Skip to main content
SpringerLink
Log in

Next-Generation Sequencing Technologies: Approaches and Applications for Crop Improvement

  • Protocol
  • First Online:
Genomics of Cereal Crops

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

The persistent efforts toward attaining food security and balanced nutrition are challenged by the deteriorating natural resources, aberrant climate changes, and increase in population, hence calling for the utilization of innovative technologies to overcome the constraints of crop production. Crop improvement through multifaceted approaches that combine conventional and genomic technologies is necessary for developing biotic and abiotic stress-tolerant varieties with high yield and desirable nutritional quality. A detailed understanding of complex plant genome and genetic diversity is necessary to meet these challenges. Before 2004, genome sequencing was mostly dependent on Sanger sequencing technology, which though accurate was not high-throughput. The successful sequencing of Arabidopsis and rice genomes encouraged the sequencing of many other crop and model plants. Since then, sequencing technologies, accompanied by application of high-power computer technology have evolved at an astounding pace and developed into more advanced, innovative, and competitive next-generation sequencing (NGS) and Next-NGS technologies. The NGS technologies are low cost, rapid, and high-throughput. The advancement of NGS and Next-NGS technologies combined with automated phenotyping techniques have accelerated the crop improvement process. NGS technology enables the generation of reference genomes and re-sequencing of related species to understand the genetic diversity, transcriptome sequencing that provides insight into complex gene networks, metagenomics, as well as high-throughput genotyping methods like genotyping by sequencing (GBS) and QTL mapping which have been successfully used in crop improvement programs.

In the present chapter, we briefly describe different generations of sequencing technologies, the current status of advanced NGS technologies, and their application in crop improvement including de novo nuclear/organellar genome assembly, re-sequencing, functional genomics, epigenetics, and marker development for introgression of important agronomic traits, population genetics, evolutionary biology, and pan-genomics.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737–738. https://doi.org/10.1038/171737a0

    Article  CAS  PubMed  Google Scholar 

  2. Holley RW, Everett GA, Madison JT, Zamir A (1965) Nucleotide sequences in the yeast alanine transfer ribonucleic acid. J Biol Chem 240:2122–2128

    Article  CAS  Google Scholar 

  3. Fiers W, Contreras R, Duerinck F et al (1976) Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature 260:500–507. https://doi.org/10.1038/260500a0

    Article  CAS  PubMed  Google Scholar 

  4. Padmanabhan R, Padmanabhan R, Wu R (1972) Nucleotide sequence analysis of DNA: IX. Use of oligonucleotides of defined sequence as primers in DNA sequence analysis. Biochem Biophys Res Commun 48:1295–1302. https://doi.org/10.1016/0006-291X(72)90852-2

    Article  CAS  PubMed  Google Scholar 

  5. Wu R (1972) Nucleotide sequence analysis of DNA. Nat New Biol 236:198–200. https://doi.org/10.1038/newbio236198a0

    Article  CAS  PubMed  Google Scholar 

  6. Wu R, Kaiser AD (1968) Structure and base sequence in the cohesive ends of bacteriophage lambda DNA. J Mol Biol 35:523–537. https://doi.org/10.1016/S0022-2836(68)80012-9

    Article  CAS  PubMed  Google Scholar 

  7. Gilbert W, Maxam A (1973) The nucleotide sequence of the lac operator. Proc Natl Acad Sci U S A 70:3581–3584. https://doi.org/10.1073/pnas.70.12.3581

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Bernreiter A (2017) Molecular diagnostics to identify fungal plant pathogens – a review of current methods. Rev Científica Ecuatoriana 4:26–35

    Google Scholar 

  9. Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci U S A 74:560–564. https://doi.org/10.1073/pnas.74.2.560

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467. https://doi.org/10.1073/pnas.74.12.5463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Sanger F, Coulson AR, Hong GF et al (1982) Nucleotide sequence of bacteriophage lambda DNA. J Mol Biol 162:729–773

    Article  CAS  Google Scholar 

  12. Smith LM, Sanders JZ, Kaiser RJ et al (1986) Fluorescence detection in automated DNA sequence analysis. Nature 321:674–679. https://doi.org/10.1038/321674a0

    Article  CAS  PubMed  Google Scholar 

  13. Hood LE, Hunkapiller MW, Smith LM (1987) Automated DNA sequencing and analysis of the human genome. Genomics 1:201–212. https://doi.org/10.1016/0888-7543(87)90046-2

    Article  CAS  PubMed  Google Scholar 

  14. Hunkapiller T, Kaiser RJ, Koop BF, Hood L (1991) Large-scale and automated DNA sequence determination. Science 254:59–67. https://doi.org/10.1126/science.1925562

    Article  CAS  PubMed  Google Scholar 

  15. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815. https://doi.org/10.1038/35048692

    Article  Google Scholar 

  16. Craig Venter J, Adams MD, Myers EW et al (2001) The sequence of the human genome. Science 291:1304–1351. https://doi.org/10.1126/science.1058040

    Article  Google Scholar 

  17. Matsumoto T, Wu J, Kanamori H et al (2005) The map-based sequence of the rice genome. Nature 436:793–800. https://doi.org/10.1038/nature03895

    Article  CAS  Google Scholar 

  18. Shendure J (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145. https://doi.org/10.1038/nbt1486

    Article  CAS  PubMed  Google Scholar 

  19. Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380. https://doi.org/10.1038/nature03959

    Article  PubMed  PubMed Central  Google Scholar 

  20. Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351. https://doi.org/10.1038/nrg.2016.49

    Article  CAS  PubMed  Google Scholar 

  21. Levene MJ, Korlach J, Turner SW et al (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299:682–686. https://doi.org/10.1126/science.1079700

    Article  CAS  PubMed  Google Scholar 

  22. Haque F, Li J, Wu H-C et al (2013) Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA. Nano Today 8:56–74. https://doi.org/10.1016/j.nantod.2012.12.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Jain M, Koren S, Miga KH et al (2018) Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol 36:338–345. https://doi.org/10.1038/nbt.4060

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Heather JM, Chain B (2016) The sequence of sequencers: the history of sequencing DNA. Genomics 107:1–8. https://doi.org/10.1016/j.ygeno.2015.11.003

    Article  CAS  PubMed  Google Scholar 

  25. Shendure J, Balasubramanian S, Church GM et al (2017) DNA sequencing at 40: past, present and future. Nature 550:345. https://doi.org/10.1038/nature24286

    Article  CAS  PubMed  Google Scholar 

  26. Kchouk M, Gibrat JF, Elloumi M (2017) Generations of sequencing technologies: from first to next generation. Biol Med 9:1. https://doi.org/10.4172/0974-8369.1000395

    Article  CAS  Google Scholar 

  27. Sanger F (1959) Chemistry of insulin. Science 129:1340–1344. https://doi.org/10.1126/science.129.3359.1340

    Article  CAS  PubMed  Google Scholar 

  28. Sanger F, Coulson AR (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94:441–448. https://doi.org/10.1016/0022-2836(75)90213-2

    Article  CAS  PubMed  Google Scholar 

  29. Sanger F, Air GM, Barrell BG et al (1977) Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265:687–695. https://doi.org/10.1038/265687a0

    Article  CAS  PubMed  Google Scholar 

  30. Mullis KB, Faloona FA (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 155:335–350. https://doi.org/10.1016/0076-6879(87)55023-6

    Article  CAS  PubMed  Google Scholar 

  31. Hyman ED (1988) A new method of sequencing DNA. Anal Biochem 174:423–436. https://doi.org/10.1016/0003-2697(88)90041-3

    Article  CAS  PubMed  Google Scholar 

  32. Edwards A, Voss H, Rice P et al (1990) Automated DNA sequencing of the human HPRT locus. Genomics 6:593–608. https://doi.org/10.1016/0888-7543(90)90493-E

    Article  CAS  PubMed  Google Scholar 

  33. Ronaghi M, Karamohamed S, Pettersson B et al (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242:84–89. https://doi.org/10.1006/abio.1996.0432

    Article  CAS  PubMed  Google Scholar 

  34. Mitra RD, Church GM (1999) In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res 27:e34. https://doi.org/10.1093/nar/27.24.e34

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Dressman D, Yan H, Traverso G et al (2003) Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci 100:8817–8822. https://doi.org/10.1073/pnas.1133470100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Shendure J, Porreca GJ, Reppas NB et al (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–1732. https://doi.org/10.1126/science.1117389

    Article  CAS  PubMed  Google Scholar 

  37. Seo TS, Bai X, Kim DH et al (2005) Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides. Proc Natl Acad Sci 102:5926–5931. https://doi.org/10.1073/pnas.0501965102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Ruparel H, Bi L, Li Z et al (2005) Design and synthesis of a 3′-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. Proc Natl Acad Sci 102:5932–5937. https://doi.org/10.1073/pnas.0501962102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Flusberg BA, Webster DR, Lee JH et al (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 7:461–465. https://doi.org/10.1038/nmeth.1459

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Huang S, He J, Chang S et al (2010) Identifying single bases in a DNA oligomer with electron tunnelling. Nat Nanotechnol 5:868–873. https://doi.org/10.1038/nnano.2010.213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Rothberg JM, Hinz W, Rearick TM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352. https://doi.org/10.1038/nature10242

    Article  CAS  PubMed  Google Scholar 

  42. Chidgeavadze ZG, Beabealashvilli RS, Atrazhev AM et al (1984) 2′,3′-Dideoxy-3′ aminonucleoside 5′-triphosphates are the terminators of DNA synthesis catalyzed by DNA polymerases. Nucleic Acids Res 12:1671–1686. https://doi.org/10.1093/nar/12.3.1671

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Prober JM, Trainor GL, Dam RJ et al (1987) A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 238:336–341. https://doi.org/10.1126/science.2443975

    Article  CAS  PubMed  Google Scholar 

  44. Zhang J, Fang Y, Hou JY et al (1995) Use of non-cross-linked polyacrylamide for four-color DNA sequencing by capillary electrophoresis separation of fragments up to 640 bases in length in two hours. Anal Chem 67:4589–4593. https://doi.org/10.1021/ac00120a026

    Article  CAS  PubMed  Google Scholar 

  45. Fleischmann RD, Adams MD, White O et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512. https://doi.org/10.1126/science.7542800

    Article  CAS  PubMed  Google Scholar 

  46. Goffeau A, Barrell BG, Bussey H et al (1996) Life with 6000 genes. Science 274:546–567. https://doi.org/10.1126/science.274.5287.546

    Article  CAS  PubMed  Google Scholar 

  47. C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012–2018. https://doi.org/10.1126/science.282.5396.2012

    Article  Google Scholar 

  48. Adams MD, Celniker SE, Holt RA et al (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195. https://doi.org/10.1126/science.287.5461.2185

    Article  PubMed  Google Scholar 

  49. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800. https://doi.org/10.1038/nature03895

    Article  CAS  Google Scholar 

  50. Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178. https://doi.org/10.1038/nature08670

    Article  CAS  PubMed  Google Scholar 

  51. Mitra RD, Shendure J, Olejnik J et al (2003) Fluorescent in situ sequencing on polymerase colonies. Anal Biochem 320:55–65. https://doi.org/10.1016/s0003-2697(03)00291-4

    Article  CAS  PubMed  Google Scholar 

  52. Ju J, Kim DH, Bi L et al (2006) Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci 103:19635–19640. https://doi.org/10.1073/pnas.0609513103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Nyrén P, Lundin A (1985) Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis. Anal Biochem 151:504–509. https://doi.org/10.1016/0003-2697(85)90211-8

    Article  PubMed  Google Scholar 

  54. Myllykangas S, Buenrostro J, Ji HP (2012) Overview of sequencing technology platforms. In: Bioinformatics for high throughput sequencing. Springer, New York, NY

    Google Scholar 

  55. Huse SM, Huber JA, Morrison HG et al (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8:R143. https://doi.org/10.1186/gb-2007-8-7-r143

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. GenomeWeb (2015) Roche shutting down 454 sequencing business. GenomeWeb. https://www.genomeweb.com/sequencing/roche-shutting-down-%20454-sequencing-bus

  57. Balasubramanian S (2015) Solexa sequencing: decoding genomes on a population scale. Clin Chem 61:21–24. https://doi.org/10.1373/clinchem.2014.221747

    Article  CAS  PubMed  Google Scholar 

  58. Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55:641–658. https://doi.org/10.1373/clinchem.2008.112789

    Article  CAS  PubMed  Google Scholar 

  59. Reuter JA, Spacek DV, Snyder MP (2015) High-throughput sequencing technologies. Mol Cell 58:586–597. https://doi.org/10.1016/j.molcel.2015.05.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Kulski JKKE-JK (2016) Next-generation sequencing — an overview of the history, tools, and “omic” applications. IntechOpen, Rijeka. Chapter 1

    Book  Google Scholar 

  61. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402. https://doi.org/10.1146/annurev.genom.9.081307.164359

    Article  CAS  PubMed  Google Scholar 

  62. Alic AS, Ruzafa D, Dopazo J, Blanquer I (2016) Objective review of de novo stand-alone error correction methods for NGS data. Wiley Interdiscip Rev Comput Mol Sci 6:111–146. https://doi.org/10.1002/wcms.1239

    Article  CAS  Google Scholar 

  63. Drmanac R, Sparks AB, Callow MJ et al (2010) Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327:78–81. https://doi.org/10.1126/science.1181498

    Article  CAS  PubMed  Google Scholar 

  64. Li Q, Zhao X, Zhang W et al (2019) Reliable multiplex sequencing with rare index mis-assignment on DNB-based NGS platform. BMC Genomics 20:1–13. https://doi.org/10.1186/s12864-019-5569-5

    Article  Google Scholar 

  65. Xu Y, Lin Z, Tang C et al (2019) A new massively parallel nanoball sequencing platform for whole exome research. BMC Bioinformatics 20:1–9. https://doi.org/10.1186/s12859-019-2751-3

    Article  Google Scholar 

  66. Salzberg SL, Yorke JA (2005) Beware of mis-assembled genomes. Bioinformatics 21:4320–4321. https://doi.org/10.1093/bioinformatics/bti769

    Article  CAS  PubMed  Google Scholar 

  67. Daber R, Sukhadia S, Morrissette JJD (2013) Understanding the limitations of next generation sequencing informatics, an approach to clinical pipeline validation using artificial data sets. Cancer Genet 206:441–448. https://doi.org/10.1016/j.cancergen.2013.11.005

    Article  CAS  PubMed  Google Scholar 

  68. van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C (2018) The third revolution in sequencing technology. Trends Genet 34:666–681. https://doi.org/10.1016/j.tig.2018.05.008

    Article  CAS  PubMed  Google Scholar 

  69. Payne A, Holmes N, Rakyan V, Loose M (2019) BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics 35:2193–2198. https://doi.org/10.1093/bioinformatics/bty841

    Article  CAS  PubMed  Google Scholar 

  70. Braslavsky I, Hebert B, Kartalov E, Quake SR (2003) Sequence information can be obtained from single DNA molecules. Proc Natl Acad Sci 100:3960–3964. https://doi.org/10.1073/pnas.0230489100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Bowers J, Mitchell J, Beer E et al (2009) Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 6:593–595. https://doi.org/10.1038/nmeth.1354

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138. https://doi.org/10.1126/science.1162986

    Article  CAS  PubMed  Google Scholar 

  73. Ip CLC, Loose M, Tyson JR et al (2015) MinION analysis and reference consortium: phase 1 data release and analysis. F1000Research 4:1075. https://doi.org/10.12688/f1000research.7201.1

    Article  PubMed  PubMed Central  Google Scholar 

  74. Travers KJ, Chin C-S, Rank DR et al (2010) A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 38:e159–e159. https://doi.org/10.1093/nar/gkq543

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Eisenstein M (2012) Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 30:295–296

    Article  CAS  Google Scholar 

  76. Loman NJ, Quinlan AR (2014) Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics 30:3399–3401. https://doi.org/10.1093/bioinformatics/btu555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Li J, Stein D, McMullan C et al (2001) Ion-beam sculpting at nanometre length scales. Nature 412:166–169. https://doi.org/10.1038/35084037

    Article  CAS  PubMed  Google Scholar 

  78. Dekker C (2007) Solid-state nanopores. Nat Nanotechnol 2:209–215. https://doi.org/10.1038/nnano.2007.27

    Article  CAS  PubMed  Google Scholar 

  79. Deamer D, Akeson M, Branton D (2016) Three decades of nanopore sequencing. Nat Biotechnol 34:518–524. https://doi.org/10.1038/nbt.3423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U S A 93:13770–13773. https://doi.org/10.1073/pnas.93.24.13770

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Branton D, Deamer DW, Marziali A et al (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26:1146–1153. https://doi.org/10.1038/nbt.1495

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Lu H, Giordano F, Ning Z (2016) Oxford nanopore MinION sequencing and genome assembly. Genom Proteom Bioinformatics 14:265–279. https://doi.org/10.1016/j.gpb.2016.05.004

    Article  Google Scholar 

  83. Jain M, Olsen HE, Paten B, Akeson M (2016) The Oxford nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 17:239. https://doi.org/10.1186/s13059-016-1103-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. McCoy RC, Taylor RW, Blauwkamp TA et al (2014) Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One 9:e106689

    Article  Google Scholar 

  85. Heger M (2016) 10X genomics, pacific biosciences Morgan, provide business updates at JP Conference. Healthcare. GenomeWeb. https://www.genomeweb.com/sequencing-technology/10x-genomics-pacific-biosciences-provide-businessupdates-jp-morgan-healthcare

  86. Belton JM, McCord RP, Gibcus JH et al (2012) Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 58:268–276. https://doi.org/10.1016/j.ymeth.2012.05.001

    Article  CAS  PubMed  Google Scholar 

  87. de Wit E, de Laat W (2012) A decade of 3C technologies: insights into nuclear organization. Genes Dev 26:11–24. https://doi.org/10.1101/gad.179804.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Aston C, Mishra B, Schwartz DC (1999) Optical mapping and its potential for large-scale sequencing projects. Trends Biotechnol 17:297–302. https://doi.org/10.1016/S0167-7799(99)01326-8

    Article  CAS  PubMed  Google Scholar 

  89. Schwartz DC, Li X, Hernandez LI et al (1993) Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262:110–114. https://doi.org/10.1126/science.8211116

    Article  CAS  PubMed  Google Scholar 

  90. Yuan Y, Chung CY-L, Chan T-F (2020) Advances in optical mapping for genomic research. Comput Struct Biotechnol J 18:2051–2062. https://doi.org/10.1016/j.csbj.2020.07.018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Hu L, Xu Z, Wang M et al (2019) The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis. Nat Commun 10:4702. https://doi.org/10.1038/s41467-019-12607-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Wang M, Tu L, Yuan D et al (2019) Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat Genet 51:224–229. https://doi.org/10.1038/s41588-018-0282-x

    Article  CAS  PubMed  Google Scholar 

  93. Jiao Y, Peluso P, Shi J et al (2017) Improved maize reference genome with single-molecule technologies. Nature 546:524–527. https://doi.org/10.1038/nature22971

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Yuan Y, Milec Z, Bayer PE et al (2018) Large-scale structural variation detection in subterranean clover subtypes using optical mapping. Front Plant Sci 9:971

    Article  Google Scholar 

  95. Wheeler DA, Srinivasan M, Egholm M et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872–876. https://doi.org/10.1038/nature06884

    Article  CAS  PubMed  Google Scholar 

  96. Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556. https://doi.org/10.1038/nature07723

    Article  CAS  PubMed  Google Scholar 

  97. Sato S, Tabata S, Hirakawa H et al (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641. https://doi.org/10.1038/nature11119

    Article  CAS  Google Scholar 

  98. Jaillon O, Aury J-M, Noel B et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467. https://doi.org/10.1038/nature06148

    Article  CAS  PubMed  Google Scholar 

  99. Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115. https://doi.org/10.1126/science.1178534

    Article  CAS  PubMed  Google Scholar 

  100. Velasco R, Zharkikh A, Affourtit J et al (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833–839. https://doi.org/10.1038/ng.654

    Article  CAS  PubMed  Google Scholar 

  101. Varshney RK, Chen W, Li Y et al (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30:83–89. https://doi.org/10.1038/nbt.2022

    Article  CAS  Google Scholar 

  102. Singh NK, Gupta DK, Jayaswal PK et al (2011) The first draft of the pigeonpea genome sequence. J Plant Biochem Biotechnol 21:98–112. https://doi.org/10.1007/s13562-011-0088-8

    Article  PubMed  PubMed Central  Google Scholar 

  103. D’Hont A, Denoeud F, Aury J-M et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488:213–217. https://doi.org/10.1038/nature11241

    Article  CAS  PubMed  Google Scholar 

  104. Mayer KFX, Waugh R, Langridge P et al (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716. https://doi.org/10.1038/nature11543

    Article  CAS  PubMed  Google Scholar 

  105. Young ND, Debellé F, Oldroyd GED et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520. https://doi.org/10.1038/nature10625

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Pootakham W, Nawae W, Naktang C et al (2021) A chromosome-scale assembly of the black gram (Vigna mungo) genome. Mol Ecol Resour 21:238–250. https://doi.org/10.1111/1755-0998.13243

    Article  CAS  PubMed  Google Scholar 

  107. Wang X, Wang H, Wang J et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039. https://doi.org/10.1038/ng.919

    Article  CAS  PubMed  Google Scholar 

  108. Varshney RK, Song C, Saxena RK et al (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246. https://doi.org/10.1038/nbt.2491

    Article  CAS  PubMed  Google Scholar 

  109. Kim S, Park M, Yeom S-I et al (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270–278. https://doi.org/10.1038/ng.2877

    Article  CAS  PubMed  Google Scholar 

  110. Argout X, Salse J, Aury J-M et al (2011) The genome of Theobroma cacao. Nat Genet 43:101–108. https://doi.org/10.1038/ng.736

    Article  CAS  PubMed  Google Scholar 

  111. Xiao Y, Xu P, Fan H et al (2017) The genome draft of coconut (Cocos nucifera). Gigascience 6:1–11. https://doi.org/10.1093/gigascience/gix095

    Article  PubMed  PubMed Central  Google Scholar 

  112. Schmutz J, McClean PE, Mamidi S et al (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46:707–713. https://doi.org/10.1038/ng.3008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Huang S, Li R, Zhang Z et al (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275–1281. https://doi.org/10.1038/ng.475

    Article  CAS  PubMed  Google Scholar 

  114. Garcia-Mas J, Benjak A, Sanseverino W et al (2012) The genome of melon (Cucumis melo L.). Proc Natl Acad Sci 109:11872–11877. https://doi.org/10.1073/pnas.1205415109

    Article  PubMed  PubMed Central  Google Scholar 

  115. Sun X, Zhu S, Li N et al (2020) A chromosome-level genome assembly of garlic (Allium sativum) provides insights into genome evolution and allicin biosynthesis. Mol Plant 13:1328–1339. https://doi.org/10.1016/j.molp.2020.07.019

    Article  CAS  PubMed  Google Scholar 

  116. Bertioli DJ, Cannon SB, Froenicke L et al (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48:438–446. https://doi.org/10.1038/ng.3517

    Article  CAS  PubMed  Google Scholar 

  117. Bertioli DJ, Jenkins J, Clevenger J et al (2019) The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 51:877–884. https://doi.org/10.1038/s41588-019-0405-z

    Article  CAS  PubMed  Google Scholar 

  118. Yang J, Liu D, Wang X et al (2016) The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet 48:1225–1232. https://doi.org/10.1038/ng.3657

    Article  CAS  PubMed  Google Scholar 

  119. Sato S, Nakamura Y, Kaneko T et al (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15:227. https://doi.org/10.1093/dnares/dsn008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Wang P, Luo Y, Huang J et al (2020) The genome evolution and domestication of tropical fruit mango. Genome Biol 21:60. https://doi.org/10.1186/s13059-020-01959-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Kang YJ, Kim SK, Kim MY et al (2014) Genome sequence of mungbean and insights into evolution within Vigna species. Nat Commun 5:5443. https://doi.org/10.1038/ncomms6443

    Article  CAS  PubMed  Google Scholar 

  122. Krishnan NM, Pattnaik S, Jain P et al (2012) A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. BMC Genomics 13:464. https://doi.org/10.1186/1471-2164-13-464

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Guo L, Winzer T, Yang X et al (2018) The opium poppy genome and morphinan production. Science 362:343–347. https://doi.org/10.1126/science.aat4096

    Article  CAS  PubMed  Google Scholar 

  124. Kreplak J, Madoui M-A, Cápal P et al (2019) A reference genome for pea provides insight into legume genome evolution. Nat Genet 51:1411–1422. https://doi.org/10.1038/s41588-019-0480-1

    Article  CAS  PubMed  Google Scholar 

  125. Verde I, Abbott AG, Scalabrin S et al (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494. https://doi.org/10.1038/ng.2586

    Article  CAS  PubMed  Google Scholar 

  126. Al-Mssallem IS, Hu S, Zhang X et al (2013) Genome sequence of the date palm Phoenix dactylifera L. Nat Commun 4:2274. https://doi.org/10.1038/ncomms3274

    Article  CAS  PubMed  Google Scholar 

  127. Ming R, VanBuren R, Wai CM et al (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 47:1435–1442. https://doi.org/10.1038/ng.3435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Zeng L, Tu XL, Dai H et al (2019) Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. Genome Biol 20:79. https://doi.org/10.1186/s13059-019-1686-3

    Article  PubMed  PubMed Central  Google Scholar 

  129. Xu X, Pan S, Cheng S et al (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195. https://doi.org/10.1038/nature10158

    Article  CAS  PubMed  Google Scholar 

  130. Rousseau-Gueutin M, Belser C, Da Silva C et al (2020) Long-read assembly of the Brassica napus reference genome Darmor-bzh. Gigascience 9:giaa137. https://doi.org/10.1093/gigascience/giaa137

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Hibrand Saint-Oyant L, Ruttink T, Hamama L et al (2018) A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nat Plants 4:473–484. https://doi.org/10.1038/s41477-018-0166-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Tang C, Yang M, Fang Y et al (2016) The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants 2:16073. https://doi.org/10.1038/nplants.2016.73

    Article  CAS  PubMed  Google Scholar 

  133. Shulaev V, Sargent DJ, Crowhurst RN et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109–116. https://doi.org/10.1038/ng.740

    Article  CAS  PubMed  Google Scholar 

  134. Edger PP, Poorten TJ, VanBuren R et al (2019) Origin and evolution of the octoploid strawberry genome. Nat Genet 51:541–547. https://doi.org/10.1038/s41588-019-0356-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Xu Q, Chen L-L, Ruan X et al (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45:59–66. https://doi.org/10.1038/ng.2472

    Article  CAS  PubMed  Google Scholar 

  136. Zhang J, Zhang X, Tang H et al (2018) Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat Genet 50:1565–1573. https://doi.org/10.1038/s41588-018-0237-2

    Article  CAS  PubMed  Google Scholar 

  137. Wei C, Yang H, Wang S et al (2018) Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. Proc Natl Acad Sci 115:E4151–E4158. https://doi.org/10.1073/pnas.1719622115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Initiative TAG (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815. https://doi.org/10.1038/35048692

    Article  Google Scholar 

  139. Sierro N, Battey JND, Ouadi S et al (2014) The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 5:3833. https://doi.org/10.1038/ncomms4833

    Article  CAS  PubMed  Google Scholar 

  140. Li F, Fan G, Lu C et al (2015) Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol 33:524–530. https://doi.org/10.1038/nbt.3208

    Article  CAS  PubMed  Google Scholar 

  141. Appels R, Eversole K, Stein N et al (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:eaar7191. https://doi.org/10.1126/science.aar7191

    Article  CAS  Google Scholar 

  142. Zimin A, Stevens KA, Crepeau MW et al (2014) Sequencing and assembly of the 22-gb loblolly pine genome. Genetics 196:875–890. https://doi.org/10.1534/genetics.113.159715

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Safár J, Bartos J, Janda J et al (2004) Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J 39:960–968. https://doi.org/10.1111/j.1365-313X.2004.02179.x

    Article  CAS  PubMed  Google Scholar 

  144. Feuillet C, Leach JE, Rogers J et al (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16:77–88. https://doi.org/10.1016/j.tplants.2010.10.005

    Article  CAS  PubMed  Google Scholar 

  145. Weigel D, Mott R (2009) The 1001 genomes project for Arabidopsis thaliana. Genome Biol 10:107. https://doi.org/10.1186/gb-2009-10-5-107

    Article  PubMed  PubMed Central  Google Scholar 

  146. The 3000 rice genomes project (2014) The 3,000 rice genomes project. Gigascience 3:7. https://doi.org/10.1186/2047-217X-3-7

    Article  CAS  Google Scholar 

  147. Wang W, Mauleon R, Hu Z et al (2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557:43–49. https://doi.org/10.1038/s41586-018-0063-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Lai J, Li R, Xu X et al (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1030. https://doi.org/10.1038/ng.684

    Article  CAS  PubMed  Google Scholar 

  149. Liang Z, Duan S, Sheng J et al (2019) Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses. Nat Commun 10:1190. https://doi.org/10.1038/s41467-019-09135-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Zhou Z, Jiang Y, Wang Z et al (2015) Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol 33:408–414. https://doi.org/10.1038/nbt.3096

    Article  CAS  PubMed  Google Scholar 

  151. Lam H-M, Xu X, Liu X et al (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42:1053–1059. https://doi.org/10.1038/ng.715

    Article  CAS  PubMed  Google Scholar 

  152. Varshney RK, Saxena RK, Upadhyaya HD et al (2017) Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits. Nat Genet 49:1082–1088. https://doi.org/10.1038/ng.3872

    Article  CAS  PubMed  Google Scholar 

  153. Varshney RK, Thudi M, Roorkiwal M et al (2019) Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nat Genet 51:857–864. https://doi.org/10.1038/s41588-019-0401-3

    Article  CAS  PubMed  Google Scholar 

  154. Varshney RK, Shi C, Thudi M et al (2017) Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol 35:969–976. https://doi.org/10.1038/nbt.3943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Causse M, Desplat N, Pascual L et al (2013) Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics 14:791. https://doi.org/10.1186/1471-2164-14-791

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Wu D, Liang Z, Yan T et al (2019) Whole-genome resequencing of a worldwide collection of rapeseed accessions reveals the genetic basis of ecotype divergence. Mol Plant 12:30–43. https://doi.org/10.1016/j.molp.2018.11.007

    Article  CAS  PubMed  Google Scholar 

  157. Slavov GT, DiFazio SP, Martin J et al (2012) Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol 196:713–725. https://doi.org/10.1111/j.1469-8137.2012.04258.x

    Article  CAS  PubMed  Google Scholar 

  158. Ossowski S, Schneeberger K, Clark RM et al (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18:2024–2033. https://doi.org/10.1101/gr.080200.108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. 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 107:22032–22037. https://doi.org/10.1073/pnas.1009526107

    Article  PubMed  PubMed Central  Google Scholar 

  160. Ramakrishna G, Kaur P, Nigam D et al (2018) Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits. BMC Plant Biol 18:141. https://doi.org/10.1186/s12870-018-1341-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Mace ES, Tai S, Gilding EK et al (2013) Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Nat Commun 4:2320. https://doi.org/10.1038/ncomms3320

    Article  PubMed  Google Scholar 

  162. He J, Zhao X, Laroche A et al (2014) Genotyping-by-sequencing (GBS), An ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5:1–8. https://doi.org/10.3389/fpls.2014.00484

    Article  Google Scholar 

  163. Elshire RJ, Glaubitz JC, Sun Q et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    Article  CAS  Google Scholar 

  164. Beissinger TM, Hirsch CN, Sekhon RS et al (2013) Marker density and read depth for genotyping populations using genotyping-by-sequencing. Genetics 193:1073–1081. https://doi.org/10.1534/genetics.112.147710

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. 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 13:281. https://doi.org/10.1186/1471-2164-13-281

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Truong HT, Ramos AM, Yalcin F et al (2012) Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations. PLoS One 7:e37565

    Article  CAS  Google Scholar 

  167. Sonah H, Bastien M, Iquira E et al (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS One 8:e54603

    Article  CAS  Google Scholar 

  168. Zhao K, Tung C-W, Eizenga GC et al (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:467. https://doi.org/10.1038/ncomms1467

    Article  CAS  PubMed  Google Scholar 

  169. Tian F, Bradbury PJ, Brown PJ et al (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43:159–162. https://doi.org/10.1038/ng.746

    Article  CAS  PubMed  Google Scholar 

  170. Huang X, Kurata N, Wei X et al (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497–501. https://doi.org/10.1038/nature11532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Huang X, Zhao Y, Wei X et al (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32–39. https://doi.org/10.1038/ng.1018

    Article  CAS  Google Scholar 

  172. Spindel J, Wright M, Chen C et al (2013) Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet 126:2699–2716. https://doi.org/10.1007/s00122-013-2166-x

    Article  CAS  PubMed  Google Scholar 

  173. Li H, Peng Z, Yang X et al (2013) Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet 45:43–50. https://doi.org/10.1038/ng.2484

    Article  CAS  PubMed  Google Scholar 

  174. Romay MC, Millard MJ, Glaubitz JC et al (2013) Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol 14:R55. https://doi.org/10.1186/gb-2013-14-6-r55

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Jia G, Huang X, Zhi H et al (2013) A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet 45:957–961. https://doi.org/10.1038/ng.2673

    Article  CAS  PubMed  Google Scholar 

  176. 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 110:453–458. https://doi.org/10.1073/pnas.1215985110

    Article  PubMed  Google Scholar 

  177. Varala K, Swaminathan K, Li Y, Hudson ME (2011) Rapid genotyping of soybean cultivars using high throughput sequencing. PLoS One 6:e24811

    Article  CAS  Google Scholar 

  178. Uitdewilligen JGAML, Wolters A-MA, D’hoop BB et al (2013) A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One 8:e62355

    Article  CAS  Google Scholar 

  179. 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. https://doi.org/10.1186/1471-2164-14-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253

    Article  CAS  Google Scholar 

  181. Liu H, Bayer M, Druka A et al (2014) An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics 15:104. https://doi.org/10.1186/1471-2164-15-104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Tettelin H, Masignani V, Cieslewicz MJ et al (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A 102:13950–13955. https://doi.org/10.1073/pnas.0506758102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  183. Golicz AA, Bayer PE, Bhalla PL et al (2020) Pangenomics comes of age: from bacteria to plant and animal applications. Trends Genet 36:132–145. https://doi.org/10.1016/j.tig.2019.11.006

    Article  CAS  PubMed  Google Scholar 

  184. Bayer PE, Golicz AA, Scheben A et al (2020) Plant pan-genomes are the new reference. Nat Plants 6:914–920. https://doi.org/10.1038/s41477-020-0733-0

    Article  PubMed  Google Scholar 

  185. Tao Y, Zhao X, Mace E et al (2019) Exploring and exploiting pan-genomics for crop improvement. Mol Plant 12:156–169. https://doi.org/10.1016/j.molp.2018.12.016

    Article  CAS  PubMed  Google Scholar 

  186. Della Coletta R, Qiu Y, Ou S et al (2021) How the pan-genome is changing crop genomics and improvement. Genome Biol 22:3. https://doi.org/10.1186/s13059-020-02224-8

    Article  PubMed  PubMed Central  Google Scholar 

  187. Li Y, Zhou G, Ma J et al (2014) De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 32:1045–1052. https://doi.org/10.1038/nbt.2979

    Article  CAS  PubMed  Google Scholar 

  188. Golicz AA, Bayer PE, Barker GC et al (2016) The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 7:13390. https://doi.org/10.1038/ncomms13390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Montenegro JD, Golicz AA, Bayer PE et al (2017) The pangenome of hexaploid bread wheat. Plant J 90:1007–1013. https://doi.org/10.1111/tpj.13515

    Article  CAS  PubMed  Google Scholar 

  190. Hurgobin B, Golicz AA, Bayer PE et al (2018) Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Plant Biotechnol J 16:1265–1274. https://doi.org/10.1111/pbi.12867

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Golicz AA, Batley J, Edwards D (2016) Towards plant pangenomics. Plant Biotechnol J 14:1099–1105. https://doi.org/10.1111/pbi.12499

    Article  PubMed  Google Scholar 

  192. Lin K, Zhang N, Severing EI et al (2014) Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. BMC Genomics 15:250. https://doi.org/10.1186/1471-2164-15-250

    Article  PubMed  PubMed Central  Google Scholar 

  193. Schatz MC, Maron LG, Stein JC et al (2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol 15:506. https://doi.org/10.1186/PREACCEPT-2784872521277375

    Article  PubMed  PubMed Central  Google Scholar 

  194. Hirsch CN, Foerster JM, Johnson JM et al (2014) Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26:121–135. https://doi.org/10.1105/tpc.113.119982

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Yao W, Li G, Zhao H et al (2015) Exploring the rice dispensable genome using a metagenome-like assembly strategy. Genome Biol 16:187. https://doi.org/10.1186/s13059-015-0757-3

    Article  PubMed  PubMed Central  Google Scholar 

  196. Gordon SP, Contreras-Moreira B, Woods DP et al (2017) Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nat Commun 8:2184. https://doi.org/10.1038/s41467-017-02292-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Zhou P, Silverstein KAT, Ramaraj T et al (2017) Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. BMC Genomics 18:261. https://doi.org/10.1186/s12864-017-3654-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  198. Ou L, Li D, Lv J et al (2018) Pan-genome of cultivated pepper (Capsicum) and its use in gene presence-absence variation analyses. New Phytol 220:360–363

    Article  Google Scholar 

  199. Zhao Q, Feng Q, Lu H et al (2018) Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat Genet 50:278–284. https://doi.org/10.1038/s41588-018-0041-z

    Article  CAS  PubMed  Google Scholar 

  200. Yu J, Golicz AA, Lu K et al (2019) Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars. Plant Biotechnol J 17:881–892. https://doi.org/10.1111/pbi.13022

    Article  CAS  PubMed  Google Scholar 

  201. Hübner S, Bercovich N, Todesco M et al (2019) Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance. Nat Plants 5:54–62. https://doi.org/10.1038/s41477-018-0329-0

    Article  CAS  PubMed  Google Scholar 

  202. Gao L, Gonda I, Sun H et al (2019) The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat Genet 51:1044. https://doi.org/10.1038/s41588-019-0410-2

    Article  CAS  PubMed  Google Scholar 

  203. Song J-M, Guan Z, Hu J et al (2020) Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat Plants 6:34–45. https://doi.org/10.1038/s41477-019-0577-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Trouern-Trend AJ, Falk T, Zaman S et al (2020) Comparative genomics of six Juglans species reveals disease-associated gene family contractions. Plant J 102:410–423. https://doi.org/10.1111/tpj.14630

    Article  CAS  PubMed  Google Scholar 

  205. Liu Y, Du H, Li P et al (2020) Pan-genome of wild and cultivated soybeans. Cell 182:162–176.e13. https://doi.org/10.1016/j.cell.2020.05.023

    Article  CAS  PubMed  Google Scholar 

  206. Zhao J, Bayer PE, Ruperao P et al (2020) Trait associations in the pangenome of pigeon pea (Cajanus cajan). Plant Biotechnol J 18:1946–1954. https://doi.org/10.1111/pbi.13354

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  207. Ruperao P, Thirunavukkarasu N, Gandham P et al (2021) Sorghum pan-genome explores the functional utility for genomic-assisted breeding to accelerate the genetic gain. Front Plant Sci 12:963

    Article  Google Scholar 

  208. Hufford MB, Seetharam AS, Woodhouse MR et al (2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373:655–662. https://doi.org/10.1126/science.abg5289

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Shomura A, Izawa T, Ebana K et al (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028. https://doi.org/10.1038/ng.169

    Article  CAS  PubMed  Google Scholar 

  210. Xu K, Xu X, Fukao T et al (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708. https://doi.org/10.1038/nature04920

    Article  CAS  PubMed  Google Scholar 

  211. Ashikawa I, Hayashi N, Yamane H et al (2008) Two adjacent nucleotide-binding site–leucine-rich repeat class genes are required to confer pikm-specific rice blast resistance. Genetics 180:2267–2276. https://doi.org/10.1534/genetics.108.095034

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    CAS  PubMed  PubMed Central  Google Scholar 

  213. Bernatzky R, Tanksley SD (1986) Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112:887–898

    Article  CAS  Google Scholar 

  214. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410. https://doi.org/10.1046/j.1365-313x.1993.04020403.x

    Article  CAS  PubMed  Google Scholar 

  215. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185. https://doi.org/10.1023/A:1003910819967

    Article  CAS  Google Scholar 

  216. Wei X, Wang L, Zhang Y et al (2014) Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey. Molecules 19:5150–5162. https://doi.org/10.3390/molecules19045150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  217. Salgado LR, Koop DM, Pinheiro DG et al (2014) De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers. BMC Genomics 15:236. https://doi.org/10.1186/1471-2164-15-236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  218. Nigam D, Saxena S, Ramakrishna G et al (2017) De novo assembly and characterization of Cajanus scarabaeoides (L.) thouars transcriptome by paired-end sequencing. Front Mol Biosci 4:48. https://doi.org/10.3389/fmolb.2017.00048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  219. Yadav CB, Bonthala VS, Muthamilarasan M et al (2015) Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database. DNA Res 22:79–90. https://doi.org/10.1093/dnares/dsu039

    Article  CAS  PubMed  Google Scholar 

  220. Bailey-Serres J, Fukao T, Ronald P et al (2010) Submergence tolerant rice: SUB1’s journey from landrace to modern cultivar. Rice 3:138–147. https://doi.org/10.1007/s12284-010-9048-5

    Article  Google Scholar 

  221. Takagi H, Abe A, Yoshida K et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183. https://doi.org/10.1111/tpj.12105

    Article  CAS  PubMed  Google Scholar 

  222. Liu S, Yeh C-T, Tang HM et al (2012) Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS One 7:e36406

    Article  CAS  Google Scholar 

  223. Hussain W, Baenziger PS, Belamkar V et al (2017) Genotyping-by-sequencing derived high-density linkage map and its application to QTL mapping of flag leaf traits in bread wheat. Sci Rep 7:16394. https://doi.org/10.1038/s41598-017-16006-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Price AH (2006) Believe it or not, QTLs are accurate! Trends Plant Sci 11:213–216. https://doi.org/10.1016/j.tplants.2006.03.006

    Article  CAS  PubMed  Google Scholar 

  225. Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5. https://doi.org/10.3835/plantgenome2008.02.0089

    Article  CAS  Google Scholar 

  226. Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630. https://doi.org/10.1016/j.tplants.2005.10.004

    Article  CAS  PubMed  Google Scholar 

  227. Varshney RK, Terauchi R, McCouch SR (2014) Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol 12:1–8. https://doi.org/10.1371/journal.pbio.1001883

    Article  Google Scholar 

  228. Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond Ser B Biol Sci 363:557–572. https://doi.org/10.1098/rstb.2007.2170

    Article  CAS  Google Scholar 

  229. Busemeyer L, Ruckelshausen A, Möller K et al (2013) Precision phenotyping of biomass accumulation in triticale reveals temporal genetic patterns of regulation. Sci Rep 3:2442. https://doi.org/10.1038/srep02442

    Article  PubMed  PubMed Central  Google Scholar 

  230. Varshney RK, Thudi M, Nayak SN et al (2014) Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theor Appl Genet 127:445–462. https://doi.org/10.1007/s00122-013-2230-6

    Article  CAS  PubMed  Google Scholar 

  231. Hayes B, Goddard M (2010) Genome-wide association and genomic selection in animal breeding. Genome 53:876–883. https://doi.org/10.1139/G10-076

    Article  CAS  PubMed  Google Scholar 

  232. Crossa J, Pérez P, Hickey J et al (2014) Genomic prediction in CIMMYT maize and wheat breeding programs. Heredity 112:48–60. https://doi.org/10.1038/hdy.2013.16

    Article  CAS  PubMed  Google Scholar 

  233. de Oliveira EJ, de Resende MDV, da Silva Santos V et al (2012) Genome-wide selection in cassava. Euphytica 187:263–276. https://doi.org/10.1007/s10681-012-0722-0

    Article  CAS  Google Scholar 

  234. Shen R, Fan J-B, Campbell D et al (2005) High-throughput SNP genotyping on universal bead arrays. Mutat Res 573:70–82. https://doi.org/10.1016/j.mrfmmm.2004.07.022

    Article  CAS  PubMed  Google Scholar 

  235. Steemers FJ, Gunderson KL (2007) Whole genome genotyping technologies on the BeadArray platform. Biotechnol J 2:41–49. https://doi.org/10.1002/biot.200600213

    Article  CAS  PubMed  Google Scholar 

  236. Matsuzaki H, Dong S, Loi H et al (2004) Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods 1:109–111. https://doi.org/10.1038/nmeth718

    Article  CAS  PubMed  Google Scholar 

  237. Ganal MW, Durstewitz G, Polley A et al (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One 6:e28334. https://doi.org/10.1371/journal.pone.0028334

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  238. Hiremath PJ, Kumar A, Penmetsa RV et al (2012) Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol J 10:716–732. https://doi.org/10.1111/j.1467-7652.2012.00710.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  239. Saxena RK, Penmetsa RV, Upadhyaya HD et al (2012) Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. DNA Res 19:449–461. https://doi.org/10.1093/dnares/dss025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  240. Sanand S, Srivastava H, Kaila T et al (2020) Methods and tools for plant organelle genome sequencing, assembly, and downstream analysis. In: Methods in molecular biology. Humana Press, Totowa, NJ, pp 49–98

    Google Scholar 

  241. Shinozaki K, Ohme M, Tanaka M et al (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049

    Article  CAS  Google Scholar 

  242. Ohyama K, Fukuzawa H, Kohchi T et al (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322:572–574. https://doi.org/10.1038/322572a0

    Article  CAS  Google Scholar 

  243. Segovia R, Pett W, Trewick S, Lavrov DV (2011) Extensive and evolutionarily persistent mitochondrial tRNA editing in Velvet Worms (phylum Onychophora). Mol Biol Evol 28:2873–2881. https://doi.org/10.1093/molbev/msr113

    Article  CAS  PubMed  Google Scholar 

  244. Fitzgerald TL, Shapter FM, McDonald S et al (2011) Genome diversity in wild grasses under environmental stress. Proc Natl Acad Sci U S A 108:21140–21145. https://doi.org/10.1073/pnas.1115203108

    Article  PubMed  PubMed Central  Google Scholar 

  245. Hardouin EA, Tautz D (2013) Increased mitochondrial mutation frequency after an island colonization: positive selection or accumulation of slightly deleterious mutations? Biol Lett 9:20121123. https://doi.org/10.1098/rsbl.2012.1123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  246. Hieter P, Boguski M (1997) Functional genomics: it’s all how you read it. Science 278:601–602. https://doi.org/10.1126/science.278.5338.601

    Article  CAS  PubMed  Google Scholar 

  247. Yamada K, Lim J, Dale JM et al (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842–846. https://doi.org/10.1126/science.1088305

    Article  CAS  PubMed  Google Scholar 

  248. Weber APM, Weber KL, Carr K et al (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144:32–42. https://doi.org/10.1104/pp.107.096677

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  249. Lowe R, Shirley N, Bleackley M et al (2017) Transcriptomics technologies. PLoS Comput Biol 13:e1005457

    Article  Google Scholar 

  250. Nejat N, Ramalingam A, Mantri N (2018) Advances in transcriptomics of plants. Adv Biochem Eng Biotechnol 164:161–185. https://doi.org/10.1007/10_2017_52

    Article  CAS  PubMed  Google Scholar 

  251. Ramakrishna G, Kaur P, Singh A et al (2021) Comparative transcriptome analyses revealed different heat stress responses in pigeonpea (Cajanus cajan) and its crop wild relatives. Plant Cell Rep 40:881. https://doi.org/10.1007/s00299-021-02686-5

    Article  CAS  PubMed  Google Scholar 

  252. Schmid M, Davison TS, Henz SR et al (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37:501–506. https://doi.org/10.1038/ng1543

    Article  CAS  PubMed  Google Scholar 

  253. Wang L, Xie W, Chen Y et al (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J 61:752–766. https://doi.org/10.1111/j.1365-313X.2009.04100.x

    Article  CAS  PubMed  Google Scholar 

  254. Severin AJ, Woody JL, Bolon YT et al (2010) RNA-Seq atlas of glycine max: a guide to the soybean transcriptome. BMC Plant Biol 10:160. https://doi.org/10.1186/1471-2229-10-160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  255. Kudapa H, Garg V, Chitikineni A, Varshney RK (2018) The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development. Plant Cell Environ 41:2209–2225. https://doi.org/10.1111/pce.13210

    Article  CAS  PubMed  Google Scholar 

  256. Pazhamala LT, Purohit S, Saxena RK et al (2017) Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation. J Exp Bot 68:2037–2054. https://doi.org/10.1093/jxb/erx010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  257. Sekhon RS, Briskine R, Hirsch CN et al (2013) Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One 8:e61005

    Article  CAS  Google Scholar 

  258. Ramírez-González RH, Borrill P, Lang D et al (2018) The transcriptional landscape of polyploid wheat. Science 361:eaar6089. https://doi.org/10.1126/science.aar6089

    Article  CAS  PubMed  Google Scholar 

  259. Allis CD, Jenuwein T (2016) The molecular hallmarks of epigenetic control. Nat Rev Genet 17:487–500. https://doi.org/10.1038/nrg.2016.59

    Article  CAS  PubMed  Google Scholar 

  260. Gu H, Smith ZD, Bock C et al (2011) Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 6:468–481. https://doi.org/10.1038/nprot.2010.190

    Article  CAS  PubMed  Google Scholar 

  261. Wang P, Xia H, Zhang Y et al (2015) Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across embryo and endosperm in Maize (Zea may). BMC Genomics 16:21. https://doi.org/10.1186/s12864-014-1204-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  262. Junaid A, Kumar H, Rao AR et al (2018) Unravelling the epigenomic interactions between parental inbreds resulting in an altered hybrid methylome in pigeonpea. DNA Res 25:361–373. https://doi.org/10.1093/dnares/dsy008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  263. Meissner A, Gnirke A, Bell GW et al (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33:5868–5877. https://doi.org/10.1093/nar/gki901

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  264. Platt A, Gugger PF, Pellegrini M, Sork VL (2015) Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations. Mol Ecol 24:3823–3830. https://doi.org/10.1111/mec.13230

    Article  CAS  PubMed  Google Scholar 

  265. Chen X, Ge X, Wang J et al (2015) Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution. Front Plant Sci 6:836. https://doi.org/10.3389/fpls.2015.00836

    Article  PubMed  PubMed Central  Google Scholar 

  266. Clark C, Palta P, Joyce CJ et al (2012) A comparison of the whole genome approach of MeDIP-Seq to the targeted approach of the infinium HumanMethylation450 BeadChip® for methylome profiling. PLoS One 7:e50233

    Article  CAS  Google Scholar 

  267. Taiwo O, Wilson GA, Morris T et al (2012) Methylome analysis using MeDIP-seq with low DNA concentrations. Nat Protoc 7:617–636. https://doi.org/10.1038/nprot.2012.012

    Article  CAS  PubMed  Google Scholar 

  268. Zhao M-T, Whyte JJ, Hopkins GM et al (2014) Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) using low amounts of genomic DNA. Cell Reprogr 16:175–184. https://doi.org/10.1089/cell.2014.0002

    Article  CAS  Google Scholar 

  269. Weng Y-I, Huang TH-M, Yan PS (2009) Methylated DNA immunoprecipitation and microarray-based analysis: detection of DNA methylation in breast cancer cell lines. Methods Mol Biol 590:165–176. https://doi.org/10.1007/978-1-60327-378-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  270. Park PJ (2009) ChIP–seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680. https://doi.org/10.1038/nrg2641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  271. Warr A, Robert C, Hume D et al (2015) Exome sequencing: current and future perspectives. G3 5:1543–1550. https://doi.org/10.1534/g3.115.018564

    Article  PubMed  PubMed Central  Google Scholar 

  272. Muraya MM, Schmutzer T, Ulpinnis C et al (2015) Targeted sequencing reveals large-scale sequence polymorphism in maize candidate genes for biomass production and composition. PLoS One 10:e0132120

    Article  Google Scholar 

  273. 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:R88. https://doi.org/10.1186/gb-2011-12-9-r88

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  274. Haun WJ, Hyten DL, Xu WW et al (2011) The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol 155:645–655. https://doi.org/10.1104/pp.110.166736

    Article  CAS  PubMed  Google Scholar 

  275. Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840. https://doi.org/10.1038/nrmicro2910

    Article  CAS  PubMed  Google Scholar 

  276. Bulgarelli D, Schlaeppi K, Spaepen S et al (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838. https://doi.org/10.1146/annurev-arplant-050312-120106

    Article  CAS  PubMed  Google Scholar 

  277. Newton AC, Fitt BDL, Atkins SD et al (2010) Pathogenesis, parasitism and mutualism in the trophic space of microbe-plant interactions. Trends Microbiol 18:365–373. https://doi.org/10.1016/j.tim.2010.06.002

    Article  CAS  PubMed  Google Scholar 

  278. Young JPW, Crossman LC, Johnston AWB et al (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 7:R34. https://doi.org/10.1186/gb-2006-7-4-r34

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  279. Sablok G, Rosselli R, Seeman T et al (2017) Draft genome sequence of the nitrogen-fixing rhizobium sullae type strain IS123T focusing on the key genes for symbiosis with its host Hedysarum coronarium L. Front Microbiol 8:1348

    Article  Google Scholar 

  280. Bromfield ESP, Cloutier S, Nguyen HDT (2019) Description and complete genome sequence of bradyrhizobium amphicarpaeae sp. Nov., harbouring photosystem and nitrogenfixation genes. Int J Syst Evol Microbiol 69:2841–2848. https://doi.org/10.1099/ijsem.0.003569

    Article  CAS  PubMed  Google Scholar 

  281. Ramachandran VK, East AK, Karunakaran R et al (2011) Adaptation of Rhizobium leguminosarumto pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biol 12:R106. https://doi.org/10.1186/gb-2011-12-10-r106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  282. Liu X, Wei S, Wang F et al (2012) Burkholderia and Cupriavidus spp. are the preferred symbionts of Mimosa spp. in southern China. FEMS Microbiol Ecol 80:417–426. https://doi.org/10.1111/j.1574-6941.2012.01310.x

    Article  CAS  PubMed  Google Scholar 

  283. Pont C, Wagner S, Kremer A et al (2019) Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA. Genome Biol 20:1–17. https://doi.org/10.1186/s13059-019-1627-1

    Article  Google Scholar 

  284. Barba-Montoya J, dos Reis M, Schneider H et al (2018) Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution. New Phytol 218:819–834. https://doi.org/10.1111/nph.15011

    Article  PubMed  PubMed Central  Google Scholar 

  285. Murat F, Armero A, Pont C et al (2017) Reconstructing the genome of the most recent common ancestor of flowering plants. Nat Genet 49:490–496. https://doi.org/10.1038/ng.3813

    Article  CAS  PubMed  Google Scholar 

  286. Raymond O, Gouzy J, Just J et al (2018) The Rosa genome provides new insights into the domestication of modern roses. Nat Genet 50:772–777. https://doi.org/10.1038/s41588-018-0110-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  287. Murat F, Louis A, Maumus F et al (2015) Understanding Brassicaceae evolution through ancestral genome reconstruction. Genome Biol 16:262. https://doi.org/10.1186/s13059-015-0814-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  288. Wu S, Shamimuzzaman M, Sun H et al (2017) The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus. Plant J 92:963–975. https://doi.org/10.1111/tpj.13722

    Article  CAS  PubMed  Google Scholar 

  289. Wang J, Sun P, Li Y et al (2017) Hierarchically aligning 10 legume genomes establishes a family-level genomics platform. Plant Physiol 174:284–300. https://doi.org/10.1104/pp.16.01981

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  290. Wang X, Wang J, Jin D et al (2015) Genome alignment spanning major poaceae lineages reveals heterogeneous evolutionary rates and alters inferred dates for key evolutionary events. Mol Plant 8:885–898. https://doi.org/10.1016/j.molp.2015.04.004

    Article  CAS  PubMed  Google Scholar 

  291. Murat F, Xu J-H, Tannier E et al (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res 20:1545–1557. https://doi.org/10.1101/gr.109744.110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  292. Ramos-Madrigal J, Smith BD, Moreno-Mayar JV et al (2016) Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication. Curr Biol 26:3195–3201. https://doi.org/10.1016/j.cub.2016.09.036

    Article  CAS  PubMed  Google Scholar 

  293. Kistler L, Maezumi SY, Gregorio de Souza J et al (2018) Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science 362:1309–1313. https://doi.org/10.1126/science.aav0207

    Article  CAS  PubMed  Google Scholar 

  294. Scott MF, Botigué LR, Brace S et al (2019) A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. Nat Plants 5:1120–1128. https://doi.org/10.1038/s41477-019-0534-5

    Article  PubMed  PubMed Central  Google Scholar 

  295. Roullier C, Benoit L, McKey DB, Lebot V (2013) Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination. Proc Natl Acad Sci 110:2205–2210. https://doi.org/10.1073/pnas.1211049110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  296. Muñoz-Rodríguez P, Carruthers T, Wood JRI et al (2018) Reconciling conflicting phylogenies in the origin of sweet potato and dispersal to polynesia. Curr Biol 28:1246–1256.e12. https://doi.org/10.1016/j.cub.2018.03.020

    Article  CAS  PubMed  Google Scholar 

  297. Gutaker RM, Weiß CL, Ellis D et al (2019) The origins and adaptation of European potatoes reconstructed from historical genomes. Nat Ecol Evol 3:1093–1101. https://doi.org/10.1038/s41559-019-0921-3

    Article  PubMed  Google Scholar 

  298. Nozaki H, Takano H, Misumi O et al (2007) A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae. BMC Biol 5:28. https://doi.org/10.1186/1741-7007-5-28

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  299. Church GM, Gao Y, Kosuri S (2012) Next-generation digital information storage in DNA. Science 337:1628. https://doi.org/10.1126/science.1226355

    Article  CAS  PubMed  Google Scholar 

  300. Arcadia CE, Kennedy E, Geiser J et al (2020) Multicomponent molecular memory. Nat Commun 11:691. https://doi.org/10.1038/s41467-020-14455-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  301. Kim J, Bae JH, Baym M, Zhang DY (2020) Metastable hybridization-based DNA information storage to allow rapid and permanent erasure. Nat Commun 11:1–8. https://doi.org/10.1038/s41467-020-18842-6

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. ICAR-National Institute for Plant Biotechnology, New Delhi, India

    Anupam Singh, Goriparthi Ramakrishna, Tanvi Kaila, Swati Saxena, Sandhya Sharma & Kishor Gaikwad

  2. Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India

    Anupam Singh & M. Z. Abdin

  3. ICAR-National Bureau of Plant Genetic Resources, New Delhi, India

    Ambika B. Gaikwad

Authors
  1. Anupam Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Goriparthi Ramakrishna
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tanvi Kaila
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Swati Saxena
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sandhya Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ambika B. Gaikwad
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. M. Z. Abdin
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Kishor Gaikwad
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Sher-e-Kashmir University of Agricultura, KHUDWANI ANANTNAG, Jammu and Kashmir, India

    Shabir Hussain Wani

  2. Dalhousie University, Halifax, Canada

    Anuj Kumar

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Singh, A. et al. (2022). Next-Generation Sequencing Technologies: Approaches and Applications for Crop Improvement. In: Wani, S.H., Kumar, A. (eds) Genomics of Cereal Crops. Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2533-0_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2533-0_3

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2532-3

  • Online ISBN: 978-1-0716-2533-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation