A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

Paux, Etienne; Sourdille, Pierre; Salse, Jérôme; Saintenac, Cyrille; Choulet, Frédéric; Leroy, Philippe; Korol, Abraham B.; Michalak, M. K.; Kianian, Shahryar F.; Spielmeyer, Wolfgang; Lagudah, Evans; Somers, Daryl J.; Kilian, Andrzej; Alaux, Michaël; Vautrin, Sonia; Bergès, Hélène; Eversole, Kellye; Appels, R.; Šafář, Jan; Šimková, Hana; Doležel, Jaroslav; Bernard, Michel; Feuillet, Catherine

doi:10.1126/science.1161847

Cited by 367 publications

(443 citation statements)

References 23 publications

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“…It is represented by a minimum tiling path (MTP) of 67,000 BAC clones. Given a genome size of 5.1 Gb 10 , more than 95% of the barley genome is represented in the physical map, comparing favourably to the 1,036 contigs that represent 80% of the 1 Gb wheat chromosome 3B 11 .…”

Section: A Sequence-enriched Barley Physical Mapmentioning

confidence: 99%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

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Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement

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Section: A Sequence-enriched Barley Physical Mapmentioning

confidence: 99%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

1,293

880

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“…The International Wheat Genome Sequencing Consortium aims at flow-sorting and sequencing the individual chromosomes of bread wheat, and significant progress has been made with several chromosomes, for example 3B (ref. 6) and 4A (ref. 7).…”

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Draft genome of the wheat A-genome progenitor Triticum urartu

Ling

Zhao

Liu

et al. 2013

Nature

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“…Initial studies were based on aneuploid stocks (deletion lines; Endo and Gill 1996) and revealed that the frequency of meiotic recombination is highly biased toward the ends of chromosomes (Paris et al 2000;Paux et al 2008;Saintenac et al 2009). However, this does not rely on the distal position since when the chromosome arms are inverted (telomeres placed at the centromeres and vice versa), COs still occur in the same region whatever its location (Lukaszewski et al 2012).…”

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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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A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

Cited by 367 publications

References 23 publications

A physical, genetic and functional sequence assembly of the barley genome

A physical, genetic and functional sequence assembly of the barley genome

Draft genome of the wheat A-genome progenitor Triticum urartu

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

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