Rapid gene isolation in barley and wheat by mutant chromosome sequencing

Sánchez‐Martín, Javier; Steuernagel, Burkhard; Ghosh, Sreya; Herren, Gerhard; Hurni, Severine; Adamski, Nikolai M; Vrána, Jan; Kubaláková, Marie; Krattinger, Simon G.; Wicker, Thomas; Doležel, Jaroslav; Keller, Beat; Wulff, Brande B. H.

doi:10.1186/s13059-016-1082-1

Cited by 286 publications

(259 citation statements)

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“…In addition, two stem rust resistance genes, Sr22 and Sr45a, were isolated in wheat using independent ethyl methane sulfonate induced suppressor lines and sequencing of libraries enriched for nucleotide binding and Leu-rich repeats . These methods enabled the identification of induced mutations without the need for positional fine mapping but still required prior knowledge of the chromosome position (Sánchez-Martín et al, 2016) or of the type of gene affected . In addition, these methods are technologically and Blue dots represent expression in vrs1, vrs4.k, int-c.5, vrs3(int-a.1), and vrs3.f ILs in cv Bowman.…”

Section: Discussionmentioning

confidence: 99%

“…Because of the genome size of barley, sequencing whole genomes in multiple mutants is not practical due to the cost and the difficulty of interpreting the large datasets. Recently, a method was presented for gene isolation in allelic barley mutants based on flow sorting and sequencing of a single chromosome that carried a known gene for the eciferum mutation (Sánchez-Martín et al, 2016). In addition, two stem rust resistance genes, Sr22 and Sr45a, were isolated in wheat using independent ethyl methane sulfonate induced suppressor lines and sequencing of libraries enriched for nucleotide binding and Leu-rich repeats .…”

Section: Discussionmentioning

confidence: 99%

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Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

et al. 2017

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The complex nature of crop genomes has long prohibited the efficient isolation of agronomically relevant genes. However, recent advances in next-generation sequencing technologies provide new ways to accelerate fine-mapping and gene isolation in crops. We used RNA sequencing of allelic six-rowed spike3 (vrs3) mutants with altered spikelet development for gene identification and functional analysis in barley (Hordeum vulgare). Variant calling in two allelic vrs3 mutants revealed that VRS3 encodes a putative histone Lys demethylase with a conserved zinc finger and Jumonji C and N domain. Sanger sequencing of this candidate gene in independent allelic vrs3 mutants revealed a series of mutations in conserved domains, thus confirming our candidate as the VRS3 gene and suggesting that the row type in barley is determined epigenetically. Global transcriptional profiling in developing shoot apical meristems of vrs3 suggested that VRS3 acts as a transcriptional activator of the row-type genes VRS1 (Hv.HOMEOBOX1) and INTERMEDIUM-C (INT-C; Hv.TEOSINTE BRANCHED1). Comparative transcriptome analysis of the row-type mutants vrs3, vrs4 (Hv.RAMOSA2), and int-c confirmed that all three genes act as transcriptional activators of VRS1 and quantitative variation in the expression levels of VRS1 in these mutants correlated with differences in the number of developed lateral spikelets. The identification of genes and pathways affecting seed number in small grain cereals will enable to further unravel the transcriptional networks controlling this important yield component.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

et al. 2017

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“…[18]. For species that require short days to trigger the reproductive phase, such as rice (Oryza sativa) and maize (Zea mays), the speed breeding technique could be used to promote rapid vegetative growth prior to reducing the photoperiod.Recent advances in genomic tools and resources [19][20][21][22][23] and the decreasing cost of sequencing have enabled plant researchers to shift their focus from model to crop plants. Despite such advances, the slow generation times of many crop plants continue to impose a high entry barrier.…”

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confidence: 99%

Speed breeding: a powerful tool to accelerate crop research and breeding

Watson

Ghosh

Williams

et al. 2017

Preprint

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The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand [1]. This slow improvement rate is attributed partly to the long generation times of crop plants. Here we present a method called 'speed breeding', . CC-BY 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/161182 doi: bioRxiv preprint first posted online Jul. 9, 2017; Watson and Ghosh et al. (2017) 2 which greatly shortens generation time and accelerates breeding and research programs.Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum), and pea (Pisum sativum) and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully-enclosed controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies, and transformation.The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent and potential for adaptation to larger-scale crop improvement programs. Cost-saving through LED supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing, and genomic selection, accelerating the rate of crop improvement.For most crop plants, the breeding of new, advanced cultivars, takes several years. Following crossing of selected parent lines, 4-6 generations of inbreeding are typically required to develop genetically stable lines for evaluation of agronomic traits and yield. This is particularly timeconsuming for field-grown crops that are often limited to only 1-2 generations per year. Here, we present flexible protocols for "speed breeding" that use prolonged photoperiods to accelerate the developmental rate of plants [2], thereby reducing generation time. We highlight the opportunity presented by speed breeding and detail protocols to inspire widespread adoption as a state-of-theart breeding and research tool.To evaluate speed breeding as a method to accelerate applied and basic research on cereal species, standard genotypes of spring bread wheat (T. aestivum), durum wheat (T. durum), barley (H. vulgare) and the model grass Brachypodium distachyon were grown in a controlled environment room with extended photoperiod (22 hours light/2 hours dark) ( Fig. 1; Methods:Speed breeding I; Supplementary Table 1). A light/dark period was chosen over a continuous photoperiod to support functional expression of circadian clock genes [3]. Growth was compare...

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“…It can be argued that lack of chromosome-specific assemblies and the construction of chromosome maps is a weakness of many genome-sequencing efforts. However, a combination of NGS and flow sorting was used successfully for chromosomal genomics studies in wheat and barley [e.g., Šimková et al, 2008;Mayer et al, 2011;Hernandez et al, 2012;Martis et al, 2012;Cápal et al, 2015;Sánchez-Martín et al, 2016] and a few mammalian species, including the Tasmanian devil [Murchison et al, 2012], Chinese hamster [Brinkrolf et al, 2013], gorilla [Tomaszkiewicz et al, 2016], cervids , and mouse [Sudbery et al, 2009]. In reptiles, shotgun sequencing of isolated chromosomes was performed only recently by Kichigin et al [2016] to determine the sequence of A. sagrei and A. carolinensis microchromosomes and extend the work done on macrochromosomes by Alföldi et al [2011].…”

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confidence: 99%

Isolating Chromosomes of the Komodo Dragon: New Tools for Comparative Mapping and Sequence Assembly

Iannucci

Altmanová

Ciofi

et al. 2019

Cytogenet Genome Res

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We developed new tools to build a high-quality chromosomal map of the Komodo dragon (Varanus komodoensis) available for cross-species phylogenomic analyses. First, we isolated chromosomes by flow sorting and determined the chromosome content of each flow karyotype peak by FISH. We then isolated additional Komodo dragon chromosomes by microdissection and amplified chromosome-specific DNA pools. The chromosome-specific DNA pools can be sequenced, assembled, and mapped by next-generation sequencing technology. The chromosome-specific paint probes can be used to investigate karyotype evolution through cross-species chromosome painting. Overall, the set of chromosome-specific DNA pools of V. komodoensis provides new tools for detailed phylogenomic analyses of Varanidae and squamates in general.

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Rapid gene isolation in barley and wheat by mutant chromosome sequencing

Cited by 286 publications

References 41 publications

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

Speed breeding: a powerful tool to accelerate crop research and breeding

Isolating Chromosomes of the Komodo Dragon: New Tools for Comparative Mapping and Sequence Assembly

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