Abstract
Narrow-leafed lupin (Lupinus angustifolius) is an important grain legume crop for some parts of the world like Australia and parts of Northern Europe where it can form an important part of sustainable farming systems, reducing the need for nitrogenous fertiliser, providing valuable disease breaks and boosting cereal yields. Through the genome revolution and in particular rapid advances in next-generation sequencing technologies, there are new powerful tools available to help with gene discovery and to rapidly accelerate pre-breeding and breeding programmes for narrow-leafed lupin and other lupin crops. This chapter provides an overview of the genomic resources available for narrow-leafed lupin with a focus on the current reference genome which underpins many of the other resources. The cultivar Tanjil was chosen as the reference accession for narrow-leafed lupin and a short-read sequencing approach coupled with BAC-end sequence data was used to assemble the first comprehensive reference genome for the species. This genome assembly captured ~610 Mb of the estimated 921 Mb genome of narrow-leafed lupin with an annotated gene set of 33,076 genes. The narrow-leafed lupin reference genome has provided valuable insight into narrow-leafed lupin evolution and important information on some of its key plant-microbe interactions. The chapter also touches on some of the genomic resources that are in the pipeline in lupins and describes the lupin genome portal, a web-based resource that houses genomic and related information for narrow-leafed lupin.
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References
Ameline-Torregrosa C, Wang B-B, O'Bleness MS, Deshpande S, Zhu H et al (2008) Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol 146:5–21
Arnoldi A, Boschin G, Zanoni C, Lammi C (2015) The health benefits of sweet lupin seed flours and isolated proteins. J Funct Foods 18:550–563
Bak RO, Gomez-Ospina N, Porteus MH (2018) Gene editing on center stage. Trends Genet 34:600–611
Barker SJ, Si P, Hodgson L, Ferguson-Hunt M, Khentry Y et al (2016) Regeneration selection improves transformation efficiency in narrow-leaf lupin. Plant Cell Tissue Organ Cult 126:219–228
Berger JD, Clements JC, Nelson MN, Kamphuis LG, Singh KB et al (2013) The essential role of genetic resources in narrow-leafed lupin improvement. Crop Pasture Sci 64:361–373
Bravo A, York T, Pumplin N, Mueller LA, Harrison MJ (2016) Genes conserved for arbuscular mycorrhizal symbiosis identified through phylogenomics. Nat Plants 2
Crossa J, Perez-Rodriguez P, Cuevas J, Montesinos-Lopez O, Jarquin D et al (2017) Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci 22:961–975
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
Donlin MJ (2009) Using the generic genome browser (GBrowse). Current protocols in bioinformatics (Chap. 9: Unit 9.9-Unit 9.9)
Drummond CS, Eastwood RJ, Miotto STS, Hughes CE (2012) Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling. Syst Biol 61:443–460
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 15:106
Gallardo C, Hufnagel B, Casset C, Alcon C, Garcia F et al (2019) Anatomical and hormonal description of rootlet primordium development along white lupin cluster root. Physiol Plant 165:4–16
Gao L-L, Hane J, Kamphuis LG, Foley R, Shi B-J 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 12:521
González-Sama A, Lucas MM, De Felipe MR, Pueyo JJ (2004) An unusual infection mechanism and nodule morphogenesis in white lupin (Lupinus albus). New Phytol 163:371–380
Hane JK, 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 15:318–330
James E, Minchin F, Iannetta P, Sprent J (1997) Temporal relationships between nitrogenase and intercellular glycoprotein in developing white lupin nodules. Ann Bot 79:493–503
Jones JDG, Dangl JL (2006) The plant immune system. Nature 444:323–329
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 13:14–25
Kasprzak A, Safar J, Janda J, Dolezel J, Wolko B et al (2006) The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.). Cell Mol Biol Lett 11:396–407
Lambers H, Clements JC, Nelson MN (2013) How a phosphorus-acquisition strategy based on carboxylate exudation powers the success and agronomic potential of lupines (Lupinus, Fabaceae). Am J Bot 100:263–288
Lambers H, Albornoz F, Kotula L, Laliberte E, Ranathunge K et al (2018) How belowground interactions contribute to the coexistence of mycorrhizal and non-mycorrhizal species in severely phosphorus-impoverished hyperdiverse ecosystems. Plant Soil 424:11–33
Lavin M, Herendeen PS, Wojciechowski MF (2005) Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst Biol 54:575–594
Lee YP, Mori TA, Sipsas S, Barden A, Puddey IB et al (2006) Lupin-enriched bread increases satiety and reduces energy intake acutely. Am J Clin Nutr 84:975–980
Lesniewska K, Ksiazkiewicz M, Nelson MN, Mahe F, Ainouche A et al (2011) Assignment of 3 genetic linkage groups to 3 chromosomes of narrow-leafed Lupin. J Hered 102:228–236
MacLean AM, Bravo A, Harrison MJ (2017) Plant signaling and metabolic pathways enabling arbuscular mycorrhizal symbiosis. Plant Cell 29:2319–2335
Oldroyd GED (2013) Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants. Nat Rev Microbiol 11:252–263
Parra G, Bradnam K, Korf I (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genornes. Bioinformatics 23:1061–1067
Priyam A, Woodcroft BJ, Rai V, Munagala A, Moghul I et al (2015) Sequenceserver: a modern graphical user interface for custom BLAST databases. https://doi.org/10.1101/033142.
Qi YP, Tsuda K, Glazebrook J, Katagiri F (2011) Physical association of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) immune receptors in Arabidopsis. Mol Plant Pathol 12:702–708
Ramirez-Prado JS, Abulfaraj AA, Rayapuram N, Benhamed M, Hirt H (2018) Plant immunity: from signaling to epigenetic control of defense. Trends Plant Sci 23:833–844
Shane MW, Lambers H (2005) Cluster roots: a curiosity in context. Plant Soil 274:101–125
Talhinhas P, Baroncelli R, Le Floch G (2016) Antrhacnose of lupins caused by Colletotrichum lupini: a recent disease and a succssful worldwide pathogen. J Plant Pathol 98:5–14
Tang C, Robson A, Dilworth M, Kuo J (1992) Microscopic evidence on how iron deficiency limits nodule initiation in Lupinus angustifolius L. New Phytol 457–467
Thomma BPHJ, Nurnberger T, Joosten MHAJ (2011) Of PAMPs and effectors: the blurred PTI-ETI dichotomy. Plant Cell 23:4–15
Varshney RK, Glaszmann JC, Leung H, Ribaut JM (2010) More genomic resources for less-studied crops. Trends Biotechnol 28:452–460
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 31:240–246
Wang HY, Yang H, Shivalila CS, Dawlaty MM, Cheng AW et al (2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153:910–918
Yang HA, Tao Y, Zheng ZQ, Shao D, Li ZZ et al (2013a) Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breeding. Theoret Appl Genet 126:511–522
Yang HA, Tao Y, Zheng ZQ, Zhang QS, Zhou GF et al (2013b) Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus angustifolius L. PLoS One 8
Yang HA, Jian JB, Li X, Renshaw D, Clements J et al (2015) Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius). BMC Genomics 16:660.
Youens-Clark K, Faga B, Yap IV, Stein L, Ware D (2009) CMap 1.01: a comparative mapping application for the internet. Bioinformatics 25:3040–3042
Acknowledgements
Narrow-leafed lupin genomic work in the authors group has been supported by Grains Research and Development Corporation (GRDC), CSIRO, Curtin University and the University of Western Australia.
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Singh, K.B., Foley, R.C., Garg, G., Kamphuis, L.G. (2020). Overview of Genomic Resources Available for Lupins with a Focus on Narrow-Leafed Lupin (Lupinus angustifolius). In: Singh, K., Kamphuis, L., Nelson, M. (eds) The Lupin Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-21270-4_3
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