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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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Mini A, Touzy G, Beauchêne K, Cohan JP, Heumez E, Oury FX, Rincent R, Lafarge S, Le Gouis J. Genetic regions determine tolerance to nitrogen deficiency in European elite bread wheats grown under contrasting nitrogen stress scenarios. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:218. [PMID: 37815653 DOI: 10.1007/s00122-023-04468-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
KEY MESSAGE Clustering 24 environments in four contrasting nitrogen stress scenarios enabled the detection of genetic regions determining tolerance to nitrogen deficiency in European elite bread wheats. Increasing the nitrogen use efficiency of wheat varieties is an important goal for breeding. However, most genetic studies of wheat grown at different nitrogen levels in the field report significant interactions with the genotype. The chromosomal regions possibly involved in these interactions are largely unknown. The objective of this study was to quantify the response of elite bread wheat cultivars to different nitrogen field stress scenarios and identify genomic regions involved in this response. For this purpose, 212 elite bread wheat varieties were grown in a multi-environment trial at different nitrogen levels. Genomic regions associated with grain yield, protein concentration and grain protein deviation responses to nitrogen deficiency were identified. Environments were clustered according to adjusted means for grain yield, yield components and grain protein concentration. Four nitrogen availability scenarios were identified: optimal condition, moderate early deficiency, severe late deficiency, and severe continuous deficiency. A large range of tolerance to nitrogen deficiency was observed among varieties, which were ranked differently in different nitrogen deficiency scenarios. The well-known negative correlation between grain yield and grain protein concentration also existed between their respective tolerance indices. Interestingly, the tolerance indices for grain yield and grain protein deviation were either null or weakly positive meaning that breeding for the two traits should be less difficult than expected. Twenty-two QTL regions were identified for the tolerance indices. By selecting associated markers, these regions may be selected separately or combined to improve the tolerance to N deficiency within a breeding programme.
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Affiliation(s)
- Agathe Mini
- UMR GDEC, INRAE, Université Clermont Auvergne, 63100, Clermont-Ferrand, France
- Biogemma, Centre de Recherche de Chappes, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Gaëtan Touzy
- Biogemma, Centre de Recherche de Chappes, Route d'Ennezat CS90216, 63720, Chappes, France
- Arvalis-Institut du Végétal, 41240, Beauce la Romaine, France
| | - Katia Beauchêne
- Arvalis-Institut du Végétal, 41240, Beauce la Romaine, France
| | - Jean-Pierre Cohan
- Arvalis-Institut du Végétal, Station Expérimentale, 91190, Villiers le Bâcle, France
| | | | | | - Renaud Rincent
- UMR GDEC, INRAE, Université Clermont Auvergne, 63100, Clermont-Ferrand, France
| | - Stéphane Lafarge
- Biogemma, Centre de Recherche de Chappes, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Jacques Le Gouis
- UMR GDEC, INRAE, Université Clermont Auvergne, 63100, Clermont-Ferrand, France.
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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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Lisker A, Maurer A, Schmutzer T, Kazman E, Cöster H, Holzapfel J, Ebmeyer E, Alqudah AM, Sannemann W, Pillen K. A Haplotype-Based GWAS Identified Trait-Improving QTL Alleles Controlling Agronomic Traits under Contrasting Nitrogen Fertilization Treatments in the MAGIC Wheat Population WM-800. PLANTS (BASEL, SWITZERLAND) 2022; 11:3508. [PMID: 36559621 PMCID: PMC9784842 DOI: 10.3390/plants11243508] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/27/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The multi-parent-advanced-generation-intercross (MAGIC) population WM-800 was developed by intercrossing eight modern winter wheat cultivars to enhance the genetic diversity present in breeding populations. We cultivated WM-800 during two seasons in seven environments under two contrasting nitrogen fertilization treatments. WM-800 lines exhibited highly significant differences between treatments, as well as high heritabilities among the seven agronomic traits studied. The highest-yielding WM-line achieved an average yield increase of 4.40 dt/ha (5.2%) compared to the best founder cultivar Tobak. The subsequent genome-wide-association-study (GWAS), which was based on haplotypes, located QTL for seven agronomic traits including grain yield. In total, 40, 51, and 46 QTL were detected under low, high, and across nitrogen treatments, respectively. For example, the effect of QYLD_3A could be associated with the haplotype allele of cultivar Julius increasing yield by an average of 4.47 dt/ha (5.2%). A novel QTL on chromosome 2B exhibited pleiotropic effects, acting simultaneously on three-grain yield components (ears-per-square-meter, grains-per-ear, and thousand-grain-weight) and plant-height. These effects may be explained by a member of the nitrate-transporter-1 (NRT1)/peptide-family, TaNPF5.34, located 1.05 Mb apart. The WM-800 lines and favorable QTL haplotypes, associated with yield improvements, are currently implemented in wheat breeding programs to develop advanced nitrogen-use efficient wheat cultivars.
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Affiliation(s)
- Antonia Lisker
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Thomas Schmutzer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Ebrahim Kazman
- Syngenta Seeds GmbH, Kroppenstedter Str. 4, 39387 Oschersleben, Germany
| | | | - Josef Holzapfel
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg an der Isar, Germany
| | - Erhard Ebmeyer
- KWS Lochow GMBH, Ferdinand-Lochow-Str. 5, 29303 Bergen, Germany
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha P.O. Box 2713, Qatar
| | - Wiebke Sannemann
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
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Leonova IN, Kiseleva AA, Berezhnaya AA, Stasyuk AI, Likhenko IE, Salina EA. Identification of QTLs for Grain Protein Content in Russian Spring Wheat Varieties. PLANTS (BASEL, SWITZERLAND) 2022; 11:437. [PMID: 35161418 PMCID: PMC8840037 DOI: 10.3390/plants11030437] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Most modern breeding programs aim to develop wheat (T. aestivum L.) varieties with a high grain protein content (GPC) due to its greater milling and cooking quality, and improved grain price. Here, we used a genome-wide association study (GWAS) to map single nucleotide polymorphisms (SNPs) associated with GPC in 93 spring bread wheat varieties developed by eight Russian Breeding Centers. The varieties were evaluated for GPC, grain weight per spike (GWS), and thousand-kernel weight (TKW) at six environments, and genotyped with 9351 polymorphic SNPs and two SNPs associated with the NAM-A1 gene. GPC varied from 9.8 to 20.0%, depending on the genotype and environment. Nearly 52% of the genotypes had a GPC > 14.5%, which is the threshold value for entry into high-class wheat varieties. Broad-sense heritability for GPC was moderate (0.42), which is due to the significant effect of environment and genotype × environment interactions. GWAS performed on mean GPC evaluated across six environments identified eleven significant marker-trait associations, of which nine were physically mapped on chromosome 6A. Screening of wheat varieties for allelic variants of the NAM-A1 gene indicated that 60% of the varieties contained the NAM-A1c allele, followed by 33% for NAM-A1d, and 5% for NAM-A1a alleles. Varieties with the NAM-A1d allele showed significantly (p < 0.01) smaller GPC than those with NAM-A1c and NAM-A1a. However, no significant differences between NAM-A1 alleles were observed for both GWS and TKW.
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Affiliation(s)
- Irina N. Leonova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia; (A.A.K.); (A.A.B.); (A.I.S.); (E.A.S.)
| | - Antonina A. Kiseleva
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia; (A.A.K.); (A.A.B.); (A.I.S.); (E.A.S.)
| | - Alina A. Berezhnaya
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia; (A.A.K.); (A.A.B.); (A.I.S.); (E.A.S.)
| | - Anatoly I. Stasyuk
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia; (A.A.K.); (A.A.B.); (A.I.S.); (E.A.S.)
| | - Ivan E. Likhenko
- Siberian Research Institute of Plant Production and Breeding—Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630501 Krasnoobsk, Russia;
| | - Elena A. Salina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia; (A.A.K.); (A.A.B.); (A.I.S.); (E.A.S.)
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6
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Nurit E, Bordes J, Balfourier F, Paux E, Piquet A, Fossati D, Branlard G. Association between SNP Markers and 11 Vitamin Contents in Grains of a Worldwide Bread Wheat Core Collection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4307-4318. [PMID: 33784092 DOI: 10.1021/acs.jafc.0c07763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The metabolomic profiling analyses of 11 vitamins' statuses of wheat grain in a subsample of 167 accessions from the INRAE worldwide bread wheat core collection planted in two contrasting environments in France (Le Moulon and Clermont-Ferrand) have been evaluated using a high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS) procedure. This has allowed us to perform a genome-wide association study (GWAS) for these nutritional traits of interest combining the phenotypic data with the genotypic data derived from the TaBW280K SNP chip. Considering both thresholds (P < 0.0003 and R2 ≥ 8%), the GWAS identified between 1 and 22 marker-trait associations (MTAs) for the individual vitamins at the individual locations, and 12 SNP markers were stable and associated with vitamin contents across two environments. Desirable alleles and superior genotypes identified in the current analysis provide novel genetic data that can be used for future research on the genetics of vitamins and their application in wheat breeding.
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Affiliation(s)
- Eric Nurit
- INRAE, UCA UMR 1095 GDEC, 5 Chemin de Beaulieu, 63100 Clermont-Ferrand, France
| | - Jacques Bordes
- INRAE, UCA UMR 1095 GDEC, 5 Chemin de Beaulieu, 63100 Clermont-Ferrand, France
| | - François Balfourier
- INRAE, UCA UMR 1095 GDEC, 5 Chemin de Beaulieu, 63100 Clermont-Ferrand, France
| | - Etienne Paux
- INRAE, UCA UMR 1095 GDEC, 5 Chemin de Beaulieu, 63100 Clermont-Ferrand, France
| | - Agnès Piquet
- Vetagro Sup, Campus Agronomique de Clermont, 89 Avenue de l'Europe, BP35, F-63370 Lempdes, France
| | - Dario Fossati
- Agroscope, Route de Duillier 50, 1260 Nyon, Switzerland
| | - Gérard Branlard
- INRAE, UCA UMR 1095 GDEC, 5 Chemin de Beaulieu, 63100 Clermont-Ferrand, France
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7
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Nitrogen Losses and Potential Mitigation Strategies for a Sustainable Agroecosystem. SUSTAINABILITY 2021. [DOI: 10.3390/su13042400] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) in the agricultural production system influences many aspects of agroecosystems and several critical ecosystem services widely depend on the N availability in the soil. Cumulative changes in regional ecosystem services may lead to global environmental changes. Thus, the soil N status in agriculture is of critical importance to strategize its most efficient use. Nitrogen is also one of the most susceptible macronutrients to environmental loss, such as ammonia volatilization (NH3), nitrous oxide (N2O) emissions, nitrate leaching (NO3), etc. Any form of N losses from agricultural systems can be major limitations for crop production, soil sustainability, and environmental safeguard. There is a need to focus on mitigation strategies to minimize global N pollution and implement agricultural management practices that encourage regenerative and sustainable agriculture. In this review, we identified the avenues of N loss into the environment caused by current agronomic practices and discussed the potential practices that can be adapted to prevent this N loss in production agriculture. This review also explored the N status in agriculture during the COVID-19 pandemic and the existing knowledge gaps and questions that need to be addressed.
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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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Shokat S, Sehgal D, Vikram P, Liu F, Singh S. Molecular Markers Associated with Agro-Physiological Traits under Terminal Drought Conditions in Bread Wheat. Int J Mol Sci 2020; 21:E3156. [PMID: 32365765 PMCID: PMC7247584 DOI: 10.3390/ijms21093156] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/19/2020] [Accepted: 04/28/2020] [Indexed: 11/25/2022] Open
Abstract
Terminal drought stress poses a big challenge to sustain wheat grain production in rain-fed environments. This study aimed to utilize the genetically diverse pre-breeding lines for identification of genomic regions associated with agro-physiological traits at terminal stage drought stress in wheat. A total of 339 pre-breeding lines panel derived from three-way crosses of 'exotics × elite × elite' lines were evaluated in field conditions at Obregon, Mexico for two years under well irrigated as well as drought stress environments. Drought stress was imposed at flowering by skipping the irrigations at pre and post anthesis stage. Results revealed that drought significantly reduced grain yield (Y), spike length (SL), number of grains spikes-1 (NGS) and thousand kernel weight (TKW), while kernel abortion (KA) was increased. Population structure analysis in this panel uncovered three sub-populations. Genome wide linkage disequilibrium (LD) decay was observed at 2.5 centimorgan (cM). The haplotypes-based genome wide association study (GWAS) identified significant associations of Y, SL, and TKW on three chromosomes; 4A (HB10.7), 2D (HB6.10) and 3B (HB8.12), respectively. Likewise, associations on chromosomes 6B (HB17.1) and 3A (HB7.11) were found for NGS while on chromosome 3A (HB7.12) for KA. The genomic analysis information generated in the study can be efficiently utilized to improve Y and/or related parameters under terminal stage drought stress through marker-assisted breeding.
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Affiliation(s)
- Sajid Shokat
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark;
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad 38000, Pakistan
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Centre (CIMMYT) km, 45, Carretera Mex-Veracruz, El-Batan, Texcoco CP 56237, Mexico;
| | - Prashant Vikram
- International Potato Center, NASC Complex, Pusa, New Delhi 110012, India;
| | - Fulai Liu
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 13, 2630 Taastrup, Denmark;
| | - Sukhwinder Singh
- International Maize and Wheat Improvement Centre (CIMMYT) km, 45, Carretera Mex-Veracruz, El-Batan, Texcoco CP 56237, Mexico;
- Geneshifters, 222 Mary Jena Lane, Pullman, WA 99163, USA
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10
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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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Li Q, Pan Z, Gao Y, Li T, Liang J, Zhang Z, Zhang H, Deng G, Long H, Yu M. Quantitative Trait Locus (QTLs) Mapping for Quality Traits of Wheat Based on High Density Genetic Map Combined With Bulked Segregant Analysis RNA-seq (BSR-Seq) Indicates That the Basic 7S Globulin Gene Is Related to Falling Number. FRONTIERS IN PLANT SCIENCE 2020; 11:600788. [PMID: 33424899 PMCID: PMC7793810 DOI: 10.3389/fpls.2020.600788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/11/2020] [Indexed: 05/14/2023]
Abstract
Numerous quantitative trait loci (QTLs) have been identified for wheat quality; however, most are confined to low-density genetic maps. In this study, based on specific-locus amplified fragment sequencing (SLAF-seq), a high-density genetic map was constructed with 193 recombinant inbred lines derived from Chuanmai 42 and Chuanmai 39. In total, 30 QTLs with phenotypic variance explained (PVE) up to 47.99% were identified for falling number (FN), grain protein content (GPC), grain hardness (GH), and starch pasting properties across three environments. Five NAM genes closely adjacent to QGPC.cib-4A probably have effects on GPC. QGH.cib-5D was the only one detected for GH with high PVE of 33.31-47.99% across the three environments and was assumed to be related to the nearest pina-D1 and pinb-D1genes. Three QTLs were identified for FN in at least two environments, of which QFN.cib-3D had relatively higher PVE of 16.58-25.74%. The positive effect of QFN.cib-3D for high FN was verified in a double-haploid population derived from Chuanmai 42 × Kechengmai 4. The combination of these QTLs has a considerable effect on increasing FN. The transcript levels of Basic 7S globulin and Basic 7S globulin 2 in QFN.cib-3D were significantly different between low FN and high FN bulks, as observed through bulk segregant RNA-seq (BSR). These QTLs and candidate genes based on the high-density genetic map would be beneficial for further understanding of the genetic mechanism of quality traits and molecular breeding of wheat.
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Affiliation(s)
- Qiao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- *Correspondence: Zhifen Pan, ; orcid.org/0000-0002-1692-5425
| | - Yuan Gao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zijin Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Rahimi Y, Bihamta MR, Taleei A, Alipour H, Ingvarsson PK. Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs. BMC PLANT BIOLOGY 2019; 19:541. [PMID: 31805861 PMCID: PMC6896361 DOI: 10.1186/s12870-019-2165-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/26/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Identification of loci for agronomic traits and characterization of their genetic architecture are crucial in marker-assisted selection (MAS). Genome-wide association studies (GWAS) have increasingly been used as potent tools in identifying marker-trait associations (MTAs). The introduction of new adaptive alleles in the diverse genetic backgrounds may help to improve grain yield of old or newly developed varieties of wheat to balance supply and demand throughout the world. Landraces collected from different climate zones can be an invaluable resource for such adaptive alleles. RESULTS GWAS was performed using a collection of 298 Iranian bread wheat varieties and landraces to explore the genetic basis of agronomic traits during 2016-2018 cropping seasons under normal (well-watered) and stressed (rain-fed) conditions. A high-quality genotyping by sequencing (GBS) dataset was obtained using either all original single nucleotide polymorphism (SNP, 10938 SNPs) or with additional imputation (46,862 SNPs) based on W7984 reference genome. The results confirm that the B genome carries the highest number of significant marker pairs in both varieties (49,880, 27.37%) and landraces (55,086, 28.99%). The strongest linkage disequilibrium (LD) between pairs of markers was observed on chromosome 2D (0.296). LD decay was lower in the D genome, compared to the A and B genomes. Association mapping under two tested environments yielded a total of 313 and 394 significant (-log10 P >3) MTAs for the original and imputed SNP data sets, respectively. Gene ontology results showed that 27 and 27.5% of MTAs of SNPs in the original set were located in protein-coding regions for well-watered and rain-fed conditions, respectively. While, for the imputed data set 22.6 and 16.6% of MTAs represented in protein-coding genes for the well-watered and rain-fed conditions, respectively. CONCLUSIONS Our finding suggests that Iranian bread wheat landraces harbor valuable alleles that are adaptive under drought stress conditions. MTAs located within coding genes can be utilized in genome-based breeding of new wheat varieties. Although imputation of missing data increased the number of MTAs, the fraction of these MTAs located in coding genes were decreased across the different sub-genomes.
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Affiliation(s)
- Yousef Rahimi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran.
| | - Alireza Taleei
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Hadi Alipour
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Abstract
Improving the end-use quality traits is one of the primary objectives in wheat breeding programs. In the current study, a population of 127 recombinant inbred lines (RILs) derived from a cross between Glenn (PI-639273) and Traverse (PI-642780) was developed and used to identify quantitative trait loci (QTL) for 16 end-use quality traits in wheat. The phenotyping of these 16 traits was performed in nine environments in North Dakota, USA. The genotyping for the RIL population was conducted using the wheat Illumina iSelect 90K SNP assay. A high-density genetic linkage map consisting of 7,963 SNP markers identified a total of 76 additive QTL (A-QTL) and 73 digenic epistatic QTL (DE-QTL) associated with these traits. Overall, 12 stable major A-QTL and three stable DE-QTL were identified for these traits, suggesting that both A-QTL and DE-QTL played an important role in controlling end-use quality traits in wheat. The most significant A-QTL (AQ.MMLPT.ndsu.1B) was detected on chromosome 1B for mixograph middle line peak time. The AQ.MMLPT.ndsu.1B A-QTL was located very close to the position of the Glu-B1 gene encoding for a subunit of high molecular weight glutenin and explained up to 24.43% of phenotypic variation for mixograph MID line peak time. A total of 23 co-localized QTL loci were detected, suggesting the possibility of the simultaneous improvement of the end-use quality traits through selection procedures in wheat breeding programs. Overall, the information provided in this study could be used in marker-assisted selection to increase selection efficiency and to improve the end-use quality in wheat.
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Nigro D, Gadaleta A, Mangini G, Colasuonno P, Marcotuli I, Giancaspro A, Giove SL, Simeone R, Blanco A. Candidate genes and genome-wide association study of grain protein content and protein deviation in durum wheat. PLANTA 2019; 249:1157-1175. [PMID: 30603787 DOI: 10.1007/s00425-018-03075-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/19/2018] [Indexed: 05/26/2023]
Abstract
Stable QTL for grain protein content co-migrating with nitrogen-related genes have been identified by the candidate genes and genome-wide association mapping approaches useful for marker-assisted selection. Grain protein content (GPC) is one of the most important quality traits in wheat, defining the nutritional and end-use properties and rheological characteristics. Over the years, a number of breeding programs have been developed aimed to improving GPC, most of them having been prevented by the negative correlation with grain yield. To overcome this issue, a collection of durum wheat germplasm was evaluated for both GPC and grain protein deviation (GPD) in seven field trials. Fourteen candidate genes involved in several processes related to nitrogen metabolism were precisely located on two high-density consensus maps of common and durum wheat, and six of them were found to be highly associated with both traits. The wheat collection was genotyped using the 90 K iSelect array, and 11 stable quantitative trait loci (QTL) for GPC were detected in at least three environments and the mean across environments by the genome-wide association mapping. Interestingly, seven QTL were co-migrating with N-related candidate genes. Four QTL were found to be significantly associated to increases of GPD, indicating that selecting for GPC could not affect final grain yield per spike. The combined approaches of candidate genes and genome-wide association mapping led to a better understanding of the genetic relationships between grain storage proteins and grain yield per spike, and provided useful information for marker-assisted selection programs.
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Affiliation(s)
- D Nigro
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - A Gadaleta
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy.
| | - G Mangini
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - P Colasuonno
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - I Marcotuli
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - A Giancaspro
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - S L Giove
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - R Simeone
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - A Blanco
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
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15
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Jiang L, Sun L, Ye M, Wang J, Wang Y, Bogard M, Lacaze X, Fournier A, Beauchêne K, Gouache D, Wu R. Functional mapping of N deficiency‐induced response in wheat yield‐component traits by implementing high‐throughput phenotyping. THE PLANT JOURNAL 2019; 97:1105-1119. [PMID: 30536457 DOI: 10.1111/tpj.14186] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/09/2018] [Accepted: 11/23/2018] [Indexed: 05/25/2023]
Affiliation(s)
- Libo Jiang
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing 100083 China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding National Engineering Research Center for Floriculture College of Landscape Architecture Beijing Forestry University Beijing 100083 China
| | - Meixia Ye
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing 100083 China
| | - Jing Wang
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing 100083 China
| | - Yaqun Wang
- Department of Biostatistics Rutgers University New Brunswick NJ 08901 USA
| | - Matthieu Bogard
- Arvalis Institut du Végétal 3‐5 Rue Joseph et Marie Hackin 75116 Paris France
| | - Xavier Lacaze
- Arvalis Institut du Végétal 3‐5 Rue Joseph et Marie Hackin 75116 Paris France
| | - Antoine Fournier
- Arvalis Institut du Végétal 3‐5 Rue Joseph et Marie Hackin 75116 Paris France
| | - Katia Beauchêne
- Arvalis Institut du Végétal 3‐5 Rue Joseph et Marie Hackin 75116 Paris France
| | - David Gouache
- Arvalis Institut du Végétal 3‐5 Rue Joseph et Marie Hackin 75116 Paris France
| | - Rongling Wu
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing 100083 China
- Center for Statistical Genetics Departments of Public Health Sciences and Statistics Pennsylvania State University Hershey PA 17033 USA
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16
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Xiong H, Guo H, Zhou C, Guo X, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Liu L. A combined association mapping and t-test analysis of SNP loci and candidate genes involving in resistance to low nitrogen traits by a wheat mutant population. PLoS One 2019; 14:e0211492. [PMID: 30699181 PMCID: PMC6353201 DOI: 10.1371/journal.pone.0211492] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/15/2019] [Indexed: 11/19/2022] Open
Abstract
Crop productivity is highly dependent on the application of N fertilizers, but ever-increasing N application is causing serious environmental impacts. To facilitate the development of new wheat cultivars that can thrive in low N growth conditions, key loci and genes associated with wheat responses to low N must be identified. In this GWAS and t-test study of 190 M6 mutant wheat lines (Jing 411-derived) based on genotype data from the wheat 660k SNP array, we identified a total of 221 significant SNPs associated four seedling phenotypic traits that have been implicated in resistance to low N: relative root length, relative shoot length, relative root weight, and relative shoot weight. Notably, we detected large numbers of significantly associated SNP in what appear to be genomic 'hotspots' for resistance to low N on chromosomes 2A and 6B, strongly suggesting that these regions are functionally related to the resistance phenotypes that we observed in some of the mutant lines. Moreover, the candidate genes, including genes encoding high-affinity nitrate transporter 2.1, gibberellin responsive protein, were identified for resistance to low N. This study raises plausible mechanistic hypotheses that can be evaluated in future applied or basic efforts by breeders or plant biologists seeking to develop new high-NUE wheat cultivars.
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Affiliation(s)
- Hongchun Xiong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Chunyun Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Xiaotong Guo
- College of Agriculture, Ludong University, Yantai, China
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Jiayu Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Shirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Yuping Ding
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
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17
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Yu Z, Islam S, She M, Diepeveen D, Zhang Y, Tang G, Zhang J, Juhasz A, Yang R, Ma W. Wheat grain protein accumulation and polymerization mechanisms driven by nitrogen fertilization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1160-1177. [PMID: 30230644 DOI: 10.1111/tpj.14096] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 05/09/2023]
Abstract
In wheat (Triticum aestivum) grain yield and grain protein content are negatively correlated, making the simultaneous increase of the two traits challenging. Apart from genetic approaches, modification of nitrogen fertilization offers a feasible option to achieve this aim. In this study, a range of traits related to nitrogen-use efficiency in six Australian bread wheat varieties were investigated under different nitrogen treatments using 3-year multisite field trials. Changes in the individual storage protein composition were detected by high-performance liquid chromatography. Our results indicated that wheat grain yield and grain protein content reacted similarly to nitrogen availability, with grain yield being slightly more sensitive than grain protein content, and that genotype is a vital determinant of grain protein yield. Measurement of the glutamine synthetase activity of flag leaves and developing grains revealed that high nitrogen availability prompted the participation of glutamine in biological processes. In addition, a more significant accumulation of gluten macropolymer was observed under the high-nitrogen treatment from 21 days post-anthesis, and the underlying mechanism was elucidated by a comparative proteomics study. A yeast two-hybrid experiment confirmed this mechanism. The results of this study revealed that peptidyl-prolyl cis-trans isomerase (PPIase) was SUMOylated with the assistance of small ubiquitin-related modifier 1 and that high nitrogen availability facilitated this connection for the subsequent protein polymerization. Additionally, luminal-binding protein 2 in the endoplasmic reticulum played a similar role to PPIase in the aggregation of protein under high-nitrogen conditions.
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Affiliation(s)
- Zitong Yu
- State Agricultural Biotechnology Centre, School of Veterinary and Life Science, Murdoch University, Perth, WA, 6150, Australia
- Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, WA, 6150, Australia
| | - Shahidul Islam
- State Agricultural Biotechnology Centre, School of Veterinary and Life Science, Murdoch University, Perth, WA, 6150, Australia
- Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, WA, 6150, Australia
| | - Maoyun She
- State Agricultural Biotechnology Centre, School of Veterinary and Life Science, Murdoch University, Perth, WA, 6150, Australia
- Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, WA, 6150, Australia
| | - Dean Diepeveen
- State Agricultural Biotechnology Centre, School of Veterinary and Life Science, Murdoch University, Perth, WA, 6150, Australia
- Western Australian Department of Agriculture and Food, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Yujuan Zhang
- State Agricultural Biotechnology Centre, School of Veterinary and Life Science, Murdoch University, Perth, WA, 6150, Australia
| | - Guixiang Tang
- State Agricultural Biotechnology Centre, School of Veterinary and Life Science, Murdoch University, Perth, WA, 6150, Australia
- Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, WA, 6150, Australia
| | - Jingjuan Zhang
- State Agricultural Biotechnology Centre, School of Veterinary and Life Science, Murdoch University, Perth, WA, 6150, Australia
- Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, WA, 6150, Australia
| | - Angela Juhasz
- State Agricultural Biotechnology Centre, School of Veterinary and Life Science, Murdoch University, Perth, WA, 6150, Australia
- Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, WA, 6150, Australia
| | - Rongchang Yang
- State Agricultural Biotechnology Centre, School of Veterinary and Life Science, Murdoch University, Perth, WA, 6150, Australia
- Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, WA, 6150, Australia
| | - Wujun Ma
- State Agricultural Biotechnology Centre, School of Veterinary and Life Science, Murdoch University, Perth, WA, 6150, Australia
- Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, WA, 6150, Australia
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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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Ovenden B, Milgate A, Wade LJ, Rebetzke GJ, Holland JB. Genome-Wide Associations for Water-Soluble Carbohydrate Concentration and Relative Maturity in Wheat Using SNP and DArT Marker Arrays. G3 (BETHESDA, MD.) 2017; 7:2821-2830. [PMID: 28655739 PMCID: PMC5555485 DOI: 10.1534/g3.117.039842] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/25/2017] [Indexed: 11/18/2022]
Abstract
Improving water-use efficiency by incorporating drought avoidance traits into new wheat varieties is an important objective for wheat breeding in water-limited environments. This study uses genome wide association studies (GWAS) to identify candidate loci for water-soluble carbohydrate accumulation-an important drought-avoidance characteristic in wheat. Phenotypes from a multi-environment trial with experiments differing in water availability and separate single nucleotide polymorphism (SNP) and diversity arrays technology (DArT) marker sets were used to perform the analyses. Significant associations for water-soluble carbohydrate accumulation were identified on chromosomes 1A, 1B, 1D, 2D, and 4A. Notably, these loci did not collocate with the major loci identified for relative maturity. Loci on chromosome 1D collocated with markers previously associated with the high molecular weight glutenin Glu-D1 locus. Genetic × environmental interactions impacted the results strongly, with significant associations for carbohydrate accumulation identified only in the water-deficit experiments. The markers associated with carbohydrate accumulation may be useful for marker-assisted selection of drought tolerance in wheat.
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Affiliation(s)
- Ben Ovenden
- New South Wales Department of Primary Industries, Yanco Agricultural Institute, New South Wales 2703, Australia
| | - Andrew Milgate
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, New South Wales 2650, Australia
| | - Len J Wade
- Charles Sturt University, Graham Centre, Wagga Wagga, New South Wales 2678, Australia
| | - Greg J Rebetzke
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
| | - James B Holland
- Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, North Carolina State University, Raleigh, North Carolina 27695-7620
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695-7620
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Lin Y, Liu S, Liu Y, Liu Y, Chen G, Xu J, Deng M, Jiang Q, Wei Y, Lu Y, Zheng Y. Genome-wide association study of pre-harvest sprouting resistance in Chinese wheat founder parents. Genet Mol Biol 2017; 40:620-629. [PMID: 28696481 PMCID: PMC5596365 DOI: 10.1590/1678-4685-gmb-2016-0207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 02/28/2017] [Indexed: 12/23/2022] Open
Abstract
Pre-harvest sprouting (PHS) is a major abiotic factor affecting grain weight and
quality, and is caused by an early break in seed dormancy. Association mapping (AM)
is used to detect correlations between phenotypes and genotypes based on linkage
disequilibrium (LD) in wheat breeding programs. We evaluated seed dormancy in 80
Chinese wheat founder parents in five environments and performed a genome-wide
association study using 6,057 markers, including 93 simple sequence repeat (SSR),
1,472 diversity array technology (DArT), and 4,492 single nucleotide polymorphism
(SNP) markers. The general linear model (GLM) and the mixed linear model (MLM) were
used in this study, and two significant markers (tPt-7980 and
wPt-6457) were identified. Both markers were located on
Chromosome 1B, with wPt-6457 having been identified in a previously
reported chromosomal position. The significantly associated loci contain essential
information for cloning genes related to resistance to PHS and can be used in wheat
breeding programs.
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Affiliation(s)
- Yu Lin
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Shihang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yujiao Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
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21
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Sehgal D, Autrique E, Singh R, Ellis M, Singh S, Dreisigacker S. Identification of genomic regions for grain yield and yield stability and their epistatic interactions. Sci Rep 2017; 7:41578. [PMID: 28145508 PMCID: PMC5286416 DOI: 10.1038/srep41578] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/21/2016] [Indexed: 12/04/2022] Open
Abstract
The task of identifying genomic regions conferring yield stability is challenging in any crop and requires large experimental data sets in conjunction with complex analytical approaches. We report findings of a first attempt to identify genomic regions with stable expression and their individual epistatic interactions for grain yield and yield stability in a large elite panel of wheat under multiple environments via a genome wide association mapping (GWAM) approach. Seven hundred and twenty lines were genotyped using genotyping-by-sequencing technology and phenotyped for grain yield and phenological traits. High gene diversity (0.250) and a moderate genetic structure (five groups) in the panel provided an excellent base for GWAM. The mixed linear model and multi-locus mixed model analyses identified key genomic regions on chromosomes 2B, 3A, 4A, 5B, 7A and 7B. Further, significant epistatic interactions were observed among loci with and without main effects that contributed to additional variation of up to 10%. Simple stepwise regression provided the most significant main effect and epistatic markers resulting in up to 20% variation for yield stability and up to 17% gain in yield with the best allelic combination.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Méx-Veracruz, El Batán, Texcoco, CP 56237, México
| | - Enrique Autrique
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Méx-Veracruz, El Batán, Texcoco, CP 56237, México
| | - Ravi Singh
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Méx-Veracruz, El Batán, Texcoco, CP 56237, México
| | - Marc Ellis
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Méx-Veracruz, El Batán, Texcoco, CP 56237, México
| | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Méx-Veracruz, El Batán, Texcoco, CP 56237, México
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Méx-Veracruz, El Batán, Texcoco, CP 56237, México
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22
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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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23
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Qin P, Lin Y, Hu Y, Liu K, Mao S, Li Z, Wang J, Liu Y, Wei Y, Zheng Y. Genome-wide association study of drought-related resistance traits in Aegilops tauschii. Genet Mol Biol 2016; 39:398-407. [PMID: 27560650 PMCID: PMC5004832 DOI: 10.1590/1678-4685-gmb-2015-0232] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/15/2015] [Indexed: 01/09/2023] Open
Abstract
The D-genome progenitor of wheat (Triticum aestivum), Aegilops tauschii, possesses numerous genes for resistance to abiotic stresses, including drought. Therefore, information on the genetic architecture of A. tauschii can aid the development of drought-resistant wheat varieties. Here, we evaluated 13 traits in 373 A. tauschii accessions grown under normal and polyethylene glycol-simulated drought stress conditions and performed a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers. We identified 208 and 28 SNPs associated with all traits using the general linear model and mixed linear model, respectively, while both models detected 25 significant SNPs with genome-wide distribution. Public database searches revealed several candidate/flanking genes related to drought resistance that were grouped into three categories according to the type of encoded protein (enzyme, storage protein, and drought-induced protein). This study provided essential information for SNPs and genes related to drought resistance in A. tauschii and wheat, and represents a foundation for breeding drought-resistant wheat cultivars using marker-assisted selection.
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Affiliation(s)
- Peng Qin
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Yu Lin
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Yaodong Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Kun Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Shuangshuang Mao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Zhanyi Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
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24
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Liu Y, Wang L, Deng M, Li Z, Lu Y, Wang J, Wei Y, Zheng Y. Genome-wide association study of phosphorus-deficiency-tolerance traits in Aegilops tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2203-12. [PMID: 26187748 DOI: 10.1007/s00122-015-2578-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/01/2015] [Indexed: 05/19/2023]
Abstract
Using GWAS, 13 significant SNPs distributed on six of the seven Aegilops tauschii chromosomes (all but 5D) were identified, and several candidate P-deficiency-responsive genes were proposed from searches of public databases. Aegilops tauschii, the wheat (Triticum aestivum) D-genome progenitor, possesses numerous genes for stress resistance, including genes for tolerance of phosphorus (P) deficiency. Investigation of the genetic architecture of A. tauschii will help in developing P-deficiency-tolerant varieties of wheat. We evaluated nine traits in a population of 380 A. tauschii specimens under conditions with and without P application, and we performed genome-wide association studies for these traits using single nucleotide polymorphism (SNP) chips containing 7185 markers. Using a general linear model, we identified 119 SNPs that were significantly associated with all nine traits, and a mixed linear model revealed 18 SNPs associated with all traits. Both models detected 13 significant markers distributed on six of the seven A. tauschii chromosomes (all but 5D). Searches of public databases revealed several candidate/flanking genes related to P-deficiency tolerance. These genes were grouped in five categories by the types of proteins they encoded: defense response proteins, enzymes, promoters and transcription factors, storage proteins, or proteins triggered by P deficiency. The identified SNPs and genes contain essential information for cloning genes related to P-deficiency tolerance in A. tauschii and wheat, and they provide a foundation for breeding P-deficiency tolerant wheat cultivars.
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Affiliation(s)
- Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Lang Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Zhanyi Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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25
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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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26
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Echeverry-Solarte M, Kumar A, Kianian S, Simsek S, Alamri MS, Mantovani EE, McClean PE, Deckard EL, Elias E, Schatz B, Xu SS, Mergoum M. New QTL alleles for quality-related traits in spring wheat revealed by RIL population derived from supernumerary × non-supernumerary spikelet genotypes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:893-912. [PMID: 25740563 DOI: 10.1007/s00122-015-2478-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 02/04/2015] [Indexed: 06/04/2023]
Abstract
A population developed from an exotic line with supernumerary spikelets was genetically dissected for eight quality traits, discovering new genes/alleles with potential use in wheat breeding programs. Identifying new QTLs and alleles in exotic germplasm is paramount for further improvement of quality traits in wheat. In the present study, an RIL population developed from a cross of an elite wheat line (WCB414) and an exotic genotype with supernumerary spikelets (SS) was used to identify QTLs and new alleles for eight quality traits. Composite interval mapping for 1,000 kernels weight (TKW), kernel volume weight (KVW), grain protein content (GPC), percent of flour extraction (FE) and four mixograph-related traits identified a total of 69 QTLs including 19 stable QTLs. These QTLs were located on 18 different chromosomes (except 4D, 5D, and 6D). Thirteen of these QTLs explained more than 15% of phenotypic variation (PV) and were considered as major QTLs. In this study, we identified 11 QTLs for TKW (R (2) = 7.2-17.1 %), 10 for KVW (R (2) = 6.7-22.5%), 11 for GPC (R (2) = 4.7-16.9%), 6 for FE (R (2) = 4.8-19%) and 31 for mixograph-related traits (R (2) = 3.2-41.2%). In this population, several previously identified QTLs for SS, nine spike-related and ten agronomic traits were co-located with the quality QTLs, suggesting pleiotropic effects or close linkage among loci. The traits GPC and mixogram-related traits were positively correlated with SS. Indeed, several loci for quality traits were co-located with QTL for SS. The exotic parent contributed positive alleles that increased PV of the traits at 56% of loci demonstrating the suitability of germplasm with SS to improve quality traits in wheat.
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27
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Jiang Y, Jiang Q, Hao C, Hou J, Wang L, Zhang H, Zhang S, Chen X, Zhang X. A yield-associated gene TaCWI, in wheat: its function, selection and evolution in global breeding revealed by haplotype analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:131-43. [PMID: 25367379 DOI: 10.1007/s00122-014-2417-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/11/2014] [Indexed: 05/18/2023]
Abstract
Wheat anther-specific invertase genes were haplotyped in wheat. Strong allelic selection occurred during wheat polyploidization, domestication and breeding because of their association with yield traits. Plant invertase hydrolyzes sucrose into glucose and fructose. Cell wall invertase (CWI), one of the three types of invertase, is essential for plant development. Based on isolated TaCWI genes from chromosomes 4A, 5B and 5D, two SNPs were detected in the promoter region of TaCWI-4A, and four SNPs and two Indels were present in the TaCWI-5D gene. No polymorphism was detected in TaCWI-5B coding or promoter regions. CAPS markers caps4A and caps5D were developed to discriminate haplotypes of TaCWI-4A and TaCWI-5D. Marker/trait association analysis indicated that Hap-5D-C at TaCWI-5D was significantly associated with higher thousand kernel weight (TKW) in 348 Chinese modern cultivars grown in multiple environments. Geographic distributions and changes over time of favored haplotypes showed that Hap-5D-C was the most frequent haplotype in modern cultivars and was strongly positively selected in six major wheat production regions worldwide. However, selection for haplotypes at TaCWI-4A was not so evident, possibly due to balancing effects of the two haplotypes on TKW and grain number per spike (GN). In rainfed production regions, Hap-4A-C was favored because it brought more seeds, but in well irrigated conditions, Hap-4A-T was favored in modern breeding because of higher TKW. Evolutionary analysis among wheat and its relatives showed that genetic diversity of TaCWI genes on chromosomes 4A and 5D declined dramatically in progression from the diploid level to modern polyploid cultivars. There was strong allelic selection during polyploidization, domestication and breeding.
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Affiliation(s)
- Yanmiao Jiang
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, China,
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28
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Ain QU, Rasheed A, Anwar A, Mahmood T, Imtiaz M, Mahmood T, Xia X, He Z, Quraishi UM. Genome-wide association for grain yield under rainfed conditions in historical wheat cultivars from Pakistan. FRONTIERS IN PLANT SCIENCE 2015; 6:743. [PMID: 26442056 PMCID: PMC4585131 DOI: 10.3389/fpls.2015.00743] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/31/2015] [Indexed: 05/18/2023]
Abstract
Genome-wide association studies (GWAS) were undertaken to identify SNP markers associated with yield and yield-related traits in 123 Pakistani historical wheat cultivars evaluated during 2011-2014 seasons under rainfed field conditions. The population was genotyped by using high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) assay, and finally 14,960 high quality SNPs were used in GWAS. Population structure examined using 1000 unlinked markers identified seven subpopulations (K = 7) that were representative of different breeding programs in Pakistan, in addition to local landraces. Forty four stable marker-trait associations (MTAs) with -log p > 4 were identified for nine yield-related traits. Nine multi-trait MTAs were found on chromosomes 1AL, 1BS, 2AL, 2BS, 2BL, 4BL, 5BL, 6AL, and 6BL, and those on 5BL and 6AL were stable across two seasons. Gene annotation and syntey identified that 14 trait-associated SNPs were linked to genes having significant importance in plant development. Favorable alleles for days to heading (DH), plant height (PH), thousand grain weight (TGW), and grain yield (GY) showed minor additive effects and their frequencies were slightly higher in cultivars released after 2000. However, no selection pressure on any favorable allele was identified. These genomic regions identified have historically contributed to achieve yield gains from 2.63 million tons in 1947 to 25.7 million tons in 2015. Future breeding strategies can be devised to initiate marker assisted breeding to accumulate these favorable alleles of SNPs associated with yield-related traits to increase grain yield. Additionally, in silico identification of 454-contigs corresponding to MTAs will facilitate fine mapping and subsequent cloning of candidate genes and functional marker development.
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Affiliation(s)
- Qurat-ul Ain
- Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam UniversityIslamabad, Pakistan
| | - Awais Rasheed
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center (CIMMYT), C/O Chinese Academy of Agricultural SciencesBeijing, China
| | - Alia Anwar
- Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam UniversityIslamabad, Pakistan
| | - Tariq Mahmood
- Higher Education Commission, Research and DevelopmentIslamabad, Pakistan
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT), C/O National Agriculture Research CenterIslamabad, Pakistan
| | - Tariq Mahmood
- Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam UniversityIslamabad, Pakistan
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center (CIMMYT), C/O Chinese Academy of Agricultural SciencesBeijing, China
| | - Umar M. Quraishi
- Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam UniversityIslamabad, Pakistan
- *Correspondence: Umar M. Quraishi, Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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29
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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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30
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Bogard M, Ravel C, Paux E, Bordes J, Balfourier F, Chapman SC, Le Gouis J, Allard V. Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5849-65. [PMID: 25148833 PMCID: PMC4203124 DOI: 10.1093/jxb/eru328] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Prediction of wheat phenology facilitates the selection of cultivars with specific adaptations to a particular environment. However, while QTL analysis for heading date can identify major genes controlling phenology, the results are limited to the environments and genotypes tested. Moreover, while ecophysiological models allow accurate predictions in new environments, they may require substantial phenotypic data to parameterize each genotype. Also, the model parameters are rarely related to all underlying genes, and all the possible allelic combinations that could be obtained by breeding cannot be tested with models. In this study, a QTL-based model is proposed to predict heading date in bread wheat (Triticum aestivum L.). Two parameters of an ecophysiological model (V sat and P base , representing genotype vernalization requirements and photoperiod sensitivity, respectively) were optimized for 210 genotypes grown in 10 contrasting location × sowing date combinations. Multiple linear regression models predicting V sat and P base with 11 and 12 associated genetic markers accounted for 71 and 68% of the variance of these parameters, respectively. QTL-based V sat and P base estimates were able to predict heading date of an independent validation data set (88 genotypes in six location × sowing date combinations) with a root mean square error of prediction of 5 to 8.6 days, explaining 48 to 63% of the variation for heading date. The QTL-based model proposed in this study may be used for agronomic purposes and to assist breeders in suggesting locally adapted ideotypes for wheat phenology.
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Affiliation(s)
- Matthieu Bogard
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Catherine Ravel
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Etienne Paux
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Jacques Bordes
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - François Balfourier
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Scott C Chapman
- CSIRO, Queensland Bioscience Precinct - St Lucia, 306 Carmody Road, St Lucia QLD 4067, Australia
| | - Jacques Le Gouis
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Vincent Allard
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
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Charmet G, Storlie E, Oury FX, Laurent V, Beghin D, Chevarin L, Lapierre A, Perretant MR, Rolland B, Heumez E, Duchalais L, Goudemand E, Bordes J, Robert O. Genome-wide prediction of three important traits in bread wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014. [PMID: 26316839 DOI: 10.1007/s11032‐014‐0143‐y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Five genomic prediction models were applied to three wheat agronomic traits-grain yield, heading date and grain test weight-in three breeding populations, each comprising about 350 doubled haploid or recombinant inbred lines evaluated in three locations during a 3-year period. The prediction accuracy, measured as the correlation between genomic estimated breeding value and observed trait, was in the range of previously published values for yield (r = 0.2-0.5), a trait with relatively low heritability. Accuracies for heading date and test weight, with relatively high heritabilities, were about 0.70. There was no improvement of prediction accuracy when two or three breeding populations were merged into one for a larger training set (e.g., for yield r ranged between 0.11 and 0.40 in the respective populations and between 0.18 and 0.35 in the merged populations). Cross-population prediction, when one population was used as the training population set and another population was used as the validation set, resulted in no prediction accuracy. This lack of cross-population prediction accuracy cannot be explained by a lower level of relatedness between populations, as measured by a shared SNP similarity, since it was only slightly lower between than within populations. Simulation studies confirm that cross-prediction accuracy decreases as the proportion of shared QTLs decreases, which can be expected from a higher level of QTL × environment interactions.
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Affiliation(s)
- Gilles Charmet
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Eric Storlie
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France ; Colorado State University, Fort Collins, CO 80523 USA
| | - François Xavier Oury
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Valérie Laurent
- Bioplante-Florimond Desprez, BP41, 59242 Cappelle en Pévèle, France
| | - Denis Beghin
- Bioplante-Florimond Desprez, BP41, 59242 Cappelle en Pévèle, France
| | - Laetitia Chevarin
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Annie Lapierre
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Marie Reine Perretant
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Bernard Rolland
- INRA-APBV, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France
| | - Emmanuel Heumez
- INRA UE Lille, 2 chaussée Brunehaut, Estrées-Mons, BP 50136, 80203 Peronne Cedex, France
| | - Laure Duchalais
- Bioplante-R2n, 60 rue Léon Beauchamp, 59930 La Chapelle d'Armentières, France
| | - Ellen Goudemand
- Bioplante-Florimond Desprez, BP41, 59242 Cappelle en Pévèle, France
| | - Jacques Bordes
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Olivier Robert
- Bioplante-Florimond Desprez, BP41, 59242 Cappelle en Pévèle, France
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32
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Charmet G, Storlie E, Oury FX, Laurent V, Beghin D, Chevarin L, Lapierre A, Perretant MR, Rolland B, Heumez E, Duchalais L, Goudemand E, Bordes J, Robert O. Genome-wide prediction of three important traits in bread wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 34:1843-1852. [PMID: 26316839 PMCID: PMC4544631 DOI: 10.1007/s11032-014-0143-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 06/30/2014] [Indexed: 05/19/2023]
Abstract
Five genomic prediction models were applied to three wheat agronomic traits-grain yield, heading date and grain test weight-in three breeding populations, each comprising about 350 doubled haploid or recombinant inbred lines evaluated in three locations during a 3-year period. The prediction accuracy, measured as the correlation between genomic estimated breeding value and observed trait, was in the range of previously published values for yield (r = 0.2-0.5), a trait with relatively low heritability. Accuracies for heading date and test weight, with relatively high heritabilities, were about 0.70. There was no improvement of prediction accuracy when two or three breeding populations were merged into one for a larger training set (e.g., for yield r ranged between 0.11 and 0.40 in the respective populations and between 0.18 and 0.35 in the merged populations). Cross-population prediction, when one population was used as the training population set and another population was used as the validation set, resulted in no prediction accuracy. This lack of cross-population prediction accuracy cannot be explained by a lower level of relatedness between populations, as measured by a shared SNP similarity, since it was only slightly lower between than within populations. Simulation studies confirm that cross-prediction accuracy decreases as the proportion of shared QTLs decreases, which can be expected from a higher level of QTL × environment interactions.
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Affiliation(s)
- Gilles Charmet
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Eric Storlie
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
- Colorado State University, Fort Collins, CO 80523 USA
| | - François Xavier Oury
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Valérie Laurent
- Bioplante-Florimond Desprez, BP41, 59242 Cappelle en Pévèle, France
| | - Denis Beghin
- Bioplante-Florimond Desprez, BP41, 59242 Cappelle en Pévèle, France
| | - Laetitia Chevarin
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Annie Lapierre
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Marie Reine Perretant
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Bernard Rolland
- INRA-APBV, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France
| | - Emmanuel Heumez
- INRA UE Lille, 2 chaussée Brunehaut, Estrées-Mons, BP 50136, 80203 Peronne Cedex, France
| | - Laure Duchalais
- Bioplante-R2n, 60 rue Léon Beauchamp, 59930 La Chapelle d’Armentières, France
| | - Ellen Goudemand
- Bioplante-Florimond Desprez, BP41, 59242 Cappelle en Pévèle, France
| | - Jacques Bordes
- UMR GDEC, INRA-Université Clermont II, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex, France
| | - Olivier Robert
- Bioplante-Florimond Desprez, BP41, 59242 Cappelle en Pévèle, France
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Cormier F, Faure S, Dubreuil P, Heumez E, Beauchêne K, Lafarge S, Praud S, Le Gouis J. A multi-environmental study of recent breeding progress on nitrogen use efficiency in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:3035-48. [PMID: 24057081 DOI: 10.1007/s00122-013-2191-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/06/2013] [Indexed: 05/19/2023]
Abstract
By comparing 195 varieties in eight trials, this study assesses nitrogen use efficiency improvement in high and low nitrogen conditions in European winter wheat over the last 25 years. In a context where European agriculture practices have to deal with environmental concerns and nitrogen (N) fertiliser cost, nitrogen use efficiency (NUE) has to be improved. This study assessed genetic progress in winter wheat (Triticum aestivum L.) NUE. Two hundred and twenty-five European elite varieties were tested in four environments under two levels of N. Global genetic progress was assessed on additive genetic values and on genotype × N interaction, covering 25 years of European breeding. To avoid sampling bias, quality, precocity and plant height were added as covariates in the analyses when needed. Genotype × environment interactions were highly significant for all the traits studied to such an extent that no additive genetic effect was detected on N uptake. Genotype × N interactions were significant for yield, grain protein content (GPC), N concentration in straw, N utilisation, and NUE. Grain yield improvement (+0.45 % year(-1)) was independent of the N treatment. GPC was stable, thus grain nitrogen yield was improved (+0.39 % year(-1)). Genetic progress on N harvest index (+0.12 % year(-1)) and on N concentration in straw (-0.52 % year(-1)) possibly revealed improvement in N remobilisation. There has been an improvement of NUE additive genetic value (+0.33 % year(-1)) linked to better N utilisation (+0.20 % year(-1)). Improved yield stability was detected as a significant improvement of NUE in low compared to high N conditions. The application of these results to breeding programs is discussed.
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Affiliation(s)
- Fabien Cormier
- Biogemma, Centre de recherche de Chappes, Route d'Ennezat CS90126, 63720, Chappes, France
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Establishing an efficient way to utilize the drought resistance germplasm population in wheat. ScientificWorldJournal 2013; 2013:489583. [PMID: 23737717 PMCID: PMC3662154 DOI: 10.1155/2013/489583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 04/10/2013] [Indexed: 11/25/2022] Open
Abstract
Drought resistance breeding provides a hopeful way to improve yield and quality of wheat in arid and semiarid regions. Constructing core collection is an efficient way to evaluate and utilize drought-resistant germplasm resources in wheat. In the present research, 1,683 wheat varieties were divided into five germplasm groups (high resistant, HR; resistant, R; moderate resistant, MR; susceptible, S; and high susceptible, HS). The least distance stepwise sampling (LDSS) method was adopted to select core accessions. Six commonly used genetic distances (Euclidean distance, Euclid; Standardized Euclidean distance, Seuclid; Mahalanobis distance, Mahal; Manhattan distance, Manhat; Cosine distance, Cosine; and Correlation distance, Correlation) were used to assess genetic distances among accessions. Unweighted pair-group average (UPGMA) method was used to perform hierarchical cluster analysis. Coincidence rate of range (CR) and variable rate of coefficient of variation (VR) were adopted to evaluate the representativeness of the core collection. A method for selecting the ideal constructing strategy was suggested in the present research. A wheat core collection for the drought resistance breeding programs was constructed by the strategy selected in the present research. The principal component analysis showed that the genetic diversity was well preserved in that core collection.
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