Dissecting the U, M, S and C genomes of wild relatives of bread wheat (<i>Aegilops</i> spp.) into chromosomes and exploring their synteny with wheat

Molnár, István; Vrána, Jan; Burešová, Veronika; Cápal, Petr; Farkas, András; Darkó, Éva; Cseh, András; Kubaláková, Marie; Molnár-Láng, Márta; Doležel, Jaroslav

doi:10.1111/tpj.13266

Cited by 69 publications

(92 citation statements)

References 81 publications

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“…The results obtained on diploid wheatgrass species agreed well with previous studies and confirmed the high transferability of COS markers between species in the Triticeae [27,39,40,63,64]. The fact that 31–50% of the amplicons obtained on perennial wheatgrass species belonging to the tertiary gene pool were polymorphic relative to those obtained in hexaploid wheat suggested that a significant part of the genetic diversity in these wild species is due to the variability of intron regions [65].…”

Section: Discussionsupporting

confidence: 90%

“…The fact that 31–50% of the amplicons obtained on perennial wheatgrass species belonging to the tertiary gene pool were polymorphic relative to those obtained in hexaploid wheat suggested that a significant part of the genetic diversity in these wild species is due to the variability of intron regions [65]. Interestingly, using the same set of COS markers a similar ratio of polymorphic loci (46–53%) was obtained in diploid Aegilops species with the U, M, S or C genomes, which are more closely related to wheat [64]. …”

Section: Discussionmentioning

confidence: 96%

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Molecular cytogenetic (FISH) and genome analysis of diploid wheatgrasses and their phylogenetic relationship

et al. 2017

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This paper reports detailed FISH-based karyotypes for three diploid wheatgrass species Agropyron cristatum (L.) Beauv., Thinopyrum bessarabicum (Savul.&Rayss) A. Löve, Pseudoroegneria spicata (Pursh) A. Löve, the supposed ancestors of hexaploid Thinopyrum intermedium (Host) Barkworth & D.R.Dewey, compiled using DNA repeats and comparative genome analysis based on COS markers. Fluorescence in situ hybridization (FISH) with repetitive DNA probes proved suitable for the identification of individual chromosomes in the diploid JJ, StSt and PP genomes. Of the seven microsatellite markers tested only the (GAA)n trinucleotide sequence was appropriate for use as a single chromosome marker for the P. spicata AS chromosome. Based on COS marker analysis, the phylogenetic relationship between diploid wheatgrasses and the hexaploid bread wheat genomes was established. These findings confirmed that the J and E genomes are in neighbouring clusters.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 96%

Molecular cytogenetic (FISH) and genome analysis of diploid wheatgrasses and their phylogenetic relationship

et al. 2017

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“…Although the effect of technical factors cannot be ruled out, especially for weakly distorted markers that were randomly distributed across the genome, clusters of significantly distorted markers in the previously reported distorted regions for many grass species are most likely caused by genetic factors. Chromosome 1U, with the most severe segregation distortion, is homeologous to wheat group 1 chromosomes (Zhang et al 1998; Molnar et al 2016) and barley chromosome 1H (Edae et al 2016). Segregation distortion regions have been reported on the short arms of wheat group 1 chromosome (Li et al 2015), Ae.…”

Section: Resultsmentioning

confidence: 99%

“…The use of alien segments that carry novel genes depends on the extent of chromosome collinearity and meiotic pairing of alien chromosomes with homeologous chromosomes (Devos et al 1993; Lukaszewski et al 2004; Devos et al 2007; Molnar et al 2016). In the current study, the level of collinearity of Ae.…”

Section: Resultsmentioning

confidence: 99%

Genotyping-by-Sequencing Facilitates a High-Density Consensus Linkage Map forAegilops umbellulata, a Wild Relative of Cultivated Wheat

Edae

Olivera

Jin

et al. 2017

G3 Genes|Genomes|Genetics

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High-density genetic maps are useful to precisely localize QTL or genes that might be used to improve traits of nutritional and/or economical importance in crops. However, high-density genetic maps are lacking for most wild relatives of crop species, including wheat. Aegilops umbellulata is a wild relative of wheat known for its potential as a source of biotic and abiotic stress resistance genes. In this work, we have developed a framework consensus genetic map using two biparental populations derived from accessions PI 298905, PI 542369, PI 5422375, and PI 554395. The framework map comprised 3009 genotype-bysequence SNPs with a total map size of 948.72 cM. On average, there were three SNPs per centimorgan for each chromosome. Chromosome 1U was the shortest (66.5 cM), with only 81 SNPs, whereas the remaining chromosomes had between 391 and 591 SNP markers. A total of 2395 unmapped SNPs were added to the linkage maps through a recombination frequency approach, and increased the number of SNPs placed on the consensus map to a total of 5404 markers. Segregation distortion was disproportionally high for chromosome 1U for both populations used to construct component linkage maps, and thus segregation distortion could be one of the probable reasons for the exceptionally reduced linkage size for chromosome 1U. From comparative analysis, Ae. umbellulata chromosomes except 4U showed moderate to strong collinearity with corresponding homeologous chromosomes of hexaploid wheat and barley. The present consensus map may serve as a reference map in QTL mapping and validation projects, and also in genome assembly to develop a reference genome sequence for Ae. umbellulata.

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“…caudata has a highly asymmetric karyotype distinct from the metacentric and submetacentric chromosomes of most Triticeae species suggesting the distortion of chromosome collinearity compared to wheat. Fluorescence in situ hybridisation (FISH) and molecular marker analysis of flow-sorted C-genome chromosomes confirmed genome rearrangements (Molnár et al, 2016; Molnár et al, 2015). A set of wheat (cv.…”

Section: Introductionmentioning

confidence: 96%

Development of Wheat-Aegilops caudataIntrogression Lines and Their Characterisation Using Genome-Specific KASP Markers

Grewal

Othmeni

Walker

et al. 2020

Preprint

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22Aegilops caudata L. [syn. Ae. markgrafii (Greuter) Hammer], a diploid wild relative of wheat 23 (2n = 2x = 14, CC), is an important source for new genetic variation for wheat improvement 24 due to a variety of disease resistance factors along with tolerance for various abiotic stresses. 25 Its practical utilisation in wheat improvement can be facilitated through the generation of 26 genome-wide introgressions leading to a variety of different wheat-Ae. caudata recombinant 27 lines. In this study, we report the generation of nine such wheat-Ae. caudata recombinant lines 28 which were characterized using wheat genome-specific KASP (Kompetitive Allele Specific 29 PCR) markers and multi-colour genomic in situ hybridization (mcGISH). Of these, six lines 30 have stable homozygous introgressions from Ae. caudata and will be used for future trait 31 analysis. Through a combination of molecular and cytological analysis of all the recombinant 32 lines, we were able to physically map 182 KASP markers onto the seven Ae. caudata 33 chromosomes, of which 155 were polymorphic specifically with only one wheat subgenome. 34Comparative analysis of the physical positions of these markers in the Ae. caudata and wheat 35 genomes confirmed that the former had chromosomal rearrangements with respect to wheat, 36 as previously reported. These wheat-Ae. caudata recombinant lines and KASP markers 37 provide a useful genetic resource for wheat improvement with the latter having a wider impact 38 as a tool for detection of introgressions from other Aegilops species into wheat. 39 40 Introgression of Aegilops caudata into wheat 71 diversity in wheat breeding. Over the past decades, however, efforts have been made to study 72 the molecular organisation of the Ae. caudata genome and its homology with wheat 73 homoeologous groups. Friebe et al. (1992) showed that Ae. caudata has a highly asymmetric 74 karyotype distinct from the metacentric and submetacentric chromosomes of most Triticeae 75 species suggesting the distortion of chromosome collinearity compared to wheat. Fluorescence 76 in situ hybridisation (FISH) and molecular marker analysis of flow-sorted C-genome 77 chromosomes confirmed genome rearrangements (Molnár et al., 2016; Molnár et al., 2015). A 78 set of wheat (cv. Alcedo)-Ae. caudata addition lines B-G (Schubert and Blüthner, 1992; 79 Schubert and Blüthner, 1995) have also been characterised extensively in previous studies 80 using cytogenetic markers (Friebe et al., 1992), isozyme analysis (Schmidt et al., 1993), Simple 81 Sequence Repeat (SSR) markers (Gong et al., 2017; Niu et al., 2018; Peil et al., 1998), FISH 82 with cDNA probes (Danilova et al., 2017), Conserved Orthologous Sequence (COS) and PCR-83 based Landmark Unique Gene (PLUG) markers (Gong et al., 2017), and sequential FISH and 84 genomic in situ hybridization (GISH) (Niu et al., 2018). Many of these studies found that the 85 Introgression of Aegilops caudata into wheat Alcedo-Ae. caudata addition lines carried several inversions and translocations although ...

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Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp.) into chromosomes and exploring their synteny with wheat

Cited by 69 publications

References 81 publications

Molecular cytogenetic (FISH) and genome analysis of diploid wheatgrasses and their phylogenetic relationship

Molecular cytogenetic (FISH) and genome analysis of diploid wheatgrasses and their phylogenetic relationship

Genotyping-by-Sequencing Facilitates a High-Density Consensus Linkage Map forAegilops umbellulata, a Wild Relative of Cultivated Wheat

Development of Wheat-Aegilops caudataIntrogression Lines and Their Characterisation Using Genome-Specific KASP Markers

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