http://hdl.handle.net/2440/34068 2021-02-25T17:36:30Z http://hdl.handle.net/2440/112727 Title: Functional genomics of seed development in cereals Author: Li, M.; Lopato, S.; Kovalchuk, N.; Langridge, P. 2013-01-01T00:00:00Z http://hdl.handle.net/2440/87068 Title: Improving crop nitrogen use in dryland farming: interactions and potential trade-offs between water- and nutrient-use efficiency Author: Garnett, T.; Rebetzke, G. Abstract: Improved nitrogen-use efficiency and water-use efficiency (WUE) of dryland farming crops are important goals for cereal breeders. There have been considerable efforts to improve these traits separately, but now there is an increasing demand for crops with improvement in both of these traits. Analysis of ecological and crop-based experimental data has identified an apparent trade-off between N-use efficiency and WUE, suggesting that the two breeding goals are not compatible. This review summarises the physiology underlying these two traits and the genetic/breeding efforts underway to improve them. It then examines the observed interaction between N-use efficiency and WUE. Understanding the nature of this interaction provides scope to maximise yields in water-limiting environments whilst minimising N losses. Strategies focussing on genetic improvement to improve both traits concurrently are then discussed. Description: Published Online: 10 JAN 2013 2013-01-01T00:00:00Z http://hdl.handle.net/2440/86580 Title: PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches Author: Watson-Haigh, N.; Kadarmideen, H.; Reverter, A. Abstract: Summary: We make the PCIT algorithm, used for detecting meaningful gene–gene associations in co-expression networks, available as an R package. Automatic detection of a suitable parallel environment is used such that scripts are portable between parallel and non-parallel environments with no modification of the script. Availability and implementation: Source code and binaries freely available (under GPL-3) for download via CRAN at http://cran.r-project.org/package=PCIT, implemented in R and supported on Linux and MS Windows. Description: First published online: December 9, 2009 2010-01-01T00:00:00Z http://hdl.handle.net/2440/86550 Title: SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments Author: Ajawatanawong, P.; Atkinson, G.; Watson-Haigh, N.; MacKenzie, B.; Baldauf, S. Abstract: Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/. Description: First published online: June 11, 2012. This article appears in: Web Server issue 2012-01-01T00:00:00Z