Development of Chromosome-Specific BAC Resources for Genomics of Bread Wheat

Šafář, Jan; Šimková, Hana; Kubaláková, Marie; Číhalíková, Jarmila; Suchánková, Pavla; Bartoš, Jan; Doležel, Jaroslav

doi:10.1159/000313072

Cited by 129 publications

(100 citation statements)

References 118 publications

(70 reference statements)

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“…Recently, methods of purifying the individual wheat chromosomes and producing chromosome-specific BAC libraries have been developed (Doležel et al 2007(Doležel et al , Šafář et al 2010. By treating each chromosome individually, the complexities of physical mapping and sequence assembly can be greatly reduced.…”

Section: Introductionmentioning

confidence: 99%

Functional features of a single chromosome arm in wheat (1AL) determined from its structure

Lucas

Šimková

Šafář

et al. 2011

Funct Integr Genomics

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Bread wheat (Triticum aestivum L.) is one of the most important crops globally and a high priority for genetic improvement, but its large and complex genome has been seen as intractable to whole genome sequencing. Isolation of individual wheat chromosome arms has facilitated large-scale sequence analyses. However, so far there is no such survey of sequences from the A genome of wheat. Greater understanding of an A chromosome could facilitate wheat improvement and future sequencing of the entire genome. We have constructed BAC library from the long arm of T. aestivum chromosome 1A (1AL) and obtained BAC end sequences from 7,470 clones encompassing the arm. We obtained 13,445 (89.99%) useful sequences with a cumulative length of 7.57 Mb, representing 1.43% of 1AL and about 0.14% of the entire A genome. The GC content of the sequences was 44.7%, and 90% of the chromosome was estimated to comprise repeat sequences, while just over 1% encoded expressed genes. From the sequence data, we identified a large number of sites suitable for development of molecular markers (362 SSR and 6,948 ISBP) which will have utility for mapping this chromosome and for marker assisted breeding. From 44 putative ISBP markers tested 23 (52.3%) were found to be useful. The BAC end sequence data also enabled the identification of genes and syntenic blocks specific to chromosome 1AL, suggesting regions of particular functional interest and targets for future research.

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Section: Introductionmentioning

confidence: 99%

Functional features of a single chromosome arm in wheat (1AL) determined from its structure

Lucas

Šimková

Šafář

et al. 2011

Funct Integr Genomics

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“…These runs comprised 25.72 Gb, 60.58 Gb and 46.26 Gb of sequence for chromosomes 5A, 5B and 5D, respectively. Based on the estimated wheat chromosome arm sizes [56], these data correspond to coverage levels of 48.35X, 104.45X and 94.41X, for chromosomes 5A, 5B and 5D, respectively.…”

Section: Simulationsmentioning

confidence: 99%

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data

Margarido

Heckerman

2015

PLoS Comput Biol

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As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft genome sequences are published at a striking pace. With well-established methodologies, larger and more complex genomes are being tackled, including polyploid plant genomes. Given the similarity between multiple copies of a basic genome in polyploid individuals, assembly of such data usually results in collapsed contigs that represent a variable number of homoeologous genomic regions. Unfortunately, such collapse is often not ideal, as keeping contigs separate can lead both to improved assembly and also insights about how haplotypes influence phenotype. Here, we describe a first step in avoiding inappropriate collapse during assembly. In particular, we describe ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, we report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencing data. We also show applicability of the method for variant calling and allele dosage estimation. Results for simulated and real datasets are discussed and provide evidence that ConPADE performs well as long as enough sequencing coverage is available, or the true contig ploidy is low. We show that ConPADE may also be used for related applications, such as the identification of duplicated genes in fragmented assemblies, although refinements are needed.

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“…Genome analysis in bread wheat poses substantial challenges; in addition to the complexity associated with its hexaploid structure, the bread wheat genome is very large (~ 17 Gb; around 40 times the size of rice, or nearly six times larger than the human genome) and consists of between 80-90% repetitive sequence (Šafář et al, 2010(Šafář et al, , Wanjugi et al, 2009). …”

Section: Introductionmentioning

confidence: 99%

Genome diversity in Triticum aestivum

Lai¹

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The aims of this PhD research are to identify and characterise genome diversity in Triticum aestivum (bread wheat).This research will establish a process for the identification of large numbers of single nucleotide polymorphisms (SNPs) and other genetic variations in Triticum aestivum.Single nucleotide polymorphisms (SNPs) are the most abundant type of molecular genetic marker and can be used for producing high-resolution genetic maps, marker-trait association studies and marker assisted breeding. Large polyploid genomes, such as wheat, present a challenge for SNP discovery due to the potential presence of multiple homoeologues for each gene.AutoSNPdb has been successfully applied to identify SNPs from Sanger sequence data for several species, including barley, rice and Brassica, but the volume of data required to accurately call SNPs in the complex genome of wheat has prevented its application to this important crop. DNA sequencing technology has been revolutionised by the introduction of next generation sequencing, and it is now possible to generate several million sequence reads in a timely and cost effective manner.Wheat transcriptome sequence data has been generated using Roche 454 Life Sciences technology. This data has been applied for SNP discovery using a modified autoSNPdb method, which integrates SNP and gene annotation information with a graphical viewer. A total of 4,694,141 sequence reads from three bread wheat varieties were assembled to identify a total of 38,928 candidate SNPs. Each SNP is within an assembly complete with annotation, enabling the selection of polymorphism within genes of interest.The discovery of large numbers of genomic SNPs across 16 Australian diverse bread wheat varieties has been completed using a novel algorithm SGSautoSNP. More than 10x whole genome shotgun Illumina paired read sequence data was generated through a bioplatforms collaboration and the data mapped to the draft assemblies of chromosomes ii 7A, 7B and 7D. Over 4 million inter-varietal SNPs were identified. SNP density varied along the lengths chromosome syntenic builds as well as between genomes.SNP density analysis and SNP transition/transversion ratio analysis provide insights into the evolution and breeding history of this important crop. Both the SNP density and SNP transition/transversion ratios across the D genome are significantly lower than across the A and B genomes. This difference reflects the evolutionary history of this crop. In addition, genes within low SNP density regions may have been selected during domestication and breeding. Furthermore, this SNP resource permits the application of high resolution skim based genotyping by sequencing (GBS), trait association and analysis of structural variation in populations.An integrated database and portal for wheat genome resource, WheatGenome.info, has been established and published online. This portal provides a variety of web-based systems hosting wheat genome and genomic data, including genomic SNPs, to support wheat research and crop improve...

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Development of Chromosome-Specific BAC Resources for Genomics of Bread Wheat

Cited by 129 publications

References 118 publications

Functional features of a single chromosome arm in wheat (1AL) determined from its structure

Functional features of a single chromosome arm in wheat (1AL) determined from its structure

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data

Genome diversity in Triticum aestivum

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