Mapping-by-sequencing accelerates forward genetics in barley

Mascher, Martin; Jost, Matthias; Kuon, Joel‐Elias; Himmelbach, Axel; Aßfalg, Axel; Beier, Sebastian; Scholz, Uwe; Graner, Andreas; Stein, Nils

doi:10.1186/gb-2014-15-6-r78

Cited by 142 publications

(118 citation statements)

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“…Targeted capture can be used to quickly anchor RAD-tag maps to hundreds of candidate genes, providing a powerful surrogate for a whole genome reference (Baxter et al 2011; Mascher et al 2014; Neves et al 2014; Fig. 2).…”

Section: When Should Targeted Capture Be Used?mentioning

confidence: 99%

Targeted capture in evolutionary and ecological genomics

2015

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The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole genome sequencing in ecological and evolutionary genomic studies. High throughput targeted capture is one such strategy that involves the parallel enrichment of pre-selected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across labs focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to 1) increase the accessibility of targeted capture to researchers working in non-model taxa by discussing capture methods that circumvent the need of a reference genome, 2) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy, and 3) discuss the future of targeted capture and other genome partitioning approaches in light of the increasing accessibility of whole genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole genome sequencing.

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Section: When Should Targeted Capture Be Used?mentioning

confidence: 99%

Targeted capture in evolutionary and ecological genomics

2015

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“…Despite some recent progress (Dabbert et al, 2010;Mascher et al, 2014), most genes underlying tillering in the Triticeae await identification.…”

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confidence: 99%

The Barley Uniculme4 Gene Encodes a BLADE-ON-PETIOLE-Like Protein That Controls Tillering and Leaf Patterning

et al. 2015

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Tillers are vegetative branches that develop from axillary buds located in the leaf axils at the base of many grasses. Genetic manipulation of tillering is a major objective in breeding for improved cereal yields and competition with weeds. Despite this, very little is known about the molecular genetic bases of tiller development in important Triticeae crops such as barley (Hordeum vulgare) and wheat (Triticum aestivum). Recessive mutations at the barley Uniculme4 (Cul4) locus cause reduced tillering, deregulation of the number of axillary buds in an axil, and alterations in leaf proximal-distal patterning. We isolated the Cul4 gene by positional cloning and showed that it encodes a BROAD-COMPLEX, TRAMTRACK, BRIC-À-BRAC-ankyrin protein closely related to Arabidopsis (Arabidopsis thaliana) BLADE-ON-PETIOLE1 (BOP1) and BOP2. Morphological, histological, and in situ RNA expression analyses indicate that Cul4 acts at axil and leaf boundary regions to control axillary bud differentiation as well as the development of the ligule, which separates the distal blade and proximal sheath of the leaf. As, to our knowledge, the first functionally characterized BOP gene in monocots, Cul4 suggests the partial conservation of BOP gene function between dicots and monocots, while phylogenetic analyses highlight distinct evolutionary patterns in the two lineages.

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“…Exome sequencing is based on NGS re-sequencing of whole-genome gene space which is captured by means of oligonucleotide probes. A barley-specific exome-capture array encompassing >60 Mb nonredundant coding sequences has been developed by the members of the International Barley Genome Sequencing Consortium (Mascher et al 2013), and it has already been utilized to clone two barley mutants (Mascher et al 2014;Pankin et al 2014). …”

Section: Applications Of Ngs Technologies To Forward Geneticsmentioning

confidence: 99%