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Your search keyword '"Spillane, Charles"' showing total 41 results
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41 results on '"Spillane, Charles"'

15. A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize.

Author

Ndlovu, Noel, Gowda, Manje, Beyene, Yoseph, Das, Biswanath, Mahabaleswara, Suresh L., Makumbi, Dan, Ogugo, Veronica, Burgueno, Juan, Crossa, Jose, Spillane, Charles, McKeown, Peter C., Brychkova, Galina, and Prasanna, Boddupalli M.

Abstract

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 association mapping panel and linkage mapping with three doubled haploid (DH) and three F3 populations of tropical maize. These populations were phenotyped for NCLB resistance across six hotspot environments in Kenya. Across environments and genotypes, NCLB scores ranged from 2.12 to 5.17 (on a scale of 1–9). NCLB disease severity scores exhibited significant genotypic variance and moderate-to-high heritability. From the six biparental populations, 23 quantitative trait loci (QTLs) were identified, each explaining between 2.7% and 15.8% of the observed phenotypic variance. Collectively, the detected QTLs explained 34.28%, 51.37%, 41.12%, 12.46%, 12.11%, and 14.66% of the total phenotypic variance in DH populations 1, 2, and 3 and F3 populations 4, 5, and 6, respectively. GWAS, using 337,110 high-quality single nucleotide polymorphisms (SNPs), identified 15 marker–trait associations and several putative candidate genes linked to NCLB resistance in maize. Joint linkage association mapping (JLAM) identified 37 QTLs for NCLB resistance. Using linkage mapping, JLAM, and GWAS, several QTLs were identified within the genomic region spanning 4 to 15 Mbp on chromosome 2. This genomic region represents a promising target for enhancing NCLB resistance via marker-assisted breeding. Genome-wide predictions revealed moderate correlations with mean values of 0.45, 0.44, 0.55, and 0.42 for within GWAS panel, DH pop1, DH pop2, and DH pop3, respectively. Prediction by incorporating marker-by-environment interactions did not show much improvement. Overall, our findings indicate that NCLB resistance is quantitative in nature and is controlled by few major-effect and many minor-effect QTLs. We conclude that genomic regions consistently detected across mapping approaches and populations should be prioritized for improving NCLB resistance, while genome-wide prediction results can help incorporate both major- and minor-effect genes. This study contributes to a deeper understanding of the genetic and molecular mechanisms driving maize resistance to NCLB. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Genotype by environment interaction across water regimes in relation to cropping season response of quinoa (Chenopodium quinoa).

Author

Nguyen, Van Loc, Luu, Hue Nhan, Phan, Thi Hong Nhung, Nguyen, Viet Long, Chu, Duc Ha, Bertero, Daniel, Curti, Néstor, McKeown, Peter C., and Spillane, Charles

Subjects
GENOTYPE-environment interaction, QUINOA, AGRICULTURAL productivity, POLYETHYLENE glycol, SOIL moisture, GRAIN yields
Abstract

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, waterlogging and drought. Waterlogging and drought treatments were artificially induced using normoxia, a combination of hypoxia-normoxia, and 10% PEG (Polyethylene glycol) under hydroponic growth conditions, respectively. Both waterlogging and drought conditions significantly reduced the plant height (PH), number of leaves (NoL) and number of branches (NoB), stem diameter (SD), leaf area (LA) and dry weight (DW) of quinoa genotypes. The genotype, water regime, and genotype by water regime effects all significantly affected the measured quinoa traits. Based on the additive main effects and multiplicative interaction (AMMI) model for DW, the genotypes G18, Puno, Q4, 2-Want, Puno, Real1 x Ruy937 and Titicaca were found to exhibit tolerance and were stable across water regimes. A second-stage evaluation was conducted to test genotype × environment interaction effects in crop production field trials, selecting two contrasting seasons based on soil moisture conditions involving a diverse set of genotypes (58 varieties in total). Our results demonstrate significant variations in both growth and yield among the quinoa genotypes across the cropping seasons. The GGE analysis for grain yield indicate that field conditions matched to G × E under hydroponic experimental conditions and the cultivars G18, Q1, Q4, NL-3, G28, 42-Test, Atlas and 59-ALC were classified within a range of high productivity. Our findings provide a basis for understanding the mechanisms of wide adaptation, while identifying germplasm that enhances the water stress tolerance of quinoa cultivars at early growth stages. [ABSTRACT FROM AUTHOR]

Published
2024
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26. Discovery of genomic regions associated with grain yield and agronomic traits in Bi-parental populations of maize (Zea mays. L) Under optimum and low nitrogen conditions

Author

Kimutai, Collins, primary, Ndlovu, Noel, additional, Chaikam, Vijay, additional, Ertiro, Berhanu Tadesse, additional, Das, Biswanath, additional, Beyene, Yoseph, additional, Kiplagat, Oliver, additional, Spillane, Charles, additional, Prasanna, Boddupalli M., additional, and Gowda, Manje, additional

Published
2023
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33. Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals

Author

Castillo-Bravo, Rosa, primary, Lucca, Noel, additional, Lai, Linyi, additional, Marlborough, Killian, additional, Brychkova, Galina, additional, Sakhteh, Maryam Shideh, additional, Lonergan, Charlie, additional, O’Grady, Justin, additional, Alikhan, Nabil-Fareed, additional, Trotter, Alexander J., additional, Page, Andrew J., additional, Smyth, Breda, additional, McKeown, Peter C., additional, Feenstra, Jelena D. M., additional, Ulekleiv, Camilla, additional, Sorel, Oceane, additional, Gandhi, Manoj, additional, and Spillane, Charles, additional

Published
2022
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40. Functional effects of inter-genome interactions on seed development in Arabidopsis thaliana

Author

Dupouy, Gilles A., Spillane, Charles, and Irish Research Council

Subjects
Organelles, Kinship, fungi, Plant Molecular Biology, Genome interaction, food and beverages, Science and Engineering, Seed size, Natural Science, Chromatin
Abstract

Plant seed size determination is of high economic interest for modern food production worldwide as many crops are mainly consumed in the form of seeds, such as rice, wheat or corn. Parental conflict and genomic imprinting have been intensively studied during the last 20 years with many reports of their manifestations to significantly affect seed size determination in plants. However it has so far mostly been studied from the point of view of the nuclear genome leaving out the organelle genomes from the mitochondria and the chloroplast. In this Ph.D. thesis we explore how the interactions between these genomes can post-zygotically influence the development of seeds in angiosperms using the plant molecular model Arabidopsis thaliana. After establishing a state-of-the-art of the current knowledge on the molecular manifestations of maternal-paternal conflict over the energy allocated to the offspring, I studied the effect of these genomic interactions using different approaches. I first studied the impact of parentally imprinted genes under positive Darwinian selection on the development of intra-species hybrid seeds of A. thaliana and revealed an essential role of the CHD3 chromatin remodeler PICKLE RELATED 2 (PKR2) on the establishment of post-hybridity F1 seed size heterosis in disregard to its imprinting status. I further studied the evolution of PKR2 in comparison to its paralog PKL and showed that PKR2 is under a process of neofunctionalization since its apparition in the Brassicaceae lineage after the duplication of PKL, explaining their previously reported antagonistic effects on seed size in A. thaliana. I then explored the impact of a disruption of cytonuclear relationships (cybridity) and showed that cybridity and hybridity have an additive effect on F1 seed size determination. Finally, I performed a case-study on the impact of cytonuclear relationships on seed development by characterising the gene PLASTID RIBOSOME PROTEIN L5 and have shown it to be necessary for post-globular embryo development in A. thaliana. These results highlight the interconnection of the different plant genomes for seed size determination as well as its importance for future plant breeding programs. 2024-01-12

Published
2022

41. Nucleolar DNA damage within the female gametophyte perturbs development and genome stability in Arabidopsis thaliana

Author

Lopez, Francesca, Spillane, Charles, and Irish Research Council

Subjects
Arabidopsis thaliana, female gametophyte, Science and Engineering, Plant and AgriBiosciences, Nucleolar DNA damage, Natural Sciences, genome stability, Biological and Chemical Sciences
Abstract

The 45S rRNA genes (rDNA) are among 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 thaliana female gametophyte, we reduced 45S rDNA copy number (CN) to a plateau of ∼10%. Two independent lines had rDNA CNs reduced by up to 90% at the T7 generation, named low copy number (LCN) lines. Despite drastic reduction of rDNA copies, rRNA transcriptional rates, and steady-state levels remained the same as wild-type plants. Gene dosage compensation of rRNA transcript levels was associated with reduction of silencing histone marks at rDNA loci and altered Nucleolar Organiser Region 2 organization. Although overall genome integrity of LCN lines appears unaffected, a chromosome segmental duplication occurred in one of the lines. Transcriptome analysis of LCN seedlings identified several shared dysregulated genes and pathways in both independent lines. Cas9 genome editing of rRNA repeats to generate LCN lines provides a powerful technique to elucidate rDNA dosage compensation mechanisms and impacts of low rDNA CN on genome stability, development, and cellular processes.

Published
2021

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