Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS

Berkman, Paul J.; Skarshewski, Adam; Lorenc, Michał T.; Lai, Kaitao; Duran, Chris; Ling, Edmund Y. S.; Stiller, Jiri; Smits, Lars; Imelfort, Michael; Manoli, Sahana; McKenzie, Megan; Kubaláková, Marie; Šimková, Hana; Batley, Jacqueline; Fleury, Delphine; Doležel, Jaroslav; Edwards, David

doi:10.1111/j.1467-7652.2010.00587.x

Cited by 108 publications

(103 citation statements)

References 40 publications

(66 reference statements)

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“…The integrative GenomeZipper approach has emerged as a key common standard for comparative genome analysis that enables the rapid development of a draft gene-augmented chromosomal template for large and complex grass genomes (Mayer et al, 2009Berkman et al, 2011;Vitulo et al, 2011;Hernandez et al, 2012). This is an important development for perennial ryegrass, since the size and complexity of its genome are major barriers toward developing a reference genome sequence.…”

Section: Discussionmentioning

confidence: 99%

“…It further integrates the genome information of sequenced grass species to construct a linear gene order model at the highest possible resolution and to resolve species-specific local rearrangements. Such synteny models have proven successful to determine gene order and orientation on both single flow-sorted chromosomes (Mayer et al, 2009;Berkman et al, 2011;Vitulo et al, 2011;Wicker et al, 2011;Hernandez et al, 2012) and whole genomes . Extending this concept to perennial ryegrass enables in silico prediction of the genome locations of unmapped genes and allows gene-based marker development in specific target regions to accelerate fine-mapping and mapbased cloning of genes or quantitative trait loci (QTL) of interest.…”

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confidence: 99%

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The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics

et al. 2012

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Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genomewide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics

et al. 2012

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“…Similarly, LG1 and LG2 were assigned to chromosomes F and G. This ability to isolate individual chromosomes will be useful in high-throughput physical mapping. This could also be used to discover genes and determine the order of low-copy genic regions on a chromosome as was done in wheat [99,100] and barley [101,102].…”

Section: Physical Mappingmentioning

confidence: 99%

Impact of Genomic Technologies on Chickpea Breeding Strategies

2012

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Abstract:The major abiotic and biotic stresses that adversely affect yield of chickpea (Cicer arietinum L.) include drought, heat, fusarium wilt, ascochyta blight and pod borer. Excellent progress has been made in developing short-duration varieties with high resistance to fusarium wilt. The early maturity helps in escaping terminal drought and heat stresses and the adaptation of chickpea to short-season environments. Ascochyta blight continues to be a major challenge to chickpea productivity in areas where chickpea is exposed to cool and wet conditions. Limited variability for pod borer resistance has been a major bottleneck in the development of pod borer resistant cultivars. The use of genomics technologies in chickpea breeding programs has been limited, since available genomic resources were not adequate and limited polymorphism was observed in the cultivated chickpea for the available molecular markers. Remarkable progress has been made in the development of genetic and genomic resources in recent years and integration of genomic technologies in chickpea breeding has now started. Marker-assisted breeding is currently being used for improving drought tolerance and combining resistance to diseases. The integration of genomic technologies is expected to improve the precision and efficiency of chickpea breeding in the development of improved cultivars with enhanced resistance to abiotic and biotic stresses, better adaptation to existing and evolving agro-ecologies and traits preferred by farmers, industries and consumers.

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“…Some SSR (kupg) markers were designed based on the survey sequence data for the short arm of chromosome 7D (Berkman et al, 2011) by searching for SSR motifs using SciRoKo version 3.4 software (Kofler et al, 2007). For mapping of leaf rust-resistance locus Lr34 (Krattinger et al, 2009), the primer pair 5'-TGCGGCGATTCTATACTACT-3' and 5'-CCGACATCAAGAACCTCC-3' was designed.…”

Section: Phenotype Evaluation As a Quantitative Traitmentioning

confidence: 99%

Fine mapping of Hch1, the causal D-genome gene for hybrid chlorosis in interspecific crosses between tetraploid wheat and Aegilops tauschii

et al. 2015

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Hybrid chlorosis, one of the reproductive barriers between tetraploid wheat and its D-genome progenitor, Aegilops tauschii, inhibits normal growth of synthetic wheat hexaploids. Hybrid chlorosis appears to be due to an epistatic interaction of two loci from the AB and D wheat genomes. Our previous study assigned the causal D-genome gene for hybrid chlorosis, Hch1, to the short arm of chromosome 7D. Here, we constructed a fine map of 7DS near Hch1 using 280 F 2 individuals from a cross of two wheat synthetic lines, one showing normal growth and the other showing hybrid chlorosis. The hybrid chlorosis phenotype was controlled by a single dominant allele of the Hch1 locus in the synthetic hexaploids. Hch1 was closely linked to four new markers within 0.2 cM, and may be localized near or within the two Ae. tauschii scaffolds containing the linked markers on 7DS. Comparative analysis of the Hch1 chromosomal region for Ae. tauschii, barley and Brachypodium showed that a local inversion occurred in the region proximal to Hch1 during the divergence between barley and Ae. tauschii, and that the Hch1 region on wheat 7DS is syntenic to Brachypodium chromosome 1. These observations provide useful information for further studies toward map-based cloning of Hch1.

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Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS

Cited by 108 publications

References 40 publications

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics

Impact of Genomic Technologies on Chickpea Breeding Strategies

Fine mapping of <i>Hch1</i>, the causal D-genome gene for hybrid chlorosis in interspecific crosses between tetraploid wheat and <i>Aegilops tauschii</i>

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