Journal article
Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus angustifolius L
PLoS ONE, Vol.8(5), e64799
2013
Abstract
Lupin (Lupinus angustifolius L.) is the most recently domesticated crop in major agricultural cultivation. Its seeds are high in protein and dietary fibre, but low in oil and starch. Medical and dietetic studies have shown that consuming lupin-enriched food has significant health benefits. We report the draft assembly from a whole genome shotgun sequencing dataset for this legume species with 26.9x coverage of the genome, which is predicted to contain 57,807 genes. Analysis of the annotated genes with metabolic pathways provided a partial understanding of some key features of lupin, such as the amino acid profile of storage proteins in seeds. Furthermore, we applied the NGS-based RAD-sequencing technology to obtain 8,244 sequence-defined markers for anchoring the genomic sequences. A total of 4,214 scaffolds from the genome sequence assembly were aligned into the genetic map. The combination of the draft assembly and a sequence-defined genetic map made it possible to locate and study functional genes of agronomic interest. The identification of co-segregating SNP markers, scaffold sequences and gene annotation facilitated the identification of a candidate R gene associated with resistance to the major lupin disease anthracnose. We demonstrated that the combination of medium-depth genome sequencing and a high-density genetic linkage map by application of NGS technology is a cost-effective approach to generating genome sequence data and a large number of molecular markers to study the genomics, genetics and functional genes of lupin, and to apply them to molecular plant breeding. This strategy does not require prior genome knowledge, which potentiates its application to a wide range of non-model species.
Details
- Title
- Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus angustifolius L
- Authors/Creators
- H Yang (Author/Creator) - Agriculture and FoodY. Tao (Author/Creator) - Beijing Genome Institute, Shenzhen, ChinaZ. Zheng (Author/Creator) - Beijing Genome Institute, Shenzhen, ChinaQ. Zhang (Author/Creator) - Agriculture and FoodG. Zhou (Author/Creator) - Agriculture and FoodM.W. Sweetingham (Author/Creator) - Agriculture and FoodJ.G. Howieson (Author/Creator) - Murdoch UniversityC. Li (Author/Creator) - Agriculture and Food
- Publication Details
- PLoS ONE, Vol.8(5), e64799
- Publisher
- Public Library of Science
- Identifiers
- 991005541504507891
- Copyright
- © 2013 Yang et al.
- Murdoch Affiliation
- Centre for Rhizobium Studies
- Language
- English
- Resource Type
- Journal article
- Note
- This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics