Biology subjects

Wilson, P. B.

Publications and source records attributed to Wilson, P. B..

6 recordsLinked to original sources

bioRxiv2020

Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse

Genetic diversity and maternal ancestry line relationships amongst a sample of 96 Cleveland Bay horses were investigated using a 479bp length of mitochondrial D-loop sequence. The analysis yielded at total of 11 haplotypes with 27 variable positions, all of which have been described in previous equine mitochondrial DNA d-loop studies. Four main haplotype clusters were present in the Cleveland Bay breed describing 89% of the total sample. This suggests that only four principal maternal ancestry lines exist in the present-day global Cleveland Bay population. Comparison of these sequences with other domestic horse haplotypes shows a close association of the Cleveland Bay horse with Northern European (Clade C), Iberian (Clade A) and North African (Clade B) horse breeds. This indicates that the Cleveland Bay horse may not have evolved exclusively from the now extinct Chapman horse, as previous work as suggested. The Cleveland Bay horse remains one of only fivedomestic horse breeds classified as Critical on the Rare Breeds Survival Trust (UK) Watchlist and our results provide important information on the origins of this breed and represent a valuable tool for conservation purposes.

genetics↗

bioRxiv2020

Genetic Analysis of The Endangered Cleveland Bay Horse: A Century of Breeding Characterised by Pedigree and Microsatellite Data

The Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. The breed is one of five equine breeds listed as "critical" (<300 registered adult breeding females) by the UK Rare Breeds Survival Trust in their annual Watchlist. Due to their critically endangered status, the current breadth of their genetic diversity is of concern, and assessment of this can lead to improved breed management strategies. Herein, both genealogical and molecular methods are combined in order to assess founder representation, lineage, and allelic diversity. Data from 16 microsatellite loci from a reference population of 402 individuals determined a loss of 91% and 48% of stallion and dam lines, respectively in the reference population. Only 3 ancestors determine 50% of the genome in the living population, with 70% of maternal lineage being derived from 3 founder females, and all paternal lineages traced back to a single founder stallion. Methods and theory are described in detail in order to demonstrate the scope of this analysis for wider conservation strategies. We quantitatively demonstrate the critical nature of the genetic resources within the breed, and offer a perspective on implementing this data in considered breed management strategies.

genetics↗

bioRxiv2020

Characterization Of Yellow Root Cassava And Food Products: Investigation Of Cyanogenic Glycosides And Pro-Vitamin A

ObjectiveCyanide is a highly toxic compound, and the consumption of products containing cyanide is of singificant public health concern. In contrast, {beta}-carotene possesses essential nutritional attributes related to human health, therefore the characterisation and quanfication of both compounds in food products is both fundamental and necessary. This investigation sought to identify the cyanide and {beta}-carotene levels in two flours produced from the roots of two varieties of cassava (Manihot esculenta crantz), namely UMUCASS-38 (TMS 01/1371) and NR 8082, and their associated food products. ResultsThe fresh tuber, raw flour and food products were analysed for levels of residual cyanide and {beta}-carotene using standard analytical methods. The cyanide content of NR 8082 (18.01{+/-}0.01 ppm) and UMUCASS 38 (17.02{+/-}0.02 ppm) flours were significantly higher (p < 0.05) than the residual cyanide levels determined in the cookies (10.00{+/-}0.00 ppm) and cake (7.10{+/-}0.14 ppm). The levels of {beta}-carotene determined in the sample varied significantly (p < 0.05). The highest levels of {beta}-carotene (6.53{+/-}0.02 {micro}g/g) were determined in raw roots of UMUCASS 38 while NR 8082 levels of {beta}-carotene were 1.12{+/-}0.02 {micro}g/g. Processing the roots into flour reduced the {beta}-carotene content to 4.78{+/-}0.01 {micro}g/g and 0.76{+/-}0.02 {micro}g/g in UMUCASS 38 and NR8082 flours, respectively. Cookies and cake produced from flour derived from the UMUCASS 38 variety had 2.15{+/-}0.01 {micro}g/g and 2.84{+/-}0.04 {micro}g/g of {beta}-carotene, respectively.

biochemistry↗

bioRxiv2019

Extending the genotype in Brachypodium by including DNA methylation reveals a joint contribution with genetics on adaptive traits

Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modelling revealed large genetic differences between families and a minor contribution of epigenomic variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation towards heritable phenotypic variation relative to genetic differences.

plant biology↗

bioRxiv2019

A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana

Field-grown plants have variable exposure to sunlight as a result of shifting cloud-cover, seasonal changes, canopy shading, and other environmental factors. As a result, they need to have developed a method for dissipating excess energy obtained from periodic excessive sunlight exposure. Non-photochemical quenching (NPQ) dissipates excess energy as heat, however the physical and molecular genetic mechanics of NPQ variation are not understood. In this study, we investigated the genetic loci involved in NPQ by first growing different Arabidopsis thaliana accessions in local and seasonal climate conditions, then measured their NPQ kinetics through development by chlorophyll fluorescence. We used genome-wide association studies (GWAS) to identify 15 significant quantitative trait loci (QTL) for a range of photosynthetic traits, including a QTL co-located with known NPQ gene PSBS (AT1G44575). We found there were large alternative regulatory segments between the PSBS promoter regions of the functional haplotypes and a significant difference in PsbS protein concentration. These findings parallel studies in rice showing recurrent regulatory evolution of this gene. The variation in the PSBS promoter and the changes underlying other QTLs could give insight to allow manipulations of NPQ in crops to improve their photosynthetic efficiency and yield. B.P. & J.B. conceived the project; B.P., J.B., P.W. and T.R. designed the research plan and analysis; P.W. supervised the experiments; T.R. performed most of the experiments and analysis; P.G., T.S., A.A. & E.A. designed and undertook experimental design, experiments and analysis for Figure 4; R.C. did the GWAS analysis; P.W., T.R. & A.A. wrote the article with contributions of all the authors. O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/539379v1_fig4.gif" ALT="Figure 4"> View larger version (57K): org.highwire.dtl.DTLVardef@12ba2f9org.highwire.dtl.DTLVardef@1d88c15org.highwire.dtl.DTLVardef@1d4f21eorg.highwire.dtl.DTLVardef@16396aa_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4:C_FLOATNO (A-D) Coverage tracks of the PSBS genomic regions from five low NPQ (A and B) and five high NPQ (C and D) Arabidopsis accessions aligned with the TAIR 10 Col-0 reference genome (low NPQ accession; A and C) and KBS-Mac-74 genome (high NPQ accession; B and D). Values along x-axes indicate the base pair distance relative to the PSBS transcription start site. Genes along the track are coloured green and the intergenic region is coloured pink. (E) Graphical view of the alignment of the TAIR 10 Col-0 and the KBS-Mac-74 PSBS genomic regions. Axis values refer to base pair positions within the respective tracks. (F) Comparison of the average relative PsbS protein abundance between low and high NPQ accessions. Error bars represent standard deviations. N=30; *** P < 0.001 with paired Students T test. C_FIG

plant biology↗

bioRxiv2018

Population structure of the Brachypodium species complex and genome wide association of agronomic traits in response to climate.

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translational to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and sequenced using genotyping by sequencing (GBS). Overall, 1,897 samples were classified into two diploid or allopolyploid species and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines were selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22 and 47 QTLs were identified for flowering time, early vigour and energy traits, respectively. Overall, the results highlight the genomic structure of the Brachypodium species complex and allow powerful complex trait dissection within this new grass model species.

plant biology↗