A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes

Yu, Yangyang; Tomkins, Jeffrey; Waugh, Robbie; Frisch, David; Kudrna, David; Kleinhofs, A.; Brueggeman, Robert; Muehlbauer, Gary J.; Wise, Roger P.; Wing, Rod A.

doi:10.1007/s001220051584

Cited by 177 publications

(146 citation statements)

References 57 publications

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“…We first obtained complete genomic sequences of VRN-1 including approximately 500 bp of the 5¢ and 300 bp of the 3¢ regions from BAC clones using overlapping PCR fragments. We sequenced this gene from BACs 631P8 (VRN-H1, AY750995) from the barley variety Morex (Yu et al 2000), 1256C17 (VRN-A1, AY747598) and 1225D16 (VRN-B1, AY747602) from the tetraploid wheat variety Langdon (Cenci et al 2003), and 22J2 (VRN-D1, AY747605) from an EcoRI BAC library of T. tauschii (Xu et al 2002).…”

Section: Cloning and Sequencingmentioning

confidence: 99%

Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat

et al. 2005

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The broad adaptability of wheat and barley is in part attributable to their flexible growth habit, in that spring forms have recurrently evolved from the ancestral winter growth habit. In diploid wheat and barley growth habit is determined by allelic variation at the VRN-1 and/or VRN-2 loci, whereas in the polyploid wheat species it is determined primarily by allelic variation at VRN-1. Dominant Vrn-A1 alleles for spring growth habit are frequently associated with mutations in the promoter region in diploid wheat and in the A genome of common wheat. However, several dominant Vrn-A1, Vrn-B1, Vrn-D1 (common wheat) and Vrn-H1 (barley) alleles show no polymorphisms in the promoter region relative to their respective recessive alleles. In this study, we sequenced the complete VRN-1 gene from these accessions and found that all of them have large deletions within the first intron, which overlap in a 4-kb region. Furthermore, a 2.8-kb segment within the 4-kb region showed high sequence conservation among the different recessive alleles. PCR markers for these deletions showed that similar deletions were present in all the accessions with known Vrn-B1 and Vrn-D1 alleles, and in 51 hexaploid spring wheat accessions previously shown to have no polymorphisms in the VRN-A1 promoter region. Twenty-four tetraploid wheat accessions had a similar deletion in VRN-A1 intron 1. We hypothesize that the 2.8-kb conserved region includes regulatory elements important for the vernalization requirement. Epistatic interactions between VRN-H2 and the VRN-H1 allele with the intron 1 deletion suggest that the deleted region may include a recognition site for the flowering repression mediated by the product of the VRN-H2 gene of barley.

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Section: Cloning and Sequencingmentioning

confidence: 99%

Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat

et al. 2005

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“…Considering average inserts of 100 kb, a five fold genome coverage of the small genomes of Arabidopsis thaliana (125 Mb) and rice (450 Mb) would require 7,000 and 23,000 BAC clones, respectively (Choi et al 1995;Zhang et al 1996). However, species with large genomes, such as barley (5,000 Mb) or diploid wheat (5,600 Mb), require 250,000 and 280,000 clones for a similar coverage (Lijavetzky et al 1999;Yu et al 2000).…”

Section: Introductionmentioning

confidence: 99%

Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum)

et al. 2003

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Durum wheat (Triticum turgidum ssp. durum, 2n = 4x = 28, genomes AB) is an economically important cereal used as the raw material to make pasta and semolina. In this paper we present the construction and characterization of a bacterial artificial chromosome (BAC) library of tetraploid durum wheat cv. Langdon. This variety was selected because of the availability of substitution lines that facilitate the assignment of BACs to the A and B genome. The selected Langdon line has a 30-cM segment of chromosome 6BS from T. turgidum ssp. dicoccoides carrying a gene for high grain protein content, the target of a positional cloning effort in our laboratory. A total of 516,096 clones were organized in 1,344 384-well plates and blotted on 28 high-density filters. Ninety-eight percent of these clones had wheat DNA inserts (0.3% chloroplast DNA, 1.4% empty clones and 0.3% empty wells). The average insert size of 500 randomly selected BAC clones was 131 kb, resulting in a coverage of 5.1-fold genome equivalents for each of the two genomes, and a 99.4% probability of recovering any gene from each of the two genomes of durum wheat. Six known copy-number probes were used to validate this theoretical coverage and gave an estimated coverage of 5.8-fold genome equivalents. Screening of the library with 11 probes related to grain storage proteins and starch biosynthesis showed that the library contains several clones for each of these genes, confirming the value of the library in characterizing the organization of these important gene families. In addition, characterization of fingerprints from colinear BACs from the A and B genomes showed a large differentiation between the A and B genomes. This library will be a useful tool for evolutionary studies in one of the best characterized polyploid systems and a source of valuable genes for wheat. Clones and high-density filters can be requested at

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“…Six large-insert BAC libraries of barley cv Morex had been constructed and characterized previously (Yu et al, 2000;Schulte et al, 2011). Additionally, genecontaining BACs had been identified in the library HVVMRXALLhA and rearrayed for fingerprinting (The International Barley Genome Sequencing Consortium, 2012).…”

Section: Assembly Of the Physical Mapmentioning

confidence: 99%

“…Six BAC libraries were used in this study (Yu et al, 2000;Schulte et al, 2011). These had been either constructed by partial enzymatic fragmentation of high-M r DNA with the restriction endonucleases HindIII, EcoRI, or MboI or after mechanical fragmentation and blunt-end ligation.…”

Section: Hicf and Automatic Contig Assemblymentioning

confidence: 99%

“…At this stage, two contigs were merged only if a minimum of two BAC clones at the end of each contig matched in a reciprocal and unique manner and shared marker information with a maximum genetic distance of 5 cM. Finally, all contigs composed of only two BAC clones were examined to identify those consisting of equivalent clones from the library HVVMRXALLhA (Yu et al, 2000) and its rearrayed subset of gene-containing clones (Madishetty et al, 2007;named HVVMRX83KhA after rearraying). By comparing the average fragment number per clone in the final map with the average insert size determined by pulsed field gel electrophoresis or BAC sequencing (The International Barley Genome Sequencing Consortium, 2012), we determined the average size of an FPC consensus band to be 1.24 kb.…”

Section: Manual Editingmentioning

confidence: 99%

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A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

et al. 2013

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Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.

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A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes

Cited by 177 publications

References 57 publications

Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat

Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat

Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum)

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

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