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Supplemental Material, sj-pdf-1-apm-10.1177_01466216221084215 for Impact of Sampling Variability When Estimating the Explained Common Variance by Björn Andersson and Hao Luo in Applied Psychological Measurement

BACKGROUND: Over the past decade, demethylation inhibitors (DMIs) and succinate dehydrogenase inhibitors (SDHIs) fungicides have been extensively used to control to septoria tritici blotch, caused by Zymoseptoria tritici on wheat. This has led to the development and selection of alterations in the target-site enzymes (CYP51 and SDH, respectively).RESULTS: Taking advantage of newly and previously developed qPCR assays, the frequency of key alterations associated with DMI (CYP51-S524T) and SDHI (SDHC-T79N/I, C-N86S and C-H152R) resistance was assessed in Z. tritici infected wheat leaf samples collected from commercial crops (n = 140) across 14 European countries prior to fungicide application in the spring of 2019. This revealed the presence of a West to East gradient in the frequencies of the most common key alterations conferring azole (S524T) and SDHI resistance (T79N and N86S), with the highest frequencies measured in Ireland and Great Britain. These observations were corroborated by sequencing (CYP51 and SDH subunits) and sensitivity phenotyping (prothioconazole-desthio and fluxapyroxad) of Z. tritici isolates collected from a selection of field samples. Additional sampling made at the end of the 2019 season confirmed the continued increase in frequency of the targeted alterations. Investigations on historical leaf DNA samples originating from different European countries revealed that the frequency of all key alterations (except C-T79I) has been gradually increasing over the past decade.CONCLUSION: Whilst these alterations are quickly becoming dominant in Ireland and Great Britain, scope still exists to delay their selection throughout the wider European population, emphasizing the need for the implementation of fungicide anti-resistance measures. This article is protected by copyright. All rights reserved.

Skeletal damage is a challenge for laying hens, as the adaptations for egg laying make them susceptible to osteoporosis. We know that activity, growth and puberty influence skeletal quality genetics. However, in this story, we follow the process of resolving a QTL for skeletal quality to a single gene. Providing both a nutritional and a genetic solution and illustrating another level of complexity. Using divergently selected populations in an F2 cross, a QTL for skeletal quality was described. Utilising a series of experiments in the commercial founder line the QTL was fine mapped on chromosome 1 and the differences in physiology of hens that segregated for markers at the locus defined e.g. tibia breaking strength 200.4 vs 218.1 Newton (p< 0.002). Transcriptome profiling of tibia from the high and low bone strength genotype revealed a highly differentially expressed gene co localising to the QTL, the enzyme cystathionine beta synthase (CBS). CBS is a component of one carbon metabolism. Plasma homocysteine, the substrate of CBS had a higher concentration in the genotype associated with poor bone quality. Homocysteine interferes with crosslinking of the collagen matrix, critical to bone formation. Homocysteine can be re-methylated into methionine, a limiting amino acid in laying hens, using betaine as a methyl donor. Testing the hypothesis that reducing plasma homocysteine by feeding betaine, a widely available feed additive, would improve bone quality in laying hens proved successful.This is just one component of a complex trait and its elucidation took us along unexpected routes. However, I am optimistic that with modern tools and an open mind we can progress more quickly. Alongside understanding the factors that determine skeletal quality genetics, the discovery of the mechanisms behind complex traits, although rarely easy, offer the potential for novel interventions to improve animal health and production.

Additional file 1: Read length distribution and assembly coverage. (A) Distribution of read lengths as generated by the 454 Genome Sequencer FLX/Titanium. The read length in base pairs (bp) is on the horizontal axis and the read count is on the vertical axis. The plot displays a bimodal curve with one peak at 250 bp and another one at 500 bp, typical for each one of the two platform types used for sequencing. (B) Shows the number of assembly positions on the vertical axis with a certain level of coverage on the horizontal axis. The plot shows that the average coverage is around 47 times. (PDF 55 KB)

Additional file 5: Evolutionary analyses of a recently acquired Giardia gene. Evolutionary analyses of a recently acquired Giardia gene. (A) A maximum likelihood tree of an acetyl transferase gene (GLP15_874). Only representatives of the homologs showing the highest similarity to the Giardia sequences are included. The tree is based on 139 unambiguously aligned amino acid positions. (B) Alignment of conserved hypothetical proteins from G. intestinalis GS (GL50581_4454) and WB (GL50803_10192) to all detected bacterial homologs. A putative amino acid sequence from a G. intestinalis P15 pseudogene is included and the positions of frameshift and in-frame termination codons are indicated. (C) A maximum likelihood tree based on 137 unambiguously aligned amino acid positions in the alignment shown in (B). Accession numbers are shown in parentheses. Only bootstrap values >50% are shown in the trees. Unambiguously aligned regions were identified manually and removed. Representative homologs with high sequence similarity to these genes were selected using the BLAST-EXPLORER software. (PDF 337 KB)

Additional file 7: VSP extended polyadenylation signal and VSP phylogenetic tree. (A) Comparative analysis of the extended polyadenylation sequence of VSP genes. The conservation of the VSP polyadenylation motif was investigated using the MEME software. Downstream regions (200 bp) of VSP genes were extracted and queried for the presence of conserved motifs. The VSP genes of all three Giardia isolates carries a very similar conserved motif that extends over at least 16 bp and is strictly positioned 0-15 bp from the translational stop codon. The P15 motif is more strictly conserved and carries a few more semi-conserved positions for a longer motif than the corresponding motifs in WB and GS. (B) A phylogenetic tree of VSP genes from P15 and WB. The VSP phylogenetic tree is based on a clustalw2 protein alignment of 156 VSP genes from WB and P15. VSP genes were selected for alignment by all-against-all BLASTP, and only VSP genes that showed at least 65% protein identity to the best-matching non-identical hit were used for the alignment (n = 156). In order to improve the alignment, sequences were trimmed (190 aa were removed from the 5' part of all sequences). Subsequent clustering was performed using maximum likelihood as implemented in the software RAxML version 7.0.4 using with the rapid bootstrap setting (-f a). The tree was rendered using the ape package for R. Black dots represent nodes with > = 50% bootstrap support. The gene id (genbank locus tag) is indicated at the tip of the branch. Blue labels represent genes from WB while black labels represent genes from P15. The tree revealed two primary groups (A and B), which are distinguished based on their distance in the tree. (PDF 172 KB)