Transcriptome Resources Paving the Way for Lupin Crop Improvement

Part of the Compendium of Plant Genomes book series (CPG)


A range of transcriptomic resources have been generated for lupins from expressed sequenced tag (EST) libraries to the more recent next generation RNA sequencing libraries. This chapter will describe these resources and how they have been utilized to (a) generate gene-based molecular markers, (b) assist with the annotation of the reference genome for narrow-leafed lupin (Lupinus angustifolius), and (c) addressed specific research questions that assess global expression under different conditions and/or tissue types. For white lupins (L. albus) these include transcriptome studies using RNA sequencing libraries to investigate cluster root formation and the plants phosphate uptake status, for narrow-leafed lupins investigations into smallRNAs, seed storage protein and alkaloid content in the grain, and for yellow lupin (L. luteus) investigations into organ abscission. While transcriptomics in lupins is still in its infancies compared to larger pulse crops, lupin transcriptome resources will no doubt grow and lay strong foundations for lupin crop improvement.


  1. Berger J, Buirchell B, Luckett D, Nelson M (2012a) Domestication bottlenecks limit genetic diversity and constrain adaptation in narrow-leafed lupin (Lupinus angustifolius L.). Theor Appl Genet 124:637–652PubMedGoogle Scholar
  2. Berger JD, Buirchell B, Luckett DJ, Palta JA, Ludwig C et al (2012b) How has narrow-leafed lupin changed in its 1st 40 years as an industrial, broadacre crop? A G x E-based characterization of yield-related traits in Australian cultivars. Field Crops Res 126:152–164Google Scholar
  3. Bunsupa S, Okada T, Saito K, Yamazaki M (2011) An acyltransferase-like gene obtained by differential gene expression profiles of quinolizidine alkaloid-producing and nonproducing cultivars of Lupinus angustifolius. Plant Biotechnol 28:89–94Google Scholar
  4. Bunsupa S, Katayama K, Ikeura E, Oikawa A, Toyooka K et al (2012) Lysine decarboxylase catalyzes the first step of quinolizidine alkaloid biosynthesis and coevolved with alkaloid production in Leguminosae. Plant Cell 24:1202–1216PubMedPubMedCentralGoogle Scholar
  5. Cannon SB, McKain MR, Harkess A, Nelson MN, Dash S et al (2015) Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes. Mol Biol Evol 32:193–210PubMedGoogle Scholar
  6. Cheng L, Bucciarelli B, Shen J, Allan D, Vance CP (2011) Update on lupin cluster roots: update on white lupin cluster root acclimation to phosphorus deficiency. Plant Physiol 156:1025–1032PubMedPubMedCentralGoogle Scholar
  7. Cowling WA, Tarr A (2004) Effect of genotype and environment on seed quality in sweet narrow-leafed lupin (Lupinus angustifolius L.). Aust J Agric Res 55:745–751Google Scholar
  8. Croxford AE, Rogers T, Caligari PD, Wilkinson MJ (2008) High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar. New Phytol 180:594–607PubMedGoogle Scholar
  9. DeBoer K, Melser S, Sperschneider J, Kamphuis LG, Garg G et al (2019) Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development. BMC Genomics 20:135PubMedPubMedCentralGoogle Scholar
  10. Duranti M, Consonni A, Magni C, Sessa F, Scarafoni A (2008) The major proteins of lupin seed: characterisation and molecular properties for use as functional and nutraceutical ingredients. Trends Food Sci Technol 19:624–633Google Scholar
  11. Edwards O, Ridsdill-Smith T, Berlandier F (2003) Aphids do not avoid resistance in Australian lupin (Lupinus angustifolius, L. luteus) varieties. Bull Entomol Res 93:403–411PubMedGoogle Scholar
  12. Fischer K, Dieterich R, Nelson MN, Kamphuis LG, Singh KB et al (2015) Characterization and mapping of LanrBo: a locus conferring anthracnose resistance in narrow-leafed lupin (Lupinus angustifolius L.). Theor Appl Genet 128:2121–2130PubMedGoogle Scholar
  13. Foley RC, Gao L-L, Spriggs A, Soo LY, Goggin DE et al (2011) Identification and characterisation of seed storage protein transcripts from Lupinus angustifolius. BMC Plant Biol 11:59PubMedPubMedCentralGoogle Scholar
  14. Foley RC, Jimenez-Lopez JC, Kamphuis LG, Hane JK, Melser S et al (2015) Analysis of conglutin seed storage proteins across lupin species using transcriptomic, protein and comparative genomic approaches. BMC Plant Biol 15:106PubMedPubMedCentralGoogle Scholar
  15. Frick KM, Kamphuis LG, Siddique KHM, Singh KB, Foley RC (2017) Quinolizidine alkaloid biosynthesis in lupins and prospects for grain quality improvement. Front Plant Sci 8:87PubMedPubMedCentralGoogle Scholar
  16. Frick KM, Foley RC, Kamphuis LG, Siddique KHM, Garg G et al (2018) Characterisation of the genetic factors affecting quinolizidine alkaloid biosynthesis and its response to abiotic stress in narrow-leafed lupin (Lupinus angustifolius L.). Plant Cell Environ 41:2155–2168PubMedGoogle Scholar
  17. Frick KM, Foley R, Siddique KHM, Singh KB, Kamphuis LG (2019) The role of jasmonate signalling in quinolizidine alkaloid biosynthesis, wounding and aphid predation response in narrow-leafed lupin. Funct Plant Biol 46:443–454PubMedGoogle Scholar
  18. Gao LL, Hane JK, Kamphuis LG, Foley R, Shi BJ et al (2011) Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing. BMC Genomics 12:521PubMedPubMedCentralGoogle Scholar
  19. Glazinska P, Wojciechowski W, Kulasek M, Glinkowski W, Marciniak K et al (2017) De novo transcriptome profiling of flowers, flower pedicels and pods of Lupinus luteus (Yellow Lupine) reveals complex expression changes during organ abscission. Front Plant Sci 8:641PubMedPubMedCentralGoogle Scholar
  20. Hane J, Ming Y, Kamphuis LG, Nelson MN, Garg G et al (2017) A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution. Plant Biotechnol J 15:318–330PubMedGoogle Scholar
  21. Hayden MJ, Nguyen TM, Waterman A, Chalmers KJ (2008) Multiplex-ready PCR: a new method for multiplexed SSR and SNP genotyping. BMC Genomics 9:80PubMedPubMedCentralGoogle Scholar
  22. Kamphuis LG, Zulak K, Gao L-L, Anderson JP, Singh KB (2013) Plant—aphid interactions with a focus on legumes. Funct Plant Biol 40:1271–1284Google Scholar
  23. Kamphuis LG, Hane JK, Nelson MN, Gao L, Atkins CA et al (2015) Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers. Plant Biotechnol J 13:14–25PubMedGoogle Scholar
  24. Kroc M, Koczyk G, Swiecicki W, Kilian A, Nelson MN (2014) New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L. (narrow-leafed lupin). Theor Appl Genet 127:1237–1249PubMedGoogle Scholar
  25. Kroc M, Czepiel K, Wilczura P, Koczyk G, Święcicki W (2019a) Alkaloid biosynthesis in lupins. In: Third international legume societ conference, Poznan, PolandGoogle Scholar
  26. Kroc M, Koczyk G, Kamel KA, Czepiel K, Fedorowicz-Strońska O et al (2019b) Transcriptome-derived investigation of biosynthesis of quinolizidine alkaloids in narrow-leafed lupin (Lupinus angustifolius L.) highlights candidate genes linked to iucundus locus. Sci Rep 19:2231Google Scholar
  27. Książkiewicz M, Nazzicari N, Yang H, Nelson MN, Renshaw D et al (2017) A high-density consensus linkage map of white lupin highlights synteny with narrow-leafed lupin and provides markers tagging key agronomic traits. Sci Rep 7:15335PubMedPubMedCentralGoogle Scholar
  28. McGinn S, Gut IG (2013) DNA sequencing - spanning the generations. Nat Biotechnol 30:366–372Google Scholar
  29. Meng ZB, You XD, Suo D, Chen YL, Tang C et al (2013) Root-derived auxin contributes to the phosphorus-deficiency-induced cluster-root formation in white lupin (Lupinus albus). Plant Physiol 148:481–489Google Scholar
  30. Mousavi-Derazmahalleh M, Bayer PE, Nevado B, Hurgobin B, Filatov D et al (2018) Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin. Theoret Appl Genet 131:887–901Google Scholar
  31. Nelson MN, Phan HT, Ellwood SR, Moolhuijzen PM, Hane J et al (2006) The first gene-based map of Lupinus angustifolius L.-location of domestication genes and conserved synteny with Medicago truncatula. Theoret Appl Genet 113:225–238Google Scholar
  32. Nelson MN, Moolhuijzen PM, Boersma JG, Chudy M, Lesniewska K et al (2010) Aligning a new reference genetic map of Lupinus angustifolius with the genome sequence of the model legume, Lotus japonicus. DNA Res 17:73–83PubMedPubMedCentralGoogle Scholar
  33. Nevado B, Atchison GW, Hughes CE, Filatov DA (2016) Widespread adaptive evolution during repeated evolutionary radiations in New World lupins. Nat Commun 7:12384PubMedPubMedCentralGoogle Scholar
  34. O’Rourke JA, Yang SS, Miller SS, Bucciarelli B, Liu J et al (2013) An RNA-seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants. Plant Physiol 161:705–724Google Scholar
  35. Parra-González L, Aravena-Abarzua G, Navarro-Navarro C, Udall J, Maughan J et al (2012) Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies. BMC Genomics 13:425Google Scholar
  36. Phan HT, Ellwood SR, Adhikari K, Nelson MN, Oliver RP (2007) The first genetic and comparative map of white lupin (Lupinus albus L.): identification of QTLs for anthracnose resistance and flowering time, and a locus for alkaloid content. DNA Res 14:59–70PubMedPubMedCentralGoogle Scholar
  37. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183PubMedGoogle Scholar
  38. Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB et al (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46:707–713PubMedPubMedCentralGoogle Scholar
  39. Secco D, Shou H, Whelan J, Berkowitz O (2014) RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin. BMC Genomics 15:230PubMedPubMedCentralGoogle Scholar
  40. Tian, L, Peel, GJ, Lei, Z, Aziz, N, Dai, X et al (2009) Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots. BMC Plant Biol 9:1Google Scholar
  41. Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK et al (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30:83–89Google Scholar
  42. Varshney RK, Song C, Saxena RK, Azam S, Yu S et al (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246Google Scholar
  43. Venuti S, Zanin L, Marroni F, Franco A, Morgante M et al (2019) Physiological and transcriptomic data highlight common features between iron and phosphorus acquisition mechanisms in white lupin roots. Plant Sci 285:110–121PubMedGoogle Scholar
  44. Wang Z, Straub D, Yang H, Kania A, Shen J et al (2014) The regulatory network of cluster-root function and development in phosphate-deficient white lupin (Lupinus albus) identified by transcriptome sequencing. Physiol Plant 151:323–338PubMedGoogle Scholar
  45. Wasternack C, Hause B (2013) Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany. Ann Bot 111:1021–1058PubMedPubMedCentralGoogle Scholar
  46. Wink M (1992) The role of quinolizidine alkaloids in plant-insect interactions. Insect-Plant Interact 4:131–166Google Scholar
  47. Yang H, Tao Y, Zheng Z, Zhang Q, Zhou G et al (2013) Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus angustifolius L. PLoS ONE 8:e64799PubMedPubMedCentralGoogle Scholar
  48. Yang T, Nagy I, Mancinotti D, Otterbach SL, Andersen TB et al (2017) Transcript profiling of a bitter variety of narrow-leafed lupin to discover alkaloid biosynthetic genes. J Exp Bot 68:5527–5537PubMedPubMedCentralGoogle Scholar
  49. Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520–524PubMedPubMedCentralGoogle Scholar
  50. Zimmermann J, Voss H, Schwager C, Stegemann J, Ansorge W (1988) Automated Sanger dideoxy sequencing reaction protocol. FEBS Lett 233:432–436PubMedGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.CSIRO Agriculture and FoodWembleyAustralia
  2. 2.Centre for Crop and Disease ManagementCurtin UniversityBentleyAustralia
  3. 3.Department of Plant and Environmental ScienceUniversity of CopenhagenCopenhagenDenmark

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