Deletion Polymorphism in Wheat Chromosome Regions With Contrasting Recombination Rates

Dvořák, Jan; Yang, Zu-Li; You, Frank M.; Luo, Ming‐Cheng

doi:10.1534/genetics.103.024927

Cited by 55 publications

(60 citation statements)

References 47 publications

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“…This change in recombination rate divides the average chromosome arm into a proximal, low-recombination interval (LR), accounting for the proximal two-thirds of the arm, and a distal, highrecombination interval (HR) accounting for its distal one-third (Akhunov et al 2003a,b). The negative correlation of synteny and recombination rate along wheat chromosomes is consistent with the observation that insertions of paralogous genes along polyploid wheat chromosomes are correlated with recombination rate (Akhunov et al 2003b) and that polymorphisms for interstitial deletions of gene loci are most frequent in distal, high-recombination regions of polyploid wheat chromosomes (Dvorak et al 2004).…”

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confidence: 86%

Tempos of Gene Locus Deletions and Duplications and Their Relationship to Recombination Rate During Diploid and Polyploid Evolution in the Aegilops-Triticum Alliance

2005

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The origin of tetraploid wheat and the divergence of diploid ancestors of wheat A and D genomes were estimated to have occurred 0.36 and 2.7 million years ago, respectively. These estimates and the evolutionary history of 3159 gene loci were used to estimate the rates with which gene loci have been deleted and duplicated during the evolution of wheat diploid ancestors and during the evolution of polyploid wheat. During diploid evolution, the deletion rate was 2.1 3 10 ÿ3 locus ÿ1 MY ÿ1 for single-copy loci and 1.0 3 10 ÿ2 locus ÿ1 MY ÿ1 for loci in paralogous sets. Loci were duplicated with a rate of 2.9 3 10 ÿ3 locus ÿ1 MY ÿ1 during diploid evolution. During polyploid evolution, locus deletion and locus duplication rates were 1.8 3 10 ÿ2 and 1.8 3 10 ÿ3 locus ÿ1 MY ÿ1 , respectively. Locus deletion and duplication rates correlated positively with the distance of the locus from the centromere and the recombination rate during diploid evolution. The functions of deleted and duplicated loci were inferred to gain insight into the surprisingly high rate of deletions of loci present apparently only once in a genome. The significance of these findings for genome evolution at the diploid and polyploid level is discussed.

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confidence: 86%

Tempos of Gene Locus Deletions and Duplications and Their Relationship to Recombination Rate During Diploid and Polyploid Evolution in the Aegilops-Triticum Alliance

2005

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“…All showed the null haplotype for the Pin genes (Table I; Supplemental Table S1; Fig. 3), confirming that Pina and Pinb have been deleted in this species (Gautier et al, 2000;Dvorak et al, 2004).…”

Section: Tetraploid Speciessupporting

confidence: 53%

Recurrent Deletions of Puroindoline Genes at the GrainHardnessLocus in Four Independent Lineages of Polyploid Wheat

Huang

Gill

2007

Plant Physiology

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Polyploidy is known to induce numerous genetic and epigenetic changes but little is known about their physiological bases. In wheat, grain texture is mainly determined by the Hardness (Ha) locus consisting of genes Puroindoline a (Pina) and b (Pinb). These genes are conserved in diploid progenitors but were deleted from the A and B genomes of tetraploid Triticum turgidum (AB). We now report the recurrent deletions of Pina-Pinb in other lineages of polyploid wheat. We analyzed the Ha haplotype structure in 90 diploid and 300 polyploid accessions of Triticum and Aegilops spp. Pin genes were conserved in all diploid species and deletion haplotypes were detected in all polyploid Triticum and most of the polyploid Aegilops spp. Two Pina-Pinb deletion haplotypes were found in hexaploid wheat (Triticum aestivum; ABD). Pina and Pinb were eliminated from the G genome, but maintained in the A genome of tetraploid Triticum timopheevii (AG). Subsequently, Pina and Pinb were deleted from the A genome but retained in the A m genome of hexaploid Triticum zhukovskyi (A m AG). Comparison of deletion breakpoints demonstrated that the Pina-Pinb deletion occurred independently and recurrently in the four polyploid wheat species. The implications of Pina-Pinb deletions for polyploid-driven evolution of gene and genome and its possible physiological significance are discussed.

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“…To prepare Southern blots, DNAs were digested with restriction endonucleases and Southern blots were hybridized as described earlier (Dvorak et al 2004).…”

Section: Methodsmentioning

confidence: 99%

Discovery and Mapping of Wheat Ph1 Suppressors

2006

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Pairing between wheat (Triticum turgidum and T. aestivum) homeologous chromosomes is prevented by the expression of the Ph1 locus on the long arm of chromosome 5B. The genome of Aegilops speltoides suppresses Ph1 expression in wheat 3 Ae. speltoides hybrids. Suppressors with major effects were mapped as Mendelian loci on the long arms of Ae. speltoides chromosomes 3S and 7S. The chromosome 3S locus was designated Su1-Ph1 and the chromosome 7S locus was designated Su2-Ph1. A QTL with a minor effect was mapped on the short arm of chromosome 5S and was designated QPh.ucd-5S. The expression of Su1-Ph1 and Su2-Ph1 increased homeologous chromosome pairing in T. aestivum 3 Ae. speltoides hybrids by 8.4 and 5.8 chiasmata/cell, respectively. Su1-Ph1 was completely epistatic to Su2-Ph1, and the two genes acting together increased homeologous chromosome pairing in T. aestivum 3 Ae. speltoides hybrids to the same level as Su1-Ph1 acting alone. QPh.ucd-5S expression increased homeologous chromosome pairing by 1.6 chiasmata/cell in T. aestivum 3 Ae. speltoides hybrids and was additive to the expression of Su2-Ph1. It is hypothesized that the products of Su1-Ph1 and Su2-Ph1 affect pairing between homeologous chromosomes by regulating the expression of Ph1 but the product of QPh.ucd-5S may primarily regulate recombination between homologous chromosomes.

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Deletion Polymorphism in Wheat Chromosome Regions With Contrasting Recombination Rates

Cited by 55 publications

References 47 publications

Tempos of Gene Locus Deletions and Duplications and Their Relationship to Recombination Rate During Diploid and Polyploid Evolution in the Aegilops-Triticum Alliance

Tempos of Gene Locus Deletions and Duplications and Their Relationship to Recombination Rate During Diploid and Polyploid Evolution in the Aegilops-Triticum Alliance

Recurrent Deletions of Puroindoline Genes at the GrainHardnessLocus in Four Independent Lineages of Polyploid Wheat

Discovery and Mapping of Wheat Ph1 Suppressors

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