Charles Spillane

National University of Ireland, Galway | NUI Galway · Plant and Agricultural Biosciences Centre

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...

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...

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...

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...

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...

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)

Beta-carotene content and dry matter (%) content for the various sweetpotato varieties. (TIF)

Questionnaire format for sensory and cultural acceptability questionnaire. (XLSX)

Background: The phenomenon of heterosis is critical to plant breeding and agricultural productivity. Heterosis occurs when F1 hybrid offspring display quantitative improvements in traits to levels that do not occur in the parents. Increasing the genome dosage (i.e. ploidy level) of F1 offspring can contribute to heterosis effects. Sugar beet (Beta...

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The discovery and use of genetic markers associated with carotenoid levels can help to more effectively exploit the genetic potential of maize for provitamin A accumulation. Provitamin A carotenoids are classes of carotenoids that are precursors of vitamin A, an essential micronutrient in humans. Vitamin A deficiency is a global public health probl...

Genomic imprinting in the seed endosperm could be due to unequal parental genome contribution effects in triploid endosperm tissue that trigger parent-of-origin specific activation and/or silencing of loci prone to genomic imprinting. To determine whether genomic imprinting is triggered by unequal parental genome contribution effects, we generated...