CONSULTANCY: Plant Science
Analysis of ordinal disease scores
- Scottish raspberries are a high quality, high value product.
Many plant diseases, such as root rot
in raspberries, are assessed visually
at regular intervals using ordered
categories such as the five point scale
from 1 (healthy) to 5 (dead). These
scores have a degree of subjectivity
and are made by different assessors on
different dates. Principal co-ordinates
analysis can combine information
across dates and assessors. Pairwise
similarities, based on all the disease
assessments, are derived for all plants.
These similarities are then condensed
into a small number of dimensions or
co-ordinates.
Variation in the first principal co-ordinate due to bed number.
In a raspberry root rot trial two cultivars and their offspring were scored on nine dates over a two-year period by three assessors. The first principal co-ordinate explained 43% of the similarity matrix and showed a strong spatial effect related to the slope of the field and consequent changes on soil moisture content. Heritabilities were calculated after removing this spatial effect and found to be significant for the first and third principal co-ordinates. By combining these principal co-ordinates with genetic marker data, quantitative trait loci for root rot resistance have been identified.
Identifying environmental influences on alternative splicing
Alternative splicing (AS) is a post-transcriptional process that increases the proteomic and functional capacity of genomes through production of alternative messenger RNA (mRNA) transcripts from the same gene. The development of RT-PCR panels that measure the changes in ratio of different alternatively spliced mRNAs simultaneously is an exciting development in plant genetics, as it allows us to monitor AS. Traditional statistical methods such as analysis of variance are an essential means of identifying real differences in AS resulting from varied experimental conditions. We have found evidence that over a quarter of 90 AS events studied so far in Arabidopsis plants exhibit environmental responses. For example, when grown under long and short day conditions, 21 AS events showed significant changes in spliced transcript ratios (p<0.10).
Concentrations of transcripts of different length from parts of individual plants exposed to long and short day lengths.
Spatial effects in plant variety trials
In plant variety trials, a complete replicate often occupies a large area of land and so is unlikely to be spatially homogeneous. Explicit inclusion of spatial effects in the analysis can complement the traditional design approach to handing this problem.
The Figure shows a variogram of the grain yield for a wheat trial after allowing for variety effects, indicating both a trend in yield across rows and a zigzag pattern across columns. A check on farm practice showed that the zigzag pattern was due to the direction of harvesting; east-west and west-east on odd and even numbered columns respectively. Two combine harvesters were also used. When these row and column effects were included in the analysis, residual variance was reduced by 40%. Accounting for the spatial effects increased the precision of the experiment and the power to detect true differences among the wheat varieties.
A variogram of the grain yield (t/ha) for a wheat trial, showing mean squared difference in residuals as a function of the number of rows and columns separating plots.