Impact of Bioinformatics on Plant Science Research and Crop Improvement

  • Amrina Shafi
  • Insha Zahoor
  • Ehtishamul Haq
  • Khalid Majid Fazili


Bioinformatics plays an indispensable role and has a number of applications in today’s plant and crop science. Powerful tools and methods are required to organize the huge data and extend our ability to analyse complex biological systems. At the same time, many researchers in plant biology are unacquainted with available bioinformatics methods, tools and databases, which could lead to unexploited opportunities or misinterpretation of the information. Omics has allowed us to come to terms with vast amounts of biological data being generated by sequencing projects and has made considerable progress in plant breeding by providing scientists and breeders access to genomic information. In plant biology, these omics tools (proteomics, genomics, transcriptomics) are helpful in improving the quality of traditional medicinal plants; improving crop nutrition quality, single gene analysis, sequence similarity, modelling of protein, crop breeding and insect resistance; improving nutritional quality; and development of drought-resistant varieties. Thus, plant genomics has assisted in the efficient exploitation of plants as biological resources. Further, the progress made in molecular plant breeding, genetics, genomic selection and genome editing has contributed to a more comprehensive understanding of molecular markers, provided deeper insights into the diversity available for crops and greatly complemented breeding stratagems. In this chapter, we describe the main bioinformatics approaches in the area of next-generation sequencing (NGS) for its impact on crop improvement and breeding programmes. We also cover some molecular and genetic marker databases, which find its application in breeding programmes. Finally, we explore a few emerging research topics in this innovative field of research.


Agricultural bioinformatics Omics technologies Crop improvement Crop breeding Fruit breeding Molecular markers Genetic markers 


  1. Ahmad P, Ashraf M, Younis M, Hu X, Kumar A, Akram NA, Al-Qurainy F (2011) Role of transgenic plants in agriculture and biopharming. Biotechnol Adv 30:525–540Google Scholar
  2. Al-Khayri JM, Jain SM, Johnson DV (2015) Advances in plant breeding strategies: breeding, biotechnology and molecular tools. Springer International PublishingGoogle Scholar
  3. Ansorge WJ (2009) Next-generation DNA sequencing techniques. Nat Biotechnol 25:195–203Google Scholar
  4. Barh D, Zambare V, Azevedo V (2013) Omics: applications in biomedical, agricultural, and environmental sciences. CRC PressGoogle Scholar
  5. Batley J, Edwards D (2016) The application of genomics and bioinformatics to accelerate crop improvement in a changing climate. Curr Opin Plant Biol 30:78–81CrossRefPubMedGoogle Scholar
  6. Bennetzen JL et al (1998) A plant genome initiative. Plant Cell 10:488–493CrossRefPubMedCentralGoogle Scholar
  7. Bernardo AN, Bradbury PJ, Ma H, Hu S, Bowden RL, Buckler ES et al (2009) Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays. BMC Genomics 10:251CrossRefPubMedPubMedCentralGoogle Scholar
  8. Blenda A, Scheffl er J, Scheffl er B, Palmer M, Lacape JM et al (2006) CMD: a cotton microsatellite database resource for Gossypium genomics. BMC Genomics 7:132CrossRefPubMedPubMedCentralGoogle Scholar
  9. Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S et al (2011) The sol genomics network (solgenomics.Net): growing tomatoes using Perl. Nucleic Acids Res 39:D1149–D1155CrossRefPubMedGoogle Scholar
  10. Brown M, Funk CC (2008) Climate. Food security under climate change. Science 319:580–581CrossRefPubMedGoogle Scholar
  11. Canaran P, Stein L, Ware D (2006) LookAlign: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics 22:885–886CrossRefPubMedGoogle Scholar
  12. Carollo V, Matthews DE, Lazo GR, Blake TK, Hummel DD, Lui N et al (2005) Grain genes 2.0. An improved resource for the smallgrains community. Plant Physiol 139:643–651CrossRefPubMedPubMedCentralGoogle Scholar
  13. Cogburn LA, Porter TE, Duclos MJ, Simon J, Burgess SC, Zhu JJ et al (2007) Functional genomics of the chicken-a model organism. Poult Sci 86:2059–2094CrossRefPubMedGoogle Scholar
  14. Cory JS, Hoover K (2006) Plant-mediated effects in insect-pathogen interactions. Trends Ecol Evol 21:278–286CrossRefPubMedGoogle Scholar
  15. De Bodt S, Maere S, Van de Peer Y (2005) Genome duplication and the origin of angiosperms. Trends Ecol Evol 20:591–597CrossRefPubMedGoogle Scholar
  16. De Filippis LF (2012) Breeding for biotic stress tolerance in plants. In: Asharaf M, Ozturk M, Ahmad MSA, Aksoy A (eds) Crop production for agricultural improvement. Springer ScienceGoogle Scholar
  17. Deckers J, Hospital F (2002) The use of molecular genetics in the improvement of agricultural populations. Nat Rev Genet 3:22–32CrossRefGoogle Scholar
  18. Dwivedi SL, Scheben A, Edwards D, Spillane C, Ortiz R (2017) Assessing and exploiting functional diversity in germplasm pools to enhance abiotic stress adaptation and yield in cereals and food legumes. Front Plant Sci 8:1461Google Scholar
  19. Ellegren H (2014) Genome sequencing and population genomics in nonmodel organisms. Trends Ecol Evol 29(1):51–63CrossRefPubMedGoogle Scholar
  20. Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV, McCouch SR (2011) Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet 7(8):e1002221CrossRefPubMedPubMedCentralGoogle Scholar
  21. Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res 14:1812–1819CrossRefPubMedPubMedCentralGoogle Scholar
  22. Futamura N, Totoki Y, Toyoda A, Igasaki T, Nanjo T, Seki M et al (2008) Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili. BMC Genomics 9:383CrossRefPubMedPubMedCentralGoogle Scholar
  23. Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int 20(15):431–487Google Scholar
  24. Grant D, Nelson RT, Cannon SB, Shoemaker RC (2010) SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res 38:D843–D846CrossRefPubMedGoogle Scholar
  25. Haas BJ, Delcher AL, Wortman JR, Salzberg SL (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20:3643–3646CrossRefPubMedPubMedCentralGoogle Scholar
  26. Hakeem K, Ozturk M, Memon AR (2012) Biotechnology as an aid for crop improvement to overcome food shortage. In: Ashraf M et al (eds) Crop production for agricultural improvement. SpringerGoogle Scholar
  27. Hakeem KR, Tombuloğlu H, Tombuloğlu G (2016) Plant omics: trends and applications. Springer International Publishing, pp 109–136Google Scholar
  28. Han B, Xue Y (2003) Genome-wide intraspecific DNA-sequence variations in rice. Curr Opin Plant Biol 6:134–138CrossRefPubMedGoogle Scholar
  29. Heesacker A, Kishore VK, Gao W, Tang S, Kolkman JM, Gingle A et al (2008) SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility. Theor Appl Genet 117:1021–1029CrossRefPubMedGoogle Scholar
  30. Hori K, Sato K, Takeda K (2007) Detection of seed dormancy QTL in multiple mapping populations derived from crosses involving novel barley germplasm. Theor Appl Genet 115:869–876CrossRefPubMedGoogle Scholar
  31. Hospital F, Bouchez A, Lecomete L, Causse M, Charcosset A (2002) Use of markers in plant breeding: lessons from genotype building experiments. 7th WCGALP, Montpellier, pp 22–25Google Scholar
  32. Hu H, Scheben A, Edwards D (2018) Advances in integrating genomics and bioinformatics in the plant breeding pipeline. Agriculture 8(6):75CrossRefGoogle Scholar
  33. Huang M (2015) In Biogpu: a high performance computing tool for genome-wide association studies, Plant and Animal Genome XXIII conference, Plant and Animal GenomeGoogle Scholar
  34. Hwang EY, Song Q, Jia G, Specht JE, Hyten DL, Costa J, Cregan PB (2014) A genome-wide association study of seed protein and oil content in soybean. BMC Genomics 15(1):1CrossRefPubMedPubMedCentralGoogle Scholar
  35. Hyten DL, Song Q, Choi IY, Yoon MS, Specht JE, Matukumalli LK et al (2008) High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet 116:945–952CrossRefPubMedGoogle Scholar
  36. Jayashree B, Buhariwalla HK, Shinde S, Crouch JH (2005) A legume genomics resource: the chickpea root expressed sequence tag database. Electron J Biotechnol 8:128–133CrossRefGoogle Scholar
  37. Kaul S, Koo HL, Jenkins J, Rizzo M, Rooney T et al (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796–815CrossRefGoogle Scholar
  38. Kingsbury N (2009) Hybrid: the history and science of plant breeding. University of Chicago PressGoogle Scholar
  39. Kobayashi M (2015) In heap: a SNPs detection tool for NGS data with special reference to GWAS and genomic prediction, Plant and Animal Genome XXIII conference, Plant and Animal GenomeGoogle Scholar
  40. Kozlov AM, Aberer AJ, Stamatakis A (2015) ExaML version 3: a tool for phylogenomic analyses on supercomputers. Bioinformatics 31(15):2577–2579CrossRefPubMedPubMedCentralGoogle Scholar
  41. Kumar S (2016) Crop breeding: bioinformatics and preparing for climate change. Apple Academic PressGoogle Scholar
  42. Kumar S, Garrick DJ, Bink MC, Whitworth C, Chagné D, Volz RK (2013) Novel genomic approaches unravel genetic architecture of complex traits in apple. BMC Genomics 14(1):393CrossRefPubMedPubMedCentralGoogle Scholar
  43. Lawrence CJ, Schaeffer ML, Seigfried TE, Campbell DA, Harper LC (2007) MaizeGDB’s new data types, resources and activities. Nucleic Acids Res 35:D895–D900CrossRefPubMedPubMedCentralGoogle Scholar
  44. Li H, Peng Z, Yang X, Wang W, Fu J, Wang J, Han Y, Chai Y, Guo T, Yang N (2013) Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet 45(1):43–50CrossRefGoogle Scholar
  45. Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T et al (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res 36:D947–D953CrossRefPubMedGoogle Scholar
  46. Lorenz AJ, Chao S, Asoro FG, Heffner EL, Hayashi T et al (2011) Genomic selection in plant breeding: knowledge and prospects. Adv Agron 110:77–123CrossRefGoogle Scholar
  47. Malav AK, Indu, Chandrawat KS (2016) Gene pyramiding: an overview. Int J Curr Res Biosci Plant Biol 3(7):22–28CrossRefGoogle Scholar
  48. Matsumoto T, Wu JZ, Kanamori H, Katayose Y, Fujisawa M et al (2005) The map-based sequence of the rice genome. Nature 436(7052):793–800CrossRefGoogle Scholar
  49. Meyer K, Mewes HW (2002) How can we deliver the large plant genomes? Strategies and perspectives. Curr Opin Plant Biol 5:173–177CrossRefGoogle Scholar
  50. Mochida K, Shinozaki K (2010) Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol 51:497–523CrossRefPubMedPubMedCentralGoogle Scholar
  51. Mochida K, Saisho D, Yoshida T, Sakurai T, Shinozaki K (2008) TriMEDB: a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae. BMC Plant Biol 8:72CrossRefPubMedPubMedCentralGoogle Scholar
  52. Morrell PL, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nat Rev Genet 13(2):85–96CrossRefGoogle Scholar
  53. Mousavi-Derazmahalleh M, Bayer PE, Hane JK, Babu V, Nguyen HT et al (2018) Adapting legume crops to climate change using genomic approaches. Plant Cell Environ 42(1):6–19CrossRefPubMedPubMedCentralGoogle Scholar
  54. Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21(8):2194–2202CrossRefPubMedPubMedCentralGoogle Scholar
  55. Organization EPS (2005) European plant science: a field of opportunities. J Exp Bot 56(417):1699–1709CrossRefGoogle Scholar
  56. Ozturk M (2010) Agricultural residues and their role in bioenergy production. Proceedings-second consultation AgroResidues-Second expert consultation ‘The utilization of agricultural residues with special emphasis on utilization of agricultural residues as biofuel’, pp 31–43Google Scholar
  57. Pandey SP, Somssich IE (2009) The role of WRKY transcription factors in plant immunity. Plant Physiol 150:1648–1655CrossRefPubMedPubMedCentralGoogle Scholar
  58. Paterson AH (2008) Genomics of sorghum. Int J Plant Genomics 200:362–451Google Scholar
  59. Plechakova O, Tranchant-Dubreuil C, Benedet F, Couderc M, Tinaut A et al (2009) MoccaDB – an integrative database for functional, comparative and diversity studies in the Rubiaceae family. BMC Plant Biol 9:123CrossRefPubMedPubMedCentralGoogle Scholar
  60. Robinson AJ, Love CG, Batley J, Barker G, Edwards D (2004) Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics 20:1475–1476CrossRefPubMedGoogle Scholar
  61. Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudie S, Morris J et al (2005) Single-feature polymorphism discovery in the barley transcriptome. Genome Biol 6:R54CrossRefPubMedPubMedCentralGoogle Scholar
  62. Schenk PM, Carvalhais LC, Kazan K (2012) Unraveling plant-microbe interactions: can multispecies transcriptomics help? Trends Biotechnol 30:177–184CrossRefPubMedGoogle Scholar
  63. Schlueter SD, Dong Q, Brendel V (2003) GeneSeqer@PlantGDB: gene structure prediction. Nucleic Acids Res 32:D354–D359Google Scholar
  64. Schuster SC (2007) Next-generation sequencing transforms today’s biology. Nature 200(8):16–18Google Scholar
  65. Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY et al (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135:1198–1205CrossRefPubMedPubMedCentralGoogle Scholar
  66. Skuse GR, Du C (2008) Bioinformatics tools for plant genomics. Int J Plant Genomics 2008:910474CrossRefPubMedGoogle Scholar
  67. Sleper DA, Poehlman JM (2006) Breeding field crops. Blackwell Publishing, Oxford, p 424Google Scholar
  68. Stanford WL, Cohn JB, Cordes SP (2001) Gene-trap mutagenesis: past, present and beyond. Nat Rev Genet 2:756–768CrossRefPubMedGoogle Scholar
  69. Steinbach D (2015) In GnpIS-Asso: a generic database for managing and exploiting plant genetic association studies results using high throughput genotyping and phenotyping data, Plant and Animal Genome XXIII conference, Plant and Animal GenomeGoogle Scholar
  70. Takeda S, Matsuoka M (2008) Genetic approaches to crop improvement: responding to environmental and population changes. Nat Rev Genet 9:444–457CrossRefPubMedGoogle Scholar
  71. Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327:818–822CrossRefPubMedPubMedCentralGoogle Scholar
  72. Van Emon JM (2016) The omics revolution in agricultural research. J Agric Food Chem 64(1):36–44CrossRefPubMedGoogle Scholar
  73. Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630CrossRefPubMedGoogle Scholar
  74. Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530CrossRefPubMedGoogle Scholar
  75. Walsh B (2001) Quantitative genetics in the age of genomics. Theor Popul Biol 59:175–184CrossRefPubMedGoogle Scholar
  76. Wang J (2015) In A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies and its application on soybean oil/protein traits, Plant and Animal Genome XXIII conference, Plant and Animal Genome. p 159–162Google Scholar
  77. Wenzl P, Raman H, Wang J, Zhou M, Huttner E, Kilian A (2007) A DArT platform for quantitative bulked segregant analysis. BMC Genomics 8:196CrossRefPubMedPubMedCentralGoogle Scholar
  78. Ye X, Al-Babili S, Klöti A et al (2000) Engineering the provitamin A (β-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science 287(5451):303–305CrossRefGoogle Scholar
  79. Zhang Z, Ober U, Erbe M, Zhang H, Gao N, He J, Li J, Simianer H (2014) Improving the accuracy of whole genome prediction for complex traits using the results of genome wide association studies. PLoS One 9(3):e93017CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Amrina Shafi
    • 1
  • Insha Zahoor
    • 2
  • Ehtishamul Haq
    • 1
  • Khalid Majid Fazili
    • 1
    • 2
  1. 1.Department of Biotechnology, School of Biological SciencesUniversity of KashmirSrinagarIndia
  2. 2.Bioinformatics CentreUniversity of KashmirSrinagarIndia

Personalised recommendations