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Fortunato S, Nigro D, Lasorella C, Marcotuli I, Gadaleta A, de Pinto MC. The Role of Glutamine Synthetase (GS) and Glutamate Synthase (GOGAT) in the Improvement of Nitrogen Use Efficiency in Cereals. Biomolecules 2023; 13:1771. [PMID: 38136642 PMCID: PMC10742212 DOI: 10.3390/biom13121771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Cereals are the most broadly produced crops and represent the primary source of food worldwide. Nitrogen (N) is a critical mineral nutrient for plant growth and high yield, and the quality of cereal crops greatly depends on a suitable N supply. In the last decades, a massive use of N fertilizers has been achieved in the desire to have high yields of cereal crops, leading to damaging effects for the environment, ecosystems, and human health. To ensure agricultural sustainability and the required food source, many attempts have been made towards developing cereal crops with a more effective nitrogen use efficiency (NUE). NUE depends on N uptake, utilization, and lastly, combining the capability to assimilate N into carbon skeletons and remobilize the N assimilated. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a crucial metabolic step of N assimilation, regulating crop yield. In this review, the physiological and genetic studies on GS and GOGAT of the main cereal crops will be examined, giving emphasis on their implications in NUE.
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Affiliation(s)
- Stefania Fortunato
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
| | - Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Cecilia Lasorella
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
| | - Ilaria Marcotuli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Agata Gadaleta
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Maria Concetta de Pinto
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
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Han X, Zhang M, Gao M, Yuan Y, Yuan Y, Zhang G, An Y, Guo Y, Kong F, Li S. QTL Mapping and Candidate Gene Identifying for N, P, and K Use Efficiency at the Maturity Stages in Wheat. Genes (Basel) 2023; 14:1168. [PMID: 37372348 DOI: 10.3390/genes14061168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Nitrogen (N), phosphorus (P), and potassium (K) are the three most important mineral nutrients for crop growth and development. We previously constructed a genetic map of unigenes (UG-Map) based on their physical positions using a RIL population derived from the cross of "TN18 × LM6" (TL-RILs). In this study, a total of 18 traits related to mineral use efficiency (MUE) of N/P/K were investigated under three growing seasons using TL-RILs. A total of 54 stable QTLs were detected, distributed across 19 chromosomes except for 3A and 5B. There were 50 QTLs associated with only one trait, and the other four QTLs were associated with two traits. A total of 73 candidate genes for stable QTLs were identified. Of these, 50 candidate genes were annotated in Chinese Spring (CS) RefSeq v1.1. The average number of candidate genes per QTL was 1.35, with 45 QTLs containing only one candidate gene and nine QTLs containing two or more candidate genes. The candidate gene TraesCS6D02G132100 (TaPTR gene) for QGnc-6D-3306 belongs to the NPF (NRT1/PTR) gene family. We speculate that the TaPTR gene should regulate the GNC trait.
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Affiliation(s)
- Xu Han
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Mingxia Zhang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Minggang Gao
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
- Key Laboratory of Biochemistry and Molecular Biology, College of Biological and Agricultural Engineering, Weifang University, Weifang 261061, China
| | - Yuanyuan Yuan
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
- Jinan Academy of Agricultural Science, Jinan 250316, China
| | - Yapei Yuan
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Guizhi Zhang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250108, China
| | - Yanrong An
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Ying Guo
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Fanmei Kong
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Sishen Li
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
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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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Pascual L, Solé-Medina A, Faci I, Giraldo P, Ruiz M, Benavente E. Development and marker-trait relationships of functional markers for glutamine synthetase GS1 and GS2 homoeogenes in bread wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:8. [PMID: 37309364 PMCID: PMC10248667 DOI: 10.1007/s11032-022-01354-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/28/2022] [Indexed: 06/14/2023]
Abstract
GS1 and GS2 genes encode, respectively, the main cytosolic and the plastidic isoforms of glutamine synthetase (GS). In the present study, the wheat GS1 and GS2 homoeogenes located in the A, B and D genome chromosomes have been sequenced in a group of 15 bread wheat varieties including landraces, old commercial varieties and modern cultivars. Phenotypic characterization by multi-environment field trials detected significant effects of specific GS homoeogenes on three of the seven agronomic and grain quality traits analyzed. Based on the gene sequence polymorphisms found, biallelic molecular markers that could facilitate marker-assisted breeding were developed for genes GS1A, GS2A and GS2D. The remaining genes encoding main wheat GS were excluded because of being monomorphic (GS1D) or too polymorphic (GS1B and GS2B) in the sequencing panel varieties. A collection of 187 Spanish bread wheat landraces was genotyped for these gene-based molecular markers. Data analyses conducted with phenotypic records reported for this germplasm collection in López-Fernández et al. (Plants-Basel 10: 620, 2021) have revealed the beneficial influence of some individual alleles on thousand-kernel weight (TKW), kernels per spike (KS) and grain protein content. Furthermore, genetic interactions between GS1A, a cytosolic GS isoform coding gene, and GS2A or GS2D, plastidic GS enzyme coding genes, were found to affect TKW and KS. The finding that some alleles at one locus may mask the effect of positive alleles at hypostatic GS loci should be kept in mind if gene pyramiding strategies are attempted for the improvement of N-use efficiency-related traits. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01354-0.
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Affiliation(s)
- Laura Pascual
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Aida Solé-Medina
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- Department of Forest Ecology & Genetics, Forest Research Centre (INIA, CSIC), Ctra. de La Coruña Km 7.5, 28040 Madrid, Spain
| | - Isabel Faci
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- John Innes Centre, Norwich Research Park, Colney, NR4 7UH UK
| | - Patricia Giraldo
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Magdalena Ruiz
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), CSIC, Autovía A2, Km. 36.2, Finca La Canaleja, Alcalá de Henares, Madrid, 28805 Spain
| | - Elena Benavente
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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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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Sandhu N, Pruthi G, Prakash Raigar O, Singh MP, Phagna K, Kumar A, Sethi M, Singh J, Ade PA, Saini DK. Meta-QTL Analysis in Rice and Cross-Genome Talk of the Genomic Regions Controlling Nitrogen Use Efficiency in Cereal Crops Revealing Phylogenetic Relationship. Front Genet 2021; 12:807210. [PMID: 34992638 PMCID: PMC8724540 DOI: 10.3389/fgene.2021.807210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
The phenomenal increase in the use of nitrogenous fertilizers coupled with poor nitrogen use efficiency is among the most important threats to the environment, economic, and social health. During the last 2 decades, a number of genomic regions associated with nitrogen use efficiency (NUE) and related traits have been reported by different research groups, but none of the stable and major effect QTL have been utilized in the marker-assisted introgression/pyramiding program. Compiling the data available in the literature could be very useful in identifying stable and major effect genomic regions associated with the root and NUE-related trait improving the rice grain yield. In the present study, we performed meta-QTL analysis on 1,330 QTL from 29 studies published in the past 2 decades. A total of 76 MQTL with a stable effect over different genetic backgrounds and environments were identified. The significant reduction in the confidence interval of the MQTL compared to the initial QTL resulted in the identification of annotated and putative candidate genes related to the traits considered in the present study. A hot spot region associated with correlated traits on chr 1, 4, and 8 and candidate genes associated with nitrate transporters, nitrogen content, and ammonium uptake on chromosomes 2, 4, 6, and 8 have been identified. The identified MQTL, putative candidate genes, and their orthologues were validated on our previous studies conducted on rice and wheat. The research-based interventions such as improving nitrogen use efficiency via identification of major genomic regions and candidate genes can be a plausible, simple, and low-cost solution to address the challenges of the crop improvement program.
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Affiliation(s)
| | | | | | | | - Kanika Phagna
- Indian Institute of Science Education and Research, Berhampur, India
| | - Aman Kumar
- Punjab Agricultural University, Ludhiana, India
| | - Mehak Sethi
- Punjab Agricultural University, Ludhiana, India
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Xiong H, Ma H, Hu B, Zhao H, Wang J, Rennenberg H, Shi X, Zhang Y. Nitrogen fertilization stimulates nitrogen assimilation and modifies nitrogen partitioning in the spring shoot leaves of citrus (Citrus reticulata Blanco) trees. JOURNAL OF PLANT PHYSIOLOGY 2021; 267:153556. [PMID: 34737128 DOI: 10.1016/j.jplph.2021.153556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
The spring shoot leaves are important sites of nitrogen (N) metabolism in citrus trees. Understanding the physiological and metabolic response of the spring shoot leaves under varying N fertilization is fundamental to the fertilization management in citrus orchards. Thus, the processes affecting N composition, the activities of N metabolism related enzymes, and the expression of relevant genes were explored in spring shoot leaves under four N levels (0, 207, 275, 413 g N tree-1 y-1, as N0, N207, N275, N413). The results showed that, compared with N0, N275 significantly increased total N by 24.81%, which was mainly attributed to enhancement of structural N by 30.92%, free amino acid N by 40.91% and nitrate N by 41.33%. The relative expression of nitrate reductase (NR) and glutamate dehydrogenase (GDH) under N275 increased by 19.32% and 73.48%, respectively, compared with that under N0 treatment. Compared with N0 treatment, the NR transcription level under N275 treatment increased by 381%. The relative transcription levels of NADP-GDH and GDH1 also increased with increasing N fertilization. However, compared with that under N275, the relative transcription of GDH2 under N413 treatment was inhibited. Therefore, the transcript abundance of NR, NADP-GDH,GDH1 and GDH2 affected the activities of NR and GDH and thereby contributed to the regulation of N composition in the leaves. In addition, the activities of glutamine synthetase and nitrite reductase were largely unaffected or even declined in the N207, N275 and N413 treatments compared with the N0. This study elucidated the mechanism of primary N metabolism and partitioning in citrus leaves and provided a theoretical basis for N management in citrus orchards.
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Affiliation(s)
- Huaye Xiong
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing, 400716, China.
| | - Haotian Ma
- College of Forensic Medicine, Xi' an Jiaotong University, Xi'an, 710061, China
| | - Bin Hu
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Huanyu Zhao
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing, 400716, China; Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, 400716, China
| | - Jie Wang
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, 400716, China; State Cultivation Base of Eco-agriculture for Southwest Mountainous Land, Southwest University, Chongqing, Chongqing, 400716, China; National Monitoring Station of Soil Fertility and Fertilizer Efficiency on Purple Soils, Southwest University, Chongqing, 400716, China
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Xiaojun Shi
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, 400716, China; State Cultivation Base of Eco-agriculture for Southwest Mountainous Land, Southwest University, Chongqing, Chongqing, 400716, China; National Monitoring Station of Soil Fertility and Fertilizer Efficiency on Purple Soils, Southwest University, Chongqing, 400716, China.
| | - Yueqiang Zhang
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, 400716, China; State Cultivation Base of Eco-agriculture for Southwest Mountainous Land, Southwest University, Chongqing, Chongqing, 400716, China; National Monitoring Station of Soil Fertility and Fertilizer Efficiency on Purple Soils, Southwest University, Chongqing, 400716, China.
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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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Gupta N, Gupta M, Akhatar J, Goyal A, Kaur R, Sharma S, Goyal P, Mukta A, Kaur N, Mittal M, Singh MP, Bharti B, Sardana VK, Banga SS. Association genetics of the parameters related to nitrogen use efficiency in Brassica juncea L. PLANT MOLECULAR BIOLOGY 2021; 105:161-175. [PMID: 32997301 DOI: 10.1007/s11103-020-01076-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Genome wide association studies allowed prediction of 17 candidate genes for association with nitrogen use efficiency. Novel information obtained may provide better understanding of genomic controls underlying germplasm variations for this trait in Indian mustard. Nitrogen use efficiency (NUE) of Indian mustard (Brassica juncea (L.) Czern & Coss.) is low and most breeding efforts to combine NUE with crop performance have not succeeded. Underlying genetics also remain unexplored. We tested 92 SNP-genotyped inbred lines for yield component traits, N uptake efficiency (NUPEFF), nitrogen utilization efficiency (NUTEFF), nitrogen harvest index (NHI) and NUE for two years at two nitrogen doses (No without added N and N100 added @100 kg/ha). Genotypes IC-2489-88, M-633, MCP-632, HUJM 1080, GR-325 and DJ-65 recorded high NUE at low N. These also showed improved crop performance under high N. One determinate mustard genotype DJ-113 DT-3 revealed maximum NUTEFF. Genome wide association studies (GWAS) facilitated recognition of 17 quantitative trait loci (QTLs). Environment specificity was high. B-genome chromosomes (B02, B03, B05, B07 and B08) harbored many useful loci. We also used regional association mapping (RAM) to supplement results from GWAS. Annotation of the genomic regions around peak SNPs helped to predict several gene candidates for root architecture, N uptake, assimilation and remobilization. CAT9 (At1g05940) was consistently envisaged for both NUE and NUPEFF. Major N transporter genes, NRT1.8 and NRT3.1 were predicted for explaining variation for NUTEFF and NUPEFF, respectively. Most significant amino acid transporter gene, AAP1 appeared associated with NUE under limited N conditions. All these candidates were predicted in the regions of high linkage disequilibrium. Sequence information of the predicted candidate genes will permit development of molecular markers to aid breeding for high NUE.
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Affiliation(s)
- Neha Gupta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Mehak Gupta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Anna Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Rimaljeet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Sanjula Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Prinka Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Archana Mukta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Navneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Mohini Prabha Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Baudh Bharti
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - V K Sardana
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India.
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10
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Sandhu N, Sethi M, Kumar A, Dang D, Singh J, Chhuneja P. Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:657629. [PMID: 34149755 PMCID: PMC8213353 DOI: 10.3389/fpls.2021.657629] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/06/2021] [Indexed: 05/22/2023]
Abstract
Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world's agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.
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11
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Nigro D, Fortunato S, Giove SL, Mazzucotelli E, Gadaleta A. Functional Validation of Glutamine synthetase and Glutamate synthase Genes in Durum Wheat near Isogenic Lines with QTL for High GPC. Int J Mol Sci 2020; 21:ijms21239253. [PMID: 33291583 PMCID: PMC7730160 DOI: 10.3390/ijms21239253] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/25/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022] Open
Abstract
Durum wheat (Triticum turgidum L. ssp. durum) is a minor crop grown on about 17 million hectares of land worldwide. Several grain characteristics determine semolina's high end-use quality, such as grain protein content (GPC) which is directly related to the final products' nutritional and technological values. GPC improvement could be pursued by considering a candidate gene approach. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a bottleneck in the first step of nitrogen assimilation. QTL for GPC have been located on all chromosomes, and several major ones have been reported on 2A and 2B chromosomes, where GS2 and Fd-GOGAT genes have been mapped. A useful and efficient method to validate a putative QTL is the constitution of near-isogenic lines (NILs) by using the marker found to be associated to that QTL. Here, we present the development of two distinct sets of heterogeneous inbred family (HIF)- based NILs segregating for GS2 and Fd-GOGAT genes obtained from heterozygous lines at those loci, as well as their genotypic and phenotypic characterizations. The results allow the validation of the previously identified GPC QTL on 2A and 2B chromosomes, along with the role of these key genes in GPC control.
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Affiliation(s)
- Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
- Correspondence: (D.N.); (A.G.); Tel.: +39-0805442997(D.N.); +39-0805442995 (A.G.)
| | | | - Stefania Lucia Giove
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70126 Bari, Italy;
| | | | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70126 Bari, Italy;
- Correspondence: (D.N.); (A.G.); Tel.: +39-0805442997(D.N.); +39-0805442995 (A.G.)
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12
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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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13
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Dellero Y. Manipulating Amino Acid Metabolism to Improve Crop Nitrogen Use Efficiency for a Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2020; 11:602548. [PMID: 33329673 PMCID: PMC7733991 DOI: 10.3389/fpls.2020.602548] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/03/2020] [Indexed: 05/06/2023]
Abstract
In a context of a growing worldwide food demand coupled to the need to develop a sustainable agriculture, it is crucial to improve crop nitrogen use efficiency (NUE) while reducing field N inputs. Classical genetic approaches based on natural allelic variations existing within crops have led to the discovery of quantitative trait loci controlling NUE under low nitrogen conditions; however, the identification of candidate genes from mapping studies is still challenging. Amino acid metabolism is the cornerstone of plant N management, which involves N uptake, assimilation, and remobilization efficiencies, and it is finely regulated during acclimation to low N conditions and other abiotic stresses. Over the last two decades, biotechnological engineering of amino acid metabolism has led to promising results for the improvement of crop NUE, and more recently under low N conditions. This review summarizes current work carried out in crops and provides perspectives on the identification of new candidate genes and future strategies for crop improvement.
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14
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Ma J, Tu Y, Zhu J, Luo W, Liu H, Li C, Li S, Liu J, Ding P, Habib A, Mu Y, Tang H, Liu Y, Jiang Q, Chen G, Wang J, Li W, Pu Z, Zheng Y, Wei Y, Kang H, Chen G, Lan X. Flag leaf size and posture of bread wheat: genetic dissection, QTL validation and their relationships with yield-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:297-315. [PMID: 31628527 DOI: 10.1007/s00122-019-03458-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/10/2019] [Indexed: 05/24/2023]
Abstract
Major and environmentally stable QTL for flag leaf-related traits in wheat were identified and validated across ten environments using six populations with different genetic backgrounds. Flag leaf size and posture are two important factors of "ideotype" in wheat. Despite numerous studies on genetic analysis of flag leaf size including flag leaf length (FLL), width (FLW), area (FLA) and the ratio of length/width (FLR), few have focused on flag leaf posture including flag leaf angle (FLANG), opening angle (FLOA) and bend angle (FLBA). Further, the numbers of major, environmentally stable and verified genetic loci for flag leaf-related traits are limited. In this study, QTL for FLL, FLW, FLA, FLR, FLANG, FLOA and FLBA were identified based on a recombinant inbred line population together with values from up to ten different environments. Totally, eight major and stably expressed QTL were identified. Three co-located chromosomal intervals for seven major QTL were identified. The five major QTL QFll.sicau-5B.3 and QFll.sicau-2D.3 for FLL, QFlr.sicau-5B for FLR, QFlw.sicau-2D for FLW and QFla.sicau-2D for FLA were successfully validated by the tightly linked Kompetitive Allele Specific PCR (KASP) markers in the other five populations with different genetic backgrounds. A few genes related to leaf growth and development in intervals for these major QTL were predicated. Significant relationships between flag leaf- and yield-related traits were evidenced by analyses of Pearson correlations, conditional QTL and genetic mapping. Taken together, these results provide valuable information for understanding flag leaf size and posture of "ideotype" as well as fine mapping and breeding utilization of promising loci in bread wheat.
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Affiliation(s)
- Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yang Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuiqin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Puyang Ding
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
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15
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Shen X, Yuan Y, Zhang H, Guo Y, Zhao Y, Li S, Kong F. The Hot QTL Locations for Potassium, Calcium, and Magnesium Nutrition and Agronomic Traits at Seedling and Maturity Stages of Wheat under Different Potassium Treatments. Genes (Basel) 2019; 10:genes10080607. [PMID: 31409015 PMCID: PMC6722954 DOI: 10.3390/genes10080607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/05/2019] [Accepted: 08/05/2019] [Indexed: 01/22/2023] Open
Abstract
Potassium (K) is one of the most important mineral nutrients for wheat. In this study, the effects of low K (LK) treatments and the quantitative trait loci (QTLs) for K, calcium (Ca), and magnesium (Mg) use efficiency traits, both at the seedling and maturity stages of wheat, were investigated. The set of “Tainong 18 × Linmai 6” recombinant inbred lines (RILs) were used to identify the QTLs under different K treatments using hydroponic culture and field trials. The majority of K concentrations and content-related traits at seedling and maturity stages decreased with reduced K supply, but the K use efficiency-related traits increased. In contrast, with reduced K supply, the contents of Ca and Mg increased, while the Ca and Mg use efficiency decreased. A total of 217 QTLs for seedling traits and 89 QTLs for adult traits were detected. Four relatively high-frequency QTLs (RHF-QTLs) and 18 QTL clusters (colocation of QTLs for more than two traits) were detected. Eight clusters were detected for K-, Ca-, and Mg-related traits simultaneously. This means that these traits might be controlled by the same QTL. In addition, we highlight that 4B might be an important chromosome regulating the nutrition of K, Ca, and Mg in wheat. The 4B chromosome and four hot QTL clusters, which located 45 QTLs, might be important potential targets for further investigation.
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Affiliation(s)
- Xing Shen
- State Key Laboratory of Crop Biology/National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Yapei Yuan
- State Key Laboratory of Crop Biology/National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Han Zhang
- State Key Laboratory of Crop Biology/National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Ying Guo
- State Key Laboratory of Crop Biology/National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology/National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Sishen Li
- State Key Laboratory of Crop Biology/National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China.
| | - Fanmei Kong
- State Key Laboratory of Crop Biology/National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China.
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16
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Bhoite R, Onyemaobi I, Si P, Siddique KHM, Yan G. Identification and validation of QTL and their associated genes for pre-emergent metribuzin tolerance in hexaploid wheat (Triticum aestivum L.). BMC Genet 2018; 19:102. [PMID: 30419811 PMCID: PMC6233490 DOI: 10.1186/s12863-018-0690-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 10/30/2018] [Indexed: 11/17/2022] Open
Abstract
Background Herbicide tolerance is an important trait that allows effective weed management in wheat crops. Genetic knowledge of metribuzin tolerance in wheat is needed to develop new cultivars for the industry. Here, we evaluated metribuzin tolerance in a recombinant inbred line (RIL) mapping population derived from Synthetic W7984 and Opata 85 over two consecutive years to identify quantitative trait loci (QTL) contributing to the trait. Herbicide tolerance was measured by two chlorophyll traits, SPAD chlorophyll content index (CCI) and visual senescence score (SNS). The markers associated with major QTL from Synthetic W7984, positively contributing to reduced phytotoxic effects under herbicide treatment were validated in two F3/4 recombinant inbred populations developed from crosses of Synthetic W7984 × Westonia and Synthetic W7984 × Lang. Results Composite interval mapping (CIM) identified four QTL, two on chromosome 4A and one each on chromosomes 2D and 1A. The chromosomal position of the two QTL mapped on 4A within 10 cM intervals was refined and validated by multiple interval mapping (MIM). The major QTL affecting both measures of tolerance jointly explained 42 and 45% of the phenotypic variation by percentage CCI reduction and SNS, respectively. The identified QTL have a pure additive effect. The metribuzin tolerant allele of markers, Xgwm33 and Xbarc343, conferred lower phytotoxicity and explained the maximum phenotypic variation of 28.8 and 24.5%, respectively. The approximate physical localization of the QTL revealed the presence of five candidate genes (ribulose-bisphosphate carboxylase, oxidoreductase (rbcS), glycosyltransferase, serine/threonine-specific protein kinase and phosphotransferase) with a direct role in photosynthesis and/or metabolic detoxification pathways. Conclusion Metribuzin causes photo-inhibition by interrupting electron flow in PSII. Consequently, chlorophyll traits enabled the measure of high proportion of genetic variability in the mapping population. The validated molecular markers associated with metribuzin tolerance mediating QTL may be used in marker-assisted breeding to select metribuzin tolerant lines. Alternatively, validated favourable alleles could be introgressed into elite wheat cultivars to enhance metribuzin tolerance and improve grain yield in dryland farming for sustainable wheat production. Electronic supplementary material The online version of this article (10.1186/s12863-018-0690-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roopali Bhoite
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6001, Australia.,The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
| | - Ifeyinwa Onyemaobi
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6001, Australia.,The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
| | - Ping Si
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6001, Australia.,The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6001, Australia. .,The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia.
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17
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Ren D, Fang X, Jiang P, Zhang G, Hu J, Wang X, Meng Q, Cui W, Lan S, Ma X, Wang H, Kong L. Genetic Architecture of Nitrogen-Deficiency Tolerance in Wheat Seedlings Based on a Nested Association Mapping (NAM) Population. FRONTIERS IN PLANT SCIENCE 2018; 9:845. [PMID: 29997636 PMCID: PMC6028695 DOI: 10.3389/fpls.2018.00845] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/31/2018] [Indexed: 05/06/2023]
Abstract
Genetic divergence for nitrogen utilization in germplasms is important in wheat breeding programs, especially for low nitrogen input management. In this study, a nested association mapping (NAM) population, derived from "Yanzhan 1" (a Chinese domesticated cultivar) crossed with "Hussar" (a British domesticated cultivar) and another three semi-wild wheat varieties, namely, "Cayazheda 29" (Triticum aestivum ssp. tibetanum Shao), "Yunnan" (T. aestivum ssp. yunnanense King), and "Yutian" (T. aestivum petropavloski Udats et Migusch), was used to detect quantitative trait loci (QTLs) for nitrogen utilization at the seedling stage. An integrated genetic map was constructed using 2,059 single nucleotide polymorphism (SNP) markers from a 90 K SNP chip, with a total coverage of 2,355.75 cM and an average marker spacing of 1.13 cM. A total of 67 QTLs for RDW (root dry weight), SDW (shoot dry weight), TDW (total dry weight), and RSDW (root to shoot ratio) were identified under normal nitrogen conditions (N+) and nitrogen deficient conditions (N-). Twenty-three of these QTLs were only detected under N- conditions. Moreover, 23 favorable QTLs were identified in the domesticated cultivar Yanzhan 1, 15 of which were detected under N+ conditions, while only four were detected under N- conditions. In contrast, the semi-wild cultivars contributed more favorable N--specific QTLs (eight from Cayazheda 29; nine from Yunnan), which could be further explored for breeding cultivars adapted to nitrogen-deficient conditions. In particular, QRSDW-5A.1 from YN should be further evaluated using high-resolution mapping.
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Affiliation(s)
- Deqiang Ren
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Xiaojian Fang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Peng Jiang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Guangxu Zhang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Junmei Hu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Xiaoqian Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Qing Meng
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Weian Cui
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Shengjie Lan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Xin Ma
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Hongwei Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
- *Correspondence: Hongwei Wang, Lingrang Kong,
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
- *Correspondence: Hongwei Wang, Lingrang Kong,
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18
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Monostori I, Szira F, Tondelli A, Árendás T, Gierczik K, Cattivelli L, Galiba G, Vágújfalvi A. Genome-wide association study and genetic diversity analysis on nitrogen use efficiency in a Central European winter wheat (Triticum aestivum L.) collection. PLoS One 2017; 12:e0189265. [PMID: 29283996 PMCID: PMC5746223 DOI: 10.1371/journal.pone.0189265] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/23/2017] [Indexed: 11/18/2022] Open
Abstract
To satisfy future demands, the increase of wheat (Triticum aestivum L.) yield is inevitable. Simultaneously, maintaining high crop productivity and efficient use of nutrients, especially nitrogen use efficiency (NUE), are essential for sustainable agriculture. NUE and its components are inherently complex and highly influenced by environmental factors, nitrogen management practices and genotypic variation. Therefore, a better understanding of their genetic basis and regulation is fundamental. To investigate NUE-related traits and their genetic and environmental regulation, field trials were evaluated in a Central European wheat collection of 93 cultivars at two nitrogen input levels across three seasons. This elite germplasm collection was genotyped on DArTseq® genotypic platform to identify loci affecting N-related complex agronomic traits. To conduct robust genome-wide association mapping, the genetic diversity, population structure and linkage disequilibrium were examined. Population structure was investigated by various methods and two subpopulations were identified. Their separation is based on the breeding history of the cultivars, while analysis of linkage disequilibrium suggested that selective pressures had acted on genomic regions bearing loci with remarkable agronomic importance. Besides NUE, genetic basis for variation in agronomic traits indirectly affecting NUE and its components, moreover genetic loci underlying response to nitrogen fertilisation were also determined. Altogether, 183 marker-trait associations (MTA) were identified spreading over almost the entire genome. We found that most of the MTAs were environmental-dependent. The present study identified several associated markers in those genomic regions where previous reports had found genes or quantitative trait loci influencing the same traits, while most of the MTAs revealed new genomic regions. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArTseq® markers, which will facilitate the understanding of the genetic basis of NUE and agronomically important traits.
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Affiliation(s)
- István Monostori
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Fruzsina Szira
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Alessandro Tondelli
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda (PC), Italy
| | - Tamás Árendás
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Krisztián Gierczik
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
- Festetics Doctoral School, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
| | - Luigi Cattivelli
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda (PC), Italy
| | - Gábor Galiba
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
- Festetics Doctoral School, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
| | - Attila Vágújfalvi
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
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19
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Allelic Variants of Glutamine Synthetase and Glutamate Synthase Genes in a Collection of Durum Wheat and Association with Grain Protein Content. DIVERSITY 2017. [DOI: 10.3390/d9040052] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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20
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Gelli M, Konda AR, Liu K, Zhang C, Clemente TE, Holding DR, Dweikat IM. Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum. BMC PLANT BIOLOGY 2017; 17:123. [PMID: 28697783 PMCID: PMC5505042 DOI: 10.1186/s12870-017-1064-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/25/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Quantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations. Also, with Illumina RNA-sequencing we checked the differential expression of gene (DEG) transcripts between parents and pools of RILs with high and low nitrogen use efficiency (NUE) and overlaid these DEGs on to the common validated QTLs to find candidate genes associated with N-stress tolerance in sorghum. RESULTS An F7 RIL population derived from a cross between CK60 (N-stress sensitive) and San Chi San (N-stress tolerant) inbred sorghum lines was used to map QTLs for 11 agronomic traits tested under different N-levels. Composite interval mapping analysis detected a total of 32 QTLs for 11 agronomic traits. Validation of these QTLs revealed that of the detected, nine QTLs from this population were consistent with the reported QTLs in earlier study using CK60/China17 RIL population. The validated QTLs were located on chromosomes 1, 6, 7, 8, and 9. In addition, root transcriptomic profiling detected 55 and 20 differentially expressed gene (DEG) transcripts between parents and pools of RILs with high and low NUE respectively. Also, overlay of these DEG transcripts on to the validated QTLs found candidate genes transcripts for NUE and also showed the expected differential expression. For example, DEG transcripts encoding Lysine histidine transporter 1 (LHT1) had abundant expression in San Chi San and the tolerant RIL pool, whereas DEG transcripts encoding seed storage albumin, transcription factor IIIC (TFIIIC) and dwarfing gene (DW2) encoding multidrug resistance-associated protein-9 homolog showed abundant expression in CK60 parent, similar to earlier study. CONCLUSIONS The validated QTLs among different mapping populations would be the most reliable and stable QTLs across germplasm. The DEG transcripts found in the validated QTL regions will serve as future candidate genes for enhancing NUE in sorghum using molecular approaches.
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Affiliation(s)
- Malleswari Gelli
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Anji Reddy Konda
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - Kan Liu
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Thomas E Clemente
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - David R Holding
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - Ismail M Dweikat
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
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21
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Marcotuli I, Gadaleta A, Mangini G, Signorile AM, Zacheo SA, Blanco A, Simeone R, Colasuonno P. Development of a High-Density SNP-Based Linkage Map and Detection of QTL for β-Glucans, Protein Content, Grain Yield per Spike and Heading Time in Durum Wheat. Int J Mol Sci 2017. [PMID: 28635630 PMCID: PMC5486150 DOI: 10.3390/ijms18061329] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
High-density genetic linkage maps of crop species are particularly useful in detecting qualitative and quantitative trait loci for important agronomic traits and in improving the power of classical approaches to identify candidate genes. The aim of this study was to develop a high-density genetic linkage map in a durum wheat recombinant inbred lines population (RIL) derived from two elite wheat cultivars and to identify, characterize and correlate Quantitative Trait Loci (QTL) for β-glucan, protein content, grain yield per spike and heading time. A dense map constructed by genotyping the RIL population with the wheat 90K iSelect array included 5444 single nucleotide polymorphism (SNP) markers distributed in 36 linkage groups. Data for β-glucan and protein content, grain yield per spike and heading time were obtained from replicated trials conducted at two locations in southern Italy. A total of 19 QTL were detected in different chromosome regions. In particular, three QTL for β-glucan content were detected on chromosomes 2A and 2B (two loci); eight QTL controlling grain protein content were detected on chromosomes 1B, 2B, 3B (two loci), 4A, 5A, 7A and 7B; seven QTL for grain yield per spike were identified on chromosomes 1A, 2B, 3A (two loci), 3B (two loci) and 6B; and one marker-trait association was detected on chromosome 2A for heading time. The last was co-located with a β-glucan QTL, and the two QTL appeared to be negatively correlated. A genome scan for genomic regions controlling the traits and SNP annotated sequences identified five putative candidate genes involved in different biosynthesis pathways (β-glucosidase, GLU1a; APETALA2, TaAP2; gigantea 3, TaGI3; 14-3-3 protein, Ta14A; and photoperiod sensitivity, Ppd-A1). This study provides additional information on QTL for important agronomic traits that could be useful for marker-assisted breeding to obtain new genotypes with commercial and nutritional relevance.
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Affiliation(s)
- Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126 Bari, Italy.
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126 Bari, Italy.
| | - Giacomo Mangini
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126 Bari, Italy.
| | - Antonio Massimo Signorile
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126 Bari, Italy.
| | - Silvana Addolorata Zacheo
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126 Bari, Italy.
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126 Bari, Italy.
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126 Bari, Italy.
| | - Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126 Bari, Italy.
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22
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Yuan Y, Gao M, Zhang M, Zheng H, Zhou X, Guo Y, Zhao Y, Kong F, Li S. QTL Mapping for Phosphorus Efficiency and Morphological Traits at Seedling and Maturity Stages in Wheat. FRONTIERS IN PLANT SCIENCE 2017; 8:614. [PMID: 28484481 PMCID: PMC5402226 DOI: 10.3389/fpls.2017.00614] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/04/2017] [Indexed: 05/21/2023]
Abstract
Phosphorus (P) efficiency (PE), which comprises phosphorus uptake (PupE) and utilization efficiency (PutE), is considered as one of the most important factors for crop yield. In the present study, 11 seedling traits and 13 maturity traits related to wheat PE and morphology were investigated using a set of recombinant inbred lines (RILs) derived from the cross of "TN 18 × LM 6," under hydroponic culture trials and field trials at low P (LP) and normal P (NP) levels in two different years, respectively. The LP input reduced of biomass, yield and PupE traits, but increased PutE traits. A total of 163 QTLs for seedling and maturity traits under different P levels and their AV, and 15 QTLs for relative traits were detected on 21 chromosomes. Of these, 49 and 63 QTLs for were detected specially in LP and NP treatments, respectively. We found 11 relatively high-frequency QTLs (RHF-QTLs) and four important QTL clusters, which may be the potential targets for marker-assisted selection (MAS) in wheat breeding programs for PE. Favorable relationships for breeding programs were found in the four important QTL clusters, which allow the possibility of improving the morphological traits and PutE simultaneously. A total of 29 markers which associated with 51 QTLs were found highly homologous with EST sequences, which suggested that they were potential functional loci. We suggested that the four biomass traits (SDW, RDW, TDW, and RSDW), five yield traits (SN, PH, TGW, GWP, and StWP) and two relative traits (Rstwp and Rgwp) can be considered as the primary indexes for the evaluation of PE for they are easy to identify on a large-scale.
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Affiliation(s)
- Yuanyuan Yuan
- State Key Laboratory of Crop Biology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural UniversityTai'an, China
- Jinan Academy of Agricultural ScienceJinan, China
| | - Minggang Gao
- State Key Laboratory of Crop Biology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural UniversityTai'an, China
- Key Laboratory of Biochemistry and Molecular Biology, College of Biological and Agricultural Engineering, Weifang UniversityWeifang, China
| | - Mingxia Zhang
- State Key Laboratory of Crop Biology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural UniversityTai'an, China
| | - Honghua Zheng
- State Key Laboratory of Crop Biology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural UniversityTai'an, China
| | - Xiuwen Zhou
- State Key Laboratory of Crop Biology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural UniversityTai'an, China
| | - Ying Guo
- State Key Laboratory of Crop Biology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural UniversityTai'an, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural UniversityTai'an, China
| | - Fangmei Kong
- State Key Laboratory of Crop Biology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural UniversityTai'an, China
- *Correspondence: Fangmei Kong
| | - Sishen Li
- State Key Laboratory of Crop Biology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural UniversityTai'an, China
- Sishen Li
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23
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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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24
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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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25
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Nigro D, Fortunato S, Giove SL, Paradiso A, Gu YQ, Blanco A, de Pinto MC, Gadaleta A. Glutamine synthetase in Durum Wheat: Genotypic Variation and Relationship with Grain Protein Content. FRONTIERS IN PLANT SCIENCE 2016; 7:971. [PMID: 27468287 PMCID: PMC4942471 DOI: 10.3389/fpls.2016.00971] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/20/2016] [Indexed: 05/29/2023]
Abstract
Grain protein content (GPC), is one of the most important trait in wheat and its characterized by a very complex genetic control. The identification of wheat varieties with high GPC (HGPC), as well as the characterization of central enzymes involved in these processes, are important for more sustainable agricultural practices. In this study, we focused on Glutamine synthetase (GS) as a candidate to study GPC in wheat. We analyzed GS expression and its enzymatic activity in different tissues and phenological stages in 10 durum wheat genotypes with different GPC. Although each genotype performed quite differently from the others, both because their genetic variability and their adaptability to specific environmental conditions, the highest GS activity and expression were found in genotypes with HGPC and vice versa the lowest ones in genotypes with low GPC (LGPC). Moreover, in genotypes contrasting in GPC bred at different nitrogen regimes (0, 60, 140 N Unit/ha) GS behaved differently in diverse organs. Nitrogen supplement increased GS expression and activity in roots of all genotypes, highlighting the key role of this enzyme in nitrogen assimilation and ammonium detoxification in roots. Otherwise, nitrogen treatments decreased GS expression and activity in the leaves of HGPC genotypes and did not affect GS in the leaves of LGPC genotypes. Finally, no changes in GS and soluble protein content occurred at the filling stage in the caryopses of all analyzed genotypes.
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Affiliation(s)
- Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo MoroBari, Italy
| | - Stefania Fortunato
- Department of Soil, Plant and Food Sciences, University of Bari Aldo MoroBari, Italy
- Department of Agricultural and Environmental Sciences, Research Unity of Genetic and Plant Biotechnology, University of Bari Aldo MoroBari, Italy
| | - Stefania L. Giove
- Department of Soil, Plant and Food Sciences, University of Bari Aldo MoroBari, Italy
| | | | - Yong Q. Gu
- Crop Improvement and Genetics Research, Western Regional Research Center, United States Department of Agriculture – Agricultural Research Service, AlbanyCA, USA
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences, University of Bari Aldo MoroBari, Italy
| | | | - Agata Gadaleta
- Department of Agricultural and Environmental Sciences, Research Unity of Genetic and Plant Biotechnology, University of Bari Aldo MoroBari, Italy
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26
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Gelli M, Mitchell SE, Liu K, Clemente TE, Weeks DP, Zhang C, Holding DR, Dweikat IM. Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum. BMC PLANT BIOLOGY 2016; 16:16. [PMID: 26759170 PMCID: PMC4710988 DOI: 10.1186/s12870-015-0696-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/21/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sorghum is an important C4 crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization. RESULTS A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha(-1) fertilizer) and low N (0 kg.ha(-1) fertilizer) conditions. A linkage map spanning 1614 cM was developed using 642 polymorphic single nucleotide polymorphisms (SNPs) detected in the population using Genotyping-By-Sequencing (GBS) technology. Composite interval mapping detected a total of 38 QTLs for 11 agronomic traits tested under different nitrogen levels. The phenotypic variation explained by individual QTL ranged from 6.2 to 50.8%. Illumina RNA sequencing data generated on seedling root tissues revealed 726 differentially expressed gene (DEG) transcripts between parents, of which 108 were mapped close to the QTL regions. CONCLUSIONS Co-localized regions affecting multiple traits were detected on chromosomes 1, 5, 6, 7 and 9. These potentially pleiotropic regions were coincident with the genomic regions of cloned QTLs, including genes associated with flowering time, Ma3 on chromosome 1 and Ma1 on chromosome 6, gene associated with plant height, Dw2 on chromosome 6. In these regions, RNA sequencing data showed differential expression of transcripts related to nitrogen metabolism (Ferredoxin-nitrate reductase), glycolysis (Phosphofructo-2-kinase), seed storage proteins, plant hormone metabolism and membrane transport. The differentially expressed transcripts underlying the pleiotropic QTL regions could be potential targets for improving sorghum performance under limited N fertilizer through marker assisted selection.
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Affiliation(s)
- Malleswari Gelli
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
| | - Sharon E Mitchell
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - Kan Liu
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - Thomas E Clemente
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Donald P Weeks
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA.
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - David R Holding
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Ismail M Dweikat
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
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27
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Garnett T, Plett D, Heuer S, Okamoto M. Genetic approaches to enhancing nitrogen-use efficiency (NUE) in cereals: challenges and future directions. FUNCTIONAL PLANT BIOLOGY : FPB 2015; 42:921-941. [PMID: 32480734 DOI: 10.1071/fp15025] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/24/2015] [Indexed: 05/03/2023]
Abstract
Over 100million tonnes of nitrogen (N) fertiliser are applied globally each year to maintain high yields in agricultural crops. The rising price of N fertilisers has made them a major cost for farmers. Inefficient use of N fertiliser leads to substantial environmental problems through contamination of air and water resources and can be a significant economic cost. Consequently, there is considerable need to improve the way N fertiliser is used in farming systems. The efficiency with which crops use applied N fertiliser - the nitrogen-use efficiency (NUE) - is currently quite low for cereals. This is the case in both high yielding environments and lower yielding environments characteristic of cereal growing regions of Australia. Multiple studies have attempted to identify the genetic basis of NUE, but the utility of the results is limited because of the complex nature of the trait and the magnitude of genotype by environment interaction. Transgenic approaches have been applied to improve plant NUE but with limited success, due, in part, to a combination of the complexity of the trait but also due to lack of accurate phenotyping methods. This review documents these two approaches and suggests future directions in improving cereal NUE with a focus on the Australian cereal industry.
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Affiliation(s)
- Trevor Garnett
- Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, University of Adelaide, Adelaide, SA 5064, Australia
| | - Darren Plett
- Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, University of Adelaide, Adelaide, SA 5064, Australia
| | - Sigrid Heuer
- Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, University of Adelaide, Adelaide, SA 5064, Australia
| | - Mamoru Okamoto
- Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, University of Adelaide, Adelaide, SA 5064, Australia
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28
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Han M, Okamoto M, Beatty PH, Rothstein SJ, Good AG. The Genetics of Nitrogen Use Efficiency in Crop Plants. Annu Rev Genet 2015; 49:269-89. [PMID: 26421509 DOI: 10.1146/annurev-genet-112414-055037] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the past 50 years, the application of synthetic nitrogen (N) fertilizer to farmland resulted in a dramatic increase in crop yields but with considerable negative impacts on the environment. New solutions are therefore needed to simultaneously increase yields while maintaining, or preferably decreasing, applied N to maximize the nitrogen use efficiency (NUE) of crops. In this review, we outline the definition of NUE, the selection and development of NUE crops, and the factors that interact with NUE. In particular, we emphasize the challenges of developing crop plants with enhanced NUE, using more classical genetic approaches based on utilizing existing allelic variation for NUE traits. The challenges of phenotyping, mapping quantitative trait loci (QTLs), and selecting candidate genes for NUE improvement are described. In addition, we highlight the importance of different factors that lead to changes in the NUE components of nitrogen uptake efficiency (NUpE) and nitrogen utilization efficiency (NUtE).
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Affiliation(s)
- Mei Han
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada; , ,
| | - Mamoru Okamoto
- Australian Center for Plant Functional Genomics, The University of Adelaide, PMB1, Glen Osmond, South Australia, 5064, Australia;
| | - Perrin H Beatty
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada; , ,
| | - Steven J Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada;
| | - Allen G Good
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada; , ,
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Cormier F, Le Gouis J, Dubreuil P, Lafarge S, Praud S. A genome-wide identification of chromosomal regions determining nitrogen use efficiency components in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2679-93. [PMID: 25326179 DOI: 10.1007/s00122-014-2407-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/03/2014] [Indexed: 05/25/2023]
Abstract
This study identified 333 genomic regions associated to 28 traits related to nitrogen use efficiency in European winter wheat using genome-wide association in a 214-varieties panel experimented in eight environments. Improving nitrogen use efficiency is a key factor to sustainably ensure global production increase. However, while high-throughput screening methods remain at a developmental stage, genetic progress may be mainly driven by marker-assisted selection. The objective of this study was to identify chromosomal regions associated with nitrogen use efficiency-related traits in bread wheat (Triticum aestivum L.) using a genome-wide association approach. Two hundred and fourteen European elite varieties were characterised for 28 traits related to nitrogen use efficiency in eight environments in which two different nitrogen fertilisation levels were tested. The genome-wide association study was carried out using 23,603 SNP with a mixed model for taking into account parentage relationships among varieties. We identified 1,010 significantly associated SNP which defined 333 chromosomal regions associated with at least one trait and found colocalisations for 39 % of these chromosomal regions. A method based on linkage disequilibrium to define the associated region was suggested and discussed with reference to false positive rate. Through a network approach, colocalisations were analysed and highlighted the impact of genomic regions controlling nitrogen status at flowering, precocity, and nitrogen utilisation on global agronomic performance. We were able to explain 40 ± 10 % of the total genetic variation. Numerous colocalisations with previously published genomic regions were observed with such candidate genes as Ppd-D1, Rht-D1, NADH-Gogat, and GSe. We highlighted selection pressure on yield and nitrogen utilisation discussing allele frequencies in associated regions.
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Affiliation(s)
- Fabien Cormier
- Centre de recherche de Chappes, Biogemma, Route d'Ennezat CS90126, 63720, Chappes, France
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Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C. Structural and functional partitioning of bread wheat chromosome 3B. Science 2014; 345:1249721. [PMID: 25035497 DOI: 10.1126/science.1249721] [Citation(s) in RCA: 389] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.
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Affiliation(s)
- Frédéric Choulet
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France.
| | - Adriana Alberti
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Sébastien Theil
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Natasha Glover
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Josquin Daron
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Lise Pingault
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Pierre Sourdille
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Etienne Paux
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Philippe Leroy
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Nicolas Guilhot
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Jacques Le Gouis
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Francois Balfourier
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Michael Alaux
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Véronique Jamilloux
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Céline Durand
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Christine Gaspin
- Biométrie et Intelligence Artificielle, INRA, Chemin de Borde Rouge, BP 27, 31326 Castanet-Tolosan, France
| | - Jan Safar
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jane Rogers
- The Genome Analysis Centre, Norwich, Norwich Research Park, Norwich NR4 7UH, UK
| | - Klaas Vandepoele
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Technologiepark 927, 9052 Gent, Belgium
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Klaus Mayer
- Munich Information Center for Protein Sequences, Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - Hélène Berges
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Hadi Quesneville
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France. CNRS UMR 8030, 2 Rue Gaston Crémieux, 91000 Evry, France. Université d'Evry, CP5706 Evry, France
| | - Catherine Feuillet
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
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Characterization of ferredoxin-dependent glutamine-oxoglutarate amidotransferase (Fd-GOGAT) genes and their relationship with grain protein content QTL in wheat. PLoS One 2014; 9:e103869. [PMID: 25099972 PMCID: PMC4123923 DOI: 10.1371/journal.pone.0103869] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/02/2014] [Indexed: 11/19/2022] Open
Abstract
Background In higher plants, inorganic nitrogen is assimilated via the glutamate synthase cycle or GS-GOGAT pathway. GOGAT enzyme occurs in two distinct forms that use NADH (NADH-GOGAT) or Fd (Fd-GOGAT) as electron carriers. The goal of the present study was to characterize wheat Fd-GOGAT genes and to assess the linkage with grain protein content (GPC), an important quantitative trait controlled by multiple genes. Results We report the complete genomic sequences of the three homoeologous A, B and D Fd-GOGAT genes from hexaploid wheat (Triticum aestivum) and their localization and characterization. The gene is comprised of 33 exons and 32 introns for all the three homoeologues genes. The three genes show the same exon/intron number and size, with the only exception of a series of indels in intronic regions. The partial sequence of the Fd-GOGAT gene located on A genome was determined in two durum wheat (Triticum turgidum ssp. durum) cvs Ciccio and Svevo, characterized by different grain protein content. Genomic differences allowed the gene mapping in the centromeric region of chromosome 2A. QTL analysis was conducted in the Svevo×Ciccio RIL mapping population, previously evaluated in 5 different environments. The study co-localized the Fd-GOGAT-A gene with the marker GWM-339, identifying a significant major QTL for GPC. Conclusions The wheat Fd-GOGAT genes are highly conserved; both among the three homoeologous hexaploid wheat genes and in comparison with other plants. In durum wheat, an association was shown between the Fd-GOGAT allele of cv Svevo with increasing GPC - potentially useful in breeding programs.
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Valluru R, Reynolds MP, Salse J. Genetic and molecular bases of yield-associated traits: a translational biology approach between rice and wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1463-89. [PMID: 24913362 DOI: 10.1007/s00122-014-2332-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 05/15/2014] [Indexed: 05/21/2023]
Abstract
Transferring the knowledge bases between related species may assist in enlarging the yield potential of crop plants. Being cereals, rice and wheat share a high level of gene conservation; however, they differ at metabolic levels as a part of the environmental adaptation resulting in different yield capacities. This review focuses on the current understanding of genetic and molecular regulation of yield-associated traits in both crop species, highlights the similarities and differences and presents the putative knowledge gaps. We focus on the traits associated with phenology, photosynthesis, and assimilate partitioning and lodging resistance; the most important drivers of yield potential. Currently, there are large knowledge gaps in the genetic and molecular control of such major biological processes that can be filled in a translational biology approach in transferring genomics and genetics informations between rice and wheat.
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Affiliation(s)
- Ravi Valluru
- Wheat Physiology, Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56130, Mexico DF, Mexico,
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Emebiri LC. Genetic variation and possible SNP markers for breeding wheat with low-grain asparagine, the major precursor for acrylamide formation in heat-processed products. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:1422-1429. [PMID: 24122675 DOI: 10.1002/jsfa.6434] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/16/2013] [Accepted: 10/04/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND In products made from wheat (Triticum aestivum) flour, acrylamide formation is almost exclusively determined by the level of free asparagine in the grain. Genetic variability for grain asparagine content was evaluated in order to assess the potential for acrylamide mitigation by breeding. RESULTS Free asparagine levels in the grains of 92 varieties varied from 137 to 471 mg kg⁻¹, representing an approximate threefold difference between the low- and high-asparagine genotypes. Heritability was low, with a value of 32%, indicating that breeding cultivars with inherently low grain asparagine would be a challenge. A genome-wide scan with single-nucleotide polymorphism (SNP) markers identified nine SNPs that were significantly (P < 0.001) associated with variation in free asparagine. The significant SNPs were localized on chromosome 5A, and explained between 14% and 24% of the observed variation. These putative SNPs are candidates for further studies to develop molecular markers. CONCLUSION Significant genetic variation exists for reducing acrylamide precursors in wheat flour, indicating that breeding and genetics could play an important role in mitigating the acrylamide risk in wheat products. The study identified a region on chromosome 5A that could provide a basis for further research to develop functional markers.
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Affiliation(s)
- Livinus C Emebiri
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
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Xu Y, Wang R, Tong Y, Zhao H, Xie Q, Liu D, Zhang A, Li B, Xu H, An D. Mapping QTLs for yield and nitrogen-related traits in wheat: influence of nitrogen and phosphorus fertilization on QTL expression. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:59-72. [PMID: 24072207 DOI: 10.1007/s00122-013-2201-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 09/17/2013] [Indexed: 05/21/2023]
Abstract
The present study identified some new important genomic regions and demonstrated the availability of conditional analysis in dissecting QTLs induced by environmental factors. The high input and low use efficiency of nutrient fertilizers require knowledge of the genetic control of crop reaction to nutrient supplements. In this study, 14 morphological and 8 physiological traits of a set of 182 wheat (Triticum aestivum L.) recombinant inbred lines (Xiaoyan 54 × Jing 411) were investigated in six environments to map quantitative trait loci (QTLs). The influence of nitrogen (N) and phosphorus (P) fertilization on QTL expression was studied by unconditional and conditional analysis. A total of 117 and 30 QTLs were detected by unconditional and conditional analysis, respectively, among which 21 were common for both methods. Thirty-four QTL clusters were identified. Eighteen conserved QTLs (15.4 % of the 117 QTLs) between years, but within nutritional treatment were found. The three major QTLs on chromosomes 2D, 4B and 6A were coincident with Rht8, Rht-B1b and TaGW2, respectively. The other two important intervals on chromosomes 4B and 7A for yield component traits were newly detected QTLs that warrant further study. By conditional analysis, spikelet number per spike was found to be induced by P fertilization mostly, whereas N fertilization had more effects on the expression of the QTLs for nitrogen concentration and utilization efficiency traits. QTLs that respond to N and P interactions were also detected. The results are helpful for understanding the genetic basis of N utilization efficiency in wheat under different N and P supplement environments and provide evidence for the availability of conditional analysis in dissecting QTLs induced by environmental factors.
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Affiliation(s)
- Yunfeng Xu
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
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Matthies IE, Weise S, Förster J, Korzun V, Stein N, Röder MS. Nitrogen-metabolism related genes in barley - haplotype diversity, linkage mapping and associations with malting and kernel quality parameters. BMC Genet 2013; 14:77. [PMID: 24007272 PMCID: PMC3766251 DOI: 10.1186/1471-2156-14-77] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 08/29/2013] [Indexed: 02/01/2023] Open
Abstract
Background Several studies report about intra-specific trait variation of nitrogen-metabolism related traits, such as N(itrogen)-use efficiency, protein content, N-storage and remobilization in barley and related grass species. The goal of this study was to assess the intra-specific genetic diversity present in primary N-metabolism genes of barley and to investigate the associations of the detected haplotype diversity with malting and kernel quality related traits. Results Partial sequences of five genes related to N-metabolism in barley (Hordeum vulgare L.) were obtained, i.e. nitrate reductase 1, glutamine synthetase 2, ferredoxin-dependent glutamate synthase, aspartate aminotransferase and asparaginase. Two to five haplotypes in each gene were discovered in a set of 190 various varieties. The development of 33 SNP markers allowed the genotyping of all these barley varieties consisting of spring and winter types. Furthermore, these markers could be mapped in several doubled haploid populations. Cluster analysis based on haplotypes revealed a more uniform pattern of the spring barleys as compared to the winter barleys. Based on linear model approaches associations to several malting and kernel quality traits including soluble N and protein were identified. Conclusions A study was conducted to investigate the presence of sequence variation of several genes related to the primary N-metabolism in barley. The detected diversity could be related to particular phenotypic traits. Specific differences between spring and winter barleys most likely reflect different breeding aims. The developed markers can be used as tool for further genetic studies and marker-assisted selection during breeding of barley.
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Affiliation(s)
- Inge E Matthies
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr, 3, 06466, Stadt Seeland, Germany.
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Zhang K, Wang J, Zhang L, Rong C, Zhao F, Peng T, Li H, Cheng D, Liu X, Qin H, Zhang A, Tong Y, Wang D. Association analysis of genomic loci important for grain weight control in elite common wheat varieties cultivated with variable water and fertiliser supply. PLoS One 2013; 8:e57853. [PMID: 23469248 PMCID: PMC3587626 DOI: 10.1371/journal.pone.0057853] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/27/2013] [Indexed: 11/18/2022] Open
Abstract
Grain weight, an essential yield component, is under strong genetic control and markedly influenced by the environment. Here, by genome-wide association analysis with a panel of 94 elite common wheat varieties, 37 loci were found significantly associated with thousand-grain weight (TGW) in one or more environments differing in water and fertiliser levels. Five loci were stably associated with TGW under all 12 environments examined. Their elite alleles had positive effects on TGW. Four, two, three, and two loci were consistently associated with TGW in the irrigated and fertilised (IF), rainfed (RF), reduced nitrogen (RN), and reduced phosphorus (RP) environments. The elite alleles of the IF-specific loci enhanced TGW under well-resourced conditions, whereas those of the RF-, RN-, or RP-specific loci conferred tolerance to the TGW decrease when irrigation, nitrogen, or phosphorus were reduced. Moreover, the elite alleles of the environment-independent and -specific loci often acted additively to enhance TGW. Four additional loci were found associated with TGW in specific locations, one of which was shown to contribute to the TGW difference between two experimental sites. Further analysis of 14 associated loci revealed that nine affected both grain length and width, whereas the remaining loci influenced either grain length or width, indicating that these loci control grain weight by regulating kernel size. Finally, the elite allele of Xpsp3152 frequently co-segregated with the larger grain haplotype of TaGW2-6A, suggesting probable genetic and functional linkages between Xpsp3152 and GW2 that are important for grain weight control in cereal plants. Our study provides new knowledge on TGW control in elite common wheat lines, which may aid the improvement of wheat grain weight trait in further research.
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Affiliation(s)
- Kunpu Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Junjun Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Liyi Zhang
- Guizhou Institute of Upland Crops, Guiyang, China
| | - Chaowu Rong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fengwu Zhao
- Dry-Land Farming Institute, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Tao Peng
- Jiyuan Institute of Agricultural Sciences, Jiyuan, China
| | - Huimin Li
- Dry-Land Farming Institute, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Dongmei Cheng
- Jiyuan Institute of Agricultural Sciences, Jiyuan, China
| | - Xin Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huanju Qin
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiping Tong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Bordes J, Ravel C, Jaubertie JP, Duperrier B, Gardet O, Heumez E, Pissavy AL, Charmet G, Le Gouis J, Balfourier F. Genomic regions associated with the nitrogen limitation response revealed in a global wheat core collection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:805-822. [PMID: 23192671 DOI: 10.1007/s00122-012-2019-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 11/05/2012] [Indexed: 05/27/2023]
Abstract
Modern wheat (Triticum aestivum L.) varieties in Western Europe have mainly been bred, and selected in conditions where high levels of nitrogen-rich fertilizer are applied. However, high input crop management has greatly increased the risk of nitrates leaching into groundwater with negative impacts on the environment. To investigate wheat nitrogen tolerance characteristics that could be adapted to low input crop management, we supplied 196 accessions of a wheat core collection of old and modern cultivars with high or moderate amounts of nitrogen fertilizer in an experimental network consisting of three sites and 2 years. The main breeding traits were assessed including grain yield and grain protein content. The response to nitrogen level was estimated for grain yield and grain number per m(2) using both the difference and the ratio between performance at the two input levels and the slope of joint regression. A large variability was observed for all the traits studied and the response to nitrogen level. Whole genome association mapping was carried out using 899 molecular markers taking into account the five ancestral group structure of the collection. We identified 54 main regions involving almost all chromosomes that influence yield and its components, plant height, heading date and grain protein concentration. Twenty-three regions, including several genes, spread over 16 chromosomes were involved in the response to nitrogen level. These chromosomal regions may be good candidates to be used in breeding programs to improve the performance of wheat varieties at moderate nitrogen input levels.
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Affiliation(s)
- Jacques Bordes
- INRA, UMR 1095 Génétique, Diversité Et Ecophysiologie Des Céréales, 234 Avenue Du Brézet, 63100, Clermont-Ferrand, France.
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Chardon F, Noël V, Masclaux-Daubresse C. Exploring NUE in crops and in Arabidopsis ideotypes to improve yield and seed quality. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:3401-12. [PMID: 22231501 DOI: 10.1093/jxb/err353] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
There is evidence that crop yields are showing a trend of stagnation in many countries. This review aims to make an inventory of the last decade's crop productions and the associated economic and environmental challenges. Manipulating nitrogen use efficiency in crops appears to be the best way to conciliate global food security, respecting environmental policies, and the need to produce biofuels. In such a context, the specifications of ideal plants for the future are discussed with regards to human needs and taking into account current physiological and genetic knowledge. The approaches undertaken so far to design an ideal crop and to find suitable new germplasms are discussed. The interest in using model plants in agronomic research is illustrated through the recent data provided by studies exploring natural variation in Arabidopsis thaliana. Efficient Arabidopsis ideotypes are proposed and discussed.
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Affiliation(s)
- Fabien Chardon
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Route de St-Cyr, Versailles Cedex, France
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Guo Y, Kong FM, Xu YF, Zhao Y, Liang X, Wang YY, An DG, Li SS. QTL mapping for seedling traits in wheat grown under varying concentrations of N, P and K nutrients. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:851-65. [PMID: 22089330 DOI: 10.1007/s00122-011-1749-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 10/28/2011] [Indexed: 05/05/2023]
Abstract
Nutrient use efficiency (NuUE), comprising nutrient uptake and utilization efficiency, is regarded as one of the most important factors for wheat yield. In the present study, six morphological, nine nutrient content and nine nutrient utilization efficiency traits were investigated at the seedling stage using a set of recombinant inbred lines (RILs), under hydroponic culture of 12 treatments including single nutrient levels and two- and three-nutrient combinations treatments of N, P and K. For the 12 designed treatments, a total of 380 quantitative trait loci (QTLs) on 20 chromosomes for the 24 traits were detected. Of these, 87, 149 and 144 QTLs for morphological, nutrient content and nutrient utilization efficiency traits were found, respectively. Using the data of the average value (AV) across 12 treatments, 70 QTLs were detected for 23 traits. Most QTLs were located in new marker regions. Twenty-six important QTL clusters were mapped on 13 chromosomes, 1A, 1B, 1D, 2B, 3A, 3B, 4A, 4B, 5D, 6A, 6B, 7A and 7B. Of these, ten clusters involved 147 QTLs (38.7%) for investigated traits, indicating that these 10 loci were more important for the NuUE of N, P and K. We found evidence for cooperative uptake and utilization (CUU) of N, P and K in the early growth period at both the phenotype and QTL level. The correlation coefficients (r) between nutrient content and nutrient utilization efficiency traits for N, P and K were almost all significantly positive correlations. A total of 32 cooperative CUU loci (L1-L32) were found, which included 190 out of the 293 QTLs (64.8%) for the nutrient uptake and utilization efficiency traits, indicating that the CUU-QTLs were common for N, P and K. The CUU-QTLs in L3, L7, L16 and L28 were relatively stable. The CUU-QTLs may explain the CUU phenotype at the QTL level.
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Affiliation(s)
- Ying Guo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
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Improving Nitrogen Use Efficiency in Crops for Sustainable Agriculture. SUSTAINABILITY 2011. [DOI: 10.3390/su3091452] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Gadaleta A, Nigro D, Giancaspro A, Blanco A. The glutamine synthetase (GS2) genes in relation to grain protein content of durum wheat. Funct Integr Genomics 2011; 11:665-70. [PMID: 21755355 DOI: 10.1007/s10142-011-0235-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 06/09/2011] [Accepted: 06/26/2011] [Indexed: 10/18/2022]
Abstract
Glutamine synthetase (GS2) is a key enzyme in plant nitrogen metabolism responsible of the first step of ammonium assimilation and transformation into glutamine (an essential compound in the amino acid-biosynthetic pathway). The goal of the present study was to isolate and characterize GS2 genes and to assess the linkage with grain protein content (GPC), an important quantitative trait controlled by multiple genes. Here, we report the isolation of the complete glutamine synthetase gene sequences and their localization on the two homeologous chromosome 2A and 2B in durum wheat cvs. Ciccio and Svevo characterized by a different grain protein content. GS2-A2 located on 2A chromosome is comprised of 13 exons separated by 12 introns, and the allele sequence in the two cultivars were different for an insertion of 5 bp located in the third exon in the cv. Ciccio. The GS2-B2 has the same intron/exon structure, but the two cultivars differ for the insertion of a 33-bp sequence located in the second intron of the cv. Svevo. Specific primers were designed in the polymorphic region and amplified in a recombinant inbred line mapping population. The study localized GS genes (GS2-A2, GS2-B2 GSe, GSr) on chromosomes 2A, 2B, 4A, and 4B, where four significant QTLs for GPC were also located.
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Affiliation(s)
- Agata Gadaleta
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola 165/A, Bari, Italy.
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Bordes J, Ravel C, Le Gouis J, Lapierre A, Charmet G, Balfourier F. Use of a global wheat core collection for association analysis of flour and dough quality traits. J Cereal Sci 2011. [DOI: 10.1016/j.jcs.2011.03.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Quraishi UM, Abrouk M, Murat F, Pont C, Foucrier S, Desmaizieres G, Confolent C, Rivière N, Charmet G, Paux E, Murigneux A, Guerreiro L, Lafarge S, Le Gouis J, Feuillet C, Salse J. Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:745-56. [PMID: 21251102 DOI: 10.1111/j.1365-313x.2010.04461.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements.
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Affiliation(s)
- Umar Masood Quraishi
- INRA/Université Blaise Pascal UMR 1095 GDEC, Domaine de Crouelle, 234 Avenue du Brézet, 63100 Clermont-Ferrand, France
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Swarbreck SM, Defoin-Platel M, Hindle M, Saqi M, Habash DZ. New perspectives on glutamine synthetase in grasses. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1511-22. [PMID: 21172814 DOI: 10.1093/jxb/erq356] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Members of the glutamine synthetase (GS) gene family have now been characterized in many crop species such as wheat, rice, and maize. Studies have shown that cytosolic GS isoforms are involved in nitrogen remobilization during leaf senescence and emphasized a role in seed production particularly in small grain crop species. Data from the sequencing of genomes for model crops and expressed sequence tag (EST) libraries from non-model species have strengthened the idea that the cytosolic GS genes are organized in three functionally and phylogenetically conserved subfamilies. Using a bioinformatic approach, the considerable publicly available information on high throughput gene expression was mined to search for genes having patterns of expression similar to GS. Interesting new hypotheses have emerged from searching for co-expressed genes across multiple unfiltered experimental data sets in rice. This approach should inform new experimental designs and studies to explore the regulation of the GS gene family further. It is expected that understanding the regulation of GS under varied climatic conditions will emerge as an important new area considering the results from recent studies that have shown nitrogen assimilation to be critical to plant acclimation to high CO(2) concentrations.
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Affiliation(s)
- Stéphanie M Swarbreck
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Masclaux-Daubresse C, Daniel-Vedele F, Dechorgnat J, Chardon F, Gaufichon L, Suzuki A. Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture. ANNALS OF BOTANY 2010; 105:1141-57. [PMID: 20299346 PMCID: PMC2887065 DOI: 10.1093/aob/mcq028] [Citation(s) in RCA: 675] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 11/13/2009] [Accepted: 12/17/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Productive agriculture needs a large amount of expensive nitrogenous fertilizers. Improving nitrogen use efficiency (NUE) of crop plants is thus of key importance. NUE definitions differ depending on whether plants are cultivated to produce biomass or grain yields. However, for most plant species, NUE mainly depends on how plants extract inorganic nitrogen from the soil, assimilate nitrate and ammonium, and recycle organic nitrogen. Efforts have been made to study the genetic basis as well as the biochemical and enzymatic mechanisms involved in nitrogen uptake, assimilation, and remobilization in crops and model plants. The detection of the limiting factors that could be manipulated to increase NUE is the major goal of such research. SCOPE An overall examination of the physiological, metabolic, and genetic aspects of nitrogen uptake, assimilation and remobilization is presented in this review. The enzymes and regulatory processes manipulated to improve NUE components are presented. Results obtained from natural variation and quantitative trait loci studies are also discussed. CONCLUSIONS This review presents the complexity of NUE and supports the idea that the integration of the numerous data coming from transcriptome studies, functional genomics, quantitative genetics, ecophysiology and soil science into explanatory models of whole-plant behaviour will be promising.
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