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Sivabharathi RC, Rajagopalan VR, Suresh R, Sudha M, Karthikeyan G, Jayakanthan M, Raveendran M. Haplotype-based breeding: A new insight in crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112129. [PMID: 38763472 DOI: 10.1016/j.plantsci.2024.112129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Haplotype-based breeding (HBB) is one of the cutting-edge technologies in the realm of crop improvement due to the increasing availability of Single Nucleotide Polymorphisms identified by Next Generation Sequencing technologies. The complexity of the data can be decreased with fewer statistical tests and a lower probability of spurious associations by combining thousands of SNPs into a few hundred haplotype blocks. The presence of strong genomic regions in breeding lines of most crop species facilitates the use of haplotypes to improve the efficiency of genomic and marker-assisted selection. Haplotype-based breeding as a Genomic Assisted Breeding (GAB) approach harnesses the genome sequence data to pinpoint the allelic variation used to hasten the breeding cycle and circumvent the challenges associated with linkage drag. This review article demonstrates ways to identify candidate genes, superior haplotype identification, haplo-pheno analysis, and haplotype-based marker-assisted selection. The crop improvement strategies that utilize superior haplotypes will hasten the breeding progress to safeguard global food security.
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Affiliation(s)
- R C Sivabharathi
- Department of Genetics and Plant breeding, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - R Suresh
- Department of Rice, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Sudha
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
| | - G Karthikeyan
- Department of Plant Pathology, CPPS, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Jayakanthan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Raveendran
- Directorate of research, Tamil Nadu Agricultural University, Coimbatore 641003, India.
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Flores-Saavedra M, Villanueva G, Gramazio P, Vilanova S, Mauceri A, Abenavoli MR, Sunseri F, Prohens J, Plazas M. Nitrogen use efficiency, growth and physiological parameters in different tomato genotypes under high and low N fertilisation conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108447. [PMID: 38417307 DOI: 10.1016/j.plaphy.2024.108447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 03/01/2024]
Abstract
Identification of novel genotypes with enhanced nitrogen use efficiency (NUE) is a key challenge for a sustainable tomato production. In this respect, the performance of a panel of thirty tomato accessions were evaluated under high (HN; 5 mM N) and low (LN; 0.5 mM N) nitrogen irrigation solutions. For each treatment, when 50% of plants reached the first flower bud stage, plant growth and biomass traits, chlorophyll, flavonol and anthocyanin indexes, nitrogen balance index (NBI), C:N ratio in leaves, stems, and roots, and NUE were evaluated. Significant (p < 0.05) effects were observed for accession, N treatment, and their interaction across all the traits. Under LN, plants showed a delayed development (40 days for HN vs. 65 days for LN) and reduced growth and biomass. On average, LN condition led to 41.8% decrease in nitrogen uptake efficiency (NUpE) but also 189.0% increase in NUtE, resulting in 62.2% overall increase in NUE. A broad range of variation among accessions was observed under both HN and LN conditions. Under LN conditions, chlorophyll index and NBI decreased, while flavonol and anthocyanin indexes increased. Leaf C:N ratio was positively correlated with nitrogen utilisation efficiency (NUtE) in both N treatments. Multi-trait analyses identified top-performing accessions under each condition, allowing to identify one accession among top performers under both conditions. Correlation analysis revealed that high root biomass and leaf C:N ratio are useful markers for selecting high NUE accessions. These findings offer valuable insights for improving tomato NUE under varying nitrogen fertilization conditions and for breeding high-NUE cultivars.
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Affiliation(s)
- Martín Flores-Saavedra
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Antonio Mauceri
- Department of Agraria, University Mediterranea of Reggio Calabria Località Feo di Vito snc, 89124, Reggio, Calabria, Italy
| | - Maria Rosa Abenavoli
- Department of Agraria, University Mediterranea of Reggio Calabria Località Feo di Vito snc, 89124, Reggio, Calabria, Italy
| | - Francesco Sunseri
- Department of Agraria, University Mediterranea of Reggio Calabria Località Feo di Vito snc, 89124, Reggio, Calabria, Italy
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain.
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
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Laidig F, Feike T, Lichthardt C, Schierholt A, Piepho HP. Breeding progress of nitrogen use efficiency of cereal crops, winter oilseed rape and peas in long-term variety trials. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:45. [PMID: 38329519 PMCID: PMC10853085 DOI: 10.1007/s00122-023-04521-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024]
Abstract
KEY MESSAGE Grain yield and NUE increased over time while nitrogen yield did not drop significantly despite reduced nitrogen input. Selection for grain and nitrogen yield is equivalent to selection for NUE. Breeding and registration of improved varieties with high yield, processing quality, disease resistance and nitrogen use efficiency (NUE) are of utmost importance for sustainable crop production to minimize adverse environmental impact and contribute to food security. Based on long-term variety trials of cereals, winter oilseed rape and grain peas tested across a wide range of environmental conditions in Germany, we quantified long-term breeding progress for NUE and related traits. We estimated the genotypic, environmental and genotype-by-environment interaction variation and correlation between traits and derived heritability coefficients. Nitrogen fertilizer application was considerably reduced between 1995 and 2021 in the range of 5.4% for winter wheat and 28.9% for spring wheat while for spring barley it was increased by 20.9%. Despite the apparent nitrogen reduction for most crops, grain yield (GYLD) and nitrogen accumulation in grain (NYLD) was increased or did not significantly decrease. NUE for GYLD increased significantly for all crops between 12.8% and 35.2% and for NYLD between 8% and 20.7%. We further showed that the genotypic rank of varieties for GYLD and NYLD was about equivalent to the genotypic rank of the corresponding traits of NUE, if all varieties in a trial were treated with the same nitrogen rate. Heritability of nitrogen yield was about the same as that of grain yield, suggesting that nitrogen yield should be considered as an additional criterion for variety testing to increase NUE and reduce negative environmental impact.
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Affiliation(s)
- F Laidig
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany.
| | - T Feike
- Julius Kühn Institute - Federal Research Centre for Cultivated Plants, Institute for Strategies and Technology Assessment, Stahnsdorfer Damm 81, 14532, Kleinmachnow, Germany
| | - C Lichthardt
- Bundessortenamt, Osterfelddamm 60, 30627, Hannover, Germany
| | - A Schierholt
- Plant Breeding Methodology, Georg-August-University Göttingen, Carl-Sprengel-Weg 1, 37075, Göttingen, Germany
| | - H P Piepho
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany
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Camenzind MP, Yu K. Multi temporal multispectral UAV remote sensing allows for yield assessment across European wheat varieties already before flowering. FRONTIERS IN PLANT SCIENCE 2024; 14:1214931. [PMID: 38235203 PMCID: PMC10791776 DOI: 10.3389/fpls.2023.1214931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 11/29/2023] [Indexed: 01/19/2024]
Abstract
High throughput field phenotyping techniques employing multispectral cameras allow extracting a variety of variables and features to predict yield and yield related traits, but little is known about which types of multispectral features are optimal to forecast yield potential in the early growth phase. In this study, we aim to identify multispectral features that are able to accurately predict yield and aid in variety classification at different growth stages throughout the season. Furthermore, we hypothesize that texture features (TFs) are more suitable for variety classification than for yield prediction. Throughout 2021 and 2022, a trial involving 19 and 18 European wheat varieties, respectively, was conducted. Multispectral images, encompassing visible, Red-edge, and near-infrared (NIR) bands, were captured at 19 and 22 time points from tillering to harvest using an unmanned aerial vehicle (UAV) in the first and second year of trial. Subsequently, orthomosaic images were generated, and various features were extracted, including single-band reflectances, vegetation indices (VI), and TFs derived from a gray level correlation matrix (GLCM). The performance of these features in predicting yield and classifying varieties at different growth stages was assessed using random forest models. Measurements during the flowering stage demonstrated superior performance for most features. Specifically, Red reflectance achieved a root mean square error (RMSE) of 52.4 g m-2 in the first year and 64.4 g m-2 in the second year. The NDRE VI yielded the most accurate predictions with an RMSE of 49.1 g m-2 and 60.6 g m-2, respectively. Moreover, TFs such as CONTRAST and DISSIMILARITY displayed the best performance in predicting yield, with RMSE values of 55.5 g m-2 and 66.3 g m-2 across the two years of trial. Combining data from different dates enhanced yield prediction and stabilized predictions across dates. TFs exhibited high accuracy in classifying low and high-yielding varieties. The CORRELATION feature achieved an accuracy of 88% in the first year, while the HOMOGENEITY feature reached 92% accuracy in the second year. This study confirms the hypothesis that TFs are more suitable for variety classification than for yield prediction. The results underscore the potential of TFs derived from multispectral images in early yield prediction and varietal classification, offering insights for HTP and precision agriculture alike.
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Affiliation(s)
- Moritz Paul Camenzind
- Precision Agriculture Lab, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Kang Yu
- Precision Agriculture Lab, School of Life Sciences, Technical University of Munich, Freising, Germany
- World Agricultural Systems Center (Hans Eisenmann-Forum for Agricultural Sciences – HEF), Technical University of Munich, Freising, Germany
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Muqaddasi QH, Muqaddasi RK, Ebmeyer E, Korzun V, Argillier O, Mirdita V, Reif JC, Ganal MW, Röder MS. Genetic control and prospects of predictive breeding for European winter wheat's Zeleny sedimentation values and Hagberg-Perten falling number. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:229. [PMID: 37874400 PMCID: PMC10598174 DOI: 10.1007/s00122-023-04450-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/16/2023] [Indexed: 10/25/2023]
Abstract
KEY MESSAGE Sedimentation values and falling number in the last decades have helped maintain high baking quality despite rigorous selection for grain yield in wheat. Allelic combinations of major loci sustained the bread-making quality while improving grain yield. Glu-D1, Pinb-D1, and non-gluten proteins are associated with sedimentation values and falling number in European wheat. Zeleny sedimentation values (ZSV) and Hagberg-Perten falling number (HFN) are among the most important parameters that help determine the baking quality classes of wheat and, thus, influence the monetary benefits for growers. We used a published data set of 372 European wheat varieties evaluated in replicated field trials in multiple environments. ZSV and HFN traits hold a wide and significant genotypic variation and high broad-sense heritability. The genetic correlations revealed positive and significant associations of ZSV and HFN with each other, grain protein content (GPC) and grain hardness; however, they were all significantly negatively correlated with grain yield. Besides, GPC appeared to be the major predictor for ZSV and HFN. Our genome-wide association analyses based on high-quality SSR, SNP, and candidate gene markers revealed a strong quantitative genetic nature of ZSV and HFN by explaining their total genotypic variance as 41.49% and 38.06%, respectively. The association of known Glutenin (Glu-1) and Puroindoline (Pin-1) with ZSV provided positive analytic proof of our studies. We report novel candidate loci associated with globulins and albumins-the non-gluten monomeric proteins in wheat. In addition, predictive breeding analyses for ZSV and HFN suggest using genomic selection in the early stages of breeding programs with an average prediction accuracy of 81 and 59%, respectively.
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Affiliation(s)
- Quddoos H Muqaddasi
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany.
- KWS SAAT SE & Co. KGaA, Einbeck, 37574, Germany.
| | - Roop Kamal Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | | | | | | | - Vilson Mirdita
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1B, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
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Zhao Y, Islam S, Alhabbar Z, Zhang J, O'Hara G, Anwar M, Ma W. Current Progress and Future Prospect of Wheat Genetics Research towards an Enhanced Nitrogen Use Efficiency. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091753. [PMID: 37176811 PMCID: PMC10180859 DOI: 10.3390/plants12091753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 05/15/2023]
Abstract
To improve the yield and quality of wheat is of great importance for food security worldwide. One of the most effective and significant approaches to achieve this goal is to enhance the nitrogen use efficiency (NUE) in wheat. In this review, a comprehensive understanding of the factors involved in the process of the wheat nitrogen uptake, assimilation and remobilization of nitrogen in wheat were introduced. An appropriate definition of NUE is vital prior to its precise evaluation for the following gene identification and breeding process. Apart from grain yield (GY) and grain protein content (GPC), the commonly recognized major indicators of NUE, grain protein deviation (GPD) could also be considered as a potential trait for NUE evaluation. As a complex quantitative trait, NUE is affected by transporter proteins, kinases, transcription factors (TFs) and micro RNAs (miRNAs), which participate in the nitrogen uptake process, as well as key enzymes, circadian regulators, cross-talks between carbon metabolism, which are associated with nitrogen assimilation and remobilization. A series of quantitative genetic loci (QTLs) and linking markers were compiled in the hope to help discover more efficient and useful genetic resources for breeding program. For future NUE improvement, an exploration for other criteria during selection process that incorporates morphological, physiological and biochemical traits is needed. Applying new technologies from phenomics will allow high-throughput NUE phenotyping and accelerate the breeding process. A combination of multi-omics techniques and the previously verified QTLs and molecular markers will facilitate the NUE QTL-mapping and novel gene identification.
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Affiliation(s)
- Yun Zhao
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang 050035, China
| | - Shahidul Islam
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Zaid Alhabbar
- Department of Field Crops, College of Agriculture and Forestry, University of Mosul, Mosul 41002, Iraq
| | - Jingjuan Zhang
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
| | - Graham O'Hara
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
| | - Masood Anwar
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
| | - Wujun Ma
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
- College of Agronomy, Qingdao Agriculture University, Qingdao 266109, China
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Wang TC, Casadebaig P, Chen TW. More than 1000 genotypes are required to derive robust relationships between yield, yield stability and physiological parameters: a computational study on wheat crop. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:34. [PMID: 36897399 PMCID: PMC10006026 DOI: 10.1007/s00122-023-04264-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/10/2022] [Indexed: 06/18/2023]
Abstract
Using in silico experiment in crop model, we identified different physiological regulations of yield and yield stability, as well as quantify the genotype and environment numbers required for analysing yield stability convincingly. Identifying target traits for breeding stable and high-yielded cultivars simultaneously is difficult due to limited knowledge of physiological mechanisms behind yield stability. Besides, there is no consensus about the adequacy of a stability index (SI) and the minimal number of environments and genotypes required for evaluating yield stability. We studied this question using the crop model APSIM-Wheat to simulate 9100 virtual genotypes grown under 9000 environments. By analysing the simulated data, we showed that the shape of phenotype distributions affected the correlation between SI and mean yield and the genotypic superiority measure (Pi) was least affected among 11 SI. Pi was used as index to demonstrate that more than 150 environments were required to estimate yield stability of a genotype convincingly and more than 1000 genotypes were necessary to evaluate the contribution of a physiological parameter to yield stability. Network analyses suggested that a physiological parameter contributed preferentially to yield or Pi. For example, soil water absorption efficiency and potential grain filling rate explained better the variations in yield than in Pi; while light extinction coefficient and radiation use efficiency were more correlated with Pi than with yield. The high number of genotypes and environments required for studying Pi highlight the necessity and potential of in silico experiments to better understand the mechanisms behind yield stability.
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Affiliation(s)
- Tien-Cheng Wang
- Section of Intensive Plant Food Systems, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt Universität zu Berlin, Berlin, Germany.
- Institut für Gartenbauliche Produktionssysteme, Leibniz Universität Hannover, Hannover, Germany.
| | - Pierre Casadebaig
- INRAE, UMR AGIR, Université de Toulouse, 31320, Castanet-Tolosan, France
| | - Tsu-Wei Chen
- Section of Intensive Plant Food Systems, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt Universität zu Berlin, Berlin, Germany.
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8
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Hartung J, Laidig F, Piepho HP. Effects of systematic data reduction on trend estimation from German registration trials. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:21. [PMID: 36688966 PMCID: PMC9870826 DOI: 10.1007/s00122-023-04266-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/22/2022] [Indexed: 06/17/2023]
Abstract
VCU trials can provide unbiased estimates of post-breeding trends given that all data is used. Dropping data of genotypes tested for up to two years may result in biased post-breeding trend estimates. Increasing yield trends are seen on-farm in Germany. The increase is based on genetic trend in registered genotypes and changes in agronomic practices and climate. To estimate both genetic and non-genetic trends, historical wheat data from variety trials evaluating a varieties' value for cultivation und use (VCU) were analyzed. VCU datasets include information on varieties as well as on genotypes that were submitted by breeders and tested in trials but could not make it to registration. Therefore, the population of registered varieties (post-registration population) is a subset of the population of genotypes tested in VCU trials (post-breeding population). To assess post-registration genetic trend, historical VCU trial datasets are often reduced, e.g. to registered varieties only. This kind of drop-out mechanism is statistically informative which affects variance component estimates and which can affect trend estimates. To investigate the effect of this informative drop-out on trend estimates, a simulation study was conducted mimicking the structure of German winter wheat VCU trials. Zero post-breeding trends were simulated. Results showed unbiased estimates of post-breeding trends when using all data. When restricting data to genotypes tested for at least three years, a positive genetic trend of 0.11 dt ha-1 year-1 and a negative non-genetic trend (- 0.11 dt ha-1 year-1) were observed. Bias increased with increasing genotype-by-year variance and disappeared with random selection. We simulated single-trait selection, whereas decisions in VCU trials consider multiple traits, so selection intensity per trait is considerably lower. Hence, our results provide an upper bound for the bias expected in practice.
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Affiliation(s)
- Jens Hartung
- Institut for Crop Science, Biostatistics Unit, University of Hohenheim, Stuttgart, Germany.
| | - Friedrich Laidig
- Institut for Crop Science, Biostatistics Unit, University of Hohenheim, Stuttgart, Germany
| | - Hans-Peter Piepho
- Institut for Crop Science, Biostatistics Unit, University of Hohenheim, Stuttgart, Germany
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Chattha MS, Ali Q, Haroon M, Afzal MJ, Javed T, Hussain S, Mahmood T, Solanki MK, Umar A, Abbas W, Nasar S, Schwartz-Lazaro LM, Zhou L. Enhancement of nitrogen use efficiency through agronomic and molecular based approaches in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:994306. [PMID: 36237509 PMCID: PMC9552886 DOI: 10.3389/fpls.2022.994306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/22/2022] [Indexed: 05/22/2023]
Abstract
Cotton is a major fiber crop grown worldwide. Nitrogen (N) is an essential nutrient for cotton production and supports efficient crop production. It is a crucial nutrient that is required more than any other. Nitrogen management is a daunting task for plants; thus, various strategies, individually and collectively, have been adopted to improve its efficacy. The negative environmental impacts of excessive N application on cotton production have become harmful to consumers and growers. The 4R's of nutrient stewardship (right product, right rate, right time, and right place) is a newly developed agronomic practice that provides a solid foundation for achieving nitrogen use efficiency (NUE) in cotton production. Cropping systems are equally crucial for increasing production, profitability, environmental growth protection, and sustainability. This concept incorporates the right fertilizer source at the right rate, time, and place. In addition to agronomic practices, molecular approaches are equally important for improving cotton NUE. This could be achieved by increasing the efficacy of metabolic pathways at the cellular, organ, and structural levels and NUE-regulating enzymes and genes. This is a potential method to improve the role of N transporters in plants, resulting in better utilization and remobilization of N in cotton plants. Therefore, we suggest effective methods for accelerating NUE in cotton. This review aims to provide a detailed overview of agronomic and molecular approaches for improving NUE in cotton production, which benefits both the environment and growers.
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Affiliation(s)
- Muhammad Sohaib Chattha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Qurban Ali
- Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | | | - Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sadam Hussain
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Tahir Mahmood
- Department of Plant Breeding & Genetics, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Manoj K. Solanki
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Aisha Umar
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Waseem Abbas
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shanza Nasar
- Department of Botany, University of Gujrat Hafiz Hayat Campus, Gujrat, Pakistan
| | - Lauren M. Schwartz-Lazaro
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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10
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Grzybowski MW, Zwiener M, Jin H, Wijewardane NK, Atefi A, Naldrett MJ, Alvarez S, Ge Y, Schnable JC. Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel. BMC PLANT BIOLOGY 2022; 22:433. [PMID: 36076172 PMCID: PMC9461132 DOI: 10.1186/s12870-022-03823-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Access to biologically available nitrogen is a key constraint on plant growth in both natural and agricultural settings. Variation in tolerance to nitrogen deficit stress and productivity in nitrogen limited conditions exists both within and between plant species. However, our understanding of changes in different phenotypes under long term low nitrogen stress and their impact on important agronomic traits, such as yield, is still limited. RESULTS Here we quantified variation in the metabolic, physiological, and morphological responses of a sorghum association panel assembled to represent global genetic diversity to long term, nitrogen deficit stress and the relationship of these responses to grain yield under both conditions. Grain yield exhibits substantial genotype by environment interaction while many other morphological and physiological traits exhibited consistent responses to nitrogen stress across the population. Large scale nontargeted metabolic profiling for a subset of lines in both conditions identified a range of metabolic responses to long term nitrogen deficit stress. Several metabolites were associated with yield under high and low nitrogen conditions. CONCLUSION Our results highlight that grain yield in sorghum, unlike many morpho-physiological traits, exhibits substantial variability of genotype specific responses to long term low severity nitrogen deficit stress. Metabolic response to long term nitrogen stress shown higher proportion of variability explained by genotype specific responses than did morpho-pysiological traits and several metabolites were correlated with yield. This suggest, that it might be possible to build predictive models using metabolite abundance to estimate which sorghum genotypes will exhibit greater or lesser decreases in yield in response to nitrogen deficit, however further research needs to be done to evaluate such model.
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Affiliation(s)
- Marcin W Grzybowski
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsw, Poland.
| | - Mackenzie Zwiener
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Hongyu Jin
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Nuwan K Wijewardane
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, USA
| | - Abbas Atefi
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, USA
- California Strawberry Commission, San Luis Obispo, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, USA
| | - Sophie Alvarez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, USA
| | - Yufeng Ge
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA.
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11
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Javed T, I I, Singhal RK, Shabbir R, Shah AN, Kumar P, Jinger D, Dharmappa PM, Shad MA, Saha D, Anuragi H, Adamski R, Siuta D. Recent Advances in Agronomic and Physio-Molecular Approaches for Improving Nitrogen Use Efficiency in Crop Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:877544. [PMID: 35574130 PMCID: PMC9106419 DOI: 10.3389/fpls.2022.877544] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/11/2022] [Indexed: 05/05/2023]
Abstract
The efficiency with which plants use nutrients to create biomass and/or grain is determined by the interaction of environmental and plant intrinsic factors. The major macronutrients, especially nitrogen (N), limit plant growth and development (1.5-2% of dry biomass) and have a direct impact on global food supply, fertilizer demand, and concern with environmental health. In the present time, the global consumption of N fertilizer is nearly 120 MT (million tons), and the N efficiency ranges from 25 to 50% of applied N. The dynamic range of ideal internal N concentrations is extremely large, necessitating stringent management to ensure that its requirements are met across various categories of developmental and environmental situations. Furthermore, approximately 60 percent of arable land is mineral deficient and/or mineral toxic around the world. The use of chemical fertilizers adds to the cost of production for the farmers and also increases environmental pollution. Therefore, the present study focused on the advancement in fertilizer approaches, comprising the use of biochar, zeolite, and customized nano and bio-fertilizers which had shown to be effective in improving nitrogen use efficiency (NUE) with lower soil degradation. Consequently, adopting precision farming, crop modeling, and the use of remote sensing technologies such as chlorophyll meters, leaf color charts, etc. assist in reducing the application of N fertilizer. This study also discussed the role of crucial plant attributes such as root structure architecture in improving the uptake and transport of N efficiency. The crosstalk of N with other soil nutrients plays a crucial role in nutrient homeostasis, which is also discussed thoroughly in this analysis. At the end, this review highlights the more efficient and accurate molecular strategies and techniques such as N transporters, transgenes, and omics, which are opening up intriguing possibilities for the detailed investigation of the molecular components that contribute to nitrogen utilization efficiency, thus expanding our knowledge of plant nutrition for future global food security.
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Affiliation(s)
- Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Indu I
- Indian Council of Agricultural Research (ICAR)-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rajesh Kumar Singhal
- Indian Council of Agricultural Research (ICAR)-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rubab Shabbir
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant Breeding and Genetics, Seed Science and Technology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Pawan Kumar
- Indian Council of Agricultural Research (ICAR)-Central Institute for Arid Horticulture, Bikaner, India
| | - Dinesh Jinger
- Research Centre, Indian Council of Agricultural Research (ICAR)-Indian Institute of Soil and Water Conservation, Anand, India
| | - Prathibha M. Dharmappa
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Horticultural Research, Bengaluru, India
| | - Munsif Ali Shad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene, Hubei Hongshan Laboratory, Wuhan, China
| | - Debanjana Saha
- Centurion University of Technology and Management, Jatni, India
| | - Hirdayesh Anuragi
- Indian Council of Agricultural Research (ICAR)- Central Agroforestry Research Institute, Jhansi, India
| | - Robert Adamski
- Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
| | - Dorota Siuta
- Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
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12
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Kaur S, Shamshad M, Jindal S, Kaur A, Singh S, sharma A, Kaur S. RNA-Seq-Based Transcriptomics Study to Investigate the Genes Governing Nitrogen Use Efficiency in Indian Wheat Cultivars. Front Genet 2022; 13:853910. [PMID: 35432475 PMCID: PMC9009086 DOI: 10.3389/fgene.2022.853910] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/18/2022] [Indexed: 11/24/2022] Open
Abstract
High NUE (nitrogen use efficiency) has great practical significance for sustainable crop production. Wheat is one of the main cultivated crops worldwide for human food and nutrition. However, wheat grain productivity is dependent upon cultivars with high NUE in addition to the application of nitrogen fertilizers. In order to understand the molecular mechanisms exhibiting a high NUE response, a comparative transcriptomics study was carried out through RNA-seq analysis to investigate the gene expression that regulates NUE, in root and shoot tissue of N-efficient (PBW677) and N-inefficient (703) cultivars under optimum and nitrogen (N) stress. Differentially expressed gene analysis revealed a total of 2,406 differentially expressed genes (DEGs) present in both the contrasting cultivars under N stress. The efficient genotype PBW677 had considerably more abundant DEGs with 1,653 (903 roots +750 shoots) compared to inefficient cultivar PBW703 with 753 (96 roots +657 shoots). Gene ontology enrichment and pathway analysis of these DEGs suggested that the two cultivars differed in terms of adaptive mechanism. Gene enrichment analysis revealed that among the upregulated and downregulated genes the overrepresented and underrepresented gene categories belonged to biological processes like DNA binding, response to abiotic stimulus, photosynthesis, carbon fixation, carbohydrate metabolic process, nitrogen compound metabolic process, nitrate transport, and translation in cultivar PBW677, while the enriched biological processes were nucleosome assembly, chromatin remodeling, DNA packaging, lipid transport, sulfur compound metabolic process, protein modifications, and protein folding and refolding in N inefficient cultivar PBW703. We found several transcription factors (MYB, WRKY, RING finger protein, zinc finger protein, transporters, NRT1, amino acid transporters, sugar), protein kinases, and genes involved in N absorption, transportation, and assimilation to be highly expressed in high NUE cultivar PBW677. In our study, we report 13 potential candidate genes which showed alternate gene expression in the two contrasting cultivars under study. These genes could serve as potential targets for future breeding programs.
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Affiliation(s)
- Sarabjit Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - M. Shamshad
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Suruchi Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Satinder Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Achla sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Achla sharma, ; Satinder Kaur,
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Achla sharma, ; Satinder Kaur,
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13
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Teng W, He X, Tong Y. Genetic Control of Efficient Nitrogen Use for High Yield and Grain Protein Concentration in Wheat: A Review. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040492. [PMID: 35214826 PMCID: PMC8878021 DOI: 10.3390/plants11040492] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 05/12/2023]
Abstract
The increasing global population and the negative effects of nitrogen (N) fertilizers on the environment challenge wheat breeding to maximize yield potential and grain protein concentration (GPC) in an economically and environmentally friendly manner. Understanding the molecular mechanisms for the response of yield components to N availability and assimilates allocation to grains provides the opportunity to increase wheat yield and GPC simultaneously. This review summarized quantitative trait loci/genes which can increase spikes and grain number by enhancing N uptake and assimilation at relative early growth stage, and 1000-grain weight and GPC by increasing post-anthesis N uptake and N allocation to grains.
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Affiliation(s)
- Wan Teng
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (W.T.); (X.H.)
| | - Xue He
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (W.T.); (X.H.)
| | - Yiping Tong
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (W.T.); (X.H.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: ; Tel.: +86-10-64806556
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14
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Ivić M, Grljušić S, Plavšin I, Dvojković K, Lovrić A, Rajković B, Maričević M, Černe M, Popović B, Lončarić Z, Bentley AR, Swarbreck SM, Šarčević H, Novoselović D. Variation for Nitrogen Use Efficiency Traits in Wheat Under Contrasting Nitrogen Treatments in South-Eastern Europe. FRONTIERS IN PLANT SCIENCE 2021; 12:682333. [PMID: 34868096 PMCID: PMC8636685 DOI: 10.3389/fpls.2021.682333] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 10/18/2021] [Indexed: 05/06/2023]
Abstract
Wheat cultivars differ in their response to nitrogen (N) fertilizer, both in terms of its uptake and utilization. Characterizing this variation is an important step in improving the N use efficiency (NUE) of future cultivars while maximizing production (yield) potential. In this study, we compared the agronomic performance of 48 diverse wheat cultivars released between 1936 and 2016 at low and high N input levels in field conditions to assess the relationship between NUE and its components. Agronomic trait values were significantly lower in the low N treatment, and the cultivars tested showed a significant variation for all traits (apart from the N remobilization efficiency), indicating that response is genotype-dependent, although significant genotype × environment effects were also observed. Overall, we show a varietal improvement in NUE over time of 0.33 and 0.30% year-1 at low and high N, respectively, and propose that this is driven predominantly by varietal selection for increased yield. More complete understanding of the components of these improvements will inform future targeted breeding and selection strategies to support a reduction in fertilizer use while maintaining productivity.
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Affiliation(s)
- Marko Ivić
- Agricultural Institute Osijek, Osijek, Croatia
| | | | - Ivana Plavšin
- Agricultural Institute Osijek, Osijek, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Zagreb, Croatia
| | | | - Ana Lovrić
- Faculty of Agriculture Zagreb, University of Zagreb, Zagreb, Croatia
| | - Bruno Rajković
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Zagreb, Croatia
- Faculty of Agriculture Zagreb, University of Zagreb, Zagreb, Croatia
| | - Marko Maričević
- BC Institute for Breeding and Production of Field Crops Zagreb, Rugvica, Croatia
| | - Marko Černe
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Zagreb, Croatia
- Institute for Agriculture and Tourism Poreč, Poreč, Croatia
| | - Brigita Popović
- Faculty of Agrobiotechnical Sciences, University of Josip Juraj Strossmayer in Osijek, Osijek, Croatia
| | - Zdenko Lončarić
- Faculty of Agrobiotechnical Sciences, University of Josip Juraj Strossmayer in Osijek, Osijek, Croatia
| | - Alison R. Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Stéphanie M. Swarbreck
- The John Bingham Lab, National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Hrvoje Šarčević
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Zagreb, Croatia
- Faculty of Agriculture Zagreb, University of Zagreb, Zagreb, Croatia
| | - Dario Novoselović
- Agricultural Institute Osijek, Osijek, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Zagreb, Croatia
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15
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Carucci F, Gatta G, Gagliardi A, De Vita P, Bregaglio S, Giuliani MM. Agronomic Strategies to Improve N Efficiency Indices in Organic Durum Wheat Grown in Mediterranean Area. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112444. [PMID: 34834811 PMCID: PMC8618784 DOI: 10.3390/plants10112444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Organic farming systems are often constrained by limited soil nitrogen (N) availability. Here we evaluated the effect of foliar organic N and sulphur (S), and selenium (Se) application on durum wheat, considering N uptake, utilization efficiency (NUtE), grain yield, and protein concentration as target variables. Field trials were conducted in 2018 and 2019 on two old (Cappelli and old Saragolla) and two modern (Marco Aurelio and Nadif) Italian durum wheat varieties. Four organic fertilization strategies were evaluated, i.e., the control (CTR, dry blood meal at sowing), the application of foliar N (CTR + N) and S (CTR + S), and their joint use (CTR + NS). Furthermore, a foliar application of sodium selenate was evaluated. Three factors-variety, fertilization strategies and selenium application-were arranged in a split-split-plot design and tested in two growing seasons. The modern variety Marco Aurelio led to the highest NUtE and grain yield in both seasons. S and N applications had a positive synergic effect, especially under drought conditions, on pre-anthesis N uptake, N translocation, NUtE, and grain yield. Se treatment improved post-anthesis N uptake and NUtE, leading to 17% yield increase in the old variety Cappelli, and to 13% and 14% yield increase in Marco Aurelio and Nadif, mainly attributed to NUtE increase. This study demonstrated that the synergistic effect of foliar applications could improve organic durum wheat yields in Mediterranean environments, especially on modern varieties.
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Affiliation(s)
- Federica Carucci
- Department of Agricultural Sciences, Food, Natural Resources and Engineering (DAFNE), University of Foggia, 71122 Foggia, Italy; (F.C.); (G.G.); (A.G.)
| | - Giuseppe Gatta
- Department of Agricultural Sciences, Food, Natural Resources and Engineering (DAFNE), University of Foggia, 71122 Foggia, Italy; (F.C.); (G.G.); (A.G.)
| | - Anna Gagliardi
- Department of Agricultural Sciences, Food, Natural Resources and Engineering (DAFNE), University of Foggia, 71122 Foggia, Italy; (F.C.); (G.G.); (A.G.)
| | - Pasquale De Vita
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy;
| | - Simone Bregaglio
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment (CREA-AA), 40128 Bologna, Italy;
| | - Marcella Michela Giuliani
- Department of Agricultural Sciences, Food, Natural Resources and Engineering (DAFNE), University of Foggia, 71122 Foggia, Italy; (F.C.); (G.G.); (A.G.)
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16
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Zhang X, Ma Q, Li F, Ding Y, Yi Y, Zhu M, Ding J, Li C, Guo W, Zhu X. Transcriptome Analysis Reveals Different Responsive Patterns to Nitrogen Deficiency in Two Wheat Near-Isogenic Lines Contrasting for Nitrogen Use Efficiency. BIOLOGY 2021; 10:biology10111126. [PMID: 34827119 PMCID: PMC8614915 DOI: 10.3390/biology10111126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/30/2022]
Abstract
Simple Summary Nitrogen (N) limitation is the key factor for wheat production worldwide. Therefore, the development of genotypes with improved nitrogen use efficiency (NUE) is a prerequisite for sustainable and productive agriculture. Exploring the molecular mechanisms of low N stress tolerance is significant for breeding wheat cultivars with high NUE. To clarify the underlying molecular mechanisms of enhanced resilience to low N in high-NUE wheat, we performed an RNA sequencing (RNA-seq) analysis. In the current research, two wheat near-isogenic lines (NILs) differing dramatically in NUE were used to measure gene expression differences under different N treatments. There was a dramatic difference between two wheat NILs in response to N deficiency at the transcriptional level, and the classification of identified candidate genes may provide new valuable insights into the resilience mechanism of wheat. Abstract The development of crop cultivars with high nitrogen use efficiency (NUE) under low-N fertilizer inputs is imperative for sustainable agriculture. However, there has been little research on the molecular mechanisms underlying enhanced resilience to low N in high-NUE plants. The comparison of the transcriptional responses of genotypes contrasting for NUE will facilitate an understanding of the key molecular mechanism of wheat resilience to low-N stress. In the current study, the RNA sequencing (RNA-seq) technique was employed to investigate the genotypic difference in response to N deficiency between two wheat NILs (1Y, high-NUE, and 1W, low-NUE). In our research, high- and low-NUE wheat NILs showed different patterns of gene expression under N-deficient conditions, and these N-responsive genes were classified into two major classes, including “frontloaded genes” and “relatively upregulated genes”. In total, 103 and 45 genes were identified as frontloaded genes in high-NUE and low-NUE wheat, respectively. In summary, our study might provide potential directions for further understanding the molecular mechanism of high-NUE genotypes adapting to low-N stress.
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Affiliation(s)
- Xinbo Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (X.Z.); (Q.M.); (F.L.); (Y.D.); (M.Z.); (J.D.); (C.L.); (W.G.)
| | - Quan Ma
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (X.Z.); (Q.M.); (F.L.); (Y.D.); (M.Z.); (J.D.); (C.L.); (W.G.)
| | - Fujian Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (X.Z.); (Q.M.); (F.L.); (Y.D.); (M.Z.); (J.D.); (C.L.); (W.G.)
| | - Yonggang Ding
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (X.Z.); (Q.M.); (F.L.); (Y.D.); (M.Z.); (J.D.); (C.L.); (W.G.)
| | - Yuan Yi
- Jiangsu Xuhuai Regional Institute of Agricultural Science, Xuzhou 221131, China;
| | - Min Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (X.Z.); (Q.M.); (F.L.); (Y.D.); (M.Z.); (J.D.); (C.L.); (W.G.)
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jinfeng Ding
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (X.Z.); (Q.M.); (F.L.); (Y.D.); (M.Z.); (J.D.); (C.L.); (W.G.)
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Chunyan Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (X.Z.); (Q.M.); (F.L.); (Y.D.); (M.Z.); (J.D.); (C.L.); (W.G.)
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Wenshan Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (X.Z.); (Q.M.); (F.L.); (Y.D.); (M.Z.); (J.D.); (C.L.); (W.G.)
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Xinkai Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (X.Z.); (Q.M.); (F.L.); (Y.D.); (M.Z.); (J.D.); (C.L.); (W.G.)
- Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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17
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Liang T, Yuan Z, Fu L, Zhu M, Luo X, Xu W, Yuan H, Zhu R, Hu Z, Wu X. Integrative Transcriptomic and Proteomic Analysis Reveals an Alternative Molecular Network of Glutamine Synthetase 2 Corresponding to Nitrogen Deficiency in Rice ( Oryza sativa L.). Int J Mol Sci 2021; 22:ijms22147674. [PMID: 34299294 PMCID: PMC8304609 DOI: 10.3390/ijms22147674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/10/2021] [Accepted: 07/15/2021] [Indexed: 01/21/2023] Open
Abstract
Nitrogen (N) is an essential nutrient for plant growth and development. The root system architecture is a highly regulated morphological system, which is sensitive to the availability of nutrients, such as N. Phenotypic characterization of roots from LY9348 (a rice variety with high nitrogen use efficiency (NUE)) treated with 0.725 mM NH4NO3 (1/4N) was remarkable, especially primary root (PR) elongation, which was the highest. A comprehensive analysis was performed for transcriptome and proteome profiling of LY9348 roots between 1/4N and 2.9 mM NH4NO3 (1N) treatments. The results indicated 3908 differential expression genes (DEGs; 2569 upregulated and 1339 downregulated) and 411 differential abundance proteins (DAPs; 192 upregulated and 219 downregulated). Among all DAPs in the proteome, glutamine synthetase (GS2), a chloroplastic ammonium assimilation protein, was the most upregulated protein identified. The unexpected concentration of GS2 from the shoot to the root in the 1/4N treatment indicated that the presence of an alternative pathway of N assimilation regulated by GS2 in LY9348 corresponded to the low N signal, which was supported by GS enzyme activity and glutamine/glutamate (Gln/Glu) contents analysis. In addition, N transporters (NRT2.1, NRT2.2, NRT2.3, NRT2.4, NAR2.1, AMT1.3, AMT1.2, and putative AMT3.3) and N assimilators (NR2, GS1;1, GS1;2, GS1;3, NADH-GOGAT2, and AS2) were significantly induced during the long-term N-deficiency response at the transcription level (14 days). Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that phenylpropanoid biosynthesis and glutathione metabolism were significantly modulated by N deficiency. Notably, many transcription factors and plant hormones were found to participate in root morphological adaptation. In conclusion, our study provides valuable information to further understand the response of rice roots to N-deficiency stress.
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Affiliation(s)
- Ting Liang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhengqing Yuan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lu Fu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Menghan Zhu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoyun Luo
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wuwu Xu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huanran Yuan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Renshan Zhu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xianting Wu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610000, China
- Correspondence: ; Tel.: +86-181-8061-4938
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18
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Meng X, Wang X, Zhang Z, Xiong S, Wei Y, Guo J, Zhang J, Wang L, Ma X, Tegeder M. Transcriptomic, proteomic, and physiological studies reveal key players in wheat nitrogen use efficiency under both high and low nitrogen supply. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4435-4456. [PMID: 33829261 DOI: 10.1093/jxb/erab153] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
The effective use of available nitrogen (N) to improve crop grain yields provides an important strategy to reduce environmental N pollution and promote sustainable agriculture. However, little is known about the common genetic basis of N use efficiency (NUE) at varying N availability. Two wheat (Triticum aestivum L.) cultivars were grown in the field with high, moderate, and low N supply. Cultivar Zhoumai 27 outperformed Aikang 58 independent of the N supply and showed improved growth, canopy leaf area index, flag leaf surface area, grain number, and yield, and enhanced NUE due to both higher N uptake and utilization efficiency. Further, transcriptome and proteome analyses were performed using flag leaves that provide assimilates for grain growth. The results showed that many genes or proteins that are up- or down-regulated under all N regimes are associated with N and carbon metabolism and transport. This was reinforced by cultivar differences in photosynthesis, assimilate phloem transport, and grain protein/starch yield. Overall, our study establishes that improving NUE at both high and low N supply requires distinct adjustments in leaf metabolism and assimilate partitioning. Identified key genes/proteins may individually or concurrently regulate NUE and are promising targets for maximizing crop NUE irrespective of the N supply.
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Affiliation(s)
- Xiaodan Meng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
- School of Biological Sciences, Washington State University, Pullman, WAUSA
| | - Xiaochun Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
| | - Zhiyong Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Shuping Xiong
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Yihao Wei
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Jianbiao Guo
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Jie Zhang
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Lulu Wang
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Xinming Ma
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WAUSA
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19
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Islam S, Zhang J, Zhao Y, She M, Ma W. Genetic regulation of the traits contributing to wheat nitrogen use efficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110759. [PMID: 33487345 DOI: 10.1016/j.plantsci.2020.110759] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/14/2020] [Accepted: 11/11/2020] [Indexed: 05/25/2023]
Abstract
High nitrogen application aimed at increasing crop yield is offset by higher production costs and negative environmental consequences. For wheat, only one third of the applied nitrogen is utilized, which indicates there is scope for increasing Nitrogen Use Efficiency (NUE). However, achieving greater NUE is challenged by the complexity of the trait, which comprises processes associated with nitrogen uptake, transport, reduction, assimilation, translocation and remobilization. Thus, knowledge of the genetic regulation of these processes is critical in increasing NUE. Although primary nitrogen uptake and metabolism-related genes have been well studied, the relative influence of each towards NUE is not fully understood. Recent attention has focused on engineering transcription factors and identification of miRNAs acting on expression of specific genes related to NUE. Knowledge obtained from model species needs to be translated into wheat using recently-released whole genome sequences, and by exploring genetic variations of NUE-related traits in wild relatives and ancient germplasm. Recent findings indicate the genetic basis of NUE is complex. Pyramiding various genes will be the most effective approach to achieve a satisfactory level of NUE in the field.
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Affiliation(s)
- Shahidul Islam
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Jingjuan Zhang
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Yun Zhao
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Maoyun She
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Wujun Ma
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia.
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20
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Galindo FS, da Silva EC, Pagliari PH, Fernandes GC, Rodrigues WL, Biagini ALC, Baratella EB, da Silva Júnior CA, Moretti Neto MJ, Silva VM, Muraoka T, Teixeira Filho MCM. Nitrogen recovery from fertilizer and use efficiency response to Bradyrhizobium sp. and Azospirillum brasilense combined with N rates in cowpea-wheat crop sequence. APPLIED SOIL ECOLOGY 2021. [DOI: 10.1016/j.apsoil.2020.103764] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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21
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Zeffa DM, Moda-Cirino V, Medeiros IA, Freiria GH, Neto JDS, Ivamoto-Suzuki ST, Delfini J, Scapim CA, Gonçalves LSA. Genetic Progress of Seed Yield and Nitrogen Use Efficiency of Brazilian carioca Common Bean Cultivars Using Bayesian Approaches. FRONTIERS IN PLANT SCIENCE 2020; 11:1168. [PMID: 32849723 PMCID: PMC7419646 DOI: 10.3389/fpls.2020.01168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/20/2020] [Indexed: 05/17/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is one of the most important crops worldwide and is considered an essential source of proteins, fibers, and minerals in the daily diet of several countries. Nitrogen (N) is considered the most important nutrient for common bean crop. On the other hand, the reduction of chemical fertilizers is a global challenge, and the development of cultivars with more N use efficiency (NUsE) is considered one of the main strategies to reduce the amount of N fertilizers. Genetic progress of NUsE has been reported in several crops; however, there was still no quantity in common bean. In this study, our goal was to analyze the genetic progress of seed yield (SY) and NUsE-related traits of 40 carioca common bean cultivars release from 1970 to 2017 in eight environments under low (zero) or high N (40 kg ha-1) in top-dressing. Genetic progress, principal component analysis, correlations among traits, and cultivar stability were analyzed using Bayesian approaches. The lowest values of the deviance information criterion (DIC) for the full model tested indicated the presence of the genotype × N × environment interaction for all evaluated traits. Nitrogen utilization efficiency (NUtE) and nitrogen uptake efficiency (NUpE) were the traits that most contributed to discriminate cultivars. The genetic progress of SY under high N (0.53% year-1, 95% HPD = 0.39; 0.65% year-1) was similar to that obtained in low N conditions (0.48% year-1, 95% HPD = 0.31; 0.64% year-1). These results indicate that modern cultivars do not demand more N fertilizers to be more productive. In addition, we observed a high genetic variability for NUsE-related traits, but there was no genetic progress for these variables. SY showed negative correlation with seed protein content (Prot) in both N conditions, and there was no reduction in Prot in modern cultivars. Both modern and old cultivars showed adaptability and stability under contrasting N conditions. Our study contributed to improve our knowledge about the genetic progress of common bean breeding program in Brazil in the last 47 years, and our data will help researchers to face the challenge of increase NUsE and Prot in the next few years.
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Affiliation(s)
- Douglas Mariani Zeffa
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil
- Laboratório de Ecofisiologia e Biotecnologia Agrícola, Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Vânia Moda-Cirino
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
| | - Isabella Arruda Medeiros
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil
- Laboratório de Ecofisiologia e Biotecnologia Agrícola, Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Gustavo Henrique Freiria
- Laboratório de Ecofisiologia e Biotecnologia Agrícola, Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - José dos Santos Neto
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
| | - Suzana Tiemi Ivamoto-Suzuki
- Laboratório de Ecofisiologia e Biotecnologia Agrícola, Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Jéssica Delfini
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Laboratório de Ecofisiologia e Biotecnologia Agrícola, Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Leandro Simões Azeredo Gonçalves
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil
- Laboratório de Ecofisiologia e Biotecnologia Agrícola, Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
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22
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Banerjee BP, Joshi S, Thoday-Kennedy E, Pasam RK, Tibbits J, Hayden M, Spangenberg G, Kant S. High-throughput phenotyping using digital and hyperspectral imaging-derived biomarkers for genotypic nitrogen response. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4604-4615. [PMID: 32185382 PMCID: PMC7382386 DOI: 10.1093/jxb/eraa143] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/17/2020] [Indexed: 05/18/2023]
Abstract
The development of crop varieties with higher nitrogen use efficiency is crucial for sustainable crop production. Combining high-throughput genotyping and phenotyping will expedite the discovery of novel alleles for breeding crop varieties with higher nitrogen use efficiency. Digital and hyperspectral imaging techniques can efficiently evaluate the growth, biophysical, and biochemical performance of plant populations by quantifying canopy reflectance response. Here, these techniques were used to derive automated phenotyping of indicator biomarkers, biomass and chlorophyll levels, corresponding to different nitrogen levels. A detailed description of digital and hyperspectral imaging and the associated challenges and required considerations are provided, with application to delineate the nitrogen response in wheat. Computational approaches for spectrum calibration and rectification, plant area detection, and derivation of vegetation index analysis are presented. We developed a novel vegetation index with higher precision to estimate chlorophyll levels, underpinned by an image-processing algorithm that effectively removed background spectra. Digital shoot biomass and growth parameters were derived, enabling the efficient phenotyping of wheat plants at the vegetative stage, obviating the need for phenotyping until maturity. Overall, our results suggest value in the integration of high-throughput digital and spectral phenomics for rapid screening of large wheat populations for nitrogen response.
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Affiliation(s)
- Bikram P Banerjee
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Sameer Joshi
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | | | - Raj K Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
- Correspondence:
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23
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Le Gouis J, Oury FX, Charmet G. How changes in climate and agricultural practices influenced wheat production in Western Europe. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2020.102960] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Ahmed M, Rauf M, Akhtar M, Mukhtar Z, Saeed NA. Hazards of nitrogen fertilizers and ways to reduce nitrate accumulation in crop plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:17661-17670. [PMID: 32180142 DOI: 10.1007/s11356-020-08236-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
In modern agriculture, farm produce accumulates a lot of nitrates that can reach toxic levels owing to the unfair use of nitrogen fertilizers, cultural methods, farming policies in multiple areas of the world, thereby increasing concerns about the availability of hygienic food supply and environmental hazards. Over the past few decades, global interest in achieving greater output through intensive fertilization has been a growing trend. The fertilizer based on urea or ammonium mainly yields ammonium, which is then transformed to nitrate through the oxidation process that is biologically mediated. Nitrate tends to accumulate differently in distinct crop plants and distinct components of agricultural commodities based on species, crop variety, genetic history, environmental circumstances, harvest phase, post-harvest storage conditions, agronomic variables, nature, and fertilizer application rate. The current article highlights various factors that could directly or indirectly contribute to the accumulation of nitrates in different parts of crop plants and discusses strategies to minimize the accumulation of nitrates in farm produce, thus ensuring healthy food supply and protecting the environment from the accumulation of nitrates.
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Affiliation(s)
- Moddassir Ahmed
- Agricultural Biotechnology Division, National Institute for Biotechnology & Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan.
| | - Muhammad Rauf
- Agricultural Biotechnology Division, National Institute for Biotechnology & Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad, Pakistan.
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea.
| | - Muhammad Akhtar
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Soil and Environmental Sciences Division, Nuclear Institute for Agriculture and Biology (NIAB), Jhang Road, Faisalabad, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology & Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Nasir Ahmad Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology & Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
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25
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Abstract
The complex formation of grain yield (GY) is related to multiple dry matter (DM) traits; however, due to their time-consuming determination, they are not readily accessible. In winter wheat (Triticum aestivum L.), both agronomic treatments and genotypic variation influence GY in interaction with the environment. Spectral proximal sensing is promising for high-throughput non-destructive phenotyping but was rarely evaluated systematically for dissecting yield-related variation in DM traits. Aiming at a temporal, spectral and organ-level optimization, 48 vegetation indices were evaluated in a high-yielding environment in 10 growth stages for the estimation of 31 previously compared traits related to GY formation—influenced by sowing time, fungicide, N fertilization, and cultivar. A quantitative index ranking was evaluated to assess the stage-independent index suitability. GY showed close linear relationships with spectral vegetation indices across and within agronomic treatments (R2 = 0.47–0.67 ***). Water band indices, followed by red edge-based indices, best used at milk or early dough ripeness, were better suited than the widely used normalized difference vegetation index (NDVI). Index rankings for many organ-level DM traits were comparable, but the relationships were often less close. Among yield components, grain number per spike (R2 = 0.24–0.34 ***) and spike density (R2 = 0.23–0.46 ***) were moderately estimated. GY was mainly estimated by detecting total DM rather than the harvest index. Across agronomic treatments and cultivars, seasonal index rankings were the most stable for GY and total DM, whereas traits related to DM allocation and translocation demanded specific index selection. The results suggest using indices with water bands, near infrared/red edge and visible light bands to increase the accuracy of in-season spectral phenotyping for GY, contributing organ-level traits, and yield components, respectively.
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Taranto F, D'Agostino N, Rodriguez M, Pavan S, Minervini AP, Pecchioni N, Papa R, De Vita P. Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm. Front Genet 2020; 11:217. [PMID: 32373150 PMCID: PMC7187681 DOI: 10.3389/fgene.2020.00217] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/24/2020] [Indexed: 01/31/2023] Open
Abstract
The first breeding program in the world for durum wheat was conceived in Italy in the early 1900s. Over the decades, pressure exerted by natural and artificial selection could have progressively reduced the genetic diversity of the durum wheat germplasm. In the present study, a large panel of Italian durum wheat accessions that includes landraces, old and modern cultivars was subjected to genotyping using the Illumina iSelect 15K wheat SNP array. The aim was to assess the impact that selection has in shaping Italian durum wheat genetic diversity and to exploit the patterns of genetic diversity between populations to identify molecular signatures of divergence and selection. Relatively small differences in genetic diversity have been observed among accessions, which have been selected and cultivated in Italy over the past 150 years. Indeed, directional selection combined with that operated by farmers/breeders resulted in the increase of linkage disequilibrium (LD) and in changes of the allelic frequencies in DNA regions that control important agronomic traits. Results from this study also show that major well-known genes and/or QTLs affecting plant height (RHT), earliness (VRN, PPD) and grain quality (GLU, PSY, PSD, LYC, PPO, LOX3) co-localized with outlier SNP loci. Interestingly, many of these SNPs fall in genomic regions where genes involved in nitrogen metabolism are. This finding highlights the key role these genes have played in the transition from landraces to modern cultivars. Finally, our study remarks on the need to fully exploit the genetic diversity of Italian landraces by intense pre-breeding activities aimed at introducing a new source of adaptability and resistance in the genetic background of modern cultivars, to contrast the effect of climate change. The list of divergent loci and loci under selection associated with useful agronomic traits represents an invaluable resource to detect new allelic variants for target genes and for guiding new genomic selection programs in durum wheat.
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Affiliation(s)
- Francesca Taranto
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, Sassari, Italy.,CBV - Interdepartmental Centre for Plant Biodiversity Conservation and Enhancement Sassari University, Alghero, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Anna P Minervini
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
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27
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Galindo FS, Pagliari PH, Buzetti S, Rodrigues WL, Santini JMK, Boleta EHM, Rosa PAL, Rodrigues Nogueira TA, Lazarini E, Filho MCMT. Can silicon applied to correct soil acidity in combination with Azospirillum brasilense inoculation improve nitrogen use efficiency in maize? PLoS One 2020; 15:e0230954. [PMID: 32267854 PMCID: PMC7141695 DOI: 10.1371/journal.pone.0230954] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 03/12/2020] [Indexed: 02/05/2023] Open
Abstract
Alternative management practices are needed to minimize the need for chemical fertilizer use in non-leguminous cropping systems. The use of biological agents that can fix atmospheric N has shown potential to improve nutrient availability in grass crops. This research was developed to investigate if inoculation with Azospirillum brasilense in combination with silicon (Si) can enhance N use efficiency (NUE) in maize. The study was set up in a Rhodic Hapludox under a no-till system, in a completely randomized block design with four replicates. Treatments were tested in a full factorial design and included: i) five side dress N rates (0 to 200 kg ha-1); ii) two liming sources (Ca and Mg silicate and dolomitic limestone); and iii) with and without seed inoculation with A. brasilense. Inoculation with A. brasilense was found to increase grain yield by 15% when N was omitted and up to 10% when N was applied. Inoculation also increased N accumulation in plant tissue. Inoculation and limestone application were found to increase leaf chlorophyll index, number of grains per ear, harvest index, and NUE. Inoculation increased harvest index and NUE by 9.5 and 19.3%, respectively, compared with non-inoculated plots. Silicon application increased leaf chlorophyll index and N-leaf concentration. The combination of Si and inoculation provided greater Si-shoot accumulation. This study showed positive improvements in maize growth production parameters as a result of inoculation, but the potential benefits of Si use were less evident. Further research should be conducted under growing conditions that provide some level of biotic or abiotic stress to study the true potential of Si application.
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Affiliation(s)
- Fernando Shintate Galindo
- Department of Plant Health, Rural Engineering, and Soils, São Paulo State University, Ilha Solteira, São Paulo, Brazil
| | - Paulo Humberto Pagliari
- Department of Soil, Water, and Climate, University of Minnesota, Southwest Research and Outreach Center, Lamberton, Minnesota, United States of America
| | - Salatiér Buzetti
- Department of Plant Health, Rural Engineering, and Soils, São Paulo State University, Ilha Solteira, São Paulo, Brazil
| | - Willian Lima Rodrigues
- Department of Plant Health, Rural Engineering, and Soils, São Paulo State University, Ilha Solteira, São Paulo, Brazil
| | | | | | - Poliana Aparecida Leonel Rosa
- Department of Plant Health, Rural Engineering, and Soils, São Paulo State University, Ilha Solteira, São Paulo, Brazil
| | | | - Edson Lazarini
- Department of Plant Health, Rural Engineering, and Soils, São Paulo State University, Ilha Solteira, São Paulo, Brazil
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28
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Pereira NCM, Galindo FS, Gazola RPD, Dupas E, Rosa PAL, Mortinho ES, Filho MCMT. Corn Yield and Phosphorus Use Efficiency Response to Phosphorus Rates Associated With Plant Growth Promoting Bacteria. FRONTIERS IN ENVIRONMENTAL SCIENCE 2020. [DOI: 10.3389/fenvs.2020.00040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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29
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Identification of quantitative trait loci associated with nitrogen use efficiency in winter wheat. PLoS One 2020; 15:e0228775. [PMID: 32092066 PMCID: PMC7039505 DOI: 10.1371/journal.pone.0228775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/22/2020] [Indexed: 11/26/2022] Open
Abstract
Maintaining winter wheat (Triticum aestivum L.) productivity with more efficient nitrogen (N) management will enable growers to increase profitability and reduce the negative environmental impacts associated with nitrogen loss. Wheat breeders would therefore benefit greatly from the identification and application of genetic markers associated with nitrogen use efficiency (NUE). To investigate the genetics underlying N response, two bi-parental mapping populations were developed and grown in four site-seasons under low and high N rates. The populations were derived from a cross between previously identified high NUE parents (VA05W-151 and VA09W-52) and a shared common low NUE parent, ‘Yorktown.’ The Yorktown × VA05W-151 population was comprised of 136 recombinant inbred lines while the Yorktown × VA09W-52 population was comprised of 138 doubled haploids. Phenotypic data was collected on parental lines and their progeny for 11 N-related traits and genotypes were sequenced using a genotyping-by-sequencing platform to detect more than 3,100 high quality single nucleotide polymorphisms in each population. A total of 130 quantitative trait loci (QTL) were detected on 20 chromosomes, six of which were associated with NUE and N-related traits in multiple testing environments. Two of the six QTL for NUE were associated with known photoperiod (Ppd-D1 on chromosome 2D) and disease resistance (FHB-4A) genes, two were reported in previous investigations, and one QTL, QNue.151-1D, was novel. The NUE QTL on 1D, 6A, 7A, and 7D had LOD scores ranging from 2.63 to 8.33 and explained up to 18.1% of the phenotypic variation. The QTL identified in this study have potential for marker-assisted breeding for NUE traits in soft red winter wheat.
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Lupini A, Preiti G, Badagliacca G, Abenavoli MR, Sunseri F, Monti M, Bacchi M. Nitrogen Use Efficiency in Durum Wheat Under Different Nitrogen and Water Regimes in the Mediterranean Basin. FRONTIERS IN PLANT SCIENCE 2020; 11:607226. [PMID: 33643329 PMCID: PMC7902889 DOI: 10.3389/fpls.2020.607226] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/28/2020] [Indexed: 05/11/2023]
Abstract
Improving nitrogen use efficiency (NUE) represents one of the main goals to reduce N input in maximizing crop yield for sustainable agriculture. A NUE key strategy is the exploitation of genetic variation in available germplasm together with the understanding of molecular mechanisms governing this complex trait. Thus, NUE, its components, nitrogen uptake efficiency (NUpE) and nitrogen utilization efficiency (NUtE), and NUE-related traits heritability were evaluated in ancient (Cappelli, Capeiti, Russello, and Mazzancoio) and modern (Messapia, Tiziana, Svevo, and Normanno) wheat genotypes for tackling nitrogen (N) and/or water limitation in both growth chamber and field experiments. Our results exhibited a reduction of NUE, NUpE, and NUtE under water and combined (nitrogen + water) stress in all the genotypes, as expected. The contribution of genetic variability on phenotypic variation was significant for NUtE, harvest index, post-anthesis nitrogen uptake (PANU), and biomass production traits. Moreover, the stress tolerance indexes, calculated and bi-plotted for N and water stresses, exhibited two distinct clusters for many traits as then confirmed by principal component analysis. Although modern varieties showed higher crop yield and NUE under conventional N and water regimes, ancient varieties exhibited best performances to cope with both stresses, mainly under water limitation. Finally, the usage index, which takes into account total biomass increase, underlined that old genotypes were less affected by both stresses during crop cycle. In particular, these genotypes showed the best performances for NUE and its components under both stresses at stem elongation and milk ripening as shown also by PANU. In addition, at these stages, nitrate and ammonium transporter gene expressions in the root were performed, showing the highest activity in ancient varieties. In conclusion, the identification of NUE traits during a specific crop cycle stage, under both N and water limitation, will help in the breeding of more resilient varieties in Mediterranean sustainable agriculture by reducing N supply.
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Nguyen GN, Maharjan P, Maphosa L, Vakani J, Thoday-Kennedy E, Kant S. A Robust Automated Image-Based Phenotyping Method for Rapid Vegetative Screening of Wheat Germplasm for Nitrogen Use Efficiency. FRONTIERS IN PLANT SCIENCE 2019; 10:1372. [PMID: 31772563 PMCID: PMC6849468 DOI: 10.3389/fpls.2019.01372] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/04/2019] [Indexed: 05/29/2023]
Abstract
Nitrogen use efficiency (NUE) in crops is generally low, with more than 60% of applied nitrogen (N) being lost to the environment, which increases production costs and affects ecosystems and human habitats. To overcome these issues, the breeding of crop varieties with improved NUE is needed, requiring efficient phenotyping methods along with molecular and genetic approaches. To develop an effective phenotypic screening method, experiments on wheat varieties under various N levels were conducted in the automated phenotyping platform at Plant Phenomics Victoria, Horsham. The results from the initial experiment showed that two relative N levels-5 mM and 20 mM, designated as low and optimum N, respectively-were ideal to screen a diverse range of wheat germplasm for NUE on the automated imaging phenotyping platform. In the second experiment, estimated plant parameters such as shoot biomass and top-view area, derived from digital images, showed high correlations with phenotypic traits such as shoot biomass and leaf area seven weeks after sowing, indicating that they could be used as surrogate measures of the latter. Plant growth analysis confirmed that the estimated plant parameters from the vegetative linear growth phase determined by the "broken-stick" model could effectively differentiate the performance of wheat varieties for NUE. Based on this study, vegetative phenotypic screens should focus on selecting wheat varieties under low N conditions, which were highly correlated with biomass and grain yield at harvest. Analysis indicated a relationship between controlled and field conditions for the same varieties, suggesting that greenhouse screens could be used to prioritise a higher value germplasm for subsequent field studies. Overall, our results showed that this phenotypic screening method is highly applicable and can be applied for the identification of N-efficient wheat germplasm at the vegetative growth phase.
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Affiliation(s)
- Giao N. Nguyen
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Pankaj Maharjan
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Lance Maphosa
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Jignesh Vakani
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | | | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Melbourne, VIC, Australia
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Prey L, Hu Y, Schmidhalter U. Temporal Dynamics and the Contribution of Plant Organs in a Phenotypically Diverse Population of High-Yielding Winter Wheat: Evaluating Concepts for Disentangling Yield Formation and Nitrogen Use Efficiency. FRONTIERS IN PLANT SCIENCE 2019; 10:1295. [PMID: 31736988 PMCID: PMC6829449 DOI: 10.3389/fpls.2019.01295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/18/2019] [Indexed: 05/13/2023]
Abstract
Enhancing crop nitrogen use efficiency (NUE) is a key requirement for both economic and ecological reasons. Consequently, the genotypic potential for NUE in winter wheat (Triticum aestivum L.) requires further exploitation. Emerging plant phenomic techniques may provide knowledge about traits contributing to grain N uptake (GNup) and grain yield (GY). However, the understanding of beneficial strategies concerning the temporal dynamics of NUE and GY formation and the role of plant organs is still scarce especially under high-yielding European conditions-particularly to discriminate interesting lines in the breeding process. Thus, screening for potentially useful NUE traits in terms of variation, stability, and contribution to target traits will be an essential prerequisite for the development of efficient phenotyping strategies. Therefore, 46 NUE and yield formation traits were assessed in a population of 75 breeding lines over 3 years from 2015 to 2017 in southern Germany, including dry matter (DM), N concentration, and N uptake at anthesis and maturity, both at the aboveground-plant and plant organ levels. Significant genotype and genotypexenvironment effects were observed for all traits. While GY was more related to post-anthesis assimilation, also DM translocation contributed substantially to GY by 31-44%. At maturity, total aboveground DM as opposed to harvest index predominantly determined GY. NUE for GY was better described by N uptake efficiency than by N utilization efficiency. GNup was greatly influenced by variation in GY, but not in grain N concentration, and by total N uptake and not the N harvest index. Post-anthesis N uptake highly depended on the year and was low in comparison to N translocation. However, post-anthesis N uptake was always correlated with GNup, suggesting the need to also consider stay-green strategies under temperate growing conditions. While anthesis traits were only moderately descriptive, GY will be enhanced by increasing total biomass and the N uptake efficiency. Similarly, targeting total N uptake, particularly at post-anthesis, seems to be a rewarding strategy to boost GNup. Thus, high-throughput phenotyping should be targeted rather toward detecting traits related to DM and N acquisition than to the internal allocation and rather to post-anthesis than to anthesis traits.
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Affiliation(s)
| | | | - Urs Schmidhalter
- Chair of Plant Nutrition, Technical University of Munich, Munich, Germany
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Touzy G, Rincent R, Bogard M, Lafarge S, Dubreuil P, Mini A, Deswarte JC, Beauchêne K, Le Gouis J, Praud S. Using environmental clustering to identify specific drought tolerance QTLs in bread wheat (T. aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2859-2880. [PMID: 31324929 DOI: 10.1007/s00122-019-03393-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 07/06/2019] [Indexed: 05/03/2023]
Abstract
Environmental clustering helps to identify QTLs associated with grain yield in different water stress scenarios. These QTLs could be useful for breeders to improve grain yields and increase genetic resilience in marginal environments. Drought is one of the main abiotic stresses limiting winter bread wheat growth and productivity around the world. The acquisition of new high-yielding and stress-tolerant varieties is therefore necessary and requires improved understanding of the physiological and genetic bases of drought resistance. A panel of 210 elite European varieties was evaluated in 35 field trials. Grain yield and its components were scored in each trial. A crop model was then run with detailed climatic data and soil water status to assess the dynamics of water stress in each environment. Varieties were registered from 1992 to 2011, allowing us to test timewise genetic progress. Finally, a genome-wide association study (GWAS) was carried out using genotyping data from a 280 K SNP chip. The crop model simulation allowed us to group the environments into four water stress scenarios: an optimal condition with no water stress, a post-anthesis water stress, a moderate-anthesis water stress and a high pre-anthesis water stress. Compared to the optimal water condition, grain yield losses in the stressed conditions were 3.3%, 12.4% and 31.2%, respectively. This environmental clustering improved understanding of the effect of drought on grain yields and explained 20% of the G × E interaction. The greatest genetic progress was obtained in the optimal condition, mostly represented in France. The GWAS identified several QTLs, some of which were specific of the different water stress patterns. Our results make breeding for improved drought resistance to specific environmental scenarios easier and will facilitate genetic progress in future environments, i.e., water stress environments.
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Affiliation(s)
- Gaëtan Touzy
- Arvalis-Institut du végétal, Biopôle Clermont Limagne, 63360, Saint-Beauzire, France
- Centre de recherche de Chappes, Biogemma, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Renaud Rincent
- INRA, UCA UMR 1095, Génétique, Diversité et Ecophysiologie des Céréales, 24 Avenue des Landais, 63177, Aubière Cedex, France
| | - Matthieu Bogard
- Arvalis-Institut du végétal, 6 Chemin de la côte vieille, 31450, Baziège, France
| | - Stephane Lafarge
- Centre de recherche de Chappes, Biogemma, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Pierre Dubreuil
- Centre de recherche de Chappes, Biogemma, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Agathe Mini
- INRA, UCA UMR 1095, Génétique, Diversité et Ecophysiologie des Céréales, 24 Avenue des Landais, 63177, Aubière Cedex, France
| | - Jean-Charles Deswarte
- Arvalis-Institut du végétal, Route de Châteaufort, ZA des graviers, 91190, Villiers-le-Bâcle, France
| | - Katia Beauchêne
- Arvalis-Institut du végétal, 45 voie Romaine, Ouzouer Le Marché, 41240, Beauce La Romaine, France
| | - Jacques Le Gouis
- INRA, UCA UMR 1095, Génétique, Diversité et Ecophysiologie des Céréales, 24 Avenue des Landais, 63177, Aubière Cedex, France
| | - Sébastien Praud
- Centre de recherche de Chappes, Biogemma, Route d'Ennezat CS90216, 63720, Chappes, France.
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Michel S, Löschenberger F, Ametz C, Pachler B, Sparry E, Bürstmayr H. Combining grain yield, protein content and protein quality by multi-trait genomic selection in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2767-2780. [PMID: 31263910 PMCID: PMC6763414 DOI: 10.1007/s00122-019-03386-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/24/2019] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE Simultaneous genomic selection for grain yield, protein content and dough rheological traits enables the development of resource-use efficient varieties that combine superior yield potential with comparably high end-use quality. Selecting simultaneously for grain yield and baking quality is a major challenge in wheat breeding, and several concepts like grain protein deviations have been developed for shifting the undesirable negative correlation between both traits. The protein quality is, however, not considered in these concepts, although it is an important aspect and might facilitate the selection of genotypes that use available resources more efficiently with respect to the quantity and quality of the final end products. A population of 480 lines from an applied wheat breeding programme that was phenotyped for grain yield, protein content, protein yield and dough rheological traits was thus used to assess the potential of using integrated genomic selection indices to ease selection decisions with regard to the plethora of quality traits. Additionally, the feasibility of achieving a simultaneous genetic improvement in grain yield, protein content and protein quality was investigated to develop more resource-use efficient varieties. Dough rheological traits related to either gluten strength or viscosity were combined in two separate indices, both of which showed a substantially smaller negative trade-off with grain yield than the protein content. Genomic selection indices based on regression deviations for the two latter traits were subsequently extended by the gluten strength or viscosity indices. They revealed a large merit for identifying resource-use efficient genotypes that combine both superior yield potential with comparably high end-use quality. Hence, genomic selection opens up the opportunity for multi-trait selection in early generations, which will most likely increase the efficiency when developing new and improved varieties.
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Affiliation(s)
- Sebastian Michel
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
| | | | - Christian Ametz
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Bernadette Pachler
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Ellen Sparry
- C&M Seeds, 6180 5th Line, Palmerston, ON, N0G 2P0, Canada
| | - Hermann Bürstmayr
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
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Galindo FS, Teixeira Filho MCM, Buzetti S, Pagliari PH, Santini JMK, Alves CJ, Megda MM, Nogueira TAR, Andreotti M, Arf O. Maize Yield Response to Nitrogen Rates and Sources Associated with
Azospirillum brasilense. AGRONOMY JOURNAL 2019. [DOI: 10.2134/agronj2018.07.0481] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Fernando S. Galindo
- Dep. of Plant Protection, Rural Engineering and Soils São Paulo State Univ. Ilha Solteira SP 15.385‐000 Brazil
| | | | - Salatiér Buzetti
- Dep. of Plant Protection, Rural Engineering and Soils São Paulo State Univ. Ilha Solteira SP 15.385‐000 Brazil
| | - Paulo H. Pagliari
- Dep. of Soil, Water, and Climate Univ. of Minnesota, Southwest Research and Outreach Center Lamberton MN 56152
| | - José M. K. Santini
- Dep. of Plant Protection, Rural Engineering and Soils São Paulo State Univ. Ilha Solteira SP 15.385‐000 Brazil
| | | | - Marcio M. Megda
- Montes Claros State Univ. College of Janaúba Janaúba MG Brazil
| | - Thiago A. R. Nogueira
- Dep. of Plant Protection, Rural Engineering and Soils São Paulo State Univ. Ilha Solteira SP 15.385‐000 Brazil
| | - Marcelo Andreotti
- Dep. of Plant Protection, Rural Engineering and Soils São Paulo State Univ. Ilha Solteira SP 15.385‐000 Brazil
| | - Orivaldo Arf
- Dep. of Plant Science, Food Technology and Social Economy São Paulo State Univ. Ilha Solteira SP Brazil
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Galindo FS, Teixeira Filho MCM, Buzetti S, Rodrigues WL, Santini JMK, Alves CJ. Nitrogen fertilisation efficiency and wheat grain yield affected by nitrogen doses and sources associated with Azospirillum brasilense. ACTA AGRICULTURAE SCANDINAVICA SECTION B-SOIL AND PLANT SCIENCE 2019. [DOI: 10.1080/09064710.2019.1628293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Fernando Shintate Galindo
- Department of Plant Health, Rural Engineering, and Soils, College of Engineering, São Paulo State University (UNESP), Ilha Solteira-SP, Brazil
| | | | - Salatiér Buzetti
- Department of Plant Health, Rural Engineering, and Soils, College of Engineering, São Paulo State University (UNESP), Ilha Solteira-SP, Brazil
| | - Willian Lima Rodrigues
- Department of Plant Health, Rural Engineering, and Soils, College of Engineering, São Paulo State University (UNESP), Ilha Solteira-SP, Brazil
| | - José Mateus Kondo Santini
- Department of Plant Health, Rural Engineering, and Soils, College of Engineering, São Paulo State University (UNESP), Ilha Solteira-SP, Brazil
| | - Cleiton José Alves
- Department of Crop Science, College of Agricultural Science, São Paulo State University (UNESP), Botucatu-SP, Brazil
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Hawkesford MJ, Griffiths S. Exploiting genetic variation in nitrogen use efficiency for cereal crop improvement. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:35-42. [PMID: 31176099 PMCID: PMC6692496 DOI: 10.1016/j.pbi.2019.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 05/18/2023]
Abstract
Cereals are the most important sources of calories and nutrition for the human population, and are an essential animal feed. Food security depends on adequate production and demands are predicted to rise as the global population rises. The need for increased yields will have to be coupled to the efficient use of resources including fertilisers such as nitrogen to underpin the sustainability of food production. Although optimally performing crops with high yields require a balanced mineral nutrition, nitrogen fundamentally drives growth and yield as well as requirements for other nutrients. It is estimated that globally only 33% of applied nitrogen fertiliser is recovered in the harvested grain, indicative of a huge waste of resource and potential major pollutant and is thus a major target for crop improvement. Both agronomy and breeding will contribute to improved nitrogen use efficiency (NUE) and an important component of the latter is harnessing germplasm variation. This review will consider the key traits involved in NUE, the potential to exploit genetic variation for these specific traits, and the approaches to be utilised.
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Michel S, Löschenberger F, Ametz C, Pachler B, Sparry E, Bürstmayr H. Simultaneous selection for grain yield and protein content in genomics-assisted wheat breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1745-1760. [PMID: 30810763 PMCID: PMC6531418 DOI: 10.1007/s00122-019-03312-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/15/2019] [Indexed: 05/10/2023]
Abstract
Large genetic improvement can be achieved by simultaneous genomic selection for grain yield and protein content when combining different breeding strategies in the form of selection indices. Genomic selection has been implemented in many national and international breeding programmes in recent years. Numerous studies have shown the potential of this new breeding tool; few have, however, taken the simultaneous selection for multiple traits into account that is though common practice in breeding programmes. The simultaneous improvement in grain yield and protein content is thereby a major challenge in wheat breeding due to a severe negative trade-off. Accordingly, the potential and limits of multi-trait selection for this particular trait complex utilizing the vast phenotypic and genomic data collected in an applied wheat breeding programme were investigated in this study. Two breeding strategies based on various genomic-selection indices were compared, which (1) aimed to select high-protein genotypes with acceptable yield potential and (2) develop high-yielding varieties, while maintaining protein content. The prediction accuracy of preliminary yield trials could be strongly improved when combining phenotypic and genomic information in a genomics-assisted selection approach, which surpassed both genomics-based and classical phenotypic selection methods both for single trait predictions and in genomic index selection across years. The employed genomic selection indices mitigated furthermore the negative trade-off between grain yield and protein content leading to a substantial selection response for protein yield, i.e. total seed nitrogen content, which suggested that it is feasible to develop varieties that combine a superior yield potential with comparably high protein content, thus utilizing available nitrogen resources more efficiently.
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Affiliation(s)
- Sebastian Michel
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
| | | | - Christian Ametz
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Bernadette Pachler
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Ellen Sparry
- C&M Seeds, 6180 5th Line, Palmerston, ON, N0G 2P0, Canada
| | - Hermann Bürstmayr
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
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Prey L, Kipp S, Hu Y, Schmidhalter U. Nitrogen Use Efficiency and Carbon Traits of High-Yielding European Hybrid vs. Line Winter Wheat Cultivars: Potentials and Limitations. FRONTIERS IN PLANT SCIENCE 2019; 9:1988. [PMID: 30705683 PMCID: PMC6344469 DOI: 10.3389/fpls.2018.01988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/20/2018] [Indexed: 05/13/2023]
Abstract
In contrast to allogamous crops, hybrid wheat has only recently been fostered by breeding companies in Europe. Hybrid cultivars are often associated with higher stress resistance, e.g. under drought conditions, but little is known about the nitrogen (N) use efficiency of modern hybrid wheat cultivars. Therefore, four high-yielding European hybrid and nine line winter wheat (Triticum aestivum L.) cultivars were grown under three N regimes in a high-yielding German environment and compared over 3 years at anthesis and maturity for 53 direct and indirect traits of yield formation and N allocation. Dry matter and N uptake were determined on the plant and plant organ levels. Commercial heterosis, expressing the performance of hybrid in comparison to line cultivars, was positive for about one-third of the 53 direct and indirect N and carbon traits. On average, hybrid cultivars yielded more grain (+5.5%), mainly due to a higher harvest index (+3.5%) together with higher post-anthesis assimilation and more grains per spike. However, grain N content was lower for hybrids (-8.5%), so their grain N uptake was not higher. This went along with comparable trait values for N translocation and the temporal N uptake of the different plant organs. Current wheat hybrids seem to be more efficient in overall N use because they are better at converting (higher N utilization efficiency) comparable amounts of N uptake (N uptake efficiency) into grain biomass. The results suggest that given increased seed costs for hybrids, the yield advantage of hybrid cultivars over locally adapted line cultivars will have to be further increased for establishing hybrids in low-stress, high-yielding environments.
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Affiliation(s)
| | | | | | - Urs Schmidhalter
- Department of Plant Sciences, Technical University of Munich, Munich, Germany
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Lei L, Li G, Zhang H, Powers C, Fang T, Chen Y, Wang S, Zhu X, Carver BF, Yan L. Nitrogen use efficiency is regulated by interacting proteins relevant to development in wheat. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1214-1226. [PMID: 29193541 PMCID: PMC5978868 DOI: 10.1111/pbi.12864] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/01/2017] [Accepted: 11/04/2017] [Indexed: 05/08/2023]
Abstract
Wheat (Triticum aestivum) has low nitrogen use efficiency (NUE). The genetic mechanisms controlling NUE are unknown. Positional cloning of a major quantitative trait locus for N-related agronomic traits showed that the vernalization gene TaVRN-A1 was tightly linked with TaNUE1, the gene shown to influence NUE in wheat. Because of an Ala180 /Val180 substitution, TaVRN-A1a and TaVRN-A1b proteins interact differentially with TaANR1, a protein encoded by a wheat orthologue of Arabidopsis nitrate regulated 1 (ANR1). The transcripts of both TaVRN-A1 and TaANR1 were down-regulated by nitrogen. TaANR1 was functionally characterized in TaANR1::RNAi transgenic wheat, and in a natural mutant with a 23-bp deletion including 10-bp at the 5' end of intron 5 and 13-bp of exon 6 in gDNA sequence in its gDNA sequence, which produced transcript that lacked the full 84-bp exon 6. Both TaANR1 and TaHOX1 bound to the Ala180 /Val180 position of TaVRN-A1. Genetically incorporating favourable alleles from TaVRN-A1, TaANR1 and TaHOX1 increased grain yield from 9.84% to 11.58% in the field. Molecular markers for allelic variation of the genes that regulate nitrogen can be used in breeding programmes aimed at improving NUE and yield in novel wheat cultivars.
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Affiliation(s)
- Lei Lei
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Genqiao Li
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
- Present address:
Wheat, Peanut and Other Field Crops Research UnitUSDA‐ARSStillwaterOKUSA
| | - Hailin Zhang
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Carol Powers
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Tilin Fang
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Yihua Chen
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Shuwen Wang
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
- Present address:
The Land InstituteSalinaKSUSA
| | - Xinkai Zhu
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
- Present address:
Key Laboratory of Crop Genetics and Physiology of Jiangsu ProvinceYangzhou UniversityYangzhouJiangsuChina
| | - Brett F. Carver
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Liuling Yan
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
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Nguyen GN, Kant S. Improving nitrogen use efficiency in plants: effective phenotyping in conjunction with agronomic and genetic approaches. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:606-619. [PMID: 32290963 DOI: 10.1071/fp17266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/04/2018] [Indexed: 05/03/2023]
Abstract
For global sustainable food production and environmental benefits, there is an urgent need to improve N use efficiency (NUE) in crop plants. Excessive and inefficient use of N fertiliser results in increased crop production costs and environmental pollution. Therefore, cost-effective strategies such as proper management of the timing and quantity of N fertiliser application, and breeding for better varieties are needed to improve NUE in crops. However, for these efforts to be feasible, high-throughput and reliable phenotyping techniques would be very useful for monitoring N status in planta, as well as to facilitate faster decisions during breeding and selection processes. This review provides an insight into contemporary approaches to phenotyping NUE-related traits and associated challenges. We discuss recent and advanced, sensor- and image-based phenotyping techniques that use a variety of equipment, tools and platforms. The review also elaborates on how high-throughput phenotyping will accelerate efforts for screening large populations of diverse genotypes in controlled environment and field conditions to identify novel genotypes with improved NUE.
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Affiliation(s)
- Giao N Nguyen
- Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, Vic. 3400, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, Vic. 3400, Australia
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42
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Tiwari JK, Plett D, Garnett T, Chakrabarti SK, Singh RK. Integrated genomics, physiology and breeding approaches for improving nitrogen use efficiency in potato: translating knowledge from other crops. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:587-605. [PMID: 32290962 DOI: 10.1071/fp17303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/06/2017] [Indexed: 05/22/2023]
Abstract
Potato plays a key role in global food and nutritional security. Potato is an N fertiliser-responsive crop, producing high tuber yields. However, excessive use of N can result in environmental damage and high production costs, hence improving nitrogen use efficiency (NUE) of potato plants is one of the sustainable options to address these issues and increase yield. Advanced efforts have been undertaken to improve NUE in other plants like Arabidopsis, rice, wheat and maize through molecular and physiological approaches. Conversely, in potato, NUE studies have predominantly focussed on agronomy or soil management, except for a few researchers who have measured gene expression and proteins relevant to N uptake or metabolism. The focus of this review is to adapt knowledge gained from other plants to inform investigation of N metabolism and associated traits in potato with the aim of improving potato NUE using integrated genomics, physiology and breeding methods.
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Affiliation(s)
- Jagesh K Tiwari
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
| | - Darren Plett
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Trevor Garnett
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Swarup K Chakrabarti
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
| | - Rajesh K Singh
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
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Qian L, Hickey LT, Stahl A, Werner CR, Hayes B, Snowdon RJ, Voss-Fels KP. Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops. FRONTIERS IN PLANT SCIENCE 2017; 8:1534. [PMID: 28928764 PMCID: PMC5591830 DOI: 10.3389/fpls.2017.01534] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/22/2017] [Indexed: 05/19/2023]
Abstract
In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP-trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool to equip modern crops with environment-tailored characteristics.
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Affiliation(s)
- Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural UniversityChangsha, China
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St LuciaQLD, Australia
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Christian R. Werner
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Ben Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St LuciaQLD, Australia
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Kai P. Voss-Fels
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St LuciaQLD, Australia
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Stahl A, Pfeifer M, Frisch M, Wittkop B, Snowdon RJ. Recent Genetic Gains in Nitrogen Use Efficiency in Oilseed Rape. FRONTIERS IN PLANT SCIENCE 2017; 8:963. [PMID: 28638399 PMCID: PMC5461335 DOI: 10.3389/fpls.2017.00963] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/22/2017] [Indexed: 05/21/2023]
Abstract
Nitrogen is essential for plant growth, and N fertilization allows farmers to obtain high yields and produce sufficient agricultural commodities. On the other hand, nitrogen losses potentially cause adverse effects to ecosystems and to human health. Increasing nitrogen use efficiency (NUE) is vital to solve the conflict between productivity, to secure the demand of a growing world population, and the protection of the environment. To ensure this, genetic improvement is considered to be a paramount aspect toward ecofriendly crop production. Winter oilseed rape (Brassica napus L.) is the second most important oilseed crop in the world and is cultivated in many regions across the temperate zones. To our knowledge, this study reports the most comprehensive field-based data generated to date for an empirical evaluation of genetic improvement in winter oilseed rape varieties under two divergent nitrogen fertilization levels (NFLs). A collection of 30 elite varieties registered between 1989 and 2014, including hybrids and open pollinated varieties, was tested in a 2-year experiment in 10 environments across Germany for changes in seed yield and seed quality traits. Furthermore, NUE was calculated. We observed a highly significant genetics-driven increase in seed yield per-se and, thus, increased NUE at both NFLs. On average, seed yield from modern open-pollinated varieties and modern hybrids was higher than from old open-pollinated varieties and old hybrids. The annual yield progress across all tested varieties was ~35 kg ha-1 year-1 at low nitrogen and 45 kg ha-1 year-1 under high nitrogen fertilization. Furthermore, in modern varieties an increased oil concentration and decreased protein concentration was observed. Despite, the significant effects of nitrogen fertilization, a surprisingly low average seed yield gap of 180 kg N ha-1 was noted between high and low nitrogen fertilization. Due to contrary effects of N fertilization on seed yield per-se and seed oil concentration an oil yield of 2.04 t ha-1 was measured at both N levels. Collectively, the data reveal that genetic improvement through modern breeding techniques in conjunction with reduced N fertilizer inputs has a tremendous potential to increase NUE of oilseed rape.
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Affiliation(s)
- Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Mara Pfeifer
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Matthias Frisch
- Department of Biometry and Population Genetics, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
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Hawkesford MJ. Genetic variation in traits for nitrogen use efficiency in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2627-2632. [PMID: 28338945 DOI: 10.1093/jxb/erx079] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Crop nutrient and especially nitrogen use efficiency (NUE) is both an economically and an environmentally highly desirable trait. It has been estimated that only a third of nitrogen inputs to cereal crop worldwide are recovered in grain for consumption, resulting in a huge waste of resource with major negative impacts on the environment. Most measures of NUE in wheat and other cereals are based on field assessments of crop yields at given N inputs, performance responses to added N fertilizer, or by quantifying N fertilizer recovery rates. However, NUE is a complex trait comprising two key major components, N uptake and N utilization efficiency, both also complex traits in themselves, each involving many physiological processes and biochemical pathways. A deeper understanding of the processes involved in NUE has been a target of the UK Wheat Genetic Improvement Network project (http://www.wgin.org.uk/). This has enabled the breakdown of characteristics contributing to NUE and an assessment of the variation present in those characteristics, predominantly in modern cultivars; a total of 13 years of data have been obtained to date. Significant but limited variation suggests a requirement for broader germplasm screening such as older varieties, landraces, and wild relatives.
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Affiliation(s)
- Malcolm J Hawkesford
- Rothamsted Research, Plant Sciences Department, Harpenden, Hertfordshire AL5 2JQ, UK
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Peña PA, Quach T, Sato S, Ge Z, Nersesian N, Changa T, Dweikat I, Soundararajan M, Clemente TE. Expression of the Maize Dof1 Transcription Factor in Wheat and Sorghum. FRONTIERS IN PLANT SCIENCE 2017; 8:434. [PMID: 28424717 PMCID: PMC5371680 DOI: 10.3389/fpls.2017.00434] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/14/2017] [Indexed: 05/03/2023]
Abstract
Nitrogen is essential for plant growth and development. Improving the ability of plants to acquire and assimilate nitrogen more efficiently is a key agronomic parameter that will augment sustainability in agriculture. A transcription factor approach was pursued to address improvement of nitrogen use efficiency in two major commodity crops. To this end, the Zea mays Dof1 (ZmDof1) transcription factor was expressed in both wheat (Triticum aestivum) and sorghum (Sorghum bicolor) either constitutively, UBI4 promoter from sugarcane, or in a tissue specific fashion via the maize rbcS1 promoter. The primary transcription activation target of ZmDof1, phosphoenolpyruvate carboxylase (PEPC), is observed in transgenic wheat events. Expression ZmDof1 under control of the rbcs1 promoter translates to increase in biomass and yield components in wheat. However, constitutive expression of ZmDof1 led to the down-regulation of genes involved in photosynthesis and the functional apparatus of chloroplasts, and an outcome that negatively impacts photosynthesis, height, and biomass in wheat. Similar patterns were also observed in sorghum transgenic events harboring the constitutive expression cassette of ZmDof1. These results indicate that transcription factor strategies to boost agronomic phenotypic outcomes in crops need to consider expression patterns of the genetic elements to be introduced.
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Affiliation(s)
- Pamela A. Peña
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincoln, NE, USA
| | - Truyen Quach
- Center for Biotechnology, University of Nebraska-LincolnLincoln, NE, USA
| | - Shirley Sato
- Center for Biotechnology, University of Nebraska-LincolnLincoln, NE, USA
| | - Zhengxiang Ge
- Center for Biotechnology, University of Nebraska-LincolnLincoln, NE, USA
| | - Natalya Nersesian
- Center for Biotechnology, University of Nebraska-LincolnLincoln, NE, USA
| | - Taity Changa
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincoln, NE, USA
| | - Ismail Dweikat
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincoln, NE, USA
| | | | - Tom E. Clemente
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-LincolnLincoln, NE, USA
- *Correspondence: Tom E. Clemente
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Laidig F, Piepho HP, Rentel D, Drobek T, Meyer U, Huesken A. Breeding progress, environmental variation and correlation of winter wheat yield and quality traits in German official variety trials and on-farm during 1983-2014. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:223-245. [PMID: 27796431 PMCID: PMC5215243 DOI: 10.1007/s00122-016-2810-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 10/08/2016] [Indexed: 05/18/2023]
Abstract
Over the last 32 years, a large gain in grain yield (24 %) was achieved in official German variety trials, and despite considerable loss in protein concentration (-7.9 %), winter wheat baking quality was partially improved over the last 32 years. On-farm gain in grain yield (32 %) exceeded gain in trials, but at yield level about 25 dt ha -1 lower. Breeding progress was very successfully transferred into both progress in grain yield and on-farm baking quality. Long-term gains in grain yield and baking quality of 316 winter wheat varieties from German official trials were evaluated. We dissected progress into a genetic and a non-genetic part to quantify the contribution of genetic improvement. We further investigated the influence of genotype and environment on total variation by estimating variance components. We also estimated genetic and phenotypic correlation between quality traits. For trial data, we found a large gain in grain yield (24%), but a strong decline in protein concentration (-8.0%) and loaf volume (-8.5%) relative to 1983. Improvement of baking quality could be achieved for falling number (5.8%), sedimentation value (7.9%), hardness (13.4%), water absorption (1.2%) and milling yield (2.4%). Grain yield, falling number and protein concentration were highly influenced by environment, whereas for sedimentation value, hardness, water absorption and loaf volume genotypes accounted for more than 60% of total variation. Strong to very strong relations exist among protein concentration, sedimentation value, and loaf volume. On-farm yields were obtained from national statistics, and grain quality data from samples collected by national harvest survey. These on-farm data were compared with trial results. On-farm gain in grain yield was 31.6%, but at a mean level about 25 dt ha-1 lower. Improvement of on-farm quality exceeded trial results considerably. A shift to varieties with improved baking quality can be considered as the main reason for this remarkable improvement of on-farm baking quality.
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Affiliation(s)
| | - Hans-Peter Piepho
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany
| | - Dirk Rentel
- Bundessortenamt, Osterfelddamm 80, 30627, Hannover, Germany
| | - Thomas Drobek
- Bundessortenamt, Osterfelddamm 80, 30627, Hannover, Germany
| | - Uwe Meyer
- Bundessortenamt, Osterfelddamm 80, 30627, Hannover, Germany
| | - Alexandra Huesken
- Department of Safety and Quality of Cereals, Federal Institute of Food and Nutrition, Schuetzenberg 12, 32756, Detmold, Germany
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48
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Effect of genotype, environment and crop management on yield and quality traits in spring wheat. J Cereal Sci 2016. [DOI: 10.1016/j.jcs.2016.09.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Mahjourimajd S, Taylor J, Sznajder B, Timmins A, Shahinnia F, Rengel Z, Khabaz-Saberi H, Kuchel H, Okamoto M, Langridge P. Genetic Basis for Variation in Wheat Grain Yield in Response to Varying Nitrogen Application. PLoS One 2016; 11:e0159374. [PMID: 27459317 PMCID: PMC4961366 DOI: 10.1371/journal.pone.0159374] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/03/2016] [Indexed: 01/15/2023] Open
Abstract
Nitrogen (N) is a major nutrient needed to attain optimal grain yield (GY) in all environments. Nitrogen fertilisers represent a significant production cost, in both monetary and environmental terms. Developing genotypes capable of taking up N early during development while limiting biomass production after establishment and showing high N-use efficiency (NUE) would be economically beneficial. Genetic variation in NUE has been shown previously. Here we describe the genetic characterisation of NUE and identify genetic loci underlying N response under different N fertiliser regimes in a bread wheat population of doubled-haploid lines derived from a cross between two Australian genotypes (RAC875 × Kukri) bred for a similar production environment. NUE field trials were carried out at four sites in South Australia and two in Western Australia across three seasons. There was genotype-by-environment-by-treatment interaction across the sites and also good transgressive segregation for yield under different N supply in the population. We detected some significant Quantitative Trait Loci (QTL) associated with NUE and N response at different rates of N application across the sites and years. It was also possible to identify lines showing positive N response based on the rankings of their Best Linear Unbiased Predictions (BLUPs) within a trial. Dissecting the complexity of the N effect on yield through QTL analysis is a key step towards elucidating the molecular and physiological basis of NUE in wheat.
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Affiliation(s)
- Saba Mahjourimajd
- Australian Centre for Plant Functional Genomics (ACPFG), The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Julian Taylor
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Beata Sznajder
- Australian Centre for Plant Functional Genomics (ACPFG), The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Andy Timmins
- Australian Centre for Plant Functional Genomics (ACPFG), The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Fahimeh Shahinnia
- Australian Centre for Plant Functional Genomics (ACPFG), The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Zed Rengel
- Soil Science and Plant Nutrition M087, School of Earth and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Hossein Khabaz-Saberi
- Soil Science and Plant Nutrition M087, School of Earth and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Haydn Kuchel
- Australian Grain Technologies, PMB1, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Mamoru Okamoto
- Australian Centre for Plant Functional Genomics (ACPFG), The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
- * E-mail: (PL); (MO)
| | - Peter Langridge
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
- * E-mail: (PL); (MO)
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Mahjourimajd S, Taylor J, Rengel Z, Khabaz-Saberi H, Kuchel H, Okamoto M, Langridge P. The Genetic Control of Grain Protein Content under Variable Nitrogen Supply in an Australian Wheat Mapping Population. PLoS One 2016; 11:e0159371. [PMID: 27438012 PMCID: PMC4954668 DOI: 10.1371/journal.pone.0159371] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/03/2016] [Indexed: 11/19/2022] Open
Abstract
Genetic variation has been observed in both protein concentration in wheat grain and total protein content (protein yield). Here we describe the genetic analysis of variation for grain protein in response to nitrogen (N) supply and locate significant genomic regions controlling grain protein components in a spring wheat population. In total, six N use efficiency (NUE) field trials were carried out for the target traits in a sub-population of doubled haploid lines derived from a cross between two Australian varieties, RAC875 and Kukri, in Southern and Western Australia from 2011 to 2013. Twenty-four putative Quantitative Trait Loci (QTL) for protein-related traits were identified at high and low N supply and ten QTL were identified for the response to N for the traits studied. These loci accounted for a significant proportion of the overall effect of N supply. Several of the regions were co-localised with grain yield QTL and are promising targets for further investigation and selection in breeding programs.
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Affiliation(s)
- Saba Mahjourimajd
- Australian Centre for Plant Functional Genomics (ACPFG), The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia
| | - Julian Taylor
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Zed Rengel
- Soil Science and Plant Nutrition M087, School of Earth and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Hossein Khabaz-Saberi
- Soil Science and Plant Nutrition M087, School of Earth and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Haydn Kuchel
- Australian Grain Technologies, PMB1, Glen Osmond, SA 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Mamoru Okamoto
- Australian Centre for Plant Functional Genomics (ACPFG), The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia
- * E-mail: (PL); (MO)
| | - Peter Langridge
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
- * E-mail: (PL); (MO)
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