ArticleBMC genomics2015
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).
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Identification of KASP markers and putative genes for herbicide (metribuzin) tolerance in common wheat (Triticum aestivum L.).BMC plant biology · 2026Article
- Development and validation of PCR marker array for molecular selection towards spring, vernalization-independent and winter, vernalization-responsive ecotypes of white lupin (Lupinus albus L.).Scientific reports · 2025Article
- Validation of SNP Markers for Diversity Analysis, Quality Control, and Trait Selection in a Biofortified Cassava Population.Plants (Basel, Switzerland) · 2024Article
- Host Resistance to Virus Diseases Provides a Key Enabler towards Fast Tracking Gains in Grain Lupin Breeding.Plants (Basel, Switzerland) · 2023Review
- Effectiveness ofInternational journal of molecular sciences · 2023Article
- Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era.Frontiers in genetics · 2022Review
- The Resistance of Narrow-Leafed Lupin toInternational journal of molecular sciences · 2021Article
- Development of PCR-based markers and whole-genome selection model for anthracnose resistance in white lupin (Lupinus albus L.).Journal of applied genetics · 2020Article
- Development of diagnostic molecular markers for marker-assisted breeding against bacterial wilt in tomato.Breeding science · 2020Article
- Genetic diversity analysis for narrow-leafed lupin (Lupinus angustifolius L.) by SSR markers.Molecular biology reports · 2020Article
- Validation of Diaporthe toxica resistance markers in European Lupinus angustifolius germplasm and identification of novel resistance donors for marker-assisted selection.Journal of applied genetics · 2020Article
- Article
- Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development.BMC genomics · 2019Article
- Resequencing of Common Bean Identifies Regions of Inter-Gene Pool Introgression and Provides Comprehensive Resources for Molecular Breeding.The plant genome · 2018Article
- Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain.Frontiers in genetics · 2018Article
- Construction of an ultra-high density consensus genetic map, and enhancement of the physical map from genome sequencing in Lupinus angustifolius.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- A high-density consensus linkage map of white lupin highlights synteny with narrow-leafed lupin and provides markers tagging key agronomic traits.Scientific reports · 2017Article
- Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application.Plant biotechnology journal · 2017Review
- Integration of Lupinus angustifolius L. (narrow-leafed lupin) genome maps and comparative mapping within legumes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2016Article
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8 authors.
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Abstract
backgroundMolecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotypes must match plant phenotypes in a wide range of breeding germplasm. In this study, we used the legume crop species Lupinus angustifolius (lupin) to demonstrate the utility of whole genome sequencing and re-sequencing on the development of diagnostic markers for molecular plant breeding.
resultsNine lupin cultivars released in Australia from 1973 to 2007 were subjected to whole genome re-sequencing. The re-sequencing data together with the reference genome sequence data were used in marker development, which revealed 180,596 to 795,735 SNP markers from pairwise comparisons among the cultivars. A total of 207,887 markers were anchored on the lupin genetic linkage map. Marker mining obtained an average of 387 SNP markers and 87 InDel markers for each of the 24 genome sequence assembly scaffolds bearing markers linked to 11 genes of agronomic interest. Using the R gene PhtjR conferring resistance to phomopsis stem blight disease as a test case, we discovered 17 candidate diagnostic markers by genotyping and selecting markers on a genetic linkage map. A further 243 candidate diagnostic markers were discovered by marker mining on a scaffold bearing non-diagnostic markers linked to the PhtjR gene. Nine out from the ten tested candidate diagnostic markers were confirmed as truly diagnostic on a broad range of commercial cultivars. Markers developed using these strategies meet the requirements for broad application in molecular plant breeding.
conclusionsWe demonstrated that low-cost genome sequencing and re-sequencing data were sufficient and very effective in the development of diagnostic markers for marker-assisted selection. The strategies used in this study may be applied to any trait or plant species. Whole genome sequencing and re-sequencing provides a powerful tool to overcome current limitations in molecular plant breeding, which will enable plant breeders to precisely pyramid favourable genes to develop super crop varieties to meet future food demands.
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