Theoretical and Applied Genetics

, Volume 128, Issue 5, pp 779–795 | Cite as

Sequencing consolidates molecular markers with plant breeding practice

  • Huaan YangEmail author
  • Chengdao Li
  • Hon-Ming Lam
  • Jonathan Clements
  • Guijun Yan
  • Shancen ZhaoEmail author


Key message

Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding.


The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.


Amplify Fragment Length Polymorphism Simple Sequence Repeat Marker Single Nucleotide Polymorphism Genomic Selection High Resolution Melting 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We greatly appreciate the two anonymous reviewers for their invaluable comments and suggestions. The research is supported by the Western Australian Government through the Lupin Molecular Marker Strategy Project to H. Y.; and the Hong Kong RGC Collaborative Research Fund (CUHK3/CRF/11G) and the Hong Kong RGC General Research Fund (468610) to H. M. L.

Conflict of interest

The authors declare that they have no conflict of interest.


  1. Akfirat FS, Ertugrul F, Hasancebi S et al (2013) Chromosomal location of genomic SSR markers associated with yellow rust resistance in Turkish bread wheat (Triticum aestivum L.). J Genet 92:233–240PubMedGoogle Scholar
  2. Andolfatto P, Davison D, Erezyilmaz D et al (2011) Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 21:610–617PubMedCentralPubMedGoogle Scholar
  3. Antony G, Zhou J, Huang S et al (2010) Rice xa13 recessive resistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3. Plant Cell 22:3864–3876PubMedCentralPubMedGoogle Scholar
  4. Atwell S, Huang YS, Vilhjálmsson BJ et al (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627–631PubMedCentralPubMedGoogle Scholar
  5. Baird NA, Etter PD, Atwood TS et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376PubMedCentralPubMedGoogle Scholar
  6. Barchi L, Lanteri S, Portis E et al (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 12:304PubMedCentralPubMedGoogle Scholar
  7. Boersma JG, Buirchell BJ, Sivasithamparam K, Yang H (2007a) Development of a PCR marker tightly linked to mollis, the gene that controls seed dormancy in Lupinus angustifolius L. Plant Breed 126:612–616Google Scholar
  8. Boersma JG, Buirchell BJ, Sivasithamparam K, Yang H (2007b) Development of two sequence-specific PCR markers linked to the le gene that reduces pod shattering in narrow-leafed Lupin (Lupinus angustifolius L.). Genet Mol Biol 30:623–629Google Scholar
  9. Boersma J, Nelson M, Sivasithamparam K, Yang H (2009) Development of sequence-specific PCR markers linked to the Tardus gene that reduces pod shattering in narrow-leafed lupin (Lupinus angustifolius L.). Mol Breed 23:259–267Google Scholar
  10. Brenchley R, Spannagl M, Pfeifer M et al (2013) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491:705–710Google Scholar
  11. Brien SJ, A CW, Potter RH et al (1999) A molecular marker for early maturity (Ku) and marker-assisted breeding of Lupinus angustifolius. In: Proceedings of the 9th international lupin conference, Klink/Muritz, Germany, pp 115–117Google Scholar
  12. Brumlop S, Finckh MR (2011) Applications and potentials of marker assisted selection (MAS) in plant breeding. BundesamtfürNaturschutz (BfN), Bonn, GermanyGoogle Scholar
  13. Brunner S, Hurni S, Streckeisen P et al (2010) Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles. Plant J 64:433–445PubMedGoogle Scholar
  14. Bus A, Hecht J, Huettel B et al (2012) High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genomics 13:281PubMedCentralPubMedGoogle Scholar
  15. Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11:215–221PubMedGoogle Scholar
  16. Chen W, Sun L, Zhao F et al (2012) The genome of Prunus mume. Nat Commun 3:1318Google Scholar
  17. Chen J, Huang Q, Gao D et al (2013) Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat Commun 4:1595–1599PubMedCentralPubMedGoogle Scholar
  18. Cheng SH, Cao LY, Yang SH, Zhai HQ (2004) Forty years’ development of hybrid rice: China’s experience. Rice Sci 11:225–230Google Scholar
  19. Chia J-M, Song C, Bradbury PJ et al (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44:803–807PubMedGoogle Scholar
  20. Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A et al (2011) Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley. BMC Genomics 12:4PubMedCentralPubMedGoogle Scholar
  21. Clements JC, Dracup M, Buirchell BJ, Smith CG (2005) Variation for seed coat and pod wall percentage and other traits in a germplasm collection and historical cultivars of lupins. Aust J Agric Res 56:75–83Google Scholar
  22. Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc B: Biol Sci 363:557–572Google Scholar
  23. Connelly CF, Akey JM (2012) On the prospects of whole-genome association mapping in Saccharomyces cerevisiae. Genetics 191:1345–1353PubMedCentralPubMedGoogle Scholar
  24. Cowling WA, Hamblin J, Wood PM, Gladstones JS (1987) Resistance to Phomopsis stem blight in Lupinus angustifolius L. Crop Sci 27:648–652Google Scholar
  25. Dai F, Nevo E, Wu D et al (2012) Tibet is one of the centers of domestication of cultivated barley. Proc Natl Acad Sci USA 109:16969–16973PubMedCentralPubMedGoogle Scholar
  26. Davey JW, Hohenlohe PA, Etter PD et al (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510PubMedGoogle Scholar
  27. Desta ZA, Ortiz R (2014) Genomic selection: genome-wide prediction in plant improvement. Trends Plant Sci 19:592–601PubMedGoogle Scholar
  28. Ellis JG, Lagudah ES, Spielmeyer W, Dodds PN (2014) The past, present and future of breeding rust resistant wheat. Front Plant Sci 5:641PubMedCentralPubMedGoogle Scholar
  29. Elshire RJ, Glaubitz JC, Sun Q et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379PubMedCentralPubMedGoogle Scholar
  30. Emerson KJ, Merz CR, Catchen JM et al (2010) Resolving postglacial phylogeography using high-throughput sequencing. Proc Natl Acad Sci USA 107:16196–16200PubMedCentralPubMedGoogle Scholar
  31. Etter PD, Preston JL, Bassham S et al (2011) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS One 6:e18561PubMedCentralPubMedGoogle Scholar
  32. Evans DE, Li C, Eglinton JK (2010) The properties and genetics of barley malt starch degrading enzymes. In: Zhang G, Li C (eds) Advanced topics in science and technology in China. Springer, Berlin, pp 143–189Google Scholar
  33. Feuillet C, Leach JE, Rogers J et al (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16:77–88PubMedGoogle Scholar
  34. Francki MG, Mullan DJ (2004) Application of comparative genomics to narrow-leafed lupin (Lupinus angustifolius L.) using sequence information from soybean and Arabidopsis. Génome 47:623–632PubMedGoogle Scholar
  35. Gao Z-Y, Zhao S-C, He W-M et al (2013) Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences. Proc Natl Acad Sci USA 110:14492–14497PubMedCentralPubMedGoogle Scholar
  36. Gebhardt C (2013) Bridging the gap between genome analysis and precision breeding in potato. Trends Genet 29:248–256PubMedGoogle Scholar
  37. Goettel W, Xia E, Upchurch R et al (2014) Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content. BMC Genomics 15:299PubMedCentralPubMedGoogle Scholar
  38. Goff SA, Ricke D, Lan T-H et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100PubMedGoogle Scholar
  39. Gore MA, Chia JM, Elshire RJ et al (2009) A first-generation haplotype map of maize. Science 326:1115–1117PubMedGoogle Scholar
  40. Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101:5–18PubMedGoogle Scholar
  41. Hayden MJ, Kuchel H, Chalmers KJ (2004) Sequence tagged microsatellites for the Xgwm533 locus provide new diagnostic markers to select for the presence of stem rust resistance gene Sr2 in bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1641–1647PubMedGoogle Scholar
  42. He XY, He ZH, Zhang LP et al (2007) Allelic variation of polyphenol oxidase (PPO) genes located on chromosomes 2A and 2D and development of functional markers for the PPO genes in common wheat. Theor Appl Genet 115:47–58PubMedGoogle Scholar
  43. Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49:1Google Scholar
  44. Huang X, Feng Q, Qian Q et al (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076PubMedCentralPubMedGoogle Scholar
  45. Hufford MB, Xu X, van Heerwaarden J et al (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44:808–811PubMedGoogle Scholar
  46. Hyten DL, Cannon SB, Song Q et al (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11:38PubMedCentralPubMedGoogle Scholar
  47. International Peach Genome Initiative, Verde I, Abbott AG et al (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494Google Scholar
  48. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800Google Scholar
  49. Iyer-Pascuzzi A, McCouch S (2007) Functional markers for xa5-mediated resistance in rice (Oryza sativa L.). Mol Breed 19:291–296Google Scholar
  50. Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177PubMedGoogle Scholar
  51. Jia J, Zhao S, Kong X et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95PubMedGoogle Scholar
  52. Jiao Y, Zhao H, Ren L et al (2012) Genome-wide genetic changes during modern breeding of maize. Nat Genet 44:812–815PubMedGoogle Scholar
  53. Juwattanasomran R, Somta P, Kaga A et al (2012) Identification of a new fragrance allele in soybean and development of its functional marker. Mol Breed 29:13–21Google Scholar
  54. Kim MY, Lee S, Van K et al (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci USA 107:22032–22037PubMedCentralPubMedGoogle Scholar
  55. Kroc M, Koczyk G, Swiecicki W et al (2014) New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L. (narrow-leafed lupin). Theor Appl Genet 127:1237–1249PubMedGoogle Scholar
  56. Kumar S, You FM, Cloutier S (2012) Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries. BMC Genomics 13:684–694PubMedCentralPubMedGoogle Scholar
  57. Li R, Zhu H, Ruan J et al (2010a) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272PubMedCentralPubMedGoogle Scholar
  58. Li X, Renshaw D, Yang H, Yan G (2010b) Development of a co-dominant DNA marker tightly linked to gene tardus conferring reduced pod shattering in narrow-leafed lupin (Lupinus angustifolius L.). Euphytica 176:49–58Google Scholar
  59. Li X, Yang H, Buirchell B, Yan G (2011) Development of a DNA marker tightly linked to low-alkaloid gene iucundus in narrow-leafed lupin (Lupinus angustifolius L.) for marker-assisted selection. Crop Pasture Sci 62:218–224Google Scholar
  60. Li X, Buirchell B, Yan G, Yang H (2012a) A molecular marker linked to the mollis gene conferring soft-seediness for marker-assisted selection applicable to a wide range of crosses in lupin (Lupinus angustifolius L.) breeding. Mol Breed 29:361–370Google Scholar
  61. Li X, Yang H, Yan G (2012b) Development of a co-dominant DNA marker linked to the gene lentus conferring reduced pod shattering for marker-assisted selection in narrow-leafed lupin (Lupinus angustifolius) breeding. Plant Breed 131:540–544Google Scholar
  62. Li Y-H, Zhao S-C, Ma J-X et al (2013) Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics 14:579PubMedCentralPubMedGoogle Scholar
  63. Li Z, Fu B-Y, Zhang G, McNally KL (2014) The 3,000 rice genomes project. GigaScience 3:1–6Google Scholar
  64. Lin T, Zhu G, Zhang J et al (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46:1220–1226PubMedGoogle Scholar
  65. Ling H-Q, Zhao S, Liu y et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87–90PubMedGoogle Scholar
  66. Lorenz AJ, Chao S, Asoro FG et al (2011) Genomic selection in plant breeding. In: Sparks DL (eds) Advances in agronomy. Elsevier, pp 77–123Google Scholar
  67. Ma J, Yan GJ, Liu CJ (2011) Development of near-isogenic lines for a major QTL on 3BL conferring Fusarium crown rot resistance in hexaploid wheat. Euphytica 183:147–152Google Scholar
  68. Mammadov J, Chen W, Ren R et al (2010) Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding. Theor Appl Genet 121:577–588PubMedGoogle Scholar
  69. Miller MR, Dunham JP, Amores A et al (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248PubMedCentralPubMedGoogle Scholar
  70. Molina J, Sikora M, Garud N et al (2011) Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci USA 108:8351–8356PubMedCentralPubMedGoogle Scholar
  71. Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969–977PubMedCentralPubMedGoogle Scholar
  72. Morris GP, Ramu P, Deshpande SP et al (2013) Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci USA 110:453–458PubMedCentralPubMedGoogle Scholar
  73. Mortimer SA, Kidwell MA, Doudna JA (2014) Insights into RNA structure and function from genome-wide studies. Nat Rev Genet 15:469–479PubMedGoogle Scholar
  74. Nakaya A, Isobe SN (2012) Will genomic selection be a practical method for plant breeding? Ann Bot 110:1303–1316PubMedCentralPubMedGoogle Scholar
  75. Nelson MN, Phan HTT, Ellwood SR et al (2006) The first gene-based map of Lupinus angustifolius L.-location of domestication genes and conserved synteny with Medicago truncatula. Theor Appl Genet 113:225–238PubMedGoogle Scholar
  76. Nelson MN, Moolhuijzen PM, Boersma JG et al (2010) Aligning a new reference genetic map of Lupinus angustifolius with the genome sequence of the model legume, Lotus japonicus. DNA Res 17:73–83PubMedCentralPubMedGoogle Scholar
  77. Nicolai M, Pisani C, Bouchet J-P et al (2012) Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum). Genet Mol Res 11:2295–2300PubMedGoogle Scholar
  78. Nielsen R, Paul JS, Albrechtsen A, Song YS (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12:443–451PubMedCentralPubMedGoogle Scholar
  79. Nielsen R, Korneliussen T, Albrechtsen A et al (2012) SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. PLoS One 7:e37558PubMedCentralPubMedGoogle Scholar
  80. Ogbonnaya FC, Subrahmanyam NC, Moullet O et al (2001) Diagnostic DNA markers for cereal cyst nematode resistance in bread wheat. Aust J Agric Res 52:1367–1374Google Scholar
  81. Park C-J, Ronald PC (2012) Cleavage and nuclear localization of the rice XA21 immune receptor. Nat Commun 3:920PubMedCentralPubMedGoogle Scholar
  82. Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556PubMedGoogle Scholar
  83. Pérez-de-Castro AM, Vilanova S, Cañizares J et al (2012) Application of genomic tools in plant breeding. Curr Genomics 13:179–195PubMedCentralPubMedGoogle Scholar
  84. Poland J, Endelman J, Dawson J et al (2012a) Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 5:103–113Google Scholar
  85. Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012b) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253PubMedCentralPubMedGoogle Scholar
  86. Qi J, Liu X, Shen D et al (2013) A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 45:1510–1515PubMedGoogle Scholar
  87. Qi X, Li M-W, Xie M et al (2014) Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun 5:4340PubMedCentralPubMedGoogle Scholar
  88. Ramirez-Gonzalez RH, Segovia V, Bird N et al (2014) RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat. Plant Biotechnol J. doi: 10.1111/pbi.12281 PubMedGoogle Scholar
  89. Rex B, Yu J (2007) Prospects for genome-wide selection for quantitative traits in maize. Crop Sci 47:1082–1090Google Scholar
  90. Ribaut J-M, de Vicente MC, Delannay X (2010) Molecular breeding in developing countries: challenges and perspectives. Curr Opin Plant Biol 13:213–218PubMedGoogle Scholar
  91. Sahu BB, Sumit R, Srivastava SK, Bhattacharyya MK (2012) Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome. BMC Genomics 13:20PubMedCentralPubMedGoogle Scholar
  92. Saintenac C, Jiang D, Wang S, Akhunov E (2013) Sequence-based mapping of the polyploid wheat genome. G3 (Bethesda) 3:1105–1114Google Scholar
  93. Schaeffer LR (2006) Strategy for applying genome-wide selection in dairy cattle. J Anim Breed Genet 123:218–223PubMedGoogle Scholar
  94. Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183PubMedGoogle Scholar
  95. Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115PubMedGoogle Scholar
  96. Shahidul I, Yang H, Yan G (2013) Molecular markers for genetics and plant breeding: the MFLP marker system and its application in narrow-leafed lupin (Lupinus angustifolius). Methods Mol Biol 1069:179–201PubMedGoogle Scholar
  97. Shankar M, Cowling WA, Sweetingham M (1996) The expression of resistance to latent stem infection by Diaporthe toxica in narrow-leafed lupin. Phytopathology 86:692–697Google Scholar
  98. Sharp PJ, Johnston S, Brown G et al (2001) Validation of molecular markers for wheat breeding. Aust J Agric Res 52:1357–1366Google Scholar
  99. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815Google Scholar
  100. The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716Google Scholar
  101. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768Google Scholar
  102. The International Wheat Genome Sequencing Consortium (IWGSC), Mayer KFX, Rogers J et al (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788Google Scholar
  103. Uitdewilligen JG, Wolters A-MA, Bjorn B et al (2013) A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One 8:e62355PubMedCentralPubMedGoogle Scholar
  104. Vales M, Dossmann J, Delgado D, Duque MC (2009) Parallel and interlaced recurrent selection (PAIRS): demonstration of the feasibility of implementing PAIRS to improve complete and partial resistance to blast (Magnaporthe grisea) and some other main traits in rice. Field Crops Res 111:173–178Google Scholar
  105. Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630PubMedGoogle Scholar
  106. Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530PubMedGoogle Scholar
  107. Varshney RK, Chen W, Li Y et al (2012a) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30:83–89Google Scholar
  108. Varshney RK, Ribaut J-M, Buckler ES et al (2012b) Can genomics boost productivity of orphan crops? Nat Biotechnol 30:1172–1176PubMedGoogle Scholar
  109. Varshney RK, Song C, Saxena RK et al (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246PubMedGoogle Scholar
  110. Velasco R, Zharkikh A, Affourtit J et al (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833–839PubMedGoogle Scholar
  111. Wang X, Wang H, Wang J et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039PubMedGoogle Scholar
  112. Wang XQ, Zhao L, Eaton DAR et al (2013) Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing. Mol Ecol Resour 13:938–945PubMedGoogle Scholar
  113. Ward JA, Bhangoo J, Fernández-Fernández F et al (2013) Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 14:2–15PubMedCentralPubMedGoogle Scholar
  114. Williamson PM, Sivasithamparam K, Cowling WA (1991) Formation of subcuticular hyphae by Phomopsis leptostromiformis upon latent infection of narrow-leafed lupins. Plant Dis 75:1023–1025Google Scholar
  115. Willing E-M, Hoffmann M, Klein JD et al (2011) Paired-end RAD-seq for de novo assembly and marker design without available reference. Bioinformatics 27:2187–2193PubMedGoogle Scholar
  116. Wolko B, Weeden NF (1994) Linkage map of isozyme and RAPD markers for the Lupinus angustifolius L. ISA Press, Lisbon, pp 42–49Google Scholar
  117. Xu Y (2010) Molecular plant breeding. CABI, Wallingford, pp 1–755Google Scholar
  118. Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407Google Scholar
  119. Xu X, Pan S, Cheng S et al (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195PubMedGoogle Scholar
  120. Xu Y, Lu Y, Xie C et al (2012) Whole-genome strategies for marker-assisted plant breeding. Mol Breed 29:833–854Google Scholar
  121. Xu Y, Xie C, Wan J et al (2013) Marker-assisted selection in cereals: platforms, strategies and examples. In: Gupta PK, Varshney RK (eds) Cereal genomics II. Springer, Netherlands, pp 375–411Google Scholar
  122. Yagi M, Kosugi S, Hirakawa H et al (2014) Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). DNA Res 21:231–241PubMedCentralPubMedGoogle Scholar
  123. Yang H, Sweetingham MW, Cowling WA, Smith PM (2001) DNA fingerprinting based on microsatellite-anchored fragment length polymorphisms, and isolation of sequence-specific PCR markers in lupin (Lupinus angustifolius L.). Mol Breed 7:203–209Google Scholar
  124. Yang H, Shankar M, Buirchell BJ et al (2002) Development of molecular markers using MFLP linked to a gene conferring resistance to Diaporthe toxica in narrow-leafed lupin (Lupinus angustifolius L.). Theor Appl Genet 105:265–270PubMedGoogle Scholar
  125. Yang H, Boersma JG, You M et al (2004) Development and implementation of a sequence-specific PCR marker linked to a gene conferring resistance to anthracnose disease in narrow-leafed lupin (Lupinus angustifolius L.). Mol Breed 14:145–151Google Scholar
  126. Yang H, Renshaw D, Thomas G et al (2008) A strategy to develop molecular markers applicable to a wide range of crosses for marker assisted selection in plant breeding: a case study on anthracnose disease resistance in lupin (Lupinus angustifolius L.). Mol Breed 21:473–483Google Scholar
  127. Yang H, Lin R, Renshaw D et al (2010) Development of sequence-specific PCR markers associated with a polygenic controlled trait for marker-assisted selection using a modified selective genotyping strategy: a case study on anthracnose disease resistance in white lupin (Lupinus albus L.). Mol Breed 25:239–249Google Scholar
  128. Yang H, Tao Y, Zheng Z et al (2012) Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics 13:318–328PubMedCentralPubMedGoogle Scholar
  129. Yang H, Tao Y, Zheng Z et al (2013a) Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breeding. Theor Appl Genet 126:511–522PubMedGoogle Scholar
  130. Yang H, Tao Y, Zheng Z et al (2013b) Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus angustifolius L. PLoS One 8:e64799PubMedCentralPubMedGoogle Scholar
  131. You M, Boersma JG, Buirchell BJ et al (2005) A PCR-based molecular marker applicable for marker-assisted selection for anthracnose disease resistance in lupin breeding. Cell Mol Biol Lett 10:123–134PubMedGoogle Scholar
  132. Young ND, Debellé F, Oldroyd GED et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520–524PubMedCentralPubMedGoogle Scholar
  133. Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92PubMedGoogle Scholar
  134. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829PubMedCentralPubMedGoogle Scholar
  135. Zhang D, Song H, Cheng H et al (2014) The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress. PLoS Genet 10:e1004061PubMedCentralPubMedGoogle Scholar
  136. Zheng Z, Wang HB, Chen GD, Yan GJ, Liu CJ (2013) A procedure allowing up to eight generations of wheat and nine generations of barley per annum. Euphytica 191:311–316Google Scholar
  137. Zhou L, Chen Z, Lang X et al (2013) Development and validation of a PCR-based functional marker system for the brown planthopper resistance gene Bph14 in rice. Breed Sci 63:347–352PubMedCentralPubMedGoogle Scholar

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© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Department of Agriculture and Food Western AustraliaSouth PerthAustralia
  2. 2.State Agricultural Biotechnology CentreMurdoch UniversityMurdochAustralia
  3. 3.Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life SciencesThe Chinese University of Hong KongShatinHong Kong
  4. 4.Faculty of Sciences and The UWA Institute of Agriculture, School of Plant BiologyThe University of Western AustraliaCrawleyAustralia
  5. 5.BGI-ShenzhenShenzhenChina

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