Molecular Mechanisms of Epigenetic Variation in Plants

doi:10.1201/b16568-19

Cited by 18 publications

(24 citation statements)

References 16 publications

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“…This first approach offers opportunity to use recent highthroughput genotyping data (Rimbert et al 2017), but in the future massive data such as those generated by genotyping by sequencing (Deschamps et al 2012) can lead to the complete recombination map in wheat, allowing the same approach of parameter detection as realized in human and Arabidopsis (Myers et al 2005(Myers et al , 2008Choi et al 2013). We could thus identify recombination breakpoints located in pericentromeric regions which could be enhanced to improve recombination in these poorly recombinogenic regions.…”

Section: Discussionmentioning

confidence: 93%

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: Discussionmentioning

confidence: 93%

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

et al. 2017

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“…Compared to the average distance between markers in previous studies, the average distance was shorter than those of findings of 2.3-19.3 cM by other authors (Eujayl et al, 1998;Rubeena et al, 2003;Duran et al, 2004;Hamwieh et al, 2005;Tanyolac et al, 2010;Gupta et al, 2012;De la Puente et al, 2013;Sharpe et al, 2013;Gujaria-Verma, 2014;Ates et al, 2016). Use of SNP-based technologies has led to increased marker frequency per linkage group (Deschamps et al, 2012). Most linkage maps of lentil have been constructed using RAPD, SSR, ISSR, and AFLP markers.…”

Section: Lentil Linkage Mapmentioning

confidence: 99%

“…GBS is used for population studies, characterization, breeding, and trait mapping in diverse organisms and is based on high-throughput, next-generation sequencing of genomic fragments derived by digesting the genome of each individual in a population with restriction enzymes (Elshire et al, 2011;Kumar et al, 2012). This type of high-throughput genotyping technology allows for the development of high-density applications in QTL characterization (Deschamps et al, 2012). For example, QTLs controlling genes for drought tolerance in chickpea were identified using GBS (Jaganathan et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Based on parental data, genotypes are assigned. After that, recombination maps are created for each RIL (Deschamps et al, 2012). GBS is used for population studies, characterization, breeding, and trait mapping in diverse organisms and is based on high-throughput, next-generation sequencing of genomic fragments derived by digesting the genome of each individual in a population with restriction enzymes (Elshire et al, 2011;Kumar et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

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QTLs for iron concentration in seeds of the cultivated lentil (Lens culinaris Medic.) via genotyping by sequencing

Aldemir¹,

Ateş²,

Temel³

et al. 2017

Turk J Agric For

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“…GBS uses an amplified subset of genome from individual lines or plants to identify base differences between them [86,87]. Using bioinformatic analyses the SNPs are found on-the-go when comparing the two sets of sequences, so no prior information about the genotypes is required.…”

Section: Genotype-by-sequencingmentioning

confidence: 99%