An Integrated Physical, Genetic and Cytogenetic Map of Brachypodium distachyon, a Model System for Grass Research

Febrer, Melanie; Goicoechea, José Luis; Wright, Jonathan; McKenzie, Neil; Song, Xiang; Lin, Juan; Collura, Kristi; Wissotski, Marina; Yu, Yeisoo; Ammiraju, Jetty S.S.; Wolny, Elżbieta; Idziak, D.; Betekhtin, Alexander; Kudrna, Dave; Hasterok, Robert; Wing, Rod A.; Bevan, Michael W.

doi:10.1371/journal.pone.0013461

Cited by 47 publications

(48 citation statements)

References 33 publications

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“…Several Brachypodium libraries have been made including BAC libraries for two different accessions. The largest BAC libraries, with a total of 56-fold genome coverage (184,320 clones), were made from line Bd21, used also for the reference genome (Huo et al, 2006(Huo et al, , 2008Febrer et al, 2010). The BACs in these libraries have been end sequenced and thus can be aligned along the genome Febrer et al, 2010).…”

Section: Dna Librariesmentioning

confidence: 99%

Brachypodium as a Model for the Grasses: Today and the Future

et al. 2011

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Model systems not only allow scientists to investigate complex processes that are difficult to study in nonmodel organisms but also serve to focus community efforts and resources, significantly advancing research. Arabidopsis (Arabidopsis thaliana) has served as a plant model system for almost 30 years and is widely considered the preeminent model plant. The success of Arabidopsis-related research has been driven not only by key features common to any model organism but also by the collaborative environment built by the Arabidopsis community. A decade after the Arabidopsis genome sequence was published, the development of model plants follows a different trajectory. In the past, the development of extensive resources and a large user community happened first and then sequencing the genome followed. Today, however, an organism is selected as a potential model and genome sequencing occurs prior to or concurrent with the development of experimental tools and a user community. Arabidopsis research has provided many scientific breakthroughs (Flavell, 2009). However, its utility as a model is limited to a certain extent when investigating monocot-specific processes.Within the monocots, grasses provide the vast majority of human calories and are increasingly utilized as a sustainable source of energy. Traits including cell wall composition, plant architecture, grain properties,

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Section: Dna Librariesmentioning

confidence: 99%

Brachypodium as a Model for the Grasses: Today and the Future

et al. 2011

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“…Recent developments in highthroughput genome technologies have provided us with a wealth of information about SNP and structural diversity both between and within species (Feuk et al, 2006;Faraut, 2008;Rowan et al, 2015). Chromosome painting studies have allowed for the detection and visualization of many translocations and inversions, for example, in the Brassicaceae family (Lysak et al, 2003(Lysak et al, , 2006(Lysak et al, , 2010, the Solanaceae family (Iovene et al, 2008;Tang et al, 2008;Anderson et al, 2010;Lou et al, 2010;Wu and Tanksley, 2010;Szinay et al, 2012) and the grass family (Hasterok, 2006;Febrer et al, 2010;Betekhtin et al, 2014). Furthermore, de novo genome assemblies of related species enabled multiple genome alignment studies giving rise to unprecedented comparative genomics with detailed information of inversions, translocations and other structural variants (Kurtz et al, 2004;Pop et al, 2004;Ohtsubo et al, 2008;Cheung et al, 2009;Darling et al, 2010;Zapata et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana

et al. 2016

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SummaryChromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17‐Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F‐box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col‐FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South‐Eastern Europe approximately 5000 years ago and the FRI‐Col allele to North‐West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The ‘American haplotype’ was identified from several European localities, potentially due to return migration.

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“…In the past, this has been as a direct result of the lack of robust high throughput screening procedures that enable the rapid identification and characterisation of introgressed chromosome segments. However, recent advances in conventional and next generation sequencing platforms and technology in combination with the sequencing of the crop and model plant genomes, for example, rice and Brachypodium (Febrer et al, 2010), are now enabling the development of strategies to fully exploit the potential of alien species for crop improvement, for example, (Griffiths et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Exploitation of interspecific diversity for monocot crop improvement

et al. 2013

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In many cultivated crop species there is limited genetic variation available for the development of new higher yielding varieties adapted to climate change and sustainable farming practises. The distant relatives of crop species provide a vast and largely untapped reservoir of genetic variation for a wide range of agronomically important traits that can be exploited by breeders for crop improvement. In this paper, in what we believe to be the largest introgression programme undertaken in the monocots, we describe the transfer of the entire genome of Festuca pratensis into Lolium perenne in overlapping chromosome segments. The L. perenne/F. pratensis introgressions were identified and characterised via 131 simple sequence repeats and 1612 SNPs anchored to the rice genome. Comparative analyses were undertaken to determine the syntenic relationship between L. perenne/ F. pratensis and rice, wheat, barley, sorghum and Brachypodium distachyon. Analyses comparing recombination frequency and gene distribution indicated that a large proportion of the genes within the genome are located in the proximal regions of chromosomes which undergo low/very low frequencies of recombination. Thus, it is proposed that past breeding efforts to produce improved varieties have centred on the subset of genes located in the distal regions of chromosomes where recombination is highest. The use of alien introgression for crop improvement is important for meeting the challenges of global food supply and the monocots such as the forage grasses and cereals, together with recent technological advances in molecular biology, can help meet these challenges.

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An Integrated Physical, Genetic and Cytogenetic Map of Brachypodium distachyon, a Model System for Grass Research

Cited by 47 publications

References 33 publications

Brachypodium as a Model for the Grasses: Today and the Future

Brachypodium as a Model for the Grasses: Today and the Future

Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana

Exploitation of interspecific diversity for monocot crop improvement

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