Physical maps and recombination frequency of six rice chromosomes

Wu, Jianzhong; Mizuno, Hiroshi; Hayashi-Tsugane, Mika; Ito, Yukiyo; Chiden, Yoshino; Fujisawa, Masaki; Katagiri, Satoshi; Saji, Shoko; Yoshiki, Shoji; Karasawa, Wataru; Yoshihara, Rie; Hayashi, Akiko; Kobayashi, Harumi; Ito, Kazue; Hamada, Masao; Okamoto, Masako; Ikeno, Maiko; Ichikawa, Yoko; Katayose, Yūichi; Yano, Masahiro; Matsumoto, Takashi; Sasaki, Takuji

doi:10.1046/j.1365-313x.2003.01903.x

Cited by 135 publications

(132 citation statements)

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“…We exploited the pseudomolecule of chromosome 3B (Choulet et al 2014) as well as high-throughput detection of SNPs (Rimbert et al 2017) to map 252 CO events in intervals of ,26 kb using genotyping data. This resolution has never been reached in wheat before and was close to the one observed for the four hotspots described in rice (Wu et al 2003). In the collared flycatcher, a songbird species, 279 COs were localized within intervals of ,10 kb (Smeds et al 2016) which was only 1.8 times more compared to our analysis (156 COs) while the wheat genome is 17 times larger.…”

Section: Discussionsupporting

confidence: 87%

“…New wheat-genomic tools allow more resolute analysis of recombination pattern Whole-genome, fine-scale recombination studies in plants have only been conducted in species for which the genome sequence was available (Wu et al 2003;Liu et al 2009;Paape et al 2012;Rodgers-Melnick et al 2015;Shilo et al 2015). However, this mainly restricted such analyses to species with small and compact genomes with low rates of TEs.…”

Section: Discussionmentioning

confidence: 99%

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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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Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

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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“…The peak of both QTLs corresponded to the previously mapped position of the mutant locus, brown pericarp, Rc (Kinoshita, 1998 Figure 1B, i). The genetic/ physical distance in this region averages 1.4 Mb/cM, much above the genome average of 200 to 250 kb/cM, as expected for a pericentromeric region (Zhao et al, 2002;Wu et al, 2003). An investigation of the genotype-phenotype relationship in 285 BC2F2 families demonstrated that all 18 families with red grain contained the O. rufipogon allele at either RM125 or the adjacent marker, RG30, suggesting that the gene underlying rg7.1 lay between these two markers.…”

Section: Rough Mapping Of Qtls and The Rc Mutantmentioning

confidence: 68%

Caught Red-Handed:RcEncodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice

et al. 2006

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Rc is a domestication-related gene required for red pericarp in rice (Oryza sativa). The red grain color is ubiquitous among the wild ancestors of O. sativa, in which it is closely associated with seed shattering and dormancy. Rc encodes a basic helix-loop-helix (bHLH) protein that was fine-mapped to an 18.5-kb region on rice chromosome 7 using a cross between Oryza rufipogon (red pericarp) and O. sativa cv Jefferson (white pericarp). Sequencing of the alleles from both mapping parents as well as from two independent genetic stocks of Rc revealed that the dominant red allele differed from the recessive white allele by a 14-bp deletion within exon 6 that knocked out the bHLH domain of the protein. A premature stop codon was identified in the second mutant stock that had a light red pericarp. RT-PCR experiments confirmed that the Rc gene was expressed in both red-and white-grained rice but that a shortened transcript was present in white varieties. Phylogenetic analysis, supported by comparative mapping in rice and maize (Zea mays), showed that Rc, a positive regulator of proanthocyanidin, is orthologous with INTENSIFIER1, a negative regulator of anthocyanin production in maize, and is not in the same clade as rice bHLH anthocyanin regulators.

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“…Crossing-over in the (peri-)centromeric regions, which may account for as much as 50% of the chromosome length, is essentially suppressed [23,36-40]. In genomes with smaller chromosomes, such as rice and Arabidopsis, cross-over suppression at the centromere is restricted within a relatively small region [4,41,42]. Like rice and Arabidopsis, the region of recombination suppression on chromosome 2 is also restricted to a relatively small region corresponding to ~30% of the chromosome length.…”

Section: Discussionmentioning

confidence: 99%

An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2

et al. 2011

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BackgroundIntegration of molecular, genetic and cytological maps is still a challenge for most plant species. Recent progress in molecular and cytogenetic studies created a basis for developing integrated maps in cucumber (Cucumis sativus L.).ResultsIn this study, eleven fosmid clones and three plasmids containing 45S rDNA, the centromeric satellite repeat Type III and the pericentriomeric repeat CsRP1 sequences respectively were hybridized to cucumber metaphase chromosomes to assign their cytological location on chromosome 2. Moreover, an integrated molecular cytogenetic map of cucumber chromosomes 2 was constructed by fluorescence in situ hybridization (FISH) mapping of 11 fosmid clones together with the cucumber centromere-specific Type III sequence on meiotic pachytene chromosomes. The cytogenetic map was fully integrated with genetic linkage map since each fosmid clone was anchored by a genetically mapped simple sequence repeat marker (SSR). The relationship between the genetic and physical distances along chromosome was analyzed.ConclusionsRecombination was not evenly distributed along the physical length of chromosome 2. Suppression of recombination was found in centromeric and pericentromeric regions. Our results also indicated that the molecular markers composing the linkage map for chromosome 2 provided excellent coverage of the chromosome.

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Physical maps and recombination frequency of six rice chromosomes

Cited by 135 publications

References 40 publications

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

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

Caught Red-Handed:RcEncodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice

An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2

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