Charles Spillane

• Professor
• Chair at Ollscoil na Gaillimhe – University of Galway

Abstract Background: Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the...

Heterosis is the phenomenon whereby hybrid offspring of genetically divergent parents display superior characteristics compared with their parents. Although hybridity and polyploidy can influence heterosis in hybrid plants, the differential contributions of hybridity vs polyploidy to heterosis effects remain unknown. To address this question, we in...

Retention of sister centromere cohesion during meiosis I and its dissolution at meiosis II is necessary for balanced chromosome segregation and reduction of chromosome number. PATRONUS1 (PANS1) has recently been proposed to regulate centromere cohesion in Arabidopsis after meiosis I, during interkinesis. pans1 mutants lose centromere cohesion prema...

Anthropogenic changes to our Earth’s climate system are amongst the most pressing challenges facing humankind. Advances in satellite systems for earth observation are revolutionizing our ability to monitor and assess environmental changes, manage natural resources and respond to global challenges, including climate change and disaster management. H...

Soil moisture content is typically measured in situ using various instruments; however, due to the heterogeneous nature of soil, these measurements are only suitable at a very local scale. To overcome this limitation, earth observation satellite remote sensing data, particularly through the inversion of the closure phases of interferometric synthet...

Genome‐edited plants, endowed with climate‐smart traits, have been promoted as tools for strengthening resilience against climate change. Successful plant gene editing (GE) requires precise regulation of the GE machinery, a process controlled by the promoters, which drives its transcription through interactions with transcription factors (TFs) and...

The extraction, processing and transport of crude oil in the Niger Delta region of Nigeria has long been associated with collateral environmental damage to the largest mangrove ecosystem in Africa. Oil pollution is impacting not only one of the planet’s most ecologically diverse regions but also the health, livelihoods, and social cohesion of the D...

The transition of city region diets to diets that are more sustainable, healthy and affordable iscritically important for environmental, health and food security outcomes. The EcoFoodSystems project aims to work with city-regional stakeholders to identify key needs and priorities for dietary transitions in Hanoi city region that can be enabled by r...

The Intergovernmental Panel on Climate Change (IPCC) is preparing a new IPCC Special Report on Climate Change and Cities, which will address issues of climate mitigation, adaptation and just transitions in cities and urban systems. In this context, accelerating the sustainable transitions of the diets and food systems of cities is critical to ensur...

Purpose The purpose of this study is to evaluate the effectiveness of “Connect the circle” systems thinking tools for improving contextualised systems thinking from sustainability perspectives. The guiding question is could “Connect the circle” improve sustainability education? Design/methodology/approach The effect of the “Connect the circle” too...

Despite the transformative power of gene editing for crop improvement, its widespread application across species and varieties is limited by the transformation bottleneck that exists for many crops. The genetic transformation of plants is hindered by a general reliance on in vitro regeneration through plant tissue culture. Tissue culture requires e...

Genotype × environment (GxE) interaction effects are one of the major challenges in identifying cultivars with stable performance across agri-environments. In this study we analysed GE interactions to identify quinoa (Chenopodium quinoa) cultivars with high and stable yields under different soil moisture regimes, representing control conditions, wa...

Northern corn leaf blight (NCLB), caused by Setosphaeria turcica, is a major fungal disease affecting maize production in sub-Saharan Africa. Utilizing host plant resistance to mitigate yield losses associated with NCLB can serve as a cost-effective strategy. In this study, we conducted a high-resolution genome-wide association study (GWAS) in an a...

Climate change is a threat multiplier for human migration, with those reliant on rain-fed agriculture being particularly vulnerable to climate change. This can manifest as increased poverty and potentially as climate-induced migration to seek alternative livelihood options. The interactions between climate vulnerability and social protection policy...

Satellite remote sensing (RS) and machine learning can be combined to develop methods for measuring the impacts of climate change on biomass and agricultural systems. From 2015 to 2023, we applied this approach in a critical earth observation-based evaluation of the Irrigation and Water Resources Management component of the Millennium Challenge Cor...

Smallholder maize farming systems in sub-Saharan Africa (SSA) are vulnerable to drought-induced yield losses, which significantly impact food security and livelihoods within these communities. Mapping and characterizing genomic regions associated with water stress tolerance in tropical maize is essential for future breeding initiatives targeting th...

Improving the salt stress tolerance of crops is an important goal in plant breeding. Changes in the number of chromosome sets (i.e. ploidy level) cause genome dosage effects which can result in enhanced or novel traits. Maternal inheritance versus paternal inheritance of the same chromosome sets can have differential epigenetic effects on traits of...

As a fundamental pillar of food security in sub-Saharan Africa (SSA), ensuring seed security is critical to empowering farmers in cultivating food and livestock feed, thereby fostering income generation from agricultural outputs. Among the crops cultivated by smallholders, legumes have the potential to deliver multifaceted benefits. Legumes are nut...

Main conclusion Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. Abstract The circadian clock senses light and temperature in day–night cycles to drive biological rhythms....

The suboptimal productivity of maize systems in sub-Saharan Africa (SSA) is a pressing issue, with far-reaching implications for food security, nutrition, and livelihood sustainability within the affected smallholder farming communities. Dissecting the genetic basis of grain protein, starch and oil content can increase our understanding of the gove...

Mushrooms are a nutritionally rich and sustainably-produced food with a growing global market. Agaricus bisporus accounts for 11% of the total world mushroom production and it is the dominant species cultivated in Europe. It faces threats from pathogens that cause important production losses, including the mycoparasite Lecanicillium fungicola, the...

In planta haploid induction (HI), which reduces the chromosome number in the progeny after fertilization, has garnered increasing attention for its significant potential in crop breeding and genetic research. Despite the identification of several natural and synthetic HI systems in different plant species, the molecular and cellular mechanisms unde...

The world’s food systems are rapidly changing due to socioeconomic, environmental, and demographic changes, globalization, and urbanization. Urban regions connect urban food consumption with rural food production and are associated with rapid dietary transitions in developing counties. Despite urbanization being a key driver of city-regional and gl...

The evolution and diversification of proteins capable of remodeling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodeling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis th...

Low soil nitrogen levels, compounded by the high costs associated with nitrogen supplementation through fertilizers, significantly contribute to food insecurity, malnutrition, and rural poverty in maize-dependent smallholder communities of sub-Saharan Africa (SSA). The discovery of genomic regions associated with low nitrogen tolerance in maize can...

Transforming global food systems to promote food and nutritional security can help alleviate both poverty and ill-health, and support sustainable development. Such transformations need to be tailored and sensitive to the vulnerabilities and needs of marginalized communities yet are hindered by knowledge gaps. In particular, the food and nutrition s...

Migration, Environment and Climate Change in Ireland

Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology and bioinfor...

Lettuce (Lactuca sativa L.) is one of the commercially important leafy vegetables worldwide. However, lettuce cultivars vary widely in their carotenoid concentrations at the time of harvest. While the carotenoid content of lettuce can depend on transcript levels of key biosynthetic enzymes, genes that can act as biomarkers for carotenoid accumulati...

The Central American Dry Corridor (CADC) is among the most climate-vulnerable regions worldwide. Climate change, commonly referred to as a “threat multiplier” of pre-existing socioeconomic issues, already undermines rural livelihoods by reducing agricultural yields and income opportunities. This paper provides a review of climate-related migration...

Regenerative agriculture aims to increase soil organic carbon (SOC) levels, soil health and biodiversity. Regenerative agriculture is often juxtaposed against “conventional” agriculture which contributes to land degradation, biodiversity loss, and greenhouse gas emissions. Although definitions of regenerative agriculture definitions may vary, commo...

Amongst the Sustainable Development Goals (SDGs), ensuring energy access in developing countries while reducing global emissions of greenhouse gases is critical. To achieve such goals, international cooperation combined with investments in research, technology, infrastructures and capacity building are paramount. The Sustainable Development Goal (S...

While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. I...

Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex...

Our food systems have performed well in the past, but they are failing us in the face of climate change and other challenges. This book tells the story of why food system transformation is needed, how it can be achieved and how research can be a catalyst for change. Written by a global interdisciplinary team of researchers, it brings together persp...

The balance between parental genome dosage is critical to offspring development in both animals and plants. In some angiosperm species, despite the imbalance between maternally and paternally inherited chromosome sets, crosses between parental lines of different ploidy may result in viable offspring. However, many plant species, like Arabidopsis th...

Systematic tools and approaches for measuring climate change adaptation at multiple scales of spatial resolution are lacking, limiting measurement of progress toward the adaptation goals of the Paris Agreement. In particular, there is a lack of adaptation measurement or tracking systems that are coherent (measuring adaptation itself), comparable (a...

Forage grasses are central feed resources for livestock globally. In Ethiopian dairy systems, they serve as feed sources during both wet and dry seasons, yet escalating climate change could threaten forage supply. Here, we investigate projected climate change impacts on three forage grasses currently recommended for Ethiopian dairy systems. We dete...

The scale of the COVID-19 pandemic highlighted the need for viral diagnostic systems that are accurate and could be deployed at large population scales. Large-scale diagnostic or surveillance testing of large numbers of people requires collection of infected biological samples that is easy and rapid.

Key message Genome-wide association study (GWAS) demonstrated that multiple genomic regions influence grain quality traits under nitrogen-starved soils. Using genomic prediction, genetic gains can be improved through selection for grain quality traits. Abstract Soils in sub-Saharan Africa are nitrogen deficient due to low fertilizer use and inadeq...

Plastid ribosomal proteins (PRPs) can play essential roles in plastid ribosome functioning that affect plant function and development. However, the roles of many PRPs remain unknown, including elucidation of which PRPs are essential or display redundancy. Here, we report that the nuclear-encoded PLASTID RIBOSOMAL PROTEIN L5 (PRPL5) is essential for...

Attributional life cycle assessment was applied to determine environmental footprints of lettuce produced across ten supply chain configurations, based on either hydroponic closed-environment agriculture (CEA) with six different electricity sources, or field supply chains involving regional, continental or inter-continental transport. Hydroponic CE...

RT-qPCR tests based on RNA extraction from nasopharyngeal swab samples are promoted as the “gold standard” for SARS-CoV-2 detection. However, self-collected saliva samples offer a non-invasive alternative more suited to high-throughput testing. This study evaluated the performance of TaqPath COVID-19 Fast PCR Combo Kit 2.0 assay for detection of SA...

Parent-of-origin effects arise when a phenotype depends on whether it is inherited maternally or paternally. Parent-of-origin effects can exert a strong influence on F1 seed size in flowering plants, an important agronomic and life-history trait that can contribute to biomass heterosis. Here we investigate the natural variation in the relative cont...

Improving the salt stress tolerance of crops is an important goal in plant breeding. Changes in the number of chromosome pairs (i.e. ploidy level) cause genome dosage effects which can result in improved traits or emergence of novel traits. The genetic and epigenetic contribution of maternal or paternal chromosomes can differentially affect physiol...

Diversification of production to strengthen resilience is a key tenet of climate-smart agriculture (CSA), which can help to address the complex vulnerabilities of agriculture-dependent rural communities. In this study, we investigated the relationship between the promotion of different CSA practices across four climate-smart villages (CSVs) in Myan...

Overwhelming scientific evidence shows agriculture is heavily impacted by negative climate change effects. While agriculture is affected, the sector is also the second-largest contributor to climate change, creating challenges in adaptation and mitigation strategies. Climate-smart agriculture (CSA) is a holistic approach to managing landscapes, uti...

Soils in sub-Saharan Africa are nitrogen deficient due to low fertilizer use and inadequate soil fertility management practices. This has resulted in a significant yield gap for the major staple crop maize, which is undermining nutritional security and livelihood sustainability across the region. Dissecting the genetic basis of grain protein, starc...

Provitamin A enrichment of staple crops through biofortification breeding is a powerful approach to mitigate the public health problem of vitamin A deficiency in developing countries. Twenty-four genetically diverse yellow and orange endosperm maize inbred lines with differing levels of provitamin A content were used for the analysis of their combi...

By structuring farmers’ informal networks of seed exchange, kinship systems play a key role in the dynamics of crop genetic diversity in smallholder farming systems. However, because many crop diseases are propagated through infected germplasm, local seed systems can also facilitate the dissemination of seedborne pathogens. Here, we investigate how...

Agroforestry has potential for strengthening the climate change resilience of smallholder farmers in Southeast Asia. In Indonesia, the food security challenges faced by smallholders will likely worsen due to climate change impacts. Agroforestry provides and option for strengthening climate change resilience, while contributing to food access, incom...

Current research on cleaner cookstoves (CCS) is focused primarily on women, thus removing men from the cookstove adoption equation despite their decision making role in households. Very little is understood about what would motivate men to purchase CCS, and whether such motivations are key factors that influence a household’s decision to acquire CC...

Seeds are valuable sources of carbohydrates, lipids, proteins, fibers, minerals, and vitamins. They provide energy and nutrition to germinating seedlings, food to humans, feed to livestock, and feedstocks to industry. High‐throughput analyses of gene expression in crops has identified many candidate genes associated with seed dormancy, longevity, g...

Situated in the Northern Mountain Region, one of the most climate-vulnerable regions of Vietnam, Yen Bai province is exposed to many climate risks. This study investigated how well Yen Bai farmers were aware of the impacts of the changing climate on production and their livelihoods and how they referred support programs from the central and local g...

The 45S rRNA genes (rDNA) are amongst the largest repetitive elements in eukaryotic genomes. rDNA consists of tandem arrays of rRNA genes, many of which are transcriptionally silenced. Silent rDNA repeats may act as 'back-up' copies for ribosome biogenesis and have nuclear organization roles. Through Cas9-mediated genome editing in the Arabidopsis...

The 45S rRNA genes (rDNA) are amongst the largest repetitive elements in eukaryotic genomes. rDNA consists of tandem arrays of rRNA genes, many of which are transcriptionally silenced. Silent rDNA repeats may act as ‘back-up’ copies for ribosome biogenesis and have nuclear organization roles. Through Cas9-mediated genome editing in the Arabidopsis...

Key message Genetically identical East African Highland banana (EAHB) clones are epigenetically diverse with heritable epialleles that can contribute to morphological diversity. Abstract Heritable epigenetic variation can contribute to agronomic traits in crops and should be considered in germplasm conservation. Despite the genetic uniformity aris...

Rumen microbiome composition and functionality is linked to animal feed efficiency, particularly for bovine ruminants. To investigate this in sheep, we compared rumen bacterial and archaeal populations (and predicted metabolic processes) of sheep divergent for the feed efficiency trait feed conversion ratio (FCR). In our study 50 Texel cross Scotti...

The adoption of the EU land use, land use change and forestry (LULUCF) regulation ensures that for the first time afforestation in Europe will contribute toward the achievement of European Union (EU) climate change commitments under the Paris Agreement. However, increased afforestation in Europe could have unintended environmental trade-offs that m...

In Ireland, agriculture accounts for 33% of national greenhouse gas (GHG) emissions. Ireland faces significant challenges in terms of emissions reduction and is well off course in terms of meeting binding European Union targets. Flexibility mechanisms will allow Ireland to offset 5.6% of its commitment via sequestration in biomass and soils and lan...

Vietnam accounts for 6% of global rice production and is exceptionally vulnerable to the impacts of climate change. This study utilises a mixed model ordinal logistic regression on farm household data collected in the Mekong and Red River deltas with the goal of quantifying their impacts on 'planned', in anticipation of gradual climate change, and...

Biofortification is an effective method to improve the nutritional content of crops and nutritional intake. Breeding for higher micronutrient mineral content in beans is correlated with an increase in phytic acid, a main inhibitor of mineral absorption in humans. Low phytic acid (lpa) beans have a 90% lower phytic acid content compared to conventio...

Biological phenomena defined as having an “epigenetic” component (according to various definitions) have been extensively studied in plant systems and illuminated many mechanisms by which gene expression is regulated and patterns of expression inherited through cell divisions. This second volume of Plant Epigenetics and Epigenomics: Methods in Mole...

Numerous extension efforts promote climate smart agriculture (CSA) in Sub-Saharan Africa. The need to focus on gender disparity within CSA is widely understood. Given the prominence of female agriculturalists in Malawi, such focus has can make a large impact on the country's rural sustainable development. This study quantifies the impact of extensi...

This second edition volume expands on the previous edition with a look at the latest techniques in plant epigenetics and epigenomic research. Chapters in this book cover topics such as whole genome methylome analysis; analysis of DNA methylation; chromatin analysis of metabolic gene clusters in plants; plant epigenetic stress memory induced by drou...

Dioecy (distinct male and female individuals) and scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are largely unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify floweri...

Key message Reproduction in triploid plants is important for understanding polyploid population dynamics. We show that genetically identical reciprocal F1 hybrid triploids can display transgenerational epigenetic effects on viable F2 seed development. Abstract The success or failure of reproductive outcomes from intra-species crosses between plant...

Amongst green leafy vegetables, new varieties of lettuce enriched in lutein and β-carotene are being developed to provide increased supply of dietary carotenoids. We investigated the effect of lettuce genotypes (varieties) and thermal treatments on lutein and β-carotene bioaccessibility to the micellar fraction (and also carotenoid bioavailability)...

Dioecy (distinct male and female individuals) combined with scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowe...

Heterosis refers to improved or altered performance observed in F1 hybrid organisms when compared to their parents. Heterosis has revolutionized agriculture by improving key agronomic traits in crop plants. However, even after decades of research in this area a unifying molecular theory of heterosis remains somewhat elusive. For many years the domi...

Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. We investigate whether...

Index insurance is an agricultural risk management tool that can provide a safety net for smallholder farmers experiencing climate risk. While uptake and scale-out of index insurance may be slow among smallholders, we can learn from experiences that demonstrate where crop insurance can protect smallholders’ livelihoods from climate risk. Integratin...

Climate change impacts on food security will involve negative impacts on crop yields, and potentially on the nutritional quality of staple crops. Common bean is the most important grain legume staple crop for human diets and nutrition worldwide. We demonstrate by crop modeling that the majority of current common bean growing areas in southeastern A...

Background Biofortified orange-fleshed sweetpotato (OFSP) varieties are being promoted to reduce vitamin A deficiencies due to their higher beta-carotene content. For OFSP varieties to have impact they need to be accepted and consumed at scale amongst populations suffering from vitamin A deficiencies. Objective We investigated the sensory and cult...

Results for the preference test with OFSP and a control yellow-fleshed sweetpotato variety among adults (n = 270) and children (n = 60) per location. (TIF)

Results for the acceptance test with 3 OFSP varieties and a control variety, per area and total. (TIF)