Bioinformatics and genomic and phenomic platform development

Armstead, Ian (Project Lead)
Swain, Martin (Researcher Co‑Lead)
Doonan, John (Researcher Co‑Lead)
Boyle, Roger (Researcher Co‑Lead)
Hegarty, Matthew (Researcher Co‑Lead)
Thomas, Ian (Researcher Co‑Lead)
Huang, Lin (Researcher Co‑Lead)
Fernandez Fuentes, Narcis (Researcher Co‑Lead)
Neal, M (Researcher Co‑Lead)
Gay, Alan (Researcher Co‑Lead)

Project: Externally funded research

Description

Technological and analytical advances in plant science are increasingly data intensive. While these offer new opportunities for understanding and developing precision plant breeding they also bring considerable challenges. One of these challenges is in developing an informatics infrastructure that can accommodate the various dataset-types generated by research from the molecule to the field and implement the necessary relational integration to mine these datasets. This work brings together process and research in order to deliver informatic-based, high-throughput and genome/phenome-scale analytical methodologies to inform both fundamental research into genome/phenome biology and germplasm improvement in the context of plant breeding.

Status	Finished
Effective start/end date	01 Apr 2012 → 31 Mar 2017

UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This project contributes towards the following SDG(s):

SDG 2 Zero Hunger
SDG 3 Good Health and Well-being
SDG 6 Clean Water and Sanitation
SDG 13 Climate Action

Access Project

42 Article
2 Chapter
1 Poster
1 Editorial
More
- 1 Literature Review

A deep learning-integrated micro-CT image analysis pipeline for quantifying rice lodging resistance-related traits
Wu, D., Wu, D., Feng, H., Duan, L., Dai, G., Liu, X., Wang, K., Yang, P., Chen, G., Gay, A. P., Doonan, J. H., Niu, Z., Xiong, L. & Yang, W., 08 Mar 2021, In: Plant Communications. 2, 2, 13 p., 100165.
Research output: Contribution to journal › Article › peer-review

Open Access
File
42 Citations (Scopus)

205 Downloads (Pure)
Drought priming effects on alleviating the photosynthetic limitations of wheat cultivars (Triticum aestivum L.) with contrasting tolerance to abiotic stresses
Mendanha, T., Rosenqvist, E., Nordentoft Hyldgaard, B., Doonan, J. H. & Ottosen, C. O., 27 Nov 2020, In: Journal of Agronomy and Crop Science. 206, 6, p. 651-664 14 p.
Research output: Contribution to journal › Article › peer-review

Open Access
File
24 Citations (Scopus)

375 Downloads (Pure)
Genotypic variations in leaf and whole-plant water use efficiencies are closely related in bread wheat genotypes under well-watered and water-limited conditions during grain filling
del Pozo, A., Méndez-Espinoza, A. M., Romero-Bravo, S., Garriga, M., Estrada, F., Alcaíno, M., Camargo-Rodriguez, A. V., Corke, F. M. K., Doonan, J. H. & Lobos, G. A., 16 Jan 2020, In: Scientific Reports. 10, 1, 460.
Research output: Contribution to journal › Article › peer-review

Open Access
File
33 Citations (Scopus)

175 Downloads (Pure)
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
Gordon, S. P., Contreras-Moreira, B., Levy, J. J., Djamei, A., Czedik-Eysenberg, A., Tartaglio, V. S., Session, A., Martin, J., Cartwright, A., Katz, A., Singan, V. R., Goltsman, E., Barry, K., Dinh-Thi, V. H., Chalhoub, B., Diaz-Perez, A., Sancho, R., Lusinska, J., Wolny, E. & Nibau, C. & 13 others, Doonan, J. H., Mur, L. A. J., Plott, C., Jenkins, J., Hazen, S. P., Lee, S. J., Shu, S., Goodstein, D., Rokhsar, D., Schmutz, J., Hasterok, R., Catalan, P. & Vogel, J. P., 29 Jul 2020, In: Nature Communications. 11, 1, 16 p., 3670.
Research output: Contribution to journal › Article › peer-review

Open Access
File
80 Citations (Scopus)

339 Downloads (Pure)
High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenne L.)
Keep, T., Sampoux, J. P., Blanco-Pastor, J. L., Dehmer, K. J., Hegarty, M. J., Ledauphin, T., Litrico, I., Muylle, H., Roldán-Ruiz, I., Roschanski, A. M., Ruttink, T., Surault, F., Willner, E. & Barre, P., 01 Sept 2020, In: G3 (Bethesda, Md.). 10, 9, p. 3347-3364 18 p.
Research output: Contribution to journal › Article › peer-review

Open Access
File
30 Citations (Scopus)

172 Downloads (Pure)
Semi-Automated Field Plot Segmentation From UAS Imagery for Experimental Agriculture
Robb, C., Hardy, A., Doonan, J. H. & Brook, J., 09 Dec 2020, In: Frontiers in Plant Science. 11, 13 p., 591886.
Research output: Contribution to journal › Article › peer-review

Open Access
File
24 Citations (Scopus)

221 Downloads (Pure)
A comparative assessment of the performance of a stay-green sorghum (Sorghum bicolor (L) Moench) introgression line developed by marker-assisted selection and its parental lines
Galyuon, I. K., Gay, A., Hash, C. T., Bidinger, F. R. & Howarth, C., 26 Jun 2019, In: African Journal of Biotechnology. 18, 26, p. 548-563 16 p., 7118D0361330.
Research output: Contribution to journal › Article › peer-review

Open Access
File
340 Downloads (Pure)
Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)
Fradera-Sola, A., Thomas, A., Gasior, D., Harper, J., Hegarty, M., Armstead, I. & Fernandez Fuentes, N., 30 Jul 2019, In: PLoS ONE. 14, 7, e0220518.
Research output: Contribution to journal › Article › peer-review

Open Access
File
8 Citations (Scopus)

217 Downloads (Pure)
Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species
Maughan, P. J., Lee, R., Walstead, R., Vickerstaff, R. J., Fogarty, M. C., Brouwer, C. R., Reid, R. R., Jay, J. J., Bekele, W. A., Jackson, E. W., Tinker, N. A., Langdon, T., Schlueter, J. A. & Jellen, E. N., 22 Nov 2019, In: BMC Biology. 17, 1, 92.
Research output: Contribution to journal › Article › peer-review

Open Access
File
63 Citations (Scopus)

214 Downloads (Pure)
Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. Perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits
Harper, J., de Vega, J., Swain, S., Heavens, D., Gasior, D., Thomas, A., Evans, C., Lovatt, A., Lister, S., Thorogood, D., Skot, L., Hegarty, M., Blackmore, T., Kudrna, D., Byrne, S., Asp, T., Powell, W., Fernandez-Fuentes, N. & Armstead, I., 08 May 2019, In: Annals of Botany. 123, 6, p. 977-992 16 p., mcy230.
Research output: Contribution to journal › Article › peer-review

Open Access
File
7 Citations (Scopus)

216 Downloads (Pure)
Physiological and biochemical basis for stay-green trait in sorghum
Galyuon, I. K. A., Gay, A., Borrell, A. K. & Howarth, C. J., 2019, In: African Crop Science Journal. 27, 4, p. 653, 677
Research output: Contribution to journal › Article › peer-review

Open Access
File

178 Downloads (Pure)

Crop Genetics, Genomics and Germplasm (C3G) ISPG
Armstead, I. (Project Lead)
Biotechnology and Biological Sciences Research Council
01 Apr 2012 → 31 Mar 2017
Project: Externally funded research
Developing tools and resources for oat breeding
Armstead, I. (Project Lead), Howarth, C. (Researcher Co‑Lead) & Langdon, T. (Researcher Co‑Lead)
01 Apr 2012 → 31 Mar 2017
Project: Externally funded research
Introgression and wide hybrid genetics, genomics and germplasm development in Lolium/Festuca (Festulolium) and white clover
Armstead, I. (Project Lead), Humphreys, M. (Researcher Co‑Lead) & Jenkins, G. (Researcher Co‑Lead)
01 Apr 2012 → 31 Mar 2017
Project: Externally funded research
C3G: Lolium and Trifolium genetics, genomics and germplasm development
Armstead, I. (Project Lead), Skot, L. (Researcher Co‑Lead), Jenkins, G. (Researcher Co‑Lead), Thomas, I. (Researcher Co‑Lead), Marshall, A. (Researcher Co‑Lead) & Thorogood, D. (Researcher Co‑Lead)
01 Apr 2012 → 31 Mar 2017
Project: Externally funded research

11 Oral presentation
5 Conference
5 Workshop, Seminar, or Course
1 Hosting a non-academic visitor
More
- 1 Hosting an academic visitor

Conservation Agriculture workshop
Armstead, I. (Speaker)
2018
Activity: Participating in or organising an event › Workshop, Seminar, or Course
DivSeek round table
Doonan, J. (Speaker)
13 Jan 2017
Activity: Participating in or organising an event › Conference
DivSeek round table
Armstead, I. (Speaker)
13 Jan 2017 → 17 Jan 2017
Activity: Participating in or organising an event › Workshop, Seminar, or Course
Essex University
2016
Activity: Hosting a visitor › Hosting an academic visitor
Series of tours of NPPC
Armstead, I. (Speaker)
2016
Activity: Talk or presentation › Oral presentation
C-DES project talk
Armstead, I. (Speaker)
2016
Activity: Talk or presentation › Oral presentation
Series of tours of the NPPC facility
Armstead, I. (Speaker)
2016
Activity: Talk or presentation › Oral presentation
Hyperspectral Imaging
Armstead, I. (Participant)
2016
Activity: Participating in or organising an event › Workshop, Seminar, or Course
Waitrose Limited
2016
Activity: Hosting a visitor › Hosting a non-academic visitor
Application of fluorescence imaging to detect contamination on carcasses;
Gay, A. (Speaker)
2016
Activity: Talk or presentation › Oral presentation
Series of tours of NPPC facilities
Armstead, I. (Speaker)
2016
Activity: Talk or presentation › Oral presentation

Bioinformatics and genomic and phenomic platform development

Project Details

Description

UN Sustainable Development Goals

Access Project

Fingerprint

A deep learning-integrated micro-CT image analysis pipeline for quantifying rice lodging resistance-related traits

Drought priming effects on alleviating the photosynthetic limitations of wheat cultivars (Triticum aestivum L.) with contrasting tolerance to abiotic stresses

Genotypic variations in leaf and whole-plant water use efficiencies are closely related in bread wheat genotypes under well-watered and water-limited conditions during grain filling

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenne L.)

Semi-Automated Field Plot Segmentation From UAS Imagery for Experimental Agriculture

A comparative assessment of the performance of a stay-green sorghum (Sorghum bicolor (L) Moench) introgression line developed by marker-assisted selection and its parental lines

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)

Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. Perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits

Physiological and biochemical basis for stay-green trait in sorghum

Crop Genetics, Genomics and Germplasm (C3G) ISPG

Developing tools and resources for oat breeding

Introgression and wide hybrid genetics, genomics and germplasm development in Lolium/Festuca (Festulolium) and white clover

C3G: Lolium and Trifolium genetics, genomics and germplasm development

Conservation Agriculture workshop

DivSeek round table

DivSeek round table

Essex University

Series of tours of NPPC

C-DES project talk

Series of tours of the NPPC facility

Hyperspectral Imaging

Waitrose Limited

Application of fluorescence imaging to detect contamination on carcasses;

Series of tours of NPPC facilities

Bioinformatics and genomic and phenomic platform development

Project Details

Description

UN Sustainable Development Goals

Access Project

Fingerprint

Research output

Projects

Activities