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Dive into the research topics where Erin E. Higgins is active.

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Featured researches published by Erin E. Higgins.


Nature Communications | 2014

The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure

Sateesh Kagale; Chushin Koh; John Nixon; Venkatesh Bollina; Wayne E. Clarke; Reetu Tuteja; Charles Spillane; Stephen J. Robinson; Matthew G. Links; Carling Clarke; Erin E. Higgins; Terry Huebert; Andrew G. Sharpe; Isobel A. P. Parkin

Camelina sativa is an oilseed with desirable agronomic and oil-quality attributes for a viable industrial oil platform crop. Here we generate the first chromosome-scale high-quality reference genome sequence for C. sativa and annotated 89,418 protein-coding genes, representing a whole-genome triplication event relative to the crucifer model Arabidopsis thaliana. C. sativa represents the first crop species to be sequenced from lineage I of the Brassicaceae. The well-preserved hexaploid genome structure of C. sativa surprisingly mirrors those of economically important amphidiploid Brassica crop species from lineage II as well as wheat and cotton. The three genomes of C. sativa show no evidence of fractionation bias and limited expression-level bias, both characteristics commonly associated with polyploid evolution. The highly undifferentiated polyploid genome of C. sativa presents significant consequences for breeding and genetic manipulation of this industrial oil crop.


PLOS ONE | 2013

Genomic DNA Enrichment Using Sequence Capture Microarrays: a Novel Approach to Discover Sequence Nucleotide Polymorphisms (SNP) in Brassica napus L

Wayne E. Clarke; Isobel A. P. Parkin; Humberto A. Gajardo; Daniel J. Gerhardt; Erin E. Higgins; Christine Sidebottom; Andrew G. Sharpe; Rod J. Snowdon; Maria L. Federico; Federico L. Iniguez-Luy

Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS) to discover single nucleotide polymorphisms (SNPs) in specific areas of the B. napus genome historically associated (via quantitative trait loci –QTL– analysis) to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 potentially useful SNPs were identified. Analysis of sequence coverage indicated a four-fold increased representation of target regions, with 57% of the filtered SNPs falling within these regions. Sixty percent of discovered SNPs corresponded to transitions while 40% were transversions. Interestingly, fifty eight percent of the SNPs were found in genic regions while 42% were found in intergenic regions. Further, a high percentage of genic SNPs was found in exons (65% and 64% for the A and C genomes, respectively). Two different genotyping assays were used to validate the discovered SNPs. Validation rates ranged from 61.5% to 84% of tested SNPs, underpinning the effectiveness of this SNP discovery approach. Most importantly, the discovered SNPs were associated with agronomically important regions of the B. napus genome generating a novel data resource for research and breeding this crop species.


Theoretical and Applied Genetics | 2017

A user guide to the Brassica 60K Illumina Infinium ™ SNP genotyping array

Annaliese S. Mason; Erin E. Higgins; Rod J. Snowdon; Jacqueline Batley; Anna Stein; Christian R. Werner; Isobel A. P. Parkin

The Brassica napus 60K Illumina Infinium™ SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies. We present data on which SNPs are locus-specific in winter, semi-winter and spring B. napus germplasm pools, rather than amplifying both an A-genome and a C-genome locus or multiple loci. Common issues that arise when analyzing array data will be discussed, particularly those unique to SNP markers and how to deal with these for practical applications in Brassica breeding applications.


BMC Plant Biology | 2015

Seedling development traits in Brassica napus examined by gene expression analysis and association mapping.

Niklas Körber; Anja Bus; Jinquan Li; Janet Higgins; Ian Bancroft; Erin E. Higgins; Isobel Alison Papworth Parkin; Bertha Salazar-Colqui; Rod J. Snowdon; Benjamin Stich

BackgroundAn optimal seedling development of Brassica napus plants leads to a higher yield stability even under suboptimal growing conditions and has therefore a high importance for plant breeders. The objectives of our study were to (i) examine the expression levels of candidate genes in seedling leaves of B. napus and correlate these with seedling development as well as (ii) detect genome regions associated with gene expression levels and seedling development traits in B. napus by genome-wide association mapping.ResultsThe expression levels of the 15 candidate genes examined in the 509 B. napus inbreds showed an averaged standard deviation of 5.6 across all inbreds and ranged from 3.2 to 8.8. The gene expression differences between the 509 B. napus inbreds were more than adequate for the correlation with phenotypic variation of seedling development. The average of the absolute value correlations of the correlation coefficients of 0.11 were observed with a range from 0.00 to 0.39. The candidate genes GER1, AILP1, PECT, and FBP were strongly correlated with the seedling development traits. In a genome-wide association study, we detected a total of 63 associations between single nucleotide polymorphisms (SNPs) and the seedling development traits and 31 SNP-gene associations for the candidate genes with a P-value < 0.0001. For the projected leaf area traits we identified five different association hot spots on the chromosomes A2, A7, C3, C6, and C7.ConclusionA total of 99.4% of the adjacent SNPs on the A genome and 93.0% of the adjacent SNPs on the C genome had a distance smaller than the average range of linkage disequilibrium. Therefore, this genome-wide association study is expected to result on average in 14.7% of the possible power. Compared to previous studies in B. napus, the SNP marker density of our study is expected to provide a higher power to detect SNP-trait/-gene associations in the B. napus diversity set. The large number of associations detected for the examined 14 seedling development traits indicated that these are genetically complex inherited. The results of our analyses suggested that the studied genes ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit (RBC) on the chromosomes A4 and C4 and fructose-1,6-bisphosphatase precursor (FBP) on the chromosomes A9 and C8 are cis-regulated.


Molecular Breeding | 2015

Single-nucleotide polymorphism identification and genotyping in Camelina sativa

Ravinder Singh; Venkatesh Bollina; Erin E. Higgins; Wayne E. Clarke; Christina Eynck; Christine Sidebottom; Richard Gugel; Rod J. Snowdon; Isobel A. P. Parkin

Camelina sativa, a largely relict crop, has recently returned to interest due to its potential as an industrial oilseed. Molecular markers are key tools that will allow C. sativa to benefit from modern breeding approaches. Two complementary methodologies, capture of 3′ cDNA tags and genomic reduced-representation libraries, both of which exploited second generation sequencing platforms, were used to develop a low density (768) Illumina GoldenGate single nucleotide polymorphism (SNP) array. The array allowed 533 SNP loci to be genetically mapped in a recombinant inbred population of C. sativa. Alignment of the SNP loci to the C. sativa genome identified the underlying sequenced regions that would delimit potential candidate genes in any mapping project. In addition, the SNP array was used to assess genetic variation among a collection of 175 accessions of C. sativa, identifying two sub-populations, yet low overall gene diversity. The SNP loci will provide useful tools for future crop improvement of C. sativa.


Genome | 2014

Genetic control of immunity to Turnip mosaic virus (TuMV) pathotype 1 in Brassica rapa (Chinese cabbage)

Derek J. Lydiate; Rachel L. Rusholme Pilcher; Erin E. Higgins; John A. Walsh

Turnip mosaic virus (TuMV) is the major virus infecting crops of the genus Brassica worldwide. A dominant resistance gene, TuRB01b, that confers immunity to the virus isolate UK 1 (a representative pathotype 1 isolate of TuMV) on Brassica rapa was identified in the Chinese cabbage cultivar Tropical Delight. The TuRB01b locus was mapped to a 2.9-cM interval on B. rapa chromosome 6 (A6) that was flanked by RFLP markers pN101e1 and pW137e1. This mapping used a first backcross (B(1)) population segregating for the resistance gene at TuRB01b and sets of RFLP markers employed in previous mapping experiments in Brassica. Virus-plant interaction phenotypes were assayed in inbred progeny derived from B(1) individuals to allow different virus isolates to be tested. Comparative mapping confirmed that A6 of B. rapa was equivalent to chromosome 6 of Brassica napus (A6) and that the map position of TuRB01b in B. rapa could be identical to that of TuRB01 in B. napus. Detailed evaluation of plant-virus interactions showed that TuRB01 and TuRB01b had indistinguishable specificities to a range of TuMV isolates. The possibility that TuRB01 and TuRB01b represent similar or identical alleles at the same A genome resistance locus suggests that B. napus acquired TuRB01 from the B. rapa gene pool.


G3: Genes, Genomes, Genetics | 2018

Detecting de Novo Homoeologous Recombination Events in Cultivated Brassica napus Using a Genome-Wide SNP Array

Erin E. Higgins; Wayne E. Clarke; Elaine C. Howell; Susan J. Armstrong; Isobel A. P. Parkin

The heavy selection pressure due to intensive breeding of Brassica napus has created a narrow gene pool, limiting the ability to produce improved varieties through crosses between B. napus cultivars. One mechanism that has contributed to the adaptation of important agronomic traits in the allotetraploid B. napus has been chromosomal rearrangements resulting from homoeologous recombination between the constituent A and C diploid genomes. Determining the rate and distribution of such events in natural B. napus will assist efforts to understand and potentially manipulate this phenomenon. The Brassica high-density 60K SNP array, which provides genome-wide coverage for assessment of recombination events, was used to assay 254 individuals derived from 11 diverse cultivated spring type B. napus. These analyses identified reciprocal allele gain and loss between the A and C genomes and allowed visualization of de novo homoeologous recombination events across the B. napus genome. The events ranged from loss/gain of 0.09 Mb to entire chromosomes, with almost 5% aneuploidy observed across all gametes. There was a bias toward sub-telomeric exchanges leading to genome homogenization at chromosome termini. The A genome replaced the C genome in 66% of events, and also featured more dominantly in gain of whole chromosomes. These analyses indicate de novo homoeologous recombination is a continuous source of variation in established Brassica napus and the rate of observed events appears to vary with genetic background. The Brassica 60K SNP array will be a useful tool in further study and manipulation of this phenomenon.


Theoretical and Applied Genetics | 2016

A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome.

Wayne E. Clarke; Erin E. Higgins; Joerg Plieske; Ralf Wieseke; Christine Sidebottom; Yogendra Khedikar; Jacqueline Batley; Dave Edwards; Jinling Meng; Ruiyuan Li; Cynthia T. Lawley; Jérôme Pauquet; Benjamin Laga; Wing Cheung; Federico L. Iniguez-Luy; Emmanuelle Dyrszka; Stephen Rae; Benjamin Stich; Rod J. Snowdon; Andrew G. Sharpe; Martin W. Ganal; Isobel A. P. Parkin


Journal of General Virology | 2007

Genetic control of broad-spectrum resistance to turnip mosaic virus in Brassica rapa (Chinese cabbage)

Rachel L. Rusholme; Erin E. Higgins; John A. Walsh; Derek J. Lydiate


Genome | 2010

Towards unambiguous transcript mapping in the allotetraploid Brassica napus.

Isobel A. P. Parkin; Wayne E. Clarke; ChristineSidebottomC. Sidebottom; WentaoZhangW. Zhang; Stephen J. Robinson; Matthew G. Links; SteveKarczS. Karcz; Erin E. Higgins; PierreFobertP. Fobert; Andrew G. Sharpe

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Isobel A. P. Parkin

Agriculture and Agri-Food Canada

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Wayne E. Clarke

Agriculture and Agri-Food Canada

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Derek J. Lydiate

Agriculture and Agri-Food Canada

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Stephen J. Robinson

Agriculture and Agri-Food Canada

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Federico L. Iniguez-Luy

University of Wisconsin-Madison

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Matthew G. Links

University of Saskatchewan

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