Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination‐poor region comprises more than half of barley chromosome 3<scp>H</scp>

Aliyeva-Schnorr, Lala; Beier, Sebastian; Karafiátová, Miroslava; Schmutzer, Thomas; Scholz, Uwe; Doležel, Jaroslav; Stein, Nils; Houben, Andreas

doi:10.1111/tpj.13006

Cited by 32 publications

(28 citation statements)

References 74 publications

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“…Fluorescence in situ hybridization was performed with H. vulgare nuclei as described earlier 72 using Arabidopsis-type telomere and barley centromere-specific [AGGGAG] 5 repeat probes 73 . Automated annotation of transcribed regions.…”

Section: Article Researchmentioning

confidence: 99%

A chromosome conformation capture ordered sequence of the barley genome

Mascher

Gundlach

Himmelbach

et al. 2017

Nature

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Barley remains dated to the dawn of agriculture have been found at several archaeological sites 1,2 . In addition to indications that barley was an important food crop, recent excavations have fuelled speculation that beverages from fermented grains may have motivated early Neolithic hunter-gatherers to erect some of humankind's oldest monuments 3,4 . Moreover, brewing beer may also have played a role in the eastward spread of the crop after its initial domestication in the Fertile Crescent 5,6 . Since 2012, both genetic research and crop improvement in barley have benefited from a partly ordered draft sequence assembly 7 . This community resource has underpinned gene isolation 8,9 and population genomic studies 10 . However, these and other efforts have also revealed limitations of the current draft assembly. The limitations are often direct consequences of two characteristic genomic features: the extreme abundance of repetitive elements, and the severely reduced frequency of meiotic recombination in pericentromeric regions 11 .These factors have limited the contiguity of whole-genome assemblies to kilobase-sized sequences originating from low-copy regions of the genome. Thus, a detailed investigation of the composition of the repetitive fraction of the genome-including expanded gene families-and of the distribution of targets of selection and crop improvement in (genetically defined) pericentromeric regions has been beyond reach.Here we present a map-based reference sequence of the barley genome including the first comprehensively ordered assembly of the pericentromeric regions of a Triticeae genome. The resource highlights a conspicuous distinction between distal and proximal regions of chromosomes that is reflected by the intranuclear chromatin organization. Moreover, chromosomal compartments are differentiated by an exponential gradient of gene density and recombination rate, striking contrasts in the distribution of retrotransposon families, and distinct patterns of genetic diversity.Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlightin...

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Section: Article Researchmentioning

confidence: 99%

A chromosome conformation capture ordered sequence of the barley genome

Mascher

Gundlach

Himmelbach

et al. 2017

Nature

Self Cite

1,261

1,506

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“…CO distribution is largely modified in Arabidopsis met1 and ddm1 mutants, which show an increase of proximal recombination events and a simultaneous decrease in pericentromeric and distal regions (Colome-Tatche et al 2012;Melamed-Bessudo and Levy 2012;Mirouze et al 2012;Yelina et al 2012). Since H3K4me3 and H2A.Z landmarks are important for promotion of gene transcription (Liu et al 2009;Yelina et al 2012;Choi et al 2013) and are associated with high recombination rates in Arabidopsis (Yelina et al 2012) as well as in barley (Aliyeva-Schnorr et al 2015;Baker et al 2015), this suggests that both recombination and DNA-transposon insertion benefit from low compaction of DNA to occur within the genome. …”

Section: Retrotransposons Associate With Reduced Recombination Ratementioning

confidence: 99%

“…In plants, no homolog to PRDM9 subfamily was found (Zhang and Ma 2012). However, most H3K4me3-methylase encoding genes are expressed in meiotic cells in Arabidopsis and rice (Zhang and Ma 2012), and this mark is associated with recombinogenic regions in Arabidopsis and barley (Choi et al 2013;Aliyeva-Schnorr et al 2015;Shilo et al 2015). This may even be a general eukaryotic regulatory mechanism and may have originated in the ancestor of eukaryotes (Zhang and Ma 2012;Mercier et al 2015).…”

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confidence: 99%

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

et al. 2017

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During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry 60-70% of the genes. Identifying sequence and/or chromosome features affecting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed fine-scale mapping of COs and revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length. We used 774 SNPs to genotype 180 varieties representative of the Asian and European genetic pools and a segregating population of 1270 F 6 lines. We observed a common location for ancestral COs (predicted through linkage disequilibrium) and the COs derived from the segregating population. We delineated 73 small intervals (,26 kb) on chromosome 3B that contained 252 COs. We observed a significant association of COs with genic features (73 and 54% in recombinant and nonrecombinant intervals, respectively) and with those expressed during meiosis (67% in recombinant intervals and 48% in nonrecombinant intervals). Moreover, while the recombinant intervals contained similar amounts of retrotransposons and DNA transposons (42 and 53%), nonrecombinant intervals had a higher level of retrotransposons (63%) and lower levels of DNA transposons (28%). Consistent with this, we observed a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals. KEYWORDS recombination; meiosis; bread wheat; linkage disequilibrium; transposon; hotspot; sequence motif M EIOTIC recombination is a process that allows reshuffling of diversity by the reciprocal exchange of DNA called a crossover (CO). This phenomenon is conserved in most eukaryotes (for a review see Mercier et al. 2015) and follows the formation of a double-strand break (DSB) of DNA generated by the topoisomerase SPO11 complex. However, the number of DSBs is at least 10-to 50-fold greater than the number of COs which rarely exceeds three per bivalent chromosome per meiosis (Mercier et al. 2015). This paucity of COs per meiosis with regards to the number of DSBs suggests the existence of a tight control and regulation of recombination in plants that promote DSB repair in a manner that does not lead to COs. For example, the study of the two helicases AtFANCM and RECQ4 (AtRECQ4A and AtRECQ4B) (Crismani et al. 2012;Knoll et al. 2012;Girard et al. 2014;Séguéla-Arnaud et al. 2015) revealed three-and sixfold CO frequency increases in the Atfancm single mutant and the Atrecq4a/Atrecq4b double mutant, respectively, compared to the wild type. These increases result from additional COs from the class-II pathway which suggests that FANCM and RECQ4 prevent CO formation and direct recombination intermediates towar...

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“…Combination of this chromosome preparation method with FISH could be widely applied to explore the genome organization in plants, for instance, for karyotyping 11 , chromosomal mapping 12 , in synthetic studies, and for the integration of physical and genetic maps 13 .…”

Section: Discussionmentioning

confidence: 99%

A Fast Air-dry Dropping Chromosome Preparation Method Suitable for FISH in Plants

Aliyeva-Schnorr

Houben

2015

JoVE

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Preparation of chromosome spreads is a prerequisite for the successful performance of fluorescence in situ hybridization (FISH). Preparation of high quality plant chromosome spreads is challenging due to the rigid cell wall. One of the approved methods for the preparation of plant chromosomes is a so-called drop preparation, also known as drop-spreading or air-drying technique. Here, we present a protocol for the fast preparation of mitotic chromosome spreads suitable for the FISH detection of single and high copy DNA probes. This method is an improved variant of the air-dry drop method performed under a relative humidity of 50%-55%. This protocol comprises a reduced number of washing steps making its application easy, efficient and reproducible. Obvious benefits of this approach are well-spread, undamaged and numerous metaphase chromosomes serving as a perfect prerequisite for successful FISH analysis. Using this protocol we obtained high-quality chromosome spreads and reproducible FISH results for Hordeum vulgare, H. bulbosum, H. marinum, H. murinum, H. pubiflorum and Secale cereale.

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Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination‐poor region comprises more than half of barley chromosome 3H

Cited by 32 publications

References 74 publications

A chromosome conformation capture ordered sequence of the barley genome

A chromosome conformation capture ordered sequence of the barley genome

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

A Fast Air-dry Dropping Chromosome Preparation Method Suitable for FISH in Plants

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