Biology subjects

MacKay, J.

Publications and source records attributed to MacKay, J..

3 recordsLinked to original sources

bioRxiv2024

Low effective population size but high heterozygosity revealed by SNP analyses in adult and juvenile Thuja plicata in UK Woodlands

Thuja plicata is a conifer tree that is appreciated for its cultural, ecological and wood quality features in its natural range in western North America. It is also used in Europe and the UK for timber production. Some T. Plicata plantations in the UK are converted to Continuous Cover Forestry (CCF) management which uses natural regeneration and concerns have been raised about the genetic diversity in both the adult trees and the offspring. We studied species diversity, stand structure, and genetic diversity in four UK woodlands planted with T. plicata which contained both adults and naturally regenerated individuals. We discovered 61,104 Single Nucleotide Polymorphisms (SNPs) using Genotyping-by-Sequencing (GBS) and retained 504 SNPs for analysis. We selected 67 SNPs for PCR-based genotyping of 163 adults and 176 juveniles. We found a large number of monomorphic sites (40.3%) most of which were restricted to adults in a single woodland, indicative of a high genetic differentiation among woodlands. The effective population size (Ne) was very low across all sites (Ne < 100), varied between adults and juveniles, and was lowest in the most diverse woodland in terms of species and structure. In contrast, heterozygosity was high overall (Ho = 0.38), except in the divergent woodland (Ho = 0.26), and did not vary between adults and juveniles. Our findings and genotyping methods provide insights into the ability of CCF-managed woodlands, including instances of low genetic diversity in T. plicata, to face environmental shifts and disease threats.

genomics↗

bioRxiv2023

Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene Betaglu-1 with large variations in white spruce but not Norway spruce

Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and {beta}glu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of {beta}glu-1-like, Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of {beta}glu-1 and Ugt5 genes. We observed very large copy numbers of {beta}glu-1, with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of {beta}glu-1 in P. glauca but not P. abies. Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences.

evolutionary biology↗

bioRxiv2017

Spontaneous mutations and transmission distortions of genic copy number variants shape the standing genetic variation in Picea glauca

Copy number variations (CNVs) are large genetic variations detected among the individuals of every multicellular organism examined so far. These variations are believed to play an important role in the evolution and adaptation of species. In plants, little is known about the characteristics of CNVs, particularly regarding the rates at which they are generated and the mechanics of their transmission from a generation to the next. Here, we used SNP-array raw intensity data for 55 two-generations families (3663 individuals) to scan the gene space of the conifer tree Picea glauca (Moench) Voss for CNVs. We were particularly interested in the abundance, inheritance, spontaneous mutation rate spectrum and the evolutionary consequences they may have on the standing genetic variation of white spruce. Our findings show that CNVs affect a small proportion of the gene space and are predominantly copy number losses. CNVs were either inherited or generated through de novo events. De novo CNVs present high rates of spontaneous mutations that vary for different genes and alleles and are correlated with gene expression levels. Most of the inherited CNVs (70%) are transmitted from the parents in violation of Mendelian expectations. These transmission distortions can cause considerable frequency changes between generations and be dependent on whether the heterozygote parents contribute as male or female. Transmission distortions were also influenced by the partner genotype and the parents genetic background. This study provides new insights into the effects of different evolutionary forces on copy number variations based on the analysis of a perennial plant.

genomics↗