Homologous Recombination in Maize

Dooner, Hugo K.; Hsia, An-Ping; Schnable, Patrick S.

doi:10.1007/978-0-387-77863-1_19

Cited by 4 publications

(4 citation statements)

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“…Both types of events cluster in genes (this study and [32]), but we have demonstrated that gene density is not sufficient to explain the non-uniform distributions of Mu insertions and recombination events along chromosomes.…”

Section: Discussionmentioning

confidence: 54%

“…Although there are some exceptions (viz., the long arms of Chr 2 and 5), overall the distributions of Mu insertions and meiotic recombination are similar, suggesting that common features may be involved in site selection for both kinds of events. Both types of events cluster in genes (this study and [32] ), but we have demonstrated that gene density is not sufficient to explain the non-uniform distributions of Mu insertions and recombination events along chromosomes.…”

Section: Discussionmentioning

confidence: 54%

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Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

et al. 2009

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The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mu transposons contain highly similar ∼215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional complexity of the Mu transposon system. The distribution of >40,000 non-redundant Mu insertion sites was strikingly non-uniform, such that rates increased in proportion to distance from the centromere. An identified putative Mu transposase binding consensus site does not explain this non-uniformity. An integrated genetic map containing more than 10,000 genetic markers was constructed and aligned to the sequence of the maize reference genome. Recombination rates (cM/Mb) are also strikingly non-uniform, with rates increasing in proportion to distance from the centromere. Mu insertion site frequencies are strongly correlated with recombination rates. Gene density does not fully explain the chromosomal distribution of Mu insertion and recombination sites, because pronounced preferences for the distal portion of chromosome are still observed even after accounting for gene density. The similarity of the distributions of Mu insertions and meiotic recombination sites suggests that common features, such as chromatin structure, are involved in site selection for both Mu insertion and meiotic recombination. The finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions marked with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination.

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Section: Discussionmentioning

confidence: 54%

Section: Discussionmentioning

confidence: 54%

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

et al. 2009

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“…here is ample evidence that most recombination in maize takes place in or around genes (1)(2)(3) and that little, if any, recombination takes place in the repetitive and methylated retrotransposon DNA that makes up the bulk of the genome (4,5). The evidence that retrotransposons are largely recombinationally inert is 2-fold: (i) when homozygous, the standard situation in inbreds, they do not contribute significantly to genetic length (4), and (ii) when hemizygous, a common situation in hybrids, no recombination junctions fall in intervals containing them (5).…”

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confidence: 99%

Haplotype structure strongly affects recombination in a maize genetic interval polymorphic for Helitron and retrotransposon insertions

Dooner

2009

Proc. Natl. Acad. Sci. U.S.A.

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We have asked here how the remarkable variation in maize haplotype structure affects recombination. We compared recombination across a genetic interval of 9S in 2 highly dissimilar heterozygotes that shared 1 parent. The genetic interval in the common haplotype is Ϸ100 kb long and contains 6 genes interspersed with gene-fragment-bearing Helitrons and retrotransposons that, together, comprise 70% of its length. In one heterozygote, most intergenic insertions are homozygous, although polymorphic, enabling us to determine whether any recombination junctions fall within them. In the other, most intergenic insertions are hemizygous and, thus, incapable of homologous recombination. Our analysis of the frequency and distribution of recombination in the interval revealed that: (i) Most junctions were circumscribed to the gene space, where they showed a highly nonuniform distribution. In both heterozygotes, more than half of the junctions fell in the stc1 gene, making it a clear recombination hotspot in the region. However, the genetic size of stc1 was 2- Ac ͉ bz locus ͉ genome ͉ hotspots ͉ methylation T here is ample evidence that most recombination in maize takes place in or around genes (1-3) and that little, if any, recombination takes place in the repetitive and methylated retrotransposon DNA that makes up the bulk of the genome (4, 5). The evidence that retrotransposons are largely recombinationally inert is 2-fold: (i) when homozygous, the standard situation in inbreds, they do not contribute significantly to genetic length (4), and (ii) when hemizygous, a common situation in hybrids, no recombination junctions fall in intervals containing them (5).The unprecedented haplotype diversity recently discovered in maize (6-8) raises several questions regarding the effect of local structural polymorphisms on recombination. In a recent pairwise comparison of 8 bz1 haplotypes, each one consisting of 8 genes spread over a stretch of DNA that averaged Ϸ90 kb, the percentage of shared sequences ranged from 25% to 84% (9). The lines differed by the existence of many polymorphic insertions in introns and intergenic regions, the main ones being LTR retrotransposons, often arranged in nests (10), miniature inverted repeat transposable elements (MITEs) (11), and Helitron transposons carrying fragments of several genes (12, 13). In addition, high SNP and indel heterozygosity would occur in most intergenic regions of hybrids made from those lines.This level of structural polymorphisms could affect recombination in multiple ways and, thus, contribute to the 2-to 3-fold variation in estimates of map distances for single genetic intervals that has been reported in different maize mapping populations (14-16). For example, the highly methylated retrotransposon clusters are probably heterochromatic, so retrotransposon hemizygosity could reduce recombination in adjacent genes; the level of small insertion and SNP affects overall sequence homology and, thus, could determine whether recombination occurs in intergenic regions lacking retrotra...

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“…A second gene known to be in the vicinity of p1 is defective kernel 1 (dek1), which was tentatively mapped at 0.8 cM proximal to p1 (Dooner 1980). The dek1 gene encodes a 2159-aa protein belonging to the calpain superfamily and is essential for kernel aleurone development (Becraft and Asuncion-Crabb 2000;Becraft et al 2002;Lid et al 2002;Wang et al 2003).…”

Section: Resultsmentioning

confidence: 99%

A Segmental Deletion Series Generated by Sister-Chromatid Transposition of Ac Transposable Elements in Maize

Zhang

Peterson

2005

Genetics

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Certain configurations of maize Ac/Ds transposon termini can undergo alternative transposition reactions leading to chromosome breakage and various types of stable chromosome rearrangements. Here, we show that a particular allele of the maize p1 gene containing an intact Ac element and a nearby terminally deleted Ac element ( fAc) can undergo sister-chromatid transposition (SCT) reactions that generate large flanking deletions. Among 35 deletions characterized, all begin at the Ac termini in the p1 gene and extend to various flanking sites proximal to p1. The deletions range in size from the smallest of 12,567 bp to the largest of .4.6 cM; .80% of the deletions removed the p2 gene, a paralog of p1 located 60 kb from p1 in the p1-vv allele and its derivatives. Sequencing of representative cases shows that the deletions have precise junctions between the transposon termini and the flanking genomic sequences. These results show that SCT events can efficiently generate interstitial deletions that are useful for in vivo dissection of local genome regions and for the rapid correlation of genetic and physical maps. Finally, we discuss evidence suggesting that deletions induced by alternative transposition reactions can occur at other genomic loci, indicating that this mechanism may have had a significant impact on genome evolution.

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Homologous Recombination in Maize

Cited by 4 publications

References 123 publications

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

Haplotype structure strongly affects recombination in a maize genetic interval polymorphic for Helitron and retrotransposon insertions

A Segmental Deletion Series Generated by Sister-Chromatid Transposition of Ac Transposable Elements in Maize

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