Overview of Genomic Resources Available for Lupins with a Focus on Narrow-Leafed Lupin (Lupinus angustifolius)
- 112 Downloads
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.
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.
- Bravo A, York T, Pumplin N, Mueller LA, Harrison MJ (2016) Genes conserved for arbuscular mycorrhizal symbiosis identified through phylogenomics. Nat Plants 2Google Scholar
- 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 20Google Scholar
- Donlin MJ (2009) Using the generic genome browser (GBrowse). Current protocols in bioinformatics (Chap. 9: Unit 9.9-Unit 9.9)Google Scholar
- 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.
- 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 98:5–14Google Scholar
- Tang C, Robson A, Dilworth M, Kuo J (1992) Microscopic evidence on how iron deficiency limits nodule initiation in Lupinus angustifolius L. New Phytol 457–467Google Scholar
- Thomma BPHJ, Nurnberger T, Joosten MHAJ (2011) Of PAMPs and effectors: the blurred PTI-ETI dichotomy. Plant Cell 23:4–15Google Scholar
- Varshney RK, Glaszmann JC, Leung H, Ribaut JM (2010) More genomic resources for less-studied crops. Trends Biotechnol 28:452–460Google Scholar
- 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 126:511–522CrossRefGoogle Scholar
- 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 8Google Scholar
- 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.Google Scholar