7 results on '"Gardiner, Laura-Jayne"'
Search Results
2. Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat
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Lu, Fu-Hao, McKenzie, Neil, Gardiner, Laura-Jayne, Luo, Ming-Cheng, Hall, Anthony, and Bevan, Michael W
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chr3DL ,AcademicSubjects/SCI02254 ,Aegilops ,Triticum aestivum ,Health Informatics ,Chromosomes, Plant ,Evolution, Molecular ,Gene Expression Regulation, Plant ,wheat ,Gene expression ,Homologous chromosome ,Aegilops tauschii ,Gene ,Triticum ,Genetics ,Ploidies ,biology ,Research ,synteny ,Computational Biology ,food and beverages ,Chromosome ,Genomics ,DNA Methylation ,Chromatin Assembly and Disassembly ,biology.organism_classification ,ATAC ,Chromatin ,Computer Science Applications ,Chromosome Arm ,AcademicSubjects/SCI00960 ,gene expression in polyploids ,Ploidy ,Genome, Plant ,Pseudogenes - Abstract
BackgroundPolyploidy is centrally important in the evolution and domestication of plants because it leads to major genomic changes, such as altered patterns of gene expression, which are thought to underlie the emergence of new traits. Despite the common occurrence of these globally altered patterns of gene expression in polyploids, the mechanisms involved are not well understood.ResultsUsing a precisely defined framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3 L chromosome arm of diploid Aegilops tauschii, we show that 70% of these gene pairs exhibited proportionately reduced gene expression, in which expression in the hexaploid context of the 3DL genes was ∼40% of the levels observed in diploid Ae tauschii. Several genes showed elevated expression during the later stages of grain development in wheat compared with Ae tauschii. Gene sequence and methylation differences probably accounted for only a few cases of differences in gene expression. In contrast, chromosome-wide patterns of reduced chromatin accessibility of genes in the hexaploid chromosome arm compared with its diploid progenitor were correlated with both reduced gene expression and the imposition of new patterns of gene expression.ConclusionsOur pilot-scale analyses show that chromatin compaction may orchestrate reduced gene expression levels in the hexaploid chromosome arm of wheat compared to its diploid progenitor chromosome arm.
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- 2020
3. A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene.
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Gardiner, Laura-Jayne, Bansept-Basler, Pauline, El-Soda, Mohamed, Hall, Anthony, and O'Sullivan, Donal M.
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STRIPE rust , *GENE mapping , *WHEAT , *GENES , *PANEL analysis , *WHEAT diseases & pests , *GENETIC recombination - Abstract
We used three approaches to map the yellow rust resistance gene Yr7 and identify associated SNPs in wheat. First, we used a traditional QTL mapping approach using a double haploid (DH) population and mapped Yr7 to a low-recombination region of chromosome 2B. To fine map the QTL, we then used an association mapping panel. Both populations were SNP array genotyped allowing alignment of QTL and genome-wide association scans based on common segregating SNPs. Analysis of the association panel spanning the QTL interval, narrowed the interval down to a single haplotype block. Finally, we used mapping-by-sequencing of resistant and susceptible DH bulks to identify a candidate gene in the interval showing high homology to a previously suggested Yr7 candidate and to populate the Yr7 interval with a higher density of polymorphisms. We highlight the power of combining mapping-by-sequencing, delivering a complete list of gene-based segregating polymorphisms in the interval with the high recombination, low LD precision of the association mapping panel. Our mapping-by-sequencing methodology is applicable to any trait and our results validate the approach in wheat, where with a near complete reference genome sequence, we are able to define a small interval containing the causative gene. [ABSTRACT FROM AUTHOR]
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- 2020
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4. Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential.
- Author
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Molero, Gemma, Joynson, Ryan, Pinera‐Chavez, Francisco J., Gardiner, Laura‐Jayne, Rivera‐Amado, Carolina, Hall, Anthony, and Reynolds, Matthew P.
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WHEAT yields ,WHEAT ,BOTANISTS ,RADIATION ,GRAIN yields ,BIOMASS - Abstract
Summary: One of the major challenges for plant scientists is increasing wheat (Triticum aestivum) yield potential (YP). A significant bottleneck for increasing YP is achieving increased biomass through optimization of radiation use efficiency (RUE) along the crop cycle. Exotic material such as landraces and synthetic wheat has been incorporated into breeding programmes in an attempt to alleviate this; however, their contribution to YP is still unclear. To understand the genetic basis of biomass accumulation and RUE, we applied genome‐wide association study (GWAS) to a panel of 150 elite spring wheat genotypes including many landrace and synthetically derived lines. The panel was evaluated for 31 traits over 2 years under optimal growing conditions and genotyped using the 35K wheat breeders array. Marker‐trait association identified 94 SNPs significantly associated with yield, agronomic and phenology‐related traits along with RUE and final biomass (BM_PM) at various growth stages that explained 7%–17% of phenotypic variation. Common SNP markers were identified for grain yield, BM_PM and RUE on chromosomes 5A and 7A. Additionally, landrace and synthetic derivative lines showed higher thousand grain weight (TGW), BM_PM and RUE but lower grain number (GM2) and harvest index (HI). Our work demonstrates the use of exotic material as a valuable resource to increase YP. It also provides markers for use in marker‐assisted breeding to systematically increase BM_PM, RUE and TGW and avoid the TGW/GM2 and BM_PM/HI trade‐off. Thus, achieving greater genetic gains in elite germplasm while also highlighting genomic regions and candidate genes for further study. [ABSTRACT FROM AUTHOR]
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- 2019
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5. Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat.
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Gardiner, Laura‐Jayne, Bansept‐Basler, Pauline, Olohan, Lisa, Joynson, Ryan, Brenchley, Rachel, Hall, Neil, O'Sullivan, Donal M., and Hall, Anthony
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STRIPE rust , *WHEAT disease & pest resistance , *BRACHYPODIUM , *HAPLOTYPES , *POLYPLOIDY in plant chromosomes , *LOCUS (Genetics) , *GENOMICS , *GENETICS - Abstract
Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat- Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo-chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo-chromosomes allow us to demonstrate the application of mapping-by-sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub-genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a smaller genic region than was previously possible; associate the interval with one wheat sub-genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user-friendly community resource for phenotype mapping. [ABSTRACT FROM AUTHOR]
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- 2016
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6. Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species.
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Gardiner, Laura‐Jayne, Gawroński, Piotr, Olohan, Lisa, Schnurbusch, Thorsten, Hall, Neil, and Hall, Anthony
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PLANT species , *PROGENITOR cells , *PLANT genetics , *NUCLEOTIDE sequence , *BRACHYPODIUM ,WHEAT genetics - Abstract
Mapping-by-sequencing analyses have largely required a complete reference sequence and employed whole genome re-sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re-sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early-flowering locus in einkorn wheat ( Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene-rich regions of hexaploid bread wheat to design a 110-Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo-chromosomes derived from the capture probe target sequence, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval. [ABSTRACT FROM AUTHOR]
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- 2014
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7. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat.
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Gardiner, Laura-Jayne, Brabbs, Thomas, Akhunov, Alina, Jordan, Katherine, Budak, Hikmet, Richmond, Todd, Singh, Sukhwinder, Catchpole, Leah, Akhunov, Eduard, and Hall, Anthony
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WHEAT , *COMPLEMENTARY DNA , *GENES , *PROMOTERS (Genetics) , *PLANT genomes , *NUCLEOTIDE sequencing - Abstract
Background Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. Results We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture. Conclusions We show that a capture design employing an "island strategy" can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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