MuDR Transposase Increases the Frequency of Meiotic Crossovers in the Vicinity of a Mu Insertion in the Maize a1 Gene

Yandeau‐Nelson, Marna D.; Zhou, Qing; Yao, Huilu; Xu, Xiaojie; Nikolau, Basil J.; Schnable, Patrick S.

doi:10.1534/genetics.104.035089

Cited by 28 publications

(24 citation statements)

References 91 publications

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“…This observation is in direct contrast to the trans-acting autonomous transposon MuDR that increased the rate of recombination at an a1 allele containing a Mu1 insertion but did not change the distribution of recombinant breakpoints compared to patterns observed in other a1 alleles (Yandeau-Nelson et al 2005). This suggests, not surprisingly, that different types of trans-acting modifiers will affect recombination in different ways.…”

Section: Discussionmentioning

confidence: 61%

Effects of trans-acting Genetic Modifiers on Meiotic Recombination Across the a1–sh2 Interval of Maize

2006

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Meiotic recombination rates are potentially affected by cis-and trans-acting factors, i.e., genotypespecific modifiers that do or do not reside in the recombining interval, respectively. Effects of trans modifiers on recombination across the $140-kb maize a1-sh2 interval of chromosome 3L were studied in the absence of polymorphic cis factors in three genetically diverse backgrounds into which a sequenceidentical a1-sh2 interval had been introgressed. Genetic distances across a1-sh2 varied twofold among genetic backgrounds. Although the existence of regions exhibiting high and low rates of recombination (hot and cold spots, respectively) was conserved across backgrounds, the absolute rates of recombination in these sequence-identical regions differed significantly among backgrounds. In addition, an intergenic hot spot had a higher rate of recombination as compared to the genome average rate of recombination in one background and not in another. Recombination rates across two genetic intervals on chromosome 1 did not exhibit the same relationships among backgrounds as was observed in a1-sh2. This suggests that at least some detected trans-acting factors do not equally affect recombination across the genome. This study establishes that trans modifier(s) polymorphic among genetic backgrounds can increase and decrease recombination in both genic and intergenic regions over relatively small genetic and physical intervals.

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Section: Discussionmentioning

confidence: 61%

Effects of trans-acting Genetic Modifiers on Meiotic Recombination Across the a1–sh2 Interval of Maize

2006

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“…This could be explained by a higher survival rate of DNA transposons inserted close to genes and a remaining opportunist and strategic processes to maintain, or even under certain conditions to increase, the number of DNA transposons. An example in maize was described at the a1 locus where MuDR, autonomous element of Mutator family which encodes a transposase, supported the capacity of DNA transposons to influence recombination (Yandeau-Nelson et al 2005).…”

Section: Retrotransposons Associate With Reduced Recombination Ratementioning

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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“…The genome might be more accessible for transposon insertions in regions of intense recombination. It remains unclear whether recombination promotes transposon insertions or, vice versa (Duret et al, 2000), although the latter explanation is supported by the finding that MuDR transposase increases the frequency of meiotic crossovers in the vicinity of Mu insertions (Yandeau-Nelson et al, 2005). The relationship between transposons and recombination (Downs and Jackson, 1999;Kapitonov and Jurka, 2005) is likely to have significant evolutionary implications, especially as many DNA transposons have an affinity to insert into genes (Bureau and Wessler, 1992;Bureau et al, 1996).…”

Section: Processes Acting In Regions Of Reduced Recombinationmentioning

confidence: 99%

The role of repetitive DNA in structure and evolution of sex chromosomes in plants

et al. 2009

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Eukaryotic genomes contain a large proportion of repetitive DNA sequences, mostly transposable elements (TEs) and tandem repeats. These repetitive sequences often colonize specific chromosomal (Y or W chromosomes, B chromosomes) or subchromosomal (telomeres, centromeres) niches. Sex chromosomes, especially non-recombining regions of the Y chromosome, are subject to different evolutionary forces compared with autosomes. In nonrecombining regions of the Y chromosome repetitive DNA sequences are accumulated, representing a dominant and early process forming the Y chromosome, probably before genes start to degenerate. Here we review the occurrence and role of repetitive DNA in Y chromosome evolution in various species with a focus on dioecious plants. We also discuss the potential link between recombination and transposition in shaping genomes.

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MuDR Transposase Increases the Frequency of Meiotic Crossovers in the Vicinity of a Mu Insertion in the Maize a1 Gene

Cited by 28 publications

References 91 publications

Effects of trans-acting Genetic Modifiers on Meiotic Recombination Across the a1–sh2 Interval of Maize

Effects of trans-acting Genetic Modifiers on Meiotic Recombination Across the a1–sh2 Interval of Maize

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

The role of repetitive DNA in structure and evolution of sex chromosomes in plants

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