Biology subjects

MacKay, J. J.

Publications and source records attributed to MacKay, J. J..

6 recordsLinked to original sources

bioRxiv2025

Environmental and transcriptomic determinants of drought response in critically endangered Siamese rosewood

Rosewoods account for up to 40% of the global illegal wildlife trade, with Dalbergia cochinchinensis (Siamese rosewood) being the most heavily exploited species in Southeast Asia. Its survival is further threatened by intensifying drought linked to climate change and hydrological alteration. Here we combine greenhouse drought experiments across six provenances with full-length cDNA-seq to uncover how water-relations and carbon-use strategies vary within this species. Multivariate trait analysis resolves a two-dimensional isohydry space, in which a water-flux stringency axis (gs-E) is largely orthogonal to a carbon-economics axis (A-WUEi). Provenances differed strikingly, where two (KKH and DN) showed a rare E{downarrow}A{uparrow} response, achieving high WUEi and maintaining growth under drought. Contrary to expectation, precipitation of the wettest month, not the driest, predicted isohydry, indicating that wet-season conditions set a developmental and hydrological floor for later drought responses. We identified 76 drought-responsive genes and two genes associated with isohydry axes, SEOR1 and a poorly characterised Notch-like protein AT4G14746. We also detected provenance-specific isoform switches, where drought favoured a loss-of-function PRX52 isoform lacking its signal peptide in the anisohydric provenance THB, and gain-of-function isoforms of ANN3 and LTPG5 in NP. These results reveal previously hidden diversity in drought strategies, identify mechanism-related markers for screening, and provide a simple climatic lever for climate-adjusted provenancing. We reveal post-transcriptional regulation as a novel candidate substrate for local adaptation in a threatened tropical tree, directly linking ecophysiology, climate, and genomics for conservation and restoration.

ecology↗

bioRxiv2024

Genetic diversity and population structure of pedunculate oaks (Quercus robur) in Wytham Woods

O_LIGenetic diversity is fundamental for adaptation to changing environments. It is particularly important in forest trees because of their significant role in natures contribution to people. However, their genetic diversity has been significantly changed by human activities in the past centuries. C_LIO_LIThis paper investigates a focal site, the Wytham Woods, one of the most researched woodlands on Earth, and presents a population genetic study on pedunculate oaks (Quercus robur), a keystone species in the ecosystem. We characterised 210 trees with Genotyping by Sequencing (GbS) and quantified levels of genetic diversity across stands with different histories and management regimes. C_LIO_LIWe detected only a weak population structure within the 218,567 SNPs, such that most genetic variation occurred within but not among stands, which included semi-natural woodland areas and plantations aged between 200 to 50 years ago. We also observed little difference in observed and expected heterozygosity among stand types, but detected some inbreeding in the youngest plantation. We discovered 26,174 SNPs (11.98%) that were highly differentiated and under potential selection. C_LIO_LIWe suggest that the life history traits of oak contribute to its resistance against genetic erosion, which is also observed in beeches, spruces, and pines. Preference for oaks as a timber tree and the tendency to use local seed source might have resulted in the homogeneous population structure. However, tree-to-tree differences may harbour variation in putative adaptive loci. Our study contributes crucial baseline information on for conservation and management of human-modified woodlands, in addition to supporting long-term ecological studies on many other species, which depend on this keystone oak species. C_LI Societal Impact StatementOur study highlights the importance of monitoring and preserving genetic diversity in forest trees, particularly in keystone species like pedunculate oaks. Human activities, including land use changes and forestry practices, could influence their genetic diversity and potentially alter natures contribution to people. We demonstrate how understanding the genetic structure of oaks in stands ranging from semi-natural to plantations could (1) shed light on the natural history and the consequence of human activities in Wytham Woods, (2) support the many continuing, long-term ecological studies including adaptational potential in the oak population, and (3) be translated for other co-occurring species and other woodlands for effective genetic monitoring at large.

genomics↗

bioRxiv2023

Contrasting levels of transcriptome-wide SNP diversity and decoupled patterns of molecular and functional adaptive variation in conifers

Adaptive convergence can arise when response to natural selection involves shared molecular or functional mechanisms among multiple taxa. Conifers are of ancient origin with delayed sexual maturity related to their woody perennial nature. Thus, they represent a relevant plant group to assess if convergence from selection may have become disconnected between molecular and functional levels. In this purpose, transcriptome-wide SNP diversity was assessed in seven partially sympatric and reproductively isolated conifer species populating the temperate and boreal forests of northeastern North America. SNP diversity was found highly heterogeneous among species, which would relate to variation in species-specific demography and history. Rapidly evolving genes with signatures of positive selection were identified, and their relative abundance among species reflected differences in transcriptome-wide SNP diversity. Their analysis also revealed very limited convergence among taxa in spite of sampling same tissues at same age. However, convergence increased gradually at the levels of gene families and biological processes, which were largely related to stress response and regulatory mechanisms in all species. Given their multiple small to large gene families and long time since inception, conifers may have had sufficient gene network flexibility and gene functional redundancy for evolving alternative adaptive genes for similar metabolic responses to environmental selection pressures. Despite a long divergence time of [~]350 Mya between conifers and Angiosperms, we also uncovered a set of 20 key genes presumably under positive selection in both lineages.

plant biology↗

bioRxiv2023

Conifers concentrate large numbers of NLR immune receptor genes on one chromosome

Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis) but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae and other gymnosperms were scanned for NLR genes using existing and customised pipelines. Discovered genes were mapped across chromosomes and linkage groups, and analysed phylogenetically for evolutionary history. Conifer genomes are characterised by dense clusters of NLR genes, highly localised on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and non-coniferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plants resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding. Plain language summaryNLR immune receptor genes are important in pest, disease and drought resistance of plants. In the giga-genomes of conifers, they concentrate on very small chromosomal regions. These regions act as important reservoirs for NLR diversity and can be used in breeding to improve the resilience of conifer trees.

genomics↗

bioRxiv2023

High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers

In species with large and complex genomes such as conifers, dense linkage maps are a useful for supporting genome assembly and laying the genomic groundwork at the structural, populational and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 SNP makers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-Seq and genotyping array SNP data for 528 individuals from two full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and P. glauca based on 27,052 makers and 11,609 gene sequences. Altogether, these two linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed herein opens new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.

genomics↗

bioRxiv2023

Range-wide differential adaptation and genomic vulnerability in critically endangered Asian rosewoods

In the billion-dollar global illegal wildlife trade, rosewoods have been the worlds most trafficked wild product since 20051. Dalbergia cochinchinensis and D. oliveri are the most sought-after rosewoods in the Greater Mekong Subregion2. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts. Here we present genome assemblies and range-wide genomic scans of adaptive variation, together with predictions of genomic vulnerability to climate change. Adaptive genomic variation was differentially associated with temperature and precipitation-related variables between the species, although their natural ranges overlap. The findings are consistent with differences in pioneering ability and in drought tolerance3. We predict their genomic offsets will increase over time and with increasing carbon emission pathway but at a faster pace in D. cochinchinensis than in D. oliveri. These results and the distinct gene-environment association in the eastern coastal edge suggest species-specific conservation actions: germplasm representation across the range in D. cochinchinensis and focused on vulnerability hotspots in D. oliveri. We translated our genomic models into a seed source matching application, seedeR, to rapidly inform restoration efforts. Our ecological genomic research uncovering contrasting selection forces acting in sympatric rosewoods is of relevance to conserving tropical trees globally and combating risks from climate change. Significant statementIn the billion-dollar global illegal wildlife trade, rosewoods have been the worlds most trafficked wild product since 2005, with Dalbergia cochinchinensis and D. oliveri being the most sought-after and endangered species in Southeast Asia. Emerging efforts for their restoration have lacked a suitable evidence base on adaptability and adaptive potential. We integrated range-wide genomic data and climate models to detect the differential adaptation between D. cochinchinensis and D. oliveri in relevance to temperature- and precipitation-related variables and projected their vulnerability until 2100. We highlighted the stronger local adaptation in the coastal edge of the species ranges suggesting conservation priority. We developed genomic resources including chromosome-level genome assemblies and a web-based application seedeR for genomic model-enabled assisted migration and restoration.

genomics↗