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Biotechnology Letters

, Volume 36, Issue 3, pp 417–426 | Cite as

From genomics to functional markers in the era of next-generation sequencing

  • R. K. SalgotraEmail author
  • B. B. Gupta
  • C. N. StewartJr.
Review

Abstract

The availability of complete genome sequences, along with other genomic resources for Arabidopsis, rice, pigeon pea, soybean and other crops, has revolutionized our understanding of the genetic make-up of plants. Next-generation DNA sequencing (NGS) has facilitated single nucleotide polymorphism discovery in plants. Functionally-characterized sequences can be identified and functional markers (FMs) for important traits can be developed at an ever-increasing ease. FMs are derived from sequence polymorphisms found in allelic variants of a functional gene. Linkage disequilibrium-based association mapping and homologous recombinants have been developed for identification of “perfect” markers for their use in crop improvement practices. Compared with many other molecular markers, FMs derived from the functionally characterized sequence genes using NGS techniques and their use provide opportunities to develop high-yielding plant genotypes resistant to various stresses at a fast pace.

Keywords

Crop plants Functional markers Genomic selection Next generation DNA sequencing Plant biotechnology, plant breeding, polymorphisms 

Notes

Acknowledgments

R. K. Salgotra is thankful to the Department of Science and Technology (DST) of Government of India for providing BOYSCAST Fellowship to carry out research at Plant Molecular Genetics Laboratory, University of Tennessee, USA.

References

  1. Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishna KV, Singh L (2007) Identification, characterization and utilization of EST-derived genetic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114:359–372PubMedCrossRefGoogle Scholar
  2. Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560PubMedCrossRefGoogle Scholar
  3. Andersen JR, Schrag T, Zein I, Melchinger AE, Lubberstedt T (2005) Functional marker validation of polymorphisms in the maize Dwarf8 gene affecting flowering time in European elite materials. Theor Appl Genet 111:206–217PubMedCrossRefGoogle Scholar
  4. Ayres NM, McClung AM, Larkin PD et al (1997) Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germ plasm. Theor Appl Genet 94:773–781CrossRefGoogle Scholar
  5. Azhaguve P, Saraswathi D, Sharma A, Varshney RK et al (2006) Methodological advancement in molecular markers to delimit the gene(s) for crop improvement. In: Azhaguvel P (ed) Advances in molecular markers for crop improvement. Global Science Books, Isleworthpp, pp 460–469Google Scholar
  6. Bagge M, Xia X, Lubberstedt T (2007) Functional markers in wheat. Curr Opin Plant Biol 10:211–216PubMedCrossRefGoogle Scholar
  7. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Mol Ecology 13:969–980CrossRefGoogle Scholar
  8. Bernatsky R, Tanksley S (1986) Towards a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genet 112:887–898Google Scholar
  9. Bligh HFJ, Till RI, Jones CA (1995) A microsatellite sequence closely linked to the waxy gene of Oryza sativa. Euphytica 86:83–85CrossRefGoogle Scholar
  10. Borevitz JO, Nordborg M (2003) The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiol 132:718–725PubMedCentralPubMedCrossRefGoogle Scholar
  11. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32:314–331PubMedCentralPubMedGoogle Scholar
  12. Brady SM, Provart NJ (2007) Extreme breeding: leveraging genomics for crop improvement. J Sci Food Agric 87:925–929CrossRefGoogle Scholar
  13. Brunner S, Keller B, Feuillet C (2003) A large rearrangement involving genes and low copy DNA interrupts the micro-collinearity between rice and barley at the Rph7 locus. Genet 164:673–683Google Scholar
  14. Chen T, Meng-xiang T, Zhang Y, Zhen Z, Zhao L, Zhao Q, Lin J, Zhou L, Wang C (2010) Development of simple functional markers for low glutelin content gene 1 (Lgc1) in rice (Oryza sativa). Rice Sci 17:173–178CrossRefGoogle Scholar
  15. Chu Z, Yuan M, Yao J et al (2007) Promoter mutations of an essential gene for pollen development result in disease resistance in rice. Genes Dev 20:1250–1255CrossRefGoogle Scholar
  16. Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans Royal Soc B: Biol Sci 363:557–572CrossRefGoogle Scholar
  17. Comai L, Young K, Till BJ et al (2004) Efficient discovery of DNA polymorphisms in natural populations by Eco-tilling. Plant J 37:778–786PubMedCrossRefGoogle Scholar
  18. Deschamp S, Llaca V, May GD (2012) Genotyping-by-sequencing in plants. Biology 1:460–483CrossRefGoogle Scholar
  19. Desmarais E, Lanneluc I, Lagnel J (1998) Direct amplification of length polymorphisms (DALP), or how to get and characterize new genetic markers in many species. Nucleic Acids Res 26:1458–1465PubMedCentralPubMedCrossRefGoogle Scholar
  20. Doebley J, Stec A, Gustus C (1995) Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141:333–346PubMedCentralPubMedGoogle Scholar
  21. Dubcovsky J (2004) Marker-assisted selection in public breeding programs: the wheat experience. Crop Sci 44:1895–1898CrossRefGoogle Scholar
  22. Dunford RP, Yano M, Kurata N, Sasaki T, Huestis G, Rocheford T, Laurie DA (2002) Comparative mapping of the barley Phd-H1 photoperiod response gene region, which lies close to a junction between two rice linkage segments. Genetics 161:825–834PubMedCentralPubMedGoogle Scholar
  23. Flint-Garcia M, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374PubMedCrossRefGoogle Scholar
  24. Francia E, Tacconi G, Crosatti C et al (2005) Marker assisted selection in crop plants. Plant Cell, Tissue Organ Cult 82:317–342CrossRefGoogle Scholar
  25. Frazier R (2004) Capillary electrophoresis in food analysis. Labtech, Business Briefing, pp 42–45Google Scholar
  26. Frisch M (2005) Optimum design of marker-assisted backcross programs. In: Loerz H, Wenzel G (eds) Biotechnology in agriculture and forestry, vol 55. Springer, Berlin, pp 319–334Google Scholar
  27. Frisch M, Bohn M, Melchinger TE (1999) Minimum sample size and optimal positioning of flanking markers in marker-assisted backcrossing for transfer of a target gene. Crop Sci 39:967–975CrossRefGoogle Scholar
  28. Gale KR (2005) Diagnostic DNA markers for quality traits in wheat. J Cereal Sci 41:181–192CrossRefGoogle Scholar
  29. Geng H, Xia X, Zhang L, Qu Y, He Z (2012) Development of functional markers for lipoxygenase gene Talox-B1 on chromosome 4 BS in common wheat. Crop Sci 52:568–576CrossRefGoogle Scholar
  30. Graner A, Jahoor A, Schondelmaier J, Siedler H et al (1991) Construction of an RFLP map of barley. Theor Appl Genet 83:250–256PubMedCrossRefGoogle Scholar
  31. Gupta PK, Rustgi S (2004) Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomics 4:139–162PubMedCrossRefGoogle Scholar
  32. Gupta PK, Varshney RK (2004) Cereal genomics: an overview. In: Gupta PK, Varshney RK (eds) Cereal genomics. Kluwer Academic Press, Dordrecht, pp 639–650Google Scholar
  33. Gupta PK, Varshney RK, Sharma PC, Ramesh B (1999) Molecular markers and their application in wheat breeding. Plant Breed 118:369–390CrossRefGoogle Scholar
  34. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485PubMedCrossRefGoogle Scholar
  35. Hausner G, Rashid KY, Kenaschuk EO, Procunier JD (1999) The development of codominant PCR/RFLP based markers for the flax rust resistance alleles at the L locus. Genome 42:1–8CrossRefGoogle Scholar
  36. Hayashi K, Yasuda N, Fujita Y, Koizumi S, Yoshida H (2010) Identification of the blast resistance gene Pit in rice cultivars using functional markers. Theor Appl Genet 121:1357–1367PubMedCrossRefGoogle Scholar
  37. Hazen SP, Kay SA (2003) Gene arrays are not just for measuring gene expression. Trends Plant Sci 8:413–416PubMedCrossRefGoogle Scholar
  38. Hodgkin T, Roviglioni R, De Vicente MC, Dudnik N (2001) Molecular methods in the conservation and use of plant genetic resources. Acta Horticult 546:107–118Google Scholar
  39. Ikeda A, Ueguchi-Tanaka M, Sonoda Y et al (2001) Slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8. Plant Cell 13:999–1010PubMedCentralPubMedCrossRefGoogle Scholar
  40. Ingvardsen CR, Schejbel B, Lubberstedt T (2008) Functional markers in resistance breeding. In: Luttge U, Beyschlag W, Murata J (eds) Progress in Botany. Springer, Berlin, pp 61–87CrossRefGoogle Scholar
  41. Iyer AS, McCouch SR (2004) The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol Plant Microbe Interact 17:1348–1354PubMedCrossRefGoogle Scholar
  42. Iyer AS, McCouch SR (2007) Functional markers for xa5 mediated resistance in rice (Oryza sativa L.). Mol Breed 19:291–296CrossRefGoogle Scholar
  43. Kaisoon O, Siriamornpun S, Meeso N (2008) Distinction between cereal genotypes based on the protein and DNA composition of the grain by capillary electrophoresis. World Applied Sci J 4:384–395Google Scholar
  44. Kole C, Quijada P, Michaels SD, Amasino RM, Osborn TC (2001) Evidence for homology of flowering-time genes VFR2 from Brassica rapa and FLC from Arabidopsis thaliana. Theor Appl Genet 102:425–430CrossRefGoogle Scholar
  45. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410PubMedCrossRefGoogle Scholar
  46. Lubberstedt T, Zein I, Andersen J, Wenzel G, Krutzfeldt B, Eder J, Ouzunova M, Chun S (2005) Development and application of functional markers in maize. Euphytica 146:101–108CrossRefGoogle Scholar
  47. Madsen LH, Collins NC, Rakwalska M et al (2003) Barley disease resistance gene analogs of the NBSLRR class: identification and mapping. Mol Genet Genomics 269:150–161PubMedGoogle Scholar
  48. McKay JR, Latta RG (2002) Adaptive divergence population: markers, QTLs and traits. Trends Ecol Evol 17:285–291CrossRefGoogle Scholar
  49. Mejlhede N, Kyjovska Z, Backes G, Burhenne K, Rasmussen SK, Jahoor A (2006) EcoTILLING for the identification of allelic variation in the powdery mildew resistance genes mlo and Mla in barley. Plant Breed 125:461–467CrossRefGoogle Scholar
  50. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829PubMedCentralPubMedGoogle Scholar
  51. Michalek W, Kunzel G, Graner A (1999) Sequence analysis and gene identification in a set of mapped RFLP markers in barley (Hordeum vulgare). Genome 42:849–853PubMedCrossRefGoogle Scholar
  52. Nesbitt TC, Tanksley SD (2002) Comparative sequencing in the genus Lycopersicon. Implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 162:365–379PubMedCentralPubMedGoogle Scholar
  53. Paran I, Michelmore RW (1993) Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet 85:985–993PubMedCrossRefGoogle Scholar
  54. Perumalsamy S, Bharani M, Sudha M et al (2010) Functional marker-assisted selection for bacterial leaf blight resistance genes in rice (Oryza sativa L.). Plant Breed 129:400–406Google Scholar
  55. Powell W, Machray G, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222CrossRefGoogle Scholar
  56. Salgotra RK, Millwood RJ, Agarwal S, Stewart CN Jr (2011) High-throughput functional marker assay for detection of Xa/xa and fgr genes in rice (Oryza sativa L.). Electrophoresis 32:2216–2222PubMedCrossRefGoogle Scholar
  57. Schmutz J, Steven B, Cannon Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183PubMedCrossRefGoogle Scholar
  58. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145PubMedCrossRefGoogle Scholar
  59. Shi W, Yang Y, Chen S, Xu M (2008) Discovery of a new fragrance allele and the development of functional markers for the breeding of fragrant rice varieties. Mol Breed 22:185–192CrossRefGoogle Scholar
  60. Singh KB, Foley RC, Sánchez LO (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5:430–436PubMedCrossRefGoogle Scholar
  61. Song WY, Pi LY, Wang GL, Gardner J, Holsten T, Ronald PC (1997) Evolution of the rice Xa21 disease resistance gene family. Plant Cell 9:1279–1287PubMedCentralPubMedCrossRefGoogle Scholar
  62. Sundaram RM, Vishnupriya MR, Biradar SK et al (2008) Marker-assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite indica rice variety. Euphytica 80:411–422CrossRefGoogle Scholar
  63. Syvanen AC (2001) Accessing genetic variation: genotyping SNPs. Nat Rev Genet 2:930–941PubMedCrossRefGoogle Scholar
  64. Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066PubMedCrossRefGoogle Scholar
  65. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  66. The Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566–1569CrossRefGoogle Scholar
  67. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler IVES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289PubMedCrossRefGoogle Scholar
  68. Tommasini L, Yahiaoui N, Srichumpa P, Keller B (2006) Development of functional markers specific for seven Pm3 resistance alleles and their validation in the bread wheat gene pool. Theor Appl Genet 114:165–175PubMedCrossRefGoogle Scholar
  69. Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630PubMedCrossRefGoogle Scholar
  70. Varshney RK, Mahendar T, Aggarwal RK, Borner A (2007) Genetic molecular markers in plants: development and applications. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement: genomics approaches and platforms. Springer, Berlin, pp 13–29CrossRefGoogle Scholar
  71. Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCentralPubMedCrossRefGoogle Scholar
  72. Wang DG, Fan JB, Siao CJ et al (1998) Large-scale identification, mapping and genotyping of single nucleotide polymorphisms in the human genome. Science 280:1077–1082PubMedCrossRefGoogle Scholar
  73. Williams J, Kubelik A, Livak K et al (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedCentralPubMedCrossRefGoogle Scholar
  74. Xu Y (2003) Developing marker-assisted selection strategies for breeding hybrid rice. Plant Breed Rev 23:73–174Google Scholar
  75. Xu Y, McCouch SR, Zhang Q (2005) How can we use genomics to improve cereals with rice as a reference genome? Plant Mol Biol 59:7–26PubMedCrossRefGoogle Scholar
  76. Yeam I, Kang BC, Lindeman W et al (2005) Allele specific CAPS markers based on point mutations in resistance alleles at the pvr1 locus encoding eIF4E in Capsicum sp. Theor Appl Genet 112:178–186PubMedCrossRefGoogle Scholar
  77. Young ND, Debellé F, Oldroyd GE et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520–524PubMedCentralPubMedCrossRefGoogle Scholar
  78. Zhao XL, Ma EW, Gale EKR et al (2007) Identification of SNPs and development of functional markers for LMW-GS genes at Glu-D3 and Glu-B3 loci in bread wheat (Triticum aestivum L.). Mol Breed 20:223–231CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • R. K. Salgotra
    • 1
    Email author
  • B. B. Gupta
    • 1
  • C. N. StewartJr.
    • 2
  1. 1.Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, ChathaJammuIndia
  2. 2.Plant Molecular Genetics, Department of Plant SciencesUniversity of TennesseeKnoxvilleUSA

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