kuang H, He G, Luo Y, Keller B, Xia Q, Lu P, Wang J, Zou H, Zhang R, Xu J, Gao J, Middleton C, Quan Z, Liu G, Wang J, Yang H, Liu X, He Z, Mao L, Wang J (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95CrossRefPubMedGoogle Scholar
  30. Jilal A, Grando S, Henry RJ, Lee LS, Rice N, Hill H, Baum M, Ceccarelli S (2008) Genetic diversity of ICARDA’s worldwide barley landrace collection. Genet Resour Crop Evol 55:1221–1230CrossRefGoogle Scholar
  31. Jones H, Lister DL, Bower MA, Leigh FJ, Smith LMJ, Jones MK (2008) Approaches and constraints of using existing landraces and extant plant material to understand agricultural spread in prehistory. Plant Genet Res 6:98–112CrossRefGoogle Scholar
  32. Li H, Vikram P, Singh RP, Kilian A, Carling J, Song J, Burgueno-Ferreira JA, Bhavani S, Huerta-Espino J, Payne T (2015) A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits. BMC Genom 16:216–230. doi:10.1186/s12864-015-1424-5 CrossRefGoogle Scholar
  33. Lopes MS, El-Basyoni I, Baenziger PS, Singh S, Royo C, Ozbek K, Aktas H, Ozer E, Ozdemir F, Manickavelu A, Ban T, Vikram P (2015) Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change. J Exp Bot. doi:10.1093/jxb/erv122 PubMedGoogle Scholar
  34. Maccaferri M, Zhang J, Bulli P, Abate Z, Chao S, Cantu D, Bossolini E, Chen X, Pumphrey M, Dubcovsky J (2015) A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.). G3 5:449–465CrossRefPubMedPubMedCentralGoogle Scholar
  35. Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L, Campbell BC, Hu W, Innes DJ, Han X, Cruickshank A, Dai C, Frère C, Zhang H, Hunt CH, Wang X, Shatte T, Wang M, Su Z, Li J, Lin X, Godwin ID, Jordan DR, Wang J (2013) Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Nat Commun. doi:10.1038/ncomms3320 Google Scholar
  36. Mackay MC (1995) One core collection or many? In: Hodgkin T, Brown AHD, Van Hintum TJL, Morales AAV (eds) Core collections of plant genetic resources. Wiley, Chichester, pp 199–210Google Scholar
  37. Mackay MC, Street K (2004) Focused identification of germplasm strategy–FIGS. In: Black CK, Panozzo JF, Rebetzke GJ (eds) Proceedings of the 54th Australian cereal chemistry conference and the 11th wheat breeders’ assembly. Royal Australian Chemical Institute, Melbourne, pp 138–141Google Scholar
  38. McIntosh RA, Hart GE, Devos KM, Gale MD, Rogers WJ (1998) Catalogue of gene symbols for wheat. In: Proceedings of the 9th international wheat genetic symposium 5, Univ. Extension Press. Univ. Saskatchewan, SaskatoonGoogle Scholar
  39. Mitrofanova OP (2012) Wheat genetic resources in Russia: current status and prebreeding studies. Russ J Genet 2:277–285CrossRefGoogle Scholar
  40. Montilla-Bascón G, Sánchez-Martín J, Rispail N, Rubiales D, Mur L, Langdon T, Griffiths I, Howarth C, Prats E (2013) Genetic diversity and population structure among oat cultivars and landraces. Plant Mol Biol Report 31:1305–1314CrossRefGoogle Scholar
  41. Motley TJ (2006) Crop plants: past present future. In: Motley TJ, Zerega N, Cross H (eds) Darwin’s harvest: new approaches to the origins, evolution and conservation of crops. Columbia University Press, New York, pp 1–27CrossRefGoogle Scholar
  42. Newton AC, Akar T, Baresel JP, Bebeli PJ, Bettencourt E, Bladenopoulos KV, Czembor JH, Fasoula DA, Katsiotis A, Koutis K, Koutsika-Sotiriou M, Kovacs G, Larsson H, Pinheiro de Carvalho MAA, Rubiales D, Russell J, Dos Santos TMM, Vaz Patto MC (2010) Cereal landraces for sustainable agriculture: a review. Agron Sustain Dev 30:237–269CrossRefGoogle Scholar
  43. Nielsen NH, Backes G, Stougaard J, Andersen SU, Jahoor A (2014) Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties. PLoS ONE 9(4):e94000. doi:10.1371/journal.pone.0094000 CrossRefPubMedPubMedCentralGoogle Scholar
  44. Pasam RK, Sharma R, Walther A, Ozkan H, Graner A, Kilian B (2014) Genetic diversity and population structure in a legacy collection of spring barley landraces adapted to a wide range of climates. PLoS ONE 9:e116164. doi:10.1371/journal.pone.0116164 CrossRefPubMedPubMedCentralGoogle Scholar
  45. Pineda-Hidalgo KV, Méndez-Marroquín KP, Alvarez EV, Chávez-Ontiveros J, Sánchez-Peña P, Garzón-Tiznado JA, Vega-García MO, López-Valenzuela JA (2013) Microsatellite-based genetic diversity among accessions of maize landraces from Sinaloa in Mexico. Hereditas 150:53–59CrossRefPubMedGoogle Scholar
  46. Poland JA, Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5:92–102CrossRefGoogle Scholar
  47. R Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org/
  48. Ray DK, Mueller ND, West PC, Foley JA (2013) Yield trends are insufficient to double global crop production by 2050. PLoS ONE 8:e66428. doi:10.1371/journal.pone.0066428 CrossRefPubMedPubMedCentralGoogle Scholar
  49. Reif JC, Hamrit S, Heckenberger M, Schipprack W, Peter Maurer H, Bohn M, Melchinger AE (2005) Genetic structure and diversity of European flint maize populations determined with SSR analyses of individuals and bulks. Theor Appl Genet 111:906–913CrossRefPubMedGoogle Scholar
  50. Reynolds A, Richards G, De la Iglesia B, Rayward-Smith V (1992) Clustering rules: a comparison of partitioning and hierarchical clustering algorithms. J Math Model Algorithm 5:475–504. doi:10.1007/s10852-005-9022-1 CrossRefGoogle Scholar
  51. Salse J, Chague V, Bolot S, Magdelenat G, Huneau C, Pont C, Belcram H, Couloux A, Gardais S, Evrard A, Segurens B, Charles M, Ravel C, Samain S, Charmet G, Boudet N, Chalhoub B (2008) New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC Genom 9:555–567. doi:10.1186/1471-2164-9-555 CrossRefGoogle Scholar
  52. Schierhorn F, Faramarzi M, Prishchepov AV, Koch FJ, Müller D (2014) Quantifying yield gaps in wheat production in Russia. Environ Res Lett 9:084017. doi:10.1088/1748-9326/9/8/084017 CrossRefGoogle Scholar
  53. Shewry P (2009) Wheat. J Exp Bot 60:1537–1553CrossRefPubMedGoogle Scholar
  54. Singh RP, Hodson DP, Huerta-Espino J, Jin Y, Bhavani S, Njau P, Herrera-Foessel S, Singh PK, Singh S, Govindan V (2011) The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production. Annu Rev Phytopathol 49:465–481CrossRefPubMedGoogle Scholar
  55. Smale M, Reynolds MP, Warburton M, Skovmand B, Trethowan R, Singh RP, Ortiz-Monasterio I, Crossa J (2002) Dimensions of diversity in modern spring bread wheat in developing countries from 1965. Crop Sci 42:1766–1779CrossRefGoogle Scholar
  56. Sthapit J, Newcomb M, Bonman JM, Chen X, See DR (2014) Genetic diversity for stripe rust resistance in wheat landraces and identification of accessions with resistance to stem rust and stripe rust. Crop Sci 54:2131–2139CrossRefGoogle Scholar
  57. Sukumaran S, Dreisigacker S, Lopes M, Chavez P, Reynolds MP (2015) Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments. Theor Appl Genet 128:353–363. doi:10.1007/s00122-014-2435-3 CrossRefPubMedGoogle Scholar
  58. Tyryshkin LG, Tyryshkina NA (2003) Resistance to diseases in wheat collection samples and somaclonal variants. Czech J Genet Plant 39:21–23Google Scholar
  59. Vavilov NI (1926) Studies on the origin of cultivated plants. Institut Botanique Appliqué et d’ Amélioration des Plantes, LeningradGoogle Scholar
  60. Voorrips RE (2002) MapChart, software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78CrossRefPubMedGoogle Scholar
  61. Voss-Fels K, Frisch M, Qian L, Kontowski S, Friedt W, Gottwald S, Snowdon RJ (2015) Subgenomic diversity patterns caused by directional selection in bread wheat gene pools. Plant Genome. doi:10.3835/plantgenome2015.03.0013 Google Scholar
  62. Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing C, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo M-C, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E (2014) Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796CrossRefPubMedPubMedCentralGoogle Scholar
  63. White J, Law J, MacKay I, Chalmers K, Smith J, Kilian A, Powell W (2008) The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome. Theor Appl Genet 116:439–453. doi:10.1007/s00122-007-0681-3 CrossRefPubMedGoogle Scholar
  64. Worland AJ, Korzun V, Röder MS, Ganal MW, Law CN (1998) Genetic analysis of the dwarfing gene Rht8 in wheat. Part II. The distribution and adaptive significance of allelic variants at the Rht8 locus of wheat as revealed by microsatellite screening. Theor Appl Genet 96:1110–1120CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Adnan Riaz
    • 1
  • Adrian Hathorn
    • 1
  • Eric Dinglasan
    • 1
  • Laura Ziems
    • 1
  • Cecile Richard
    • 1
  • Dharmendra Singh
    • 1
  • Olga Mitrofanova
    • 2
  • Olga Afanasenko
    • 3
  • Elizabeth Aitken
    • 4
  • Ian Godwin
    • 4
  • Lee Hickey
    • 1
  1. 1.Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandSt LuciaAustralia
  2. 2.N. I. Vavilov Institute of Plant Genetic ResourcesSaint PetersburgRussia
  3. 3.Department of Plant Resistance to DiseasesAll Russian Research Institute for Plant ProtectionPushkinRussia
  4. 4.School of Agriculture and Food SciencesThe University of QueenslandSt LuciaAustralia

Personalised recommendations