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PAG XXV: Worldwide plant genomics

The Earlham Institute will be at the largest plant and animal genomics conference in the world, based in San Diego, US.

January 13, 2017

Among the 2000 talks and 140 workshops, EI Faculty will be sharing their latest advancements and expertise in crop and plant research in wheat, potatoes, brassica, yams and peas. New cutting edge genomics and bioinformatics studies, tools and methods will be presented to assist the scientific community and breeders industry, and in turn, benefit the public.

See below for what we have in store at PAG XXV:

Saturday 14 January

From Zero to Many: Assembling Wheat Genomes with w2rap

Bernardo Clavijo Di Palma Group.
11:50, Triticeae Genetics and Genomics, Session 1: Progress in structural and functional genomics workshop.

A year ago, we presented a CS42 whole genome shotgun assembly, publicly available on Ensemble Plants, and currently, is the most accessed dataset. During that project, we developed w2rap, a pipeline for short-read assembly capable of assembling the complex wheat genome consistently.

Moving into the multi-reference era, we are now presenting five more wheat genomes assembled with w2rap. However, the multi-genome wheat era will come with specific challenges; with data integration and standard formats to play a key role in unlocking the potential of these massive datasets. We will discuss the future strategies for seamless integration of genome assemblies, to develop the tools that will allow us to build, and interrogate multi-genome datasets.

Read more, here: Can we produce a better wheat crop to feed the world? Single to multiple wheat genomics

Genotype-to-Phenotype Associations in Common Pea and Wild Relatives

Kirstie Hetherington, Di Palma Group
14:00, Cool Season Legumes workshop

Peas (Pisum sativum) are an important crop plant and are important for food security. These cool season legumes are the second most important family of crops and are high in protein making them important for food and animal fodder. Furthermore, peas are useful in crop rotation as they can symbiotically fix nitrogen, reducing the need for fertiliser.

Challenges and Opportunities in Plant Science Data Management

Rob Davey, Davey Group.
16:00, Data Stewardship in the Life Sciences workshop.

Open data and integrative data sharing are fundamental factors in order to address the challenges of modern data-intensive science. There is a clear need to develop and maintain community-focussed, semantically-aware data stewardship and management platforms, such as COPO, that are able to cope with the description and sharing of potentially huge data sets arising from the life sciences. Once made available, it is not sufficient to assume that researchers around the globe have requisite skills and resources to analyse these data.

Sunday 15 January

Scalable-Infield Phenotyping for DNA Measurements of Performance Related Traits to Study Gene Introgression in Bread Wheat

Ji Zhou, Anthony Hall Group.
08:25, Gene Introgression workshop

Automated in-field phenotyping can provide continuous and precise measures of adaptation and performance traits that are key to today’s breeding pipelines and agricultural practices. Here, we will introduce our integrated field phenotyping systems at EI and the John Innes Centre, including UAV (unmanned aerial vehicles), 3D scanning crop phenotyping platform (Phenospex), cost-effective CropQuant workstations and other novel hardware/software solutions that facilitate high-resolution and high-frequency crop phenotyping.

Monday 16 January

CyVerse for Brassica: Performing Associative Transcriptomics by Integrating with Sequence and Phenotype Repositories

Annemarie Eckes, Davey Group
19:25, CyVerse - Software, Tools, and Services for Data-Driven Discovery workshop

Associative Transcriptomics (AT) is a method that links a physical genome, via the transcriptome, to quantitative phenotypic information. For complex polyploid crops such as Brassica napus, AT can be used to facilitate the identification of SNP markers. However, there are certain problems in performing AT for the Brassica Community. We are developing a reproducible workflow to make AT analysis available to the UK Brassica Community and beyond. The aim is to integrate phenotyping data stored in the Brassica Information Portal (BIP) (https://bip.earlham.ac.uk/) and sequence data from sequence repositories to establish an AT analysis framework, powered by tools and resources available within CyVerse (http://cyverseuk.org/).

Tuesday 17 January

Improved Methodology for Large Fragment Plant Resistance-Gene Capture

Michael Giolai, Clark Group
14:20, MYcroarray - Advances in Target Capture for NGS workshop

Plant resistance genes (R-genes) are the genetic basis of many disease resistances. Pathogen evolution rates typically outpace the rate at which resistant plant varieties can be generated. An alternative to traditional breeding strategies is finding novel resistances in wild relatives followed by marker assisted selection, or transgenic technology (especially as resistance is normally a dominant trait). Resistance gene enrichment sequencing (Ren-seq) is an approach to efficiently characterise a plants R-gene repertoire by targeted sequence enrichment.

Read more, here: Forming a second line of plant defence - capturing disease-resistant DNA

Wednesday 18 January

Addressing the challenges and opportunities for information and data sharing associated with plant germplasm

Rob Davey, Davey Group
11:30, DivSeek: Data Standards for Interoperable Tools

The DivSeek Data Standards for Interoperable Tools Working Group will promote best practice in data sharing in the plant sciences, through the use of open and interoperable software powered by the adoption of open standards, i.e. programmatic interoperability standards (APIs), controlled vocabularies, trait dictionaries, metadata standards, and ontologies.

Identifying Sex Determination Loci in the Highly Heterozygous White Guinea Yam (Dioscorea rotundata Poir)

Ben White, Haerty Group
12:35, Sweetpotato and Yam Genomics

White Guinea yam (Dioscorea rotundata Poir.) is a staple crop of great agricultural, cultural and economic significance to Africa, the Americas, the Caribbean, South Pacific and Asia. While demand for yam in sub-Saharan Africa is high, there is a continuing decline in production due to pests, reduced soil fertility and disease. Despite the importance of this crop, there are currently limited genomics resources available for yam that could facilitate breeding initiatives, nor comprehensive phylogenetic or evolutionary studies.

Discovery and Visualisation of Homologous Genes and Gene Families Using Galaxy

Anil Thanki, Davey Group
14:00, DivSeek: Data Standards for Interoperable Tools

The phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of gene families and plays a vital role in finding ancestral gene duplication events as well as identifying regions that are under positive selection within species. Available at: https://github.com/TGAC/earlham-galaxytools.

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