Advertisement

From markers to genome-based breeding in wheat

  • Awais Rasheed
  • Xianchun XiaEmail author
Review Article
Part of the following topical collections:
  1. New technologies for plant breeding
  2. New technologies for plant breeding

Abstract

Key message

Recent technological advances in wheat genomics provide new opportunities to uncover genetic variation in traits of breeding interest and enable genome-based breeding to deliver wheat cultivars for the projected food requirements for 2050.

Abstract

There has been tremendous progress in development of whole-genome sequencing resources in wheat and its progenitor species during the last 5 years. High-throughput genotyping is now possible in wheat not only for routine gene introgression but also for high-density genome-wide genotyping. This is a major transition phase to enable genome-based breeding to achieve progressive genetic gains to parallel to projected wheat production demands. These advances have intrigued wheat researchers to practice less pursued analytical approaches which were not practiced due to the short history of genome sequence availability. Such approaches have been successful in gene discovery and breeding applications in other crops and animals for which genome sequences have been available for much longer. These strategies include, (i) environmental genome-wide association studies in wheat genetic resources stored in genbanks to identify genes for local adaptation by using agroclimatic traits as phenotypes, (ii) haplotype-based analyses to improve the statistical power and resolution of genomic selection and gene mapping experiments, (iii) new breeding strategies for genome-based prediction of heterosis patterns in wheat, and (iv) ultimate use of genomics information to develop more efficient and robust genome-wide genotyping platforms to precisely predict higher yield potential and stability with greater precision. Genome-based breeding has potential to achieve the ultimate objective of ensuring sustainable wheat production through developing high yielding, climate-resilient wheat cultivars with high nutritional quality.

Notes

Acknowledgements

The authors are grateful to Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for critical review of this manuscript. This work was funded by the National Natural Science Foundation of China (31461143021, 31550110212), and CAAS Science and Technology Innovation Program.

Compliance with ethical standards

Conflict of interest

We declare no conflict of interest

Ethical standard

We declare that these works complied with the ethical standards in China.

References

  1. Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang SY et al (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420CrossRefPubMedGoogle Scholar
  2. Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor Appl Genet 119:507–517CrossRefPubMedPubMedCentralGoogle Scholar
  3. Allen AM, Winfield MO, Burridge AJ, Downie RC, Benbow HR, Barker GL et al (2017) Characterization of a Wheat Breeders’ Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). Plant Biotechnol J 15:390–401CrossRefPubMedGoogle Scholar
  4. Arruda MP, Lipka AE, Brown PJ, Krill AM, Thurber C, Brown-Guedira G et al (2016) Comparing genomic selection and marker-assisted selection for Fusarium head blight resistance in wheat (Triticum aestivum L.). Mol Breeding 36:84CrossRefGoogle Scholar
  5. Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H et al (2017) Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357:93–97CrossRefPubMedGoogle Scholar
  6. Baloch FS, Alsaleh A, Shahid MQ, Ciftci V, Sáenz de Miera LE, Aasim M et al (2017) A whole genome DArTseq and SNP analysis for genetic diversity assessment in durum wheat from central fertile crescent. PLoS ONE 12:e0167821CrossRefPubMedPubMedCentralGoogle Scholar
  7. Battenfield SD, Guzmán C, Gaynor RC, Singh RP, Peña RJ, Dreisigacker S et al (2016) Genomic selection for processing and end-use quality traits in the CIMMYT spring bread wheat breeding program. Plant Genome.  https://doi.org/10.3835/plantgenome2016.01.0005 CrossRefPubMedGoogle Scholar
  8. Beales J, Turner A, Griffiths S, Snape JW, Laurie DA (2007) A Pseudo-Response Regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theor Appl Genet 115:721–733CrossRefPubMedGoogle Scholar
  9. Belamkar V, Guttieri MJ, Hussain W, Jarquín D, El-basyoni I, Poland J et al (2018) Genomic selection in preliminary yield trials in a winter wheat breeding program. Genes Genom Genet.  https://doi.org/10.1534/g3.118.200415 CrossRefGoogle Scholar
  10. Bernardo R (2016) Bandwagons I, too, have known. Theor Appl Genet 129:2323–2332CrossRefPubMedGoogle Scholar
  11. Bevan MW, Uauy C, Wulff BB, Zhou J, Krasileva K, Clark MD (2017) Genomic innovation for crop improvement. Nature 543:346–354CrossRefPubMedGoogle Scholar
  12. Blake VC, Birkett C, Matthews DE, Hane DL, Bradbury P, Jannink JL (2016) The Triticeae Toolbox: combining phenotype and genotype data to advance small-grains breeding. Plant Genome.  https://doi.org/10.3835/plantgenome2014.12.0099 CrossRefPubMedGoogle Scholar
  13. Boeven PHG, Longin CFH, Leiser WL, Kollers S, Ebmeyer E, Würschum T (2016) Genetic architecture of male floral traits required for hybrid wheat breeding. Theor Appl Genet 129:2343–2357CrossRefPubMedGoogle Scholar
  14. Börner A, Ogbonnaya FC, Röder MS, Rasheed A, Periyannan S, Lagudah ES (2015) Aegilops tauschii introgressions in wheat. In: Molnár-Láng M, Ceoloni C, Doležel J (eds) Alien introgression in wheat. Springer International, Switzerland, pp 245–271Google Scholar
  15. Borrill P, Ramirez-Gonzalez R, Uauy C (2016) expVIP: a customizable RNA-seq data analysis and visualization platform. Plant Physiol 170:2172–2186CrossRefPubMedPubMedCentralGoogle Scholar
  16. Brenchley R, Spannagl M, Pfeifer M, Barker GLA, D’Amore R, Allen AM et al (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491:705–710CrossRefPubMedPubMedCentralGoogle Scholar
  17. Cavanagh CR, Chao SM, Wang SC, Huang BE, Stephen S, Kiani S et al (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci USA 110:8057–8062CrossRefPubMedGoogle Scholar
  18. Chao SM, Dubcovsky J, Dvorak J, Luo MC, Baenziger SP, Matnyazov R et al (2010) Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics 11:727CrossRefPubMedPubMedCentralGoogle Scholar
  19. Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A et al (2015) A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 16:26CrossRefPubMedPubMedCentralGoogle Scholar
  20. Charmet G, Storlie E, Oury FX, Laurent V, Beghin D, Chevarin L et al (2014) Genome-wide prediction of three important traits in bread wheat. Mol Breeding 34:1843–1852CrossRefGoogle Scholar
  21. Chen F, Gao M, Zhang J, Zuo A, Shang X, Cui D (2013a) Molecular characterization of vernalization and response genes in bread wheat from the Yellow and Huai Valley of China. BMC Plant Biol 13:199CrossRefPubMedPubMedCentralGoogle Scholar
  22. Chen S, Huang Z, Dai Y, Qin S, Gao Y, Zhang L et al (2013b) The development of 7E chromosome-specific molecular markers for Thinopyrum elongatum based on SLAF-seq technology. PLoS ONE 8:e65122CrossRefPubMedPubMedCentralGoogle Scholar
  23. Cheng F, Sun R, Hou X, Zheng H, Zhang F, Zhang Y et al (2016) Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat Genet 48:1218–1224CrossRefPubMedGoogle Scholar
  24. Chhetri M, Bariana H, Wong D, Sohail Y, Hayden M, Bansal U (2017) Development of robust molecular markers for marker-assisted selection of leaf rust resistance gene Lr23 in common and durum wheat breeding programs. Mol Breeding 37:21CrossRefGoogle Scholar
  25. Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J et al (2014) Structural and functional partitioning of bread wheat chromosome 3B. Science 345:288–294CrossRefGoogle Scholar
  26. Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J et al (2017) An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Res 27:885–896CrossRefPubMedPubMedCentralGoogle Scholar
  27. Cormier F, Throude M, Ravel C, Gouis J, Leveugle M, Lafarge S et al (2015) Detection of NAM-A1 natural variants in bread wheat reveals differences in haplotype distribution between a worldwide core collection and European elite germplasm. Agronomy 5:143CrossRefGoogle Scholar
  28. Crossa J, Jarquin D, Franco J, Perez-Rodriguez P, Burgueno J, Saint-Pierre C et al (2016) Genomic prediction of gene bank wheat landraces. Genes Genom Genet 6:1819–1834Google Scholar
  29. Crossa J, Perez-Rodriguez P, Cuevas J, Montesinos-Lopez O, Jarquin D, de Los Campos G et al (2017) Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci 22:961–975CrossRefPubMedGoogle Scholar
  30. Cui F, Zhang N, Fan XL, Zhang W, Zhao CX, Yang LJ et al (2017) Utilization of a Wheat660 K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep-UK 7:3788CrossRefGoogle Scholar
  31. Daetwyler HD, Bansal UK, Bariana HS, Hayden MJ, Hayes BJ (2014) Genomic prediction for rust resistance in diverse wheat landraces. Theor Appl Genet 127:1795–1803CrossRefPubMedGoogle Scholar
  32. Dawson JC, Endelman JB, Heslot N, Crossa J, Poland J, Dreisigacker S, Manès Y, Sorrells ME, Jannink J-L (2013) The use of unbalanced historical data for genomic selection in an international wheat breeding program. Field Crop Res 154:12–22CrossRefGoogle Scholar
  33. Dedryver F, Jubier M-F, Thouvenin J, Goyeau H (1996) Molecular markers linked to the leaf rust resistance gene Lr24 in different wheat cultivars. Genome 39:830–835CrossRefPubMedGoogle Scholar
  34. Devos KM, Gale MD (1992) The use of random amplified polymorphic DNA markers in wheat. Theor Appl Genet 84:567–572CrossRefPubMedGoogle Scholar
  35. Deynze AEV, Dubcovsky J, Gill KS, Nelson JC, Sorrells ME, Dvořák J et al (1995) Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. Genome 38:45–59CrossRefPubMedGoogle Scholar
  36. Dong H, Wang R, Yuan Y, Anderson J, Pumphrey M, Zhang Z, Chen J (2018) Evaluation of the potential for genomic selection to improve spring wheat resistance to Fusarium head blight in the Pacific Northwest. Front Plant Sci 9:911CrossRefPubMedPubMedCentralGoogle Scholar
  37. Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316:1862–1866CrossRefPubMedPubMedCentralGoogle Scholar
  38. Elshire RJ, Glaubitz JC, Poland JA, Kawamoto K, Buckler E, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379CrossRefPubMedPubMedCentralGoogle Scholar
  39. FAO (2017) FAOSTAT. http://www.fao.org/faostat/en/
  40. Fischer R, Byerlee D, Edmeades G (2014) Crop yields and global food security. ACIAR: Canberra, ACT, pp 8–11Google Scholar
  41. Gao C (2018) The future of CRISPR technologies in agriculture. Nat Rev Mol Cell Bio 19:275CrossRefGoogle Scholar
  42. Gardner KA, Lukas M, Mackay IJ (2016) A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments. Plant Biotechnol J 14:1406–1417CrossRefPubMedPubMedCentralGoogle Scholar
  43. Gupta PK, Varshney RK, Sharma PC, Ramesh B (1999) Molecular markers and their applications in wheat breeding. Plant Breeding 118:369–390CrossRefGoogle Scholar
  44. Haile JK, N’Diaye A, Clarke F, Clarke J, Knox R, Rutkoski J, Bassi FM, Pozniak CJ (2018) Genomic selection for grain yield and quality traits in durum wheat. Mol Breeding 38:75CrossRefGoogle Scholar
  45. Hanif M, Gao FM, Liu J, Wen W, Zhang Y, Rasheed A et al (2015) TaTGW6-A1, an ortholog of rice TGW6, is associated with grain weight and yield in bread wheat. Mol Breeding 36:1–8CrossRefGoogle Scholar
  46. Hassani-Pak K, Rawlings C (2017) Knowledge discovery in biological databases for revealing candidate genes linked to complex phenotypes. J Integr Bioinform.  https://doi.org/10.1515/jib-2016-0002 CrossRefPubMedGoogle Scholar
  47. Hayes BJ, Panozzo J, Walker CK, Choy AL, Kant S, Wong D et al (2017) Accelerating wheat breeding for end-use quality with multi-trait genomic predictions incorporating near infrared and nuclear magnetic resonance-derived phenotypes. Theor Appl Genet 130:2505–2519CrossRefPubMedGoogle Scholar
  48. He XY, He ZH, Ma W, Appels R, Xia XC (2009) Allelic variants of phytoene synthase 1 (Psy1) genes in Chinese and CIMMYT wheat cultivars and development of functional markers for flour colour. Mol Breeding 23:553–563CrossRefGoogle Scholar
  49. Heffner EL, Jannink J-L, Sorrells ME (2011a) Genomic Selection Accuracy using multifamily prediction models in a wheat breeding program. Plant Genome 4:65–75CrossRefGoogle Scholar
  50. Heffner EL, Jannink JL, Iwata H, Souza E, Sorrells ME (2011b) Genomic selection accuracy for grain quality traits in biparental wheat populations. Crop Sci 51:2597–2606CrossRefGoogle Scholar
  51. Hickey JM, Chiurugwi T, Mackay I, Powell W (2017) Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery. Nat Genet 49:1297CrossRefPubMedGoogle Scholar
  52. Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B et al (2014) Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26:121–135CrossRefPubMedPubMedCentralGoogle Scholar
  53. Hou J, Jiang Q, Hao C, Wang Y, Zhang H, Zhang X (2014) Global selection on sucrose synthase haplotypes during a century of wheat breeding. Plant Physiol 164:1918–1929CrossRefPubMedPubMedCentralGoogle Scholar
  54. Huang L, Brooks SA, Li W, Fellers JP, Trick HN, Gill BS (2003) Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. Genetics 164:655–664PubMedPubMedCentralGoogle Scholar
  55. Huang M, Cabrera A, Hoffstetter A, Griffey C, Van Sanford D, Costa J et al (2016) Genomic selection for wheat traits and trait stability. Theor Appl Genet 129:1697–1710CrossRefPubMedGoogle Scholar
  56. IWGSC (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:eaar7191CrossRefGoogle Scholar
  57. Jafarzadeh J, Bonnett D, Jannink JL, Akdemir D, Dreisigacker S, Sorrells ME (2016) Breeding value of primary synthetic wheat genotypes for grain yield. PLoS ONE 11:e0162860CrossRefPubMedPubMedCentralGoogle Scholar
  58. Jatayev S, Kurishbayev A, Zotova L, Khasanova G, Serikbay D, Zhubatkanov A et al (2017) Advantages of Amplifluor-like SNP markers over KASP in plant genotyping. BMC Plant Biol 17:254CrossRefPubMedPubMedCentralGoogle Scholar
  59. Jia JZ, Zhao SC, Kong XY, Li YR, Zhao GY, He WM et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95CrossRefPubMedGoogle Scholar
  60. Jiang Y, Schmidt RH, Zhao Y, Reif JC (2017a) A quantitative genetic framework highlights the role of epistatic effects for grain-yield heterosis in bread wheat. Nat Genet 49:1741–1746CrossRefPubMedGoogle Scholar
  61. Jiang Y, Schulthess AW, Rodemann B, Ling J, Plieske J, Kollers S et al (2017b) Validating the prediction accuracies of marker-assisted and genomic selection of Fusarium head blight resistance in wheat using an independent sample. Theor Appl Genet 130:471–482CrossRefPubMedGoogle Scholar
  62. Jiang Y, Schmidt RH, Reif JC (2018) Haplotype-based genome-wide prediction models exploit local epistatic interactions among markers. Genes Genom Genet 8:1687–1699Google Scholar
  63. Jin H, Wen W, Liu J, Zhai S, Zhang Y, Yan J et al (2016) Genome-wide QTL mapping for wheat processing quality parameters in a Gaocheng 8901/Zhoumai 16 recombinant inbred line population. Front Plant Sci 7:1032PubMedPubMedCentralGoogle Scholar
  64. Jordan KW, Wang S, Lun Y, Gardiner L-J, MacLachlan R, Hucl P et al (2015) A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol 16:48CrossRefPubMedPubMedCentralGoogle Scholar
  65. Juliana P, Singh RP, Singh PK, Crossa J, Huerta-Espino J, Lan C et al (2017) Genomic and pedigree-based prediction for leaf, stem, and stripe rust resistance in wheat. Theor Appl Genet 130:1415–1430CrossRefPubMedPubMedCentralGoogle Scholar
  66. Kage U, Kumar A, Dhokane D, Karre S, Kushalappa AC (2016) Functional molecular markers for crop improvement. Crit Rev Biotechnol 36:917–930CrossRefPubMedGoogle Scholar
  67. Kassa MT, You FM, Hiebert CW, Pozniak CJ, Fobert PR, Sharpe AG et al (2017) Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16. BMC Plant Biol 17:45CrossRefPubMedPubMedCentralGoogle Scholar
  68. Kempe K, Rubtsova M, Gils M (2014) Split-gene system for hybrid wheat seed production. Proc Natl Acad Sci USA 111:9097–9102CrossRefPubMedGoogle Scholar
  69. Khlestkina EK (2014) Current applications of wheat and wheat–alien precise genetic stocks. Mol Breeding 34:273–281CrossRefGoogle Scholar
  70. King J, Grewal S, Yang CY, Hubbart S, Scholefield D, Ashling S et al (2016) A step change in the transfer of interspecific variation into wheat from Amblyopyrum muticum. Plant Biotechnol J 15:217–226CrossRefPubMedPubMedCentralGoogle Scholar
  71. Krasileva KV, Vasquez-Gross HA, Howell T, Bailey P, Paraiso F, Clissold L et al (2017) Uncovering hidden variation in polyploid wheat. Proc Natl Acad Sci USA 114:E913–E921CrossRefPubMedGoogle Scholar
  72. Kristensen PS, Jahoor A, Andersen JR, Cericola F, Orabi J, Janss LL, Jensen J (2018) Genome-wide association studies and comparison of models and cross-validation strategies for genomic prediction of quality traits in advanced winter wheat breeding lines. Front Plant Sci 9:69CrossRefPubMedPubMedCentralGoogle Scholar
  73. Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT, Bonnette J et al (2015) Genome-environment associations in sorghum landraces predict adaptive traits. Sci Adv 1:e1400218CrossRefPubMedPubMedCentralGoogle Scholar
  74. Li YH, Zhou G, Ma J, Jiang W, Jin LG, Zhang Z et al (2014) De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 32:1045CrossRefPubMedGoogle Scholar
  75. Li H, Vikram P, Singh RP, Kilian A, Carling J, Song J et al (2015) A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits. BMC Genom 16:216CrossRefGoogle Scholar
  76. Li H, Rasheed A, Hickey L, He Z (2018) Fast-forwarding genetic gain. Trends Plant Sci 23:184–186CrossRefPubMedGoogle Scholar
  77. Ling HQ, Zhao SC, Liu DC, Wang JY, Sun H, Zhang C et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87–90CrossRefPubMedGoogle Scholar
  78. Ling HQ, Ma B, Shi X, Liu H, Dong L, Sun H et al (2018) Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature 557:424–428CrossRefPubMedGoogle Scholar
  79. Liu YN, He ZH, Appels R, Xia XC (2012) Functional markers in wheat: current status and future prospects. Theor Appl Genet 125:1–10CrossRefPubMedGoogle Scholar
  80. Liu S, Sehgal SK, Li J, Lin M, Trick HN, Yu J et al (2013) Cloning and characterization of a critical regulator for preharvest sprouting in wheat. Genetics 195:263–273CrossRefPubMedPubMedCentralGoogle Scholar
  81. Long YM, Chao WS, Ma GJ, Xu SS, Qi LL (2016) An innovative SNP genotyping method adapting to multiple platforms and throughputs. Theor Appl Genet 130:597–607CrossRefPubMedGoogle Scholar
  82. Longin CF, Gowda M, Muhleisen J, Ebmeyer E, Kazman E, Schachschneider R et al (2013) Hybrid wheat: quantitative genetic parameters and consequences for the design of breeding programs. Theor Appl Genet 126:2791–2801CrossRefPubMedGoogle Scholar
  83. Lorenz AJ, Hamblin MT, Jannink JL (2010) Performance of single nucleotide polymorphisms versus haplotypes for genome-wide association analysis in barley. PLoS ONE 5:e14079CrossRefPubMedPubMedCentralGoogle Scholar
  84. Lu QX, Lillemo M, Skinnes H, He XY, Shi JR, Ji F et al (2013) Anther extrusion and plant height are associated with Type I resistance to Fusarium head blight in bread wheat line ‘Shanghai-3/Catbird’. Theor Appl Genet 126:317–334CrossRefPubMedGoogle Scholar
  85. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:1–6CrossRefGoogle Scholar
  86. Luo MC, Gu YQ, You FM, Deal KR, Ma YQ, Hu YQ et al (2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proc Natl Acad Sci USA 110:7940–7945CrossRefPubMedGoogle Scholar
  87. Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR et al (2017) Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551:498–502PubMedGoogle Scholar
  88. Ma DY, Yan J, He ZH, Wu L, Xia XC (2012) Characterization of a cell wall invertase gene TaCwi-A1 on common wheat chromosome 2A and development of functional markers. Mol Breeding 29:43–52CrossRefGoogle Scholar
  89. Ma L, Tian L, Hao C, Wang Y, Chen X, Zhang XY (2016) TaGS5-3A, a grain size gene selected during wheat improvement for larger kernel and yield. Plant Biotechnol J 14:1269–1280CrossRefPubMedGoogle Scholar
  90. Manickavelu A, Hattori T, Yamaoka S, Yoshimura K, Kondou Y, Onogi A et al (2017) Genetic nature of elemental contents in wheat grains and its genomic prediction: toward the effective use of wheat landraces from Afghanistan. PLoS ONE 12:e0169416CrossRefPubMedPubMedCentralGoogle Scholar
  91. Mayer KFX, Rogers J, Dolezel J, Pozniak C, Eversole K, Feuillet C et al (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194):1251788CrossRefGoogle Scholar
  92. Michel S, Ametz C, Gungor H, Akgöl B, Epure D, Grausgruber H et al (2017) Genomic assisted selection for enhancing line breeding: merging genomic and phenotypic selection in winter wheat breeding programs with preliminary yield trials. Theor Appl Genet 130:363–376CrossRefPubMedGoogle Scholar
  93. Michel S, Kummer C, Gallee M, Hellinger J, Ametz C, Akgöl B, Epure D, Löschenberger F, Buerstmayr H (2018) Improving the baking quality of bread wheat by genomic selection in early generations. Theor Appl Genet 131:477–493CrossRefPubMedGoogle Scholar
  94. Mirdita V, He S, Zhao Y, Korzun V, Bothe R, Ebmeyer E, Reif JC, Jiang Y (2015) Potential and limits of whole genome prediction of resistance to Fusarium head blight and Septoria tritici blotch in a vast Central European elite winter wheat population. Theor Appl Genet 128:2471–2481CrossRefPubMedGoogle Scholar
  95. Montenegro JD, Golicz AA, Bayer PE, Hurgobin B, Lee HT, Chon-Kit KC et al (2017) The pangenome of hexaploid bread wheat. Plant J 90:1007–1013CrossRefPubMedGoogle Scholar
  96. Moore G (2015) Strategic pre-breeding for wheat improvement. Nat Plants 1:15018CrossRefPubMedGoogle Scholar
  97. Moore JW, Herrera-Foessel S, Lan C, Schnippenkoetter W, Ayliffe M, Huerta-Espino J et al (2015) A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat Genet 47:1494CrossRefPubMedGoogle Scholar
  98. Moore JK, Manmathan HK, Anderson VA, Poland JA, Morris CF, Haley SD (2017) Improving genomic prediction for pre-harvest sprouting tolerance in wheat by weighting large-effect quantitative trait loci. Crop Sci 57:1315–1324CrossRefGoogle Scholar
  99. Moose SP, Mumm R (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969–977CrossRefPubMedPubMedCentralGoogle Scholar
  100. Mujeeb-Kazi A, Kazi AG, Dundas I, Rasheed A, Ogbonnaya F, Kishii M et al (2013) Genetic diversity for wheat improvement as a conduit to food security. Adv Agron 122:179–257CrossRefGoogle Scholar
  101. Myburg AA, Cawood M, Wingfield BD, Botha AM (1998) Development of RAPD and SCAR markers linked to the Russian wheat aphid resistance gene Dn2 in wheat. Theor Appl Genet 96:1162–1169CrossRefGoogle Scholar
  102. Naik S, Gill VS, Rao VSP, Gupta VS, Tamhankar SA, Pujar S et al (1998) Identification of a STS marker linked to the Aegilops speltoides-derived leaf rust resistance gene Lr28 in wheat. Theor Appl Genet 97:535–540CrossRefGoogle Scholar
  103. Navarro JAR, Willcox M, Burgueño J, Romay C, Swarts K, Trachsel S et al (2017) A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nat Genet 49:476–480CrossRefGoogle Scholar
  104. Ni F, Qi J, Hao Q, Lyu B, Luo M-C, Wang Y et al (2017) Wheat Ms2 encodes for an orphan protein that confers male sterility in grass species. Nat Commun 8:15121CrossRefPubMedPubMedCentralGoogle Scholar
  105. Norman A, Taylor J, Tanaka E, Telfer P, Edwards J, Martinant J-P, Kuchel H (2017) Increased genomic prediction accuracy in wheat breeding using a large Australian panel. Theor Appl Genet 130:2543–2555CrossRefPubMedPubMedCentralGoogle Scholar
  106. Odell SG, Lazo GR, Woodhouse MR, Hane DL, Sen TZ (2017) The art of curation at a biological database: principles and application. Curr Plant Biol 11–12:2–11CrossRefGoogle Scholar
  107. Ogbonnaya FC, Abdalla O, Mujeeb-Kazi A, Alvina GK, Xu SS, Gosman N et al (2013) Synthetic hexaploids: harnessing species of the primary gene pool for wheat improvement. Plant Breeding Rev 37:35–122CrossRefGoogle Scholar
  108. Ornella L, Singh S, Perez P, Burgueño J, Singh R, Tapia E, Bhavani S, Dreisigacker S, Braun H-J, Mathews K, Crossa J (2012) Genomic prediction of genetic values for resistance to wheat rusts. Plant Genome 5:136–148CrossRefGoogle Scholar
  109. Pasam RK, Bansal U, Daetwyler HD, Forrest KL, Wong D, Petkowski J et al (2017) Detection and validation of genomic regions associated with resistance to rust diseases in a worldwide hexaploid wheat landrace collection using BayesR and mixed linear model approaches. Theor Appl Genet 130:777–793CrossRefPubMedGoogle Scholar
  110. Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P et al (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322:101–104CrossRefPubMedGoogle Scholar
  111. Pearce S, Vazquez-Gross H, Herin SY, Hane D, Wang Y, Gu YQ, Dubcovsky J (2015) WheatExp: an RNA-seq expression database for polyploid wheat. BMC Plant Biol 15:299CrossRefPubMedPubMedCentralGoogle Scholar
  112. Poland J, Endelman J, Dawson J, Rutkoski J, Wu S, Manes Y et al (2012a) Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 5:103–113CrossRefGoogle Scholar
  113. Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012b) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7:e32253CrossRefPubMedPubMedCentralGoogle Scholar
  114. Qian L, Hickey LT, Stahl A, Werner CR, Hayes B, Snowdon RJ, Voss-Fels KP (2017) Exploring and harnessing haplotype diversity to improve yield stability in crops. Front Plant Sci 8:1534CrossRefPubMedPubMedCentralGoogle Scholar
  115. Ramirez-Gonzalez RH, Uauy C, Caccamo M (2015) PolyMarker: a fast polyploid primer design pipeline. Bioinformatics 31:2038–2039CrossRefPubMedPubMedCentralGoogle Scholar
  116. Rapp M, Lein V, Lacoudre F, Lafferty J, Müller E, Vida G, Bozhanova V, Ibraliu A, Thorwarth P, Piepho HP, Leiser WL, Würschum T, Longin CFH (2018) Simultaneous improvement of grain yield and protein content in durum wheat by different phenotypic indices and genomic selection. Theor Appl Genet 131:1315–1329CrossRefPubMedGoogle Scholar
  117. Rasheed A, Wen W, Gao FM, Zhai S, Jin H, Liu JD et al (2016) Development and validation of KASP assays for functional genes underpinning key economic traits in wheat. Theor Appl Genet 129:1843–1860CrossRefPubMedGoogle Scholar
  118. Rasheed A, Hao Y, Xia XC, Khan A, Xu Y, Varshney RK et al (2017) Crop breeding chips and genotyping platforms: progress, challenges and perspectives. Mol Plant 10:1047–1064CrossRefPubMedGoogle Scholar
  119. Rasheed A, Mujeeb-Kazi A, Ogbonnaya FC, He ZH, Rajaram S (2018a) Wheat genetic resources in the post-genomics era: promise and challenges. Ann Bot-London 121:603–616CrossRefGoogle Scholar
  120. Rasheed A, Ogbonnaya FC, Lagudah E, Appels R, He ZH (2018b) The goat grass genome’s role in wheat improvement. Nat Plants 4:56–58CrossRefPubMedGoogle Scholar
  121. Rasheed A, Jin H, Xiao Y, Zhang Y, Hao Y, Zhang Y, Hickey LT, Morgounov AI, Xia X, He Z (2019) Allelic effects and variations for key bread-making quality genes in bread wheat using high-throughput molecular markers. J Cereal Sci 85:305–309CrossRefGoogle Scholar
  122. Riaz A, Hathorn A, Dinglasan E, Ziems L, Richard C, Singh D et al (2017) Into the vault of the Vavilov wheats: old diversity for new alleles. Genet Resour Crop Ev 64:531–544CrossRefGoogle Scholar
  123. Rimbert H, Darrier B, Navarro J, Kitt J, Choulet F, Leveugle M et al (2018) High throughput SNP discovery and genotyping in hexaploid wheat. PLoS ONE 13:e0186329CrossRefPubMedPubMedCentralGoogle Scholar
  124. Röder MS, Plaschke J, König SU, Börner A, Sorrells ME, Tanksley SD et al (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327–333CrossRefPubMedGoogle Scholar
  125. Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P et al (1998) A microsatellite map of wheat. Genetics 149:2007–2023PubMedPubMedCentralGoogle Scholar
  126. Rossetto M, Henry RJ (2014) Escape from the laboratory: new horizons for plant genetics. Trends Plant Sci 19:554–555CrossRefPubMedGoogle Scholar
  127. Rutkoski JE, Heffner EL, Sorrells ME (2011) Genomic selection for durable stem rust resistance in wheat. Euphytica 179:161–173CrossRefGoogle Scholar
  128. Rutkoski JE, Poland JA, Singh RP, Huerta-Espino J, Bhavani S, Barbier H, Rouse MN, Jannink J-L, Sorrells ME (2014) Genomic selection for quantitative adult plant stem rust resistance in wheat. Plant Genome 7:1–10CrossRefGoogle Scholar
  129. Šafář J, Šimková H, Kubaláková M, Číhalíková J, Suchánková P, Bartoš J et al (2010) Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res 129:211–223CrossRefPubMedGoogle Scholar
  130. Saintenac C, Jiang D, Akhunov ED (2011) Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol 12:R88CrossRefPubMedPubMedCentralGoogle Scholar
  131. Scheben A, Batley J, Edwards D (2016) Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnol J 15:149–161CrossRefGoogle Scholar
  132. Sehgal D, Vikram P, Sansaloni CP, Ortiz C, Pierre CS, Payne T et al (2015) Exploring and mobilizing the gene bank biodiversity for wheat improvement. PLoS ONE 10:e0132112CrossRefPubMedPubMedCentralGoogle Scholar
  133. Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breeding 33:1–14CrossRefGoogle Scholar
  134. Shi F, Tibbits J, Pasam RK, Kay P, Wong D, Petkowski J et al (2017) Exome sequence genotype imputation in globally diverse hexaploid wheat accessions. Theor Appl Genet 130:1393–1404CrossRefPubMedGoogle Scholar
  135. Song J, Carver BF, Powers C, Yan L, Klápště J, El-Kassaby YA, Chen C (2017) Practical application of genomic selection in a doubled-haploid winter wheat breeding program. Mol Breeding 37:117CrossRefGoogle Scholar
  136. Sorrells ME, Gustafson JP, Somers D, Chao S, Benscher D, Guedira-Brown G et al (2011) Reconstruction of the Synthetic W7984 × Opata M85 wheat reference population. Genome 54:875–882CrossRefPubMedGoogle Scholar
  137. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE et al (2001) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293:489–493CrossRefPubMedGoogle Scholar
  138. Steuernagel B, Periyannan SK, Hernandez-Pinzon I, Witek K, Rouse MN, Yu G et al (2016) Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nat Biotechnol 34:652–655CrossRefPubMedGoogle Scholar
  139. Sun CW, Zhang FY, Yan XF, Zhang XF, Dong ZD, Cui DQ, Chen F (2017) Genome-wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China. Plant Biotechnol J 15:953–969CrossRefPubMedPubMedCentralGoogle Scholar
  140. Tabbita F, Pearce S, Barneix AJ (2017) Breeding for increased grain protein and micronutrient content in wheat: ten years of the GPC-B1 gene. J Cereal Sci 73:183–191CrossRefGoogle Scholar
  141. Thind AK, Wicker T, Simkova H, Fossati D, Moullet O, Brabant C et al (2017) Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nat Biotechnol 35:793–796CrossRefPubMedGoogle Scholar
  142. Tucker EJ, Baumann U, Kouidri A, Suchecki R, Baes M, Garcia M et al (2017) Molecular identification of the wheat male fertility gene Ms1 and its prospects for hybrid breeding. Nat Commun 8:869CrossRefPubMedPubMedCentralGoogle Scholar
  143. Uauy C (2017) Wheat genomics comes of age. Curr Opin Plant Biol 36:142–148CrossRefPubMedGoogle Scholar
  144. Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 314:1298–1301CrossRefPubMedPubMedCentralGoogle Scholar
  145. Valluru R, Reynolds MP, Salse J (2014) Genetic and molecular bases of yield-associated traits: a translational biology approach between rice and wheat. Theor Appl Genet 127:1463–1489CrossRefPubMedGoogle Scholar
  146. Velu G, Crossa J, Singh RP, Hao Y, Dreisigacker S, Perez-Rodriguez P et al (2016) Genomic prediction for grain zinc and iron concentrations in spring wheat. Theor Appl Genet 129:1595–1605CrossRefPubMedGoogle Scholar
  147. Vikram P, Franco J, Burgueño-Ferreira J, Li H, Sehgal D, Saint Pierre C et al (2016) Unlocking the genetic diversity of Creole wheats. Sci Rep 6:23092CrossRefPubMedPubMedCentralGoogle Scholar
  148. Wang SC, Wong DB, Forrest K, Allen A, Chao SM, Huang BE et al (2014) Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796CrossRefPubMedPubMedCentralGoogle Scholar
  149. Wang Z, Li J, Chen S, Heng Y, Chen Z, Yang J et al (2017) Poaceae-specific MS1 encodes a phospholipid-binding protein for male fertility in bread wheat. Proc Natl Acad Sci USA 114:12614–12619CrossRefPubMedGoogle Scholar
  150. Watson A, Ghosh S, Williams M, Cuddy WS, Simmonds J, Rey M-D et al (2018) Speed breeding is a powerful tool to accelerate crop research and breeding. Nat Plants.  https://doi.org/10.1038/s41477-017-0083-8 CrossRefPubMedGoogle Scholar
  151. Wen WE, He ZH, Gao FM, Liu JD, Jin H, Zhai SN, Qu YY, Xia XC (2017) A high-density consensus map of common wheat integrating four mapping populations scanned by the 90 K SNP array. Front Plant Sci 8:1389CrossRefPubMedPubMedCentralGoogle Scholar
  152. Winfield MO, Allen AM, Burridge AJ, Barker GL, Benbow HR, Wilkinson PA et al (2016) High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnol J 14:1195–1206CrossRefPubMedGoogle Scholar
  153. Worland AJ, Borner A, Korzun V, Li WM, Petrovic S, Sayers EJ (1998) The influence of photoperiod genes on the adaptability of European winter wheats (Reprinted from Wheat: prospects for global improvement, 1998). Euphytica 100:385–394CrossRefGoogle Scholar
  154. Wu Z, Wang B, Chen X, Wu J, King GJ, Xiao Y, Liu K (2016) Evaluation of linkage disequilibrium pattern and association study on seed oil content in Brassica napus using ddRAD sequencing. PLoS ONE 11:e0146383CrossRefPubMedPubMedCentralGoogle Scholar
  155. Wu J, Zeng Q, Wang Q, Liu S, Yu S, Mu J et al (2018) SNP-based pool genotyping and haplotype analysis accelerate fine-mapping of the wheat genomic region containing stripe rust resistance gene Yr26. Theor Appl Genet 131:1481–1496CrossRefPubMedGoogle Scholar
  156. Wurschum T, Boeven PH, Langer SM, Longin CF, Leiser WL (2015) Multiply to conquer: copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat. BMC Genet 16:96CrossRefPubMedPubMedCentralGoogle Scholar
  157. Würschum T, Liu G, Boeven PHG, Longin CFH, Mirdita V, Kazman E et al (2018a) Exploiting the Rht portfolio for hybrid wheat breeding. Theor Appl Genet 131:1433–1442CrossRefPubMedGoogle Scholar
  158. Würschum T, Langer SM, Longin CFH, Tucker MR, Leiser WL (2018b) A three-component system incorporating Ppd-D1, copy number variation at Ppd-B1, and numerous small-effect quantitative trait loci facilitates adaptation of heading time in winter wheat cultivars of worldwide origin. Plant, Cell Environ 41:1407–1416CrossRefGoogle Scholar
  159. Xia C, Zhang LC, Zou C, Gu YQ, Duan JL, Zhao GY et al (2017) A TRIM insertion in the promoter of Ms2 causes male sterility in wheat. Nat Commun 8:15407CrossRefPubMedPubMedCentralGoogle Scholar
  160. Xie WB, Wang GW, Yuan M, Yao W, Lyu K, Zhao H et al (2015) Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection. Proc Natl Acad Sci USA 112:E5411–E5419CrossRefPubMedGoogle Scholar
  161. Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407CrossRefGoogle Scholar
  162. Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268CrossRefPubMedGoogle Scholar
  163. Yuan Y, Bayer PE, Batley J, Edwards D (2017) Improvements in genomic technologies: application to crop genomics. Trends Biotechnol 35:547–558CrossRefPubMedGoogle Scholar
  164. Zhang CY, Dong CH, He XY, Zhang LP, Xia XC, He ZH (2011) Allelic Variants at the TaZds-D1 Locus on Wheat Chromosome 2DL and their Association with Yellow Pigment Content. Crop Sci 51:1580–1590CrossRefGoogle Scholar
  165. Zhang YJ, Liu JD, Xia XC, He ZH (2014) TaGS-D1, an ortholog of rice OsGS3, is associated with grain weight and grain length in common wheat. Mol Breeding 34:1097–1107CrossRefGoogle Scholar
  166. Zhang Y, Zhang J, Huang L, Gao A, Zhang J, Yang X et al (2015) A high-density genetic map for P genome of Agropyron Gaertn. based on specific-locus amplified fragment sequencing (SLAF-seq). Planta 242:1335–1347CrossRefPubMedGoogle Scholar
  167. Zhang X, Sallam A, Gao L, Kantarski T, Poland J, DeHaan LR et al (2016) Establishment and optimization of genomic selection to accelerate the domestication and improvement of intermediate wheatgrass. Plant Genome 9:1–18Zhao YS, Zeng J, Fernando R, Reif JC (2013) Genomic prediction of hybrid wheat performance. Crop Sci 53:802–810Google Scholar
  168. Zhao Y, Li Z, Liu G, Jiang Y, Maurer HP, Wurschum T et al (2015) Genome-based establishment of a high-yielding heterotic pattern for hybrid wheat breeding. Proc Natl Acad Sci USA 112:15624–15629PubMedGoogle Scholar
  169. Zhao G, Zou C, Li K, Wang K, Li T, Gao L et al (2017) The Aegilops tauschii genome reveals multiple impacts of transposons. Nat Plants 3:946–955CrossRefPubMedGoogle Scholar
  170. Zhou S, Zhang J, Che Y, Liu W, Lu Y, Yang X et al (2018) Construction of Agropyron Gaertn. genetic linkage maps using a wheat 660 K SNP array reveals a homoeologous relationship with the wheat genome. Plant Biotechnol J 16:818–827CrossRefPubMedGoogle Scholar
  171. Zhu J, Pearce S, Burke A, See DR, Skinner DZ, Dubcovsky J et al (2014) Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat. Theor Appl Genet 127:1183–1197CrossRefPubMedPubMedCentralGoogle Scholar
  172. Zikhali M, Wingen LU, Griffiths S (2016) Delimitation of the Earliness per se D1 (Eps-D1) flowering gene to a subtelomeric chromosomal deletion in bread wheat (Triticum aestivum). J Exp Bot 67:287–299CrossRefPubMedGoogle Scholar
  173. Zimin AV, Puiu D, Hall R, Kingan S, Clavijo BJ, Salzberg SL (2017a) The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. GigaScience 6:1–7PubMedPubMedCentralGoogle Scholar
  174. Zimin AV, Puiu D, Luo M-C, Zhu T, Koren S, Marçais G et al (2017b) Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm. Genome Res 27:787–792CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of Crop Sciences, National Wheat Improvement CenterChinese Academy of Agricultural Sciences (CAAS)BeijingChina
  2. 2.International Maize and Wheat Improvement Center (CIMMYT)BeijingChina
  3. 3.Department of Plant SciencesQuaid-i-Azam UniversityIslamabadPakistan

Personalised recommendations