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Unveiling novel QTLs for nitrogen use efficiency in temperate Japonica rice
Get PDFBackground
Nitrogen (N) is essential for rice growth and has driven yield increases since the 1950s. However, excessive use of mineral N fertilizers has led to considerable environmental and economic concerns. Enhancing nitrogen use efficiency (NUE) is essential for reducing these impacts and ensuring global food security. Decades of breeding under high N application have reduced the fertilizer responsiveness of modern temperate japonica rice varieties, further contributing to NUE inefficiencies. This study aimed to uncover the genetic components underlaying NUE in temperate-adapted japonica rice varieties.
Results
A genome-wide association study (GWAS) with PCA and kinship matrix was conducted on a panel of 153 temperate japonica rice accessions using 97,244 single-nucleotide polymorphisms (SNPs) to detect quantitative trait loci (QTLs) for NUE. Phenotypic evaluations were conducted under two distinct nitrogen levels across three different field environments. Significant influences of both nitrogen level and environment were observed on trait expression. A total of 14 marker trait associations (MTAs) were identified and grouped into eight QTLs. Within these regions 350 genes were identified and among them three candidate genes were pinpointed including a gene involved in N uptake and transport (OsNAR2.1) and two transcription factors related to N use and metabolism or regulated by the N availability (OsARF19 and OsMADS27). In addition, three novel loci associated with enhanced NUE (chr02:22969295, chr01:33259076, and chr09:17345345) emerged as promising targets for marker-assisted selection. A phylogenetic analysis of the allele distribution for the candidate genes across the collection revealed significant variation in NUE among the genetic clusters, with one cluster exhibiting superior NUE performance under the tested conditions highlighting the genetic components of NUE.
Conclusions
This study provides genetic insights into NUE in temperate japonica rice. We have identified QTLs associated with NUE traits, some of which co-localized with previously identified genes, while also providing novel molecular markers. The identified loci and candidate genes offer valuable genetic resources to support molecular breeding strategies aimed at improving NUE in japonica rice cultivars adapted to temperate climates.This work was supported by MICIU/AEI/https://doi.org/10.13039/501100011033, and “European Union Next Generation EU/PRTR” (grant PLEC2021-007786) as well as J.G.R. fellowship PRE209-089034. Also funded by the Consolidated Research Group (grant 2021 SGR 01429, Technologies and crop solutions for drought mitigation—AGRI DROUGHT HUB), awarded to IRTA and by Generalitat Valenciana co-financed by the European Union through the ERDF Program 2021–2027 Comunitat Valenciana (grant IVIA-GVA 52201). We also acknowledge financial support from Generalitat de Catalunya through the CERCA Program and K.M. fellowship IRTA SP 2022.info:eu-repo/semantics/publishedVersio
Development of return, a manure redistribution optimisation tool: description and application context
Get PDFCONTEXT: Collaborative agreements for manure management would enable intensive and specialized livestock
farms to expand the agricultural area available for manure distribution by transporting manure to arable farms,
thus increasing nitrogen and carbon recycling, reducing environmental pollution and decreasing farms’
dependence on external inputs. The economic and environmental viability of such collaborative arrangements
depends on the balance between the manure transport costs and emissions (and thus the distances between
farms) and the saving in mineral fertiliser purchase costs and production emissions.
OBJECTIVE: The objective of this study is to present a software tool (ReturN) designed to assess the opportunities
for moving he nitrogen (N) in manure from locations where the amount exceeds the utilization capacity of the
crops to locations with spare utilization capacity. ReturN allows the optimisation of manure fluxes at a local or
regional scale, on the basis of a multi-criteria balance that considers both economic and environmental criteria.
The tool is applied in three European case studies thus showcasing the tool applicability options.
METHODS: The ReturN multi-criteria balance considers manure transport costs and emissions (and thus the
distances between source and recipient locations) and the saving in mineral N fertiliser purchase costs and production emissions. The locations among which manure-N fluxes are optimised can be farms or municipalities,
based on the aggregation level of the manure data. The tool outputs, linked to each flux of manure from a source
to a recipient location, are the amount of transported N, the monetary costs, and the associated fossil carbon
dioxide (CO2) emissions. The ReturN tool was applied to the optimisation of manure fluxes in 3 real European
case studies, and the sensitivity of its outputs to parameters was assessed using the modified Morris sensitivity
analysis method.
RESULTS AND CONCLUSIONS: The application of the ReturN tool successfully optimised manure-N redistribution
under varying conditions of deficits and surpluses and for different geographical areas shapes. The reduction
in costs associated with the purchase of mineral N fertilisers and the decrease in fossil CO2 emissions (due to the
transportation of manure and the production of mineral N fertilisers) achieved through the optimisation of
manure-N fluxes were found to be primarily dependent on the initial manure surplus condition and secondly on
mineral N fertiliser price and manure characteristics (density and N concentration).
SIGNIFICANCE: The flexibility of the ReturN tool’s settings, along with its limited input requirements, ensures its
suitability for direct application by end users in practical contexts thus enabling both the economic and environmental
assessment of the cost-effectiveness of manure transport.The authors acknowledge the financial support for the PROENV Project through the partners of the Joint Call of the Cofund ERA-Nets SusCrop (Grant N° 771134), FACCE ERA-GAS (Grant N° 696356), ICT-AGRI-FOOD (Grant N° 862665) and SusAn (Grant N° 696231). In Spain, this study is part of the PCI2021-122060-2A project, funded by MCIN/AEI/10.13039/501100011033 and the EU's “Next Generation EU”/PRTR Initiative. We gratefully thank the Regional Agency for Agricultural and Forestry Development of Lombardy Region (ERSAF), Lombardia Region, who kindly provided input data for the province of Cremona case study. We thank the Department of Agriculture of the Government of Catalonia which have provided input data for the Girona case study.info:eu-repo/semantics/publishedVersio
Conservation Challenges Under Taxonomic Uncertainty: Introgression Patterns and Environmental Correlates in Mediterranean Brown Trout
Get PDFThe Mediterranean brown trout (Salmo trutta species complex) comprises genetically and ecologically distinct lineages primarily distributed across the Western Mediterranean region. Conservation of the Mediterranean brown trout is complicated by unresolved taxonomy. Although some populations have recently been recognised as distinct species, most—including those in the Iberian Peninsula—remain classified under the nominal S. trutta, which is currently listed as Least Concern by the IUCN. This taxonomic ambiguity masks severe conservation threats, particularly the widespread genetic introgression from stocked Atlantic-origin trout. In this study, we assessed introgression patterns, environmental drivers and conservation implications for Mediterranean brown trout populations in Catalonia (northeastern Iberian Peninsula). Genetic data from 134 sites were analysed using microsatellite markers and LDH-C1* allele frequencies, and the influence of historical stocking intensity and climatic variables on introgression was evaluated using hierarchical partitioning and regression models. Our results revealed extensive introgression, with only 10.4% of the populations retaining genetic purity. Stocking intensity was the primary predictor of introgression, followed by temperature and precipitation seasonality. Although the overall distribution of brown trout in the region remains stable, genetically pure Mediterranean populations have experienced severe range contraction, with a 61.5% reduction in extent of occurrence (EOO) and an 89.6% reduction in area of occupancy (AOO). This decline might meet IUCN criterion B for Endangered, although a formal assessment is currently impeded by taxonomic uncertainty and data limitations. The recognition of Mediterranean brown trout as a distinct species, alongside urgent measures to halt ongoing introgression and preserve remaining pure populations, is essential for its long-term conservation.This work was supported by the Generalitat de Catalunya (CERCA programme) and by grants PID2023-146173NB-C21, RED2022-134338-T, TED2021-129889B-I00, PID2022-141549OB-I00, and RTI2018-095760-B-C22 funded by MICIU/AEI/10.13039/501100011033 and the European Union by “ERDF A way of making Europe” and “NextGenerationEU/PRTR”.info:eu-repo/semantics/publishedVersio
La formación no mejora, lo que la naturaleza no da
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Fasting, crowding and temperature effects on the cardiac activity of European seabass during ice-slurry slaughtering procedure
Get PDFAquaculture production continues to expand rapidly, highlighting the need to improve welfare standards during harvesting procedures. Pre-slaughter operations such as fasting and crowding, along with slaughter procedures, represent critical points with significant welfare implications. In this study, the effects of pre-slaughter protocols and seasonal temperature on cardiac responses during slaughter in European seabass (Dicentrarchus labrax) were evaluated. To monitor cardiac activity, biologgers were surgically implanted in pre-adult seabass subjected to fasting periods and crowding protocols, followed by slaughter in ice slurry or ikejime (a rapid killing method involving brain destruction) at different seasonal temperatures (summer and winter). Results revealed that fasting significantly reduced the time to loss of cardiac function during ice slurry slaughter, particularly under warmer conditions, as fasted individuals lost cardiac activity 14 min earlier than controls, likely due to energy depletion. Crowding elevated heart rate during ice slurry slaughter, counteracting the expected bradycardic response to ice, particularly in summer, where crowded fish lost cardiac signal 11 min earlier than controls. Seasonal variation in water temperature strongly influenced physiological outcomes: winter trials resulted in markedly prolonged cardiac activity during ice exposure, with cessation of cardiac activity times up to 219 min in fasted fish, compared to 32 min in summer. Additionally, crowded fish in summer showed sustained high heart rates and faster cardiac cesssation, indicating acute stress despite shortened duration. These findings suggest that pre-slaughter stressors and environmental conditions interact to shape welfare outcomes. While fasting may improve slaughter efficiency during summer, crowding under high temperatures poses a welfare concern. From a welfare-oriented perspective, minimising crowding and tailoring fasting protocols to seasonal conditions are recommended to improve slaughter efficiency and reduce stress in seabass aquaculture.This study is part of the WELLSTUN project: "Improvement of the slaughter process in farmed fish: Welfare indicators and product quality", funded by the National Aquaculture Plan of the Ministry of Agriculture, Fisheries, and Food from the Spanish Government coordinated by AR. Additionally, EH-A was supported by a “SOIB-Recerca i Innovació” contract, P. A-L was supported by a Ramón y Cajal contract (RYC2020–029629-I) from the State Research Agency of the Spanish Government, and M.J.C-A received Portuguese national funds from FCT - Foundation for Science and Technology through projects UIDB/04326/2020 (DOI:10.54499/UIDB/04326/2020) and LA/P/0101/2020 (DOI:10.54499/LA/P/0101/2020). The authors acknowledge the staff of IRTA for their support and assistance during the experiments.info:eu-repo/semantics/publishedVersio
Rootstock effect on horticultural performance and fruit quality is not uniform across five commercial apple cultivars in western New York
Get PDFIntroduction: The interactive effect of different apple scions with commonly used rootstocks could result in growers selecting an inferior option for tree survival, yield, and fruit quality.
Methods: The long-term tree performance and fruit quality interactions of 19 rootstocks (including Budagovsky, Geneva, and Malling series) and 5 apple cultivars (‘Empire’, ‘Gala’, ‘Honeycrisp’, ‘Mustu’, and ‘Delicious’) were explored in two orchards in Western New York. The first orchard examined the five cultivars on dwarfing rootstocks (B.9, CG.4210, G.11, G.16, G.202, G.41, G.65, G.814, M.26, M.9Pajam2, and M.9T337) and was planted at a spacing of 1.22 m x 3.66 m (2,243 trees ha-1). The second orchard examined the same cultivars on semi-dwarfing rootstocks (B.118, G.214, G.30, G.210, G.935, G.222, M.26, and M.7) and was planted at a spacing of 1.83 m x 4.27 m (1,282 trees ha-1).
Results: Following 17 years, the variables of tree mortality, growth, cumulative yield, and cumulative yield efficiency each resulted in a significant interaction between cultivar and rootstock in both orchards. There were no significant interactions on quality variables measured except fruit color of the 3 bi-colored ‘Gala’, ‘Honeycrisp’ and ‘Delicious’ for both the dwarfing and semi-dwarfing rootstocks.
Discussion/Conclusions: The implications of the interactions observed are that apple producers should pair specific rootstocks with specific cultivars to optimize orchard performance.The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was funded by a grant from the New York Apple Research and Development Program.info:eu-repo/semantics/publishedVersio
Exploring the epidemiology and genetic complexity of Escherichia coli in vertically integrated pig production systems using whole genome sequencing
Get PDFEscherichia coli is a major pathogen responsible for enteric diseases in swine. This study aims to assess the genetic diversity, virulence factors, and antimicrobial resistance genes of E. coli isolated from diarrheic pigs within Spanish integrated production systems. Metadata, including epidemiological data and minimum inhibitory concentration (MIC), was collected for 350 clinical isolates reported to the laboratory between 2018 and 2022. MIC analysis using Ward’s hierarchical clustering identified 17 phenotypic resistance clusters. A subset of 206 isolates, representing different production pyramids and phenotypic clusters, was selected for whole genome sequencing (WGS). In silico serotyping and multilocus sequence typing revealed high genetic diversity, with predominant serotypes O138:H14, O147:H14, O141:H4, and O108:H39, and sequence types ST10 and ST42. Only three ST131 isolates were found in a single production pyramid suggesting that swine associated ST131 is not contributing significantly to the epidemiology of human infections associated to this ST. Isolates were classified into six phylogroups, with phylogroup A being the most represented. AMR profiling identified a high percentage of resistance (> 50 %) to tetracyclines, aminoglycosides, quinolones, trimethoprim and sulphonamides, while resistance to third-generation cephalosporins and colistin remained low (< 25 %). Comparative genomic analysis demonstrated high genetic diversity within production pyramids, although, some clones persisted over time, suggesting transmission within batches. Statistical analyses found no association between genetic traits and farm origins, although outbreaks often involved clones with minimal SNP differences. This study underscores the complexity of E. coli transmission in swine and highlights the need for genomic surveillance to monitor AMR.This study was partially funded by AEMPS/PRAN with the European funds “Mecanismo de recuperación y resilencia (C18.I2.P3.S2)” and the CERCA program. Anna Vilaró is supported by the Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR) of the Catalan Government though the industrial doctorate grant 2021DI 86. This study was carried out with the support of Grup de Sanejament Porcí, Lleida (GSP).info:eu-repo/semantics/publishedVersio
Complementariedad entre sensores satelitales y proximales para optimizar la agricultura de precisión en el cultivo del arroz
Get PDFPara facilitar la transición hacia tecnologías más eficientes, este estudio evalúa la complementariedad entre los datos satelitales proporcionados por Sentinel-2 y uno de los sensores proximales más utilizados (Greenseeker), proponiendo el uso de los datos satelitales como una alternativa de mayor cobertura, rápida adquisición, menor coste y fácil manejo. El ensayo se efectuó en campos de arroz del delta del Ebro entre los años 2016 y 2023.info:eu-repo/semantics/publishedVersio
Growth, Physiological Response, and Gill Health of Spotted Rose Snapper (Lutjanus guttatus) Reared at Different Salinities
Get PDFThe physiological and gill health responses of juvenile spotted rose snapper (Lutjanus guttatus) were evaluated at four salinities—8, 16, 24, and 32‰—over a 70-day period. Fish reared at 8‰ exhibited the highest final body weight (126.8 ± 2.6 g), which was significantly higher than their congeners kept at 24‰ (116.0 ± 2.3 g) and 32‰ (116.0 ± 2.3 g). This superior growth at 8‰ coincides with the complete absence of parasitic monogenean infestations. In contrast, parasite prevalence increased with salinity, reaching 87.5% at 24‰, and was associated with gill pathologies like hyperplasia. Plasma osmolality and chloride levels decreased at lower salinities, while sodium and potassium levels showed a compensatory increase. Plasma cortisol and glucose levels remained stable across all treatments, indicating an absence of chronic stress. These findings suggest that the optimal rearing salinity for juvenile L. guttatus is near 8‰. The enhanced growth at this salinity appears to be the result of a net energy gain, stemming from a trade-off between the minor cost of osmoregulation in a hypo-osmotic environment and the major energetic benefit of avoiding parasitic disease.Financial support of this work by the Vice-Rector for Research at the National University (UNA) of Costa Rica.info:eu-repo/semantics/publishedVersio
Compositional and nutritional value of lupin cultivars: Identifying high-protein seeds for enhanced protein isolate production and phytochemical valorisation
Get PDFThe rising global demand for sustainable protein sources has increased the interest in legumes, particularly lupin, due to its nutritional and technological advantages. Beyond the high protein content, some phytochemicals in lupin seeds such as quinolizidine alkaloids (QAs), saponins, phytic acid, and total phenolic compounds (TPC) warrant further exploration due to their potential for valorisation following a seed protein isolation process, offering opportunities for their use in functional foods, nutraceuticals, or other high-value applications. This work evaluated eight cultivars from different cultivated lupin species —L. albus (Estoril, Celina, and Frieda), L. angustifolius (Giribita and Carabor), and L. luteus (Acos, Cardiga, and a commercial mixture)— in Europe as alternative protein sources. Each cultivar was assessed in terms of proximate composition, phytochemical content, and protein extraction yield. The findings revealed significant inter- and intra-species variability in protein, total dietary fibre, and fat content among the studied cultivars. Lupin protein profile was found to be particularly rich in essential amino acids, including leucine and lysine, as well as beneficial unsaturated fatty acids across all evaluated cultivars. The studied phytochemicals, especially quinolizidine alkaloids, vary significantly among species, while cultivars within the same species showed a more consistent profile. The wet extraction process yielded high-purity protein isolates with favourable extraction efficiency. These findings highlight the potential of lupin for diverse applications in the food and industrial sectors. Cultivar selection is essential to enhance protein extraction yields and colour, as well as to consider lupin as a source of various phytochemicals for valorisation.This research was supported by the LUPIPROTECH project, grant PID2020-114422RR-C51, funded by Spanish Ministerio de Ciencia, Innovación y Universidades and the Agencia Estatal de Investigación MICIU/AEI/10.13039/501100011033 and by the European Union. Additionally, the CERCA program from the Catalan Government Generalitat de Catalunya. Pau Taberner-Pibernat received the grant FI_B 00093 (2022) doctoral contract grant funded by the Catalan Government Generalitat de Catalunya and the grant FPU22/00656 funded by the Spanish Ministerio de Ciencia, Innovación y Universidades and the Agencia Estatal de Investigación MICIU/AEI/10.13039/501100011033 and by ESF investing in your future.info:eu-repo/semantics/publishedVersio