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Noor MMA, Tahjib-Ul-Arif M, Alim SMA, Islam MM, Hasan MT, Babar MA, Hossain MA, Jewel ZA, Murata Y, Mostofa MG. Lentil adaptation to drought stress: response, tolerance, and breeding approaches. FRONTIERS IN PLANT SCIENCE 2024; 15:1403922. [PMID: 39228838 PMCID: PMC11368723 DOI: 10.3389/fpls.2024.1403922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 07/05/2024] [Indexed: 09/05/2024]
Abstract
Lentil (Lens culinaris Medik.) is a cool season legume crop that plays vital roles in food and nutritional security, mostly in the least developed countries. Lentil is often cultivated in dry and semi-dry regions, where the primary abiotic factor is drought, which negatively impacts lentil growth and development, resulting in a reduction of yield. To withstand drought-induced multiple negative effects, lentil plants evolved a variety of adaptation strategies that can be classified within three broad categories of drought tolerance mechanisms (i.e., escape, avoidance, and tolerance). Lentil adapts to drought by the modulation of various traits in the root system, leaf architecture, canopy structure, branching, anatomical features, and flowering process. Furthermore, the activation of certain defensive biochemical pathways as well as the regulation of gene functions contributes to lentil drought tolerance. Plant breeders typically employ conventional and mutational breeding approaches to develop lentil varieties that can withstand drought effects; however, little progress has been made in developing drought-tolerant lentil varieties using genomics-assisted technologies. This review highlights the current understanding of morpho-physiological, biochemical, and molecular mechanisms of lentil adaptation to drought stress. We also discuss the potential application of omics-assisted breeding approaches to develop lentil varieties with superior drought tolerance traits.
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Affiliation(s)
- Md. Mahmud Al Noor
- Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture, Mymensingh, Bangladesh
| | - Md. Tahjib-Ul-Arif
- Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, Japan
| | - S. M. Abdul Alim
- Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture, Mymensingh, Bangladesh
| | - Md. Mohimenul Islam
- Horticulture Division, Bangladesh Institute of Nuclear Agriculture, Mymensingh, Bangladesh
| | - Md. Toufiq Hasan
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Ali Babar
- Agronomy Departments, University of Florida, Gainesville, FL, United States
| | - Mohammad Anwar Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Zilhas Ahmed Jewel
- Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Yoshiyuki Murata
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, Japan
| | - Mohammad Golam Mostofa
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
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Haelterman L, Louvieaux J, Chiodi C, Bouchet AS, Kupcsik L, Stahl A, Rousseau-Gueutin M, Snowdon R, Laperche A, Nesi N, Hermans C. Genetic control of root morphology in response to nitrogen across rapeseed diversity. PHYSIOLOGIA PLANTARUM 2024; 176:e14315. [PMID: 38693794 DOI: 10.1111/ppl.14315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 05/03/2024]
Abstract
Rapeseed (Brassica napus L.) is an oil-containing crop of great economic value but with considerable nitrogen requirement. Breeding root systems that efficiently absorb nitrogen from the soil could be a driver to ensure genetic gains for more sustainable rapeseed production. The aim of this study is to identify genomic regions that regulate root morphology in response to nitrate availability. The natural variability offered by 300 inbred lines was screened at two experimental locations. Seedlings grew hydroponically with low or elevated nitrate levels. Fifteen traits related to biomass production and root morphology were measured. On average across the panel, a low nitrate level increased the root-to-shoot biomass ratio and the lateral root length. A large phenotypic variation was observed, along with important heritability values and genotypic effects, but low genotype-by-nitrogen interactions. Genome-wide association study and bulk segregant analysis were used to identify loci regulating phenotypic traits. The first approach nominated 319 SNPs that were combined into 80 QTLs. Three QTLs identified on the A07 and C07 chromosomes were stable across nitrate levels and/or experimental locations. The second approach involved genotyping two groups of individuals from an experimental F2 population created by crossing two accessions with contrasting lateral root lengths. These individuals were found in the tails of the phenotypic distribution. Co-localized QTLs found in both mapping approaches covered a chromosomal region on the A06 chromosome. The QTL regions contained some genes putatively involved in root organogenesis and represent selection targets for redesigning the root morphology of rapeseed.
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Affiliation(s)
- Loïc Haelterman
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Julien Louvieaux
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
- Laboratory of Applied Plant Ecophysiology, Haute Ecole Provinciale de Hainaut Condorcet, Centre pour l'Agronomie et l'Agro-industrie de la Province de Hainaut (CARAH), Belgium
| | - Claudia Chiodi
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Anne-Sophie Bouchet
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Laszlo Kupcsik
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Andreas Stahl
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Mathieu Rousseau-Gueutin
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Rod Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Germany
| | - Anne Laperche
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Nathalie Nesi
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Christian Hermans
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
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Biradar SS, Patil MK, Desai SA, Singh SK, Naik VR, Lamani K, Joshi AK. Nitrogen use efficiency in bread wheat: Genetic variation and prospects for improvement. PLoS One 2024; 19:e0294755. [PMID: 38598487 PMCID: PMC11006162 DOI: 10.1371/journal.pone.0294755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/08/2023] [Indexed: 04/12/2024] Open
Abstract
Nitrogen (N) is one of the primary macronutrients required for crop growth and yield. This nutrient is especially limiting wheat yields in the dry and low fertile agro-ecologies having low N in the root zone soil strata. Moreover, majority of farmers in India and South Asia are small to marginal with meagre capacity to invest in costly nitrogen fertilizers. Therefore, there is an immense need to identify lines that use nitrogen efficiently. A set of 50 diverse wheat genotypes consisting of indigenous germplasm lines (05), cultivars released for commercial cultivation (23) and selected elite lines from CIMMYT nurseries (22) were evaluated in an alpha-lattice design with two replications, a six-rowed plot of 2.5m length for 24 agro morphological, physiological and NUE related traits during two consecutive crop seasons in an N-depleted precision field under two different N levels of 50%-N50 (T1) and 100%-N100 (T2) of recommended N, i.e., 100 kg/ha. Analysis of variance revealed significant genetic variation among genotypes for all the traits studied. About 11.36% yield reduction was observed at reduced N levels. Significant correlations among NUE traits and yield component traits were observed which indicated pivotal role of N remobilization to the grain in enhancing yield levels. Among N-insensitive genotypes identified based on their yielding ability at low N levels, UASBW13356, UASBW13358, UASBW13354, UASBW13357 and KRL1-4 showed their inherent genotypic plasticity toward N application. The genotypes with more yield and high to moderate NUtE can be used as parents for the breeding of N efficient genotypes for marginal agro-ecologies. Low N tolerant genotypes identified from the current investigation may be further utilized in the identification of genomic regions responsible for NUE and its deployment in wheat breeding programs. The comprehensive data of 24 traits under different nitrogen levels for diverse genotypes from India and global sources (mainly CIMMYT) should be useful for supporting breeding for NUE and thus will be of great help for small and marginal farmers in India and South Asia.
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Affiliation(s)
- Suma S. Biradar
- AICRP on Wheat, MARS, University of Agricultural Sciences, Dharwad, India
| | - Mahalaxmi K. Patil
- Department of Genetics & Plant Breeding, University of Agricultural Sciences, Dharwad, India
| | - S. A. Desai
- Department of Genetics & Plant Breeding, University of Agricultural Sciences, Dharwad, India
| | - Sanjay K. Singh
- Genetics Division, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - V. Rudra Naik
- Directorate of Research, University of Agricultural Sciences, Dharwad, India
| | - Kumar Lamani
- Department of Agronomy, University of Agricultural Sciences, Dharwad, India
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Blancon J, Buet C, Dubreuil P, Tixier MH, Baret F, Praud S. Maize green leaf area index dynamics: genetic basis of a new secondary trait for grain yield in optimal and drought conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:68. [PMID: 38441678 PMCID: PMC10914915 DOI: 10.1007/s00122-024-04572-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2024] [Indexed: 03/07/2024]
Abstract
KEY MESSAGE Green Leaf Area Index dynamics is a promising secondary trait for grain yield and drought tolerance. Multivariate GWAS is particularly well suited to identify the genetic determinants of the green leaf area index dynamics. Improvement of maize grain yield is impeded by important genotype-environment interactions, especially under drought conditions. The use of secondary traits, that are correlated with yield, more heritable and less prone to genotype-environment interactions, can increase breeding efficiency. Here, we studied the genetic basis of a new secondary trait: the green leaf area index (GLAI) dynamics over the maize life cycle. For this, we used an unmanned aerial vehicle to characterize the GLAI dynamics of a diverse panel in well-watered and water-deficient trials in two years. From the dynamics, we derived 24 traits (slopes, durations, areas under the curve), and showed that six of them were heritable traits representative of the panel diversity. To identify the genetic determinants of GLAI, we compared two genome-wide association approaches: a univariate (single-trait) method and a multivariate (multi-trait) method combining GLAI traits, grain yield, and precocity. The explicit modeling of correlation structure between secondary traits and grain yield in the multivariate mixed model led to 2.5 times more associations detected. A total of 475 quantitative trait loci (QTLs) were detected. The genetic architecture of GLAI traits appears less complex than that of yield with stronger-effect QTLs that are more stable between environments. We also showed that a subset of GLAI QTLs explains nearly one fifth of yield variability across a larger environmental network of 11 water-deficient trials. GLAI dynamics is a promising grain yield secondary trait in optimal and drought conditions, and the detected QTLs could help to increase breeding efficiency through a marker-assisted approach.
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Affiliation(s)
- Justin Blancon
- UMR GDEC, INRAE, Université Clermont Auvergne, 63000, Clermont-Ferrand, France.
- Biogemma, Centre de Recherche de Chappes, 63720, Chappes, France.
| | - Clément Buet
- Biogemma, Centre de Recherche de Chappes, 63720, Chappes, France
| | - Pierre Dubreuil
- Biogemma, Centre de Recherche de Chappes, 63720, Chappes, France
| | | | | | - Sébastien Praud
- Biogemma, Centre de Recherche de Chappes, 63720, Chappes, France
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Lavoignat M, Cassan C, Pétriacq P, Gibon Y, Heumez E, Duque C, Momont P, Rincent R, Blancon J, Ravel C, Le Gouis J. Different wheat loci are associated to heritable free asparagine content in grain grown under different water and nitrogen availability. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:46. [PMID: 38332254 DOI: 10.1007/s00122-024-04551-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: 10/13/2023] [Accepted: 01/07/2024] [Indexed: 02/10/2024]
Abstract
KEY MESSAGE Different wheat QTLs were associated to the free asparagine content of grain grown in four different conditions. Environmental effects are a key factor when selecting for low acrylamide-forming potential. The amount of free asparagine in grain of a wheat genotype determines its potential to form harmful acrylamide in derivative food products. Here, we explored the variation in the free asparagine, aspartate, glutamine and glutamate contents of 485 accessions reflecting wheat worldwide diversity to define the genetic architecture governing the accumulation of these amino acids in grain. Accessions were grown under high and low nitrogen availability and in water-deficient and well-watered conditions, and plant and grain phenotypes were measured. Free amino acid contents of grain varied from 0.01 to 1.02 mg g-1 among genotypes in a highly heritable way that did not correlate strongly with grain yield, protein content, specific weight, thousand-kernel weight or heading date. Mean free asparagine content was 4% higher under high nitrogen and 3% higher in water-deficient conditions. After genotyping the accessions, single-locus and multi-locus genome-wide association study models were used to identify several QTLs for free asparagine content located on nine chromosomes. Each QTL was associated with a single amino acid and growing environment, and none of the QTLs colocalised with genes known to be involved in the corresponding amino acid metabolism. This suggests that free asparagine content is controlled by several loci with minor effects interacting with the environment. We conclude that breeding for reduced asparagine content is feasible, but should be firmly based on multi-environment field trials. KEY MESSAGE Different wheat QTLs were associated to the free asparagine content of grain grown in four different conditions. Environmental effects are a key factor when selecting for low acrylamide-forming potential.
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Affiliation(s)
- Mélanie Lavoignat
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France
- AgroParisTech, 75005, Paris, France
| | - Cédric Cassan
- Université Bordeaux, INRAE, UMR 1332 BFP, 33883, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Pierre Pétriacq
- Université Bordeaux, INRAE, UMR 1332 BFP, 33883, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Yves Gibon
- Université Bordeaux, INRAE, UMR 1332 BFP, 33883, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | | | | | | | - Renaud Rincent
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Justin Blancon
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France
| | - Catherine Ravel
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France
| | - Jacques Le Gouis
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France.
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Mastrangelo AM, Hartings H, Lanzanova C, Balconi C, Locatelli S, Cassol H, Valoti P, Petruzzino G, Pecchioni N. Genetic Diversity within a Collection of Italian Maize Inbred Lines: A Resource for Maize Genomics and Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:336. [PMID: 38337869 PMCID: PMC10857507 DOI: 10.3390/plants13030336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
Genetic diversity is fundamental for studying the complex architecture of the traits of agronomic importance, controlled by major and minor loci. Moreover, well-characterized germplasm collections are essential tools for dissecting and analyzing genetic and phenotypic diversity in crops. A panel of 360 entries, a subset of a larger collection maintained within the GenBank at CREA Bergamo, which includes the inbreds derived from traditional Italian maize open-pollinated (OP) varieties and advanced breeding ones (Elite Inbreds), was analyzed to identify SNP markers using the tGBS® genotyping-by-sequencing technology. A total of 797,368 SNPs were found during the initial analysis. Imputation and filtering processes were carried out based on the percentage of missing data, redundant markers, and rarest allele frequencies, resulting in a final dataset of 15,872 SNP markers for which a physical map position was identified. Using this dataset, the inbred panel was characterized for linkage disequilibrium (LD), genetic diversity, population structure, and genetic relationships. LD decay at a genome-wide level indicates that the collection is a suitable resource for association mapping. Population structure analyses, which were carried out with different clustering methods, showed stable grouping statistics for four groups, broadly corresponding to 'Insubria', 'Microsperma', and 'Scagliolino' genotypes, with a fourth group composed prevalently of elite accessions derived from Italian and US breeding programs. Based on these results, the CREA Italian maize collection, genetically characterized in this study, can be considered an important tool for the mapping and characterization of useful traits and associated loci/alleles, to be used in maize breeding programs.
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Affiliation(s)
- Anna Maria Mastrangelo
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
| | - Hans Hartings
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Chiara Lanzanova
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Carlotta Balconi
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Sabrina Locatelli
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Helga Cassol
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Paolo Valoti
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Giuseppe Petruzzino
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
| | - Nicola Pecchioni
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
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Soto-Cerda BJ, Larama G, Cloutier S, Fofana B, Inostroza-Blancheteau C, Aravena G. The Genetic Dissection of Nitrogen Use-Related Traits in Flax ( Linum usitatissimum L.) at the Seedling Stage through the Integration of Multi-Locus GWAS, RNA-seq and Genomic Selection. Int J Mol Sci 2023; 24:17624. [PMID: 38139451 PMCID: PMC10743809 DOI: 10.3390/ijms242417624] [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: 11/03/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Nitrogen (N), the most important macro-nutrient for plant growth and development, is a key factor that determines crop yield. Yet its excessive applications pollute the environment and are expensive. Hence, studying nitrogen use efficiency (NUE) in crops is fundamental for sustainable agriculture. Here, an association panel consisting of 123 flax accessions was evaluated for 21 NUE-related traits at the seedling stage under optimum N (N+) and N deficiency (N-) treatments to dissect the genetic architecture of NUE-related traits using a multi-omics approach integrating genome-wide association studies (GWAS), transcriptome analysis and genomic selection (GS). Root traits exhibited significant and positive correlations with NUE under N- conditions (r = 0.33 to 0.43, p < 0.05). A total of 359 QTLs were identified, accounting for 0.11% to 23.1% of the phenotypic variation in NUE-related traits. Transcriptomic analysis identified 1034 differentially expressed genes (DEGs) under contrasting N conditions. DEGs involved in N metabolism, root development, amino acid transport and catabolism and others, were found near the QTLs. GS models to predict NUE stress tolerance index (NUE_STI) trait were tested using a random genome-wide SNP dataset and a GWAS-derived QTLs dataset. The latter produced superior prediction accuracy (r = 0.62 to 0.79) compared to the genome-wide SNP marker dataset (r = 0.11) for NUE_STI. Our results provide insights into the QTL architecture of NUE-related traits, identify candidate genes for further studies, and propose genomic breeding tools to achieve superior NUE in flax under low N input.
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Affiliation(s)
- Braulio J. Soto-Cerda
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile
| | - Giovanni Larama
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile;
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada;
| | - Bourlaye Fofana
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada
| | - Claudio Inostroza-Blancheteau
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile
| | - Gabriela Aravena
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
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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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Valente J, Gerin F, Mini A, Richard R, Le Gouis J, Prigent-Combaret C, Moënne-Loccoz Y. Symbiotic Variations among Wheat Genotypes and Detection of Quantitative Trait Loci for Molecular Interaction with Auxin-Producing Azospirillum PGPR. Microorganisms 2023; 11:1615. [PMID: 37375117 DOI: 10.3390/microorganisms11061615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Crop varieties differ in their ability to interact with Plant Growth-Promoting Rhizobacteria (PGPR), but the genetic basis for these differences is unknown. This issue was addressed with the PGPR Azospirillum baldaniorum Sp245, using 187 wheat accessions. We screened the accessions based on the seedling colonization by the PGPR and the expression of the phenylpyruvate decarboxylase gene ppdC (for synthesis of the auxin indole-3-acetic acid), using gusA fusions. Then, the effects of the PGPR on the selected accessions stimulating Sp245 (or not) were compared in soil under stress. Finally, a genome-wide association approach was implemented to identify the quantitative trait loci (QTL) associated with PGPR interaction. Overall, the ancient genotypes were more effective than the modern genotypes for Azospirillum root colonization and ppdC expression. In non-sterile soil, A. baldaniorum Sp245 improved wheat performance for three of the four PGPR-stimulating genotypes and none of the four non-PGPR-stimulating genotypes. The genome-wide association did not identify any region for root colonization but revealed 22 regions spread on 11 wheat chromosomes for ppdC expression and/or ppdC induction rate. This is the first QTL study focusing on molecular interaction with PGPR bacteria. The molecular markers identified provide the possibility to improve the capacity of modern wheat genotypes to interact with Sp245, as well as, potentially, other Azospirillum strains.
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Affiliation(s)
- Jordan Valente
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Agathe Mini
- GDEC, INRAE, UCA, F-63000 Clermont-Ferrand, France
| | | | | | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
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10
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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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11
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Sharma A, Arif MAR, Shamshad M, Rawale KS, Brar A, Burgueño J, Shokat S, Kaur R, Vikram P, Srivastava P, Sandhu N, Singh J, Kaur S, Chhuneja P, Singh S. Preliminary Dissection of Grain Yield and Related Traits at Differential Nitrogen Levels in Diverse Pre-Breeding Wheat Germplasm Through Association Mapping. Mol Biotechnol 2023; 65:116-130. [PMID: 35908127 DOI: 10.1007/s12033-022-00535-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/14/2022] [Indexed: 01/11/2023]
Abstract
Development of nutrient efficient cultivars depends on effective identification and utilization of genetic variation. We characterized a set of 276 pre-breeding lines (PBLs) for several traits at different levels of nitrogen application. These PBLs originate from synthetic wheats and landraces. We witnessed significant variation in various traits among PBLs to different nitrogen doses. There was ~ 4-18% variation range in different agronomic traits in response to nitrogen application, with the highest variation for the biological yield (BY) and the harvest index. Among various agronomic traits measured, plant height, tiller number, and BY showed a positive correlation with nitrogen applications. GWAS analysis detected 182 marker-trait associations (MTAs) (at p-value < 0.001), out of which 8 MTAs on chromosomes 5D, 4A, 6A, 1B, and 5B explained more than 10% phenotypic variance. Out of all, 40 MTAs observed for differential nitrogen application response were contributed by the synthetic derivatives. Moreover, 20 PBLs exhibited significantly higher grain yield than checks and can be selected as potential donors for improved plant nitrogen use efficiency (pNUE).
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Affiliation(s)
- Achla Sharma
- Punjab Agricultural University, Ludhiana, India.
| | - Mian A R Arif
- Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan
| | - M Shamshad
- Punjab Agricultural University, Ludhiana, India
| | | | | | - Juan Burgueño
- CIMMYT, Carretera México Veracruz Km. 45, El Batán, 56237, Texcoco, CP, Mexico
| | - Sajid Shokat
- Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan
| | | | - Parsahnt Vikram
- International Center for Biosaline Agriculture, Academic City, Dubai, UAE
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12
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Govindasamy P, Muthusamy SK, Bagavathiannan M, Mowrer J, Jagannadham PTK, Maity A, Halli HM, G. K. S, Vadivel R, T. K. D, Raj R, Pooniya V, Babu S, Rathore SS, L. M, Tiwari G. Nitrogen use efficiency-a key to enhance crop productivity under a changing climate. FRONTIERS IN PLANT SCIENCE 2023; 14:1121073. [PMID: 37143873 PMCID: PMC10151540 DOI: 10.3389/fpls.2023.1121073] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/20/2023] [Indexed: 05/06/2023]
Abstract
Nitrogen (N) is an essential element required for the growth and development of all plants. On a global scale, N is agriculture's most widely used fertilizer nutrient. Studies have shown that crops use only 50% of the applied N effectively, while the rest is lost through various pathways to the surrounding environment. Furthermore, lost N negatively impacts the farmer's return on investment and pollutes the water, soil, and air. Therefore, enhancing nitrogen use efficiency (NUE) is critical in crop improvement programs and agronomic management systems. The major processes responsible for low N use are the volatilization, surface runoff, leaching, and denitrification of N. Improving NUE through agronomic management practices and high-throughput technologies would reduce the need for intensive N application and minimize the negative impact of N on the environment. The harmonization of agronomic, genetic, and biotechnological tools will improve the efficiency of N assimilation in crops and align agricultural systems with global needs to protect environmental functions and resources. Therefore, this review summarizes the literature on nitrogen loss, factors affecting NUE, and agronomic and genetic approaches for improving NUE in various crops and proposes a pathway to bring together agronomic and environmental needs.
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Affiliation(s)
- Prabhu Govindasamy
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Muthukumar Bagavathiannan, ; Prabhu Govindasamy,
| | - Senthilkumar K. Muthusamy
- Division of Crop Improvement, Indian Council of Agricultural Research (ICAR)-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - Muthukumar Bagavathiannan
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Muthukumar Bagavathiannan, ; Prabhu Govindasamy,
| | - Jake Mowrer
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | | | - Aniruddha Maity
- Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Hanamant M. Halli
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Pune, India
| | - Sujayananad G. K.
- Crop Protection, Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulse Research, Kanpur, India
| | - Rajagopal Vadivel
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Pune, India
| | - Das T. K.
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rishi Raj
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Vijay Pooniya
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Subhash Babu
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sanjay Singh Rathore
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Muralikrishnan L.
- Division of Agricultural Extension, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gopal Tiwari
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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13
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Diversity matters in wheat mixtures: A genomic survey of the impact of genetic diversity on the performance of 12 way durum wheat mixtures grown in two contrasted and controlled environments. PLoS One 2022; 17:e0276223. [PMID: 36490260 PMCID: PMC9733896 DOI: 10.1371/journal.pone.0276223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/04/2022] [Indexed: 12/13/2022] Open
Abstract
In ecology, an increase in genetic diversity within a community in natural ecosystems increases its productivity, while in evolutionary biology, kinship selection predicts that relatedness on social traits improves fitness. Varietal mixtures, where different genotypes are grown together, show contrasting results, especially for grain yield where both positive and negative effects of mixtures have been reported. To understand the effect of diversity on field performance, we grew 96 independent mixtures each composed with 12 durum wheat (Triticum turgidum ssp. durum Thell.) inbred lines, under two contrasting environmental conditions for water availability. Using dense genotyping, we imputed allelic frequencies and a genetic diversity index on more than 96000 loci for each mixture. We then analyzed the effect of genetic diversity on agronomic performance using a genome-wide approach. We explored the stress gradient hypothesis, which proposes that the greater the unfavourable conditions, the more beneficial the effect of diversity on mixture performance. We found that diversity on average had a negative effect on yield and its components while it was beneficial on grain weight. There was little support for the stress gradient theory. We discuss how to use genomic data to improve the assembly of varietal mixtures.
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14
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Shi H, Chen M, Gao L, Wang Y, Bai Y, Yan H, Xu C, Zhou Y, Xu Z, Chen J, Tang W, Wang S, Shi Y, Wu Y, Sun D, Jia J, Ma Y. Genome-wide association study of agronomic traits related to nitrogen use efficiency in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4289-4302. [PMID: 36136127 DOI: 10.1007/s00122-022-04218-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
GWAS identified 347 QTLs associated with eight traits related to nitrogen use efficiency in a 389-count wheat panel. Four novel candidate transcription factor genes were verified using qRT-PCR. Nitrogen is an essential nutrient for plants that determines crop yield. Improving nitrogen use efficiency (NUE) should considerably increase wheat yield and reduce the use of nitrogen fertilisers. However, knowledge on the genetic basis of NUE during wheat maturity is limited. In this study, a diversity panel incorporating 389 wheat accessions was phenotyped for eight NUE-related agronomic traits across five different environments. A total of 347 quantitative trait loci (QTLs) for low nitrogen tolerance indices (ratio of agronomic characters under low and high nitrogen conditions) were identified through a genome-wide association study utilising 397,384 single nucleotide polymorphisms (SNPs) within the MLM (Q + K) model, including 11 stable QTLs. Furthermore, 69 candidate genes were predicted for low nitrogen tolerance indices of best linear unbiased predictions values of the eight studied agronomic traits, and four novel candidate transcription factors (TraesCS5A02G237500 for qFsnR5A.2, TraesCS5B02G384500 and TraesCS5B02G384600 for qSLR5B.1, and TraesCS3B02G068800 for qTKWR3B.1) showed differing expression patterns in contrasting low-nitrogen-tolerant wheat genotypes. Moreover, the number of favourable marker alleles calculated using NUE that were significantly related to SNP in accessions decreased over the decades, indicating a decline in the NUE of the 389 wheat varieties. These findings denote promising NUE markers that could be useful in breeding high-NUE wheat varieties, and the candidate genes could further detail the NUE-related regulation network in wheat.
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Affiliation(s)
- Huawei Shi
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Lifeng Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Research Center of Wheat Engineering Technology of Hebei, Shijiazhuang, 050041, Hebei, China
| | - Yanming Bai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Huishu Yan
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Chengjie Xu
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yongbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Zhaoshi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Wensi Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Shuguang Wang
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yugang Shi
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yuxiang Wu
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Daizhen Sun
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Jizeng Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
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15
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Shi X, Zhou Z, Li W, Qin M, Yang P, Hou J, Huang F, Lei Z, Wu Z, Wang J. Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2022; 22:229. [PMID: 35508960 PMCID: PMC9066855 DOI: 10.1186/s12870-022-03602-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/15/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Hexaploid wheat (Triticum aestivum L.) is a leading cereal crop worldwide. Understanding the mechanism of calcium (Ca) accumulation in wheat is important to reduce the risk of human micronutrient deficiencies. However, the mechanisms of Ca accumulation in wheat grain are only partly understood. RESULTS Here, a genome-wide association study (GWAS) was performed to dissect the genetic basis of Ca accumulation in wheat grain using an association population consisting of 207 varieties, with phenotypic data from three locations. In total, 11 non-redundant genetic loci associated with Ca concentration were identified and they explained, on average, 9.61-26.93% of the phenotypic variation. Cultivars containing more superior alleles had increased grain Ca concentrations. Notably, four non-redundant loci were mutually verified by different statistical models in at least two environments, indicating their stability across different environments. Four putative candidate genes linked to Ca accumulation were revealed from the stable genetic loci. Among them, two genes, associated with the stable genetic loci on chromosomes 4A (AX-108912427) and 3B (AX-110922471), encode the subunits of V-type Proton ATPase (TraesCS4A02G428900 and TraesCS3B02G241000), which annotated as the typical generators of a proton gradient that might be involved in Ca homeostasis in wheat grain. CONCLUSION To identify genetic loci associated with Ca accumulation, we conducted GWAS on Ca concentrations and detected 11 genetic loci; whereas four genetic loci were stable across different environments. A genetic loci hot spot exists at the end of chromosome 4A and associated with the putative candidate gene TraesCS4A02G428900. The candidate gene TraesCS4A02G428900 encodes V-type proton ATPase subunit e and highly expressed in wheat grains, and it possibly involved in Ca accumulation. This study increases our understanding of the genetic architecture of Ca accumulation in wheat grains, which is potentially helpful for wheat Ca biofortification pyramid breeding.
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Affiliation(s)
- Xia Shi
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhengfu Zhou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Wenxu Li
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Maomao Qin
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Pan Yang
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Jinna Hou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Fangfang Huang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhensheng Lei
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China.
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China.
| | - Zhengqing Wu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Jiansheng Wang
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China.
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Shrestha V, Chhetri HB, Kainer D, Xu Y, Hamilton L, Piasecki C, Wolfe B, Wang X, Saha M, Jacobson D, Millwood RJ, Mazarei M, Stewart CN. The Genetic Architecture of Nitrogen Use Efficiency in Switchgrass ( Panicum virgatum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:893610. [PMID: 35586220 PMCID: PMC9108870 DOI: 10.3389/fpls.2022.893610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Switchgrass (Panicum virgatum L.) has immense potential as a bioenergy crop with the aim of producing biofuel as an end goal. Nitrogen (N)-related sustainability traits, such as nitrogen use efficiency (NUE) and nitrogen remobilization efficiency (NRE), are important factors affecting switchgrass quality and productivity. Hence, it is imperative to develop nitrogen use-efficient switchgrass accessions by exploring the genetic basis of NUE in switchgrass. For that, we used 331 diverse field-grown switchgrass accessions planted under low and moderate N fertility treatments. We performed a genome wide association study (GWAS) in a holistic manner where we not only considered NUE as a single trait but also used its related phenotypic traits, such as total dry biomass at low N and moderate N, and nitrogen use index, such as NRE. We have evaluated the phenotypic characterization of the NUE and the related traits, highlighted their relationship using correlation analysis, and identified the top ten nitrogen use-efficient switchgrass accessions. Our GWAS analysis identified 19 unique single nucleotide polymorphisms (SNPs) and 32 candidate genes. Two promising GWAS candidate genes, caffeoyl-CoA O-methyltransferase (CCoAOMT) and alfin-like 6 (AL6), were further supported by linkage disequilibrium (LD) analysis. Finally, we discussed the potential role of nitrogen in modulating the expression of these two genes. Our findings have opened avenues for the development of improved nitrogen use-efficient switchgrass lines.
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Affiliation(s)
- Vivek Shrestha
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hari B. Chhetri
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David Kainer
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Yaping Xu
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Lance Hamilton
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Ben Wolfe
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xueyan Wang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Malay Saha
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Daniel Jacobson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Reginald J. Millwood
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Mitra Mazarei
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - C. Neal Stewart
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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17
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Colombo M, Roumet P, Salon C, Jeudy C, Lamboeuf M, Lafarge S, Dumas AV, Dubreuil P, Ngo W, Derepas B, Beauchêne K, Allard V, Le Gouis J, Rincent R. Genetic Analysis of Platform-Phenotyped Root System Architecture of Bread and Durum Wheat in Relation to Agronomic Traits. FRONTIERS IN PLANT SCIENCE 2022; 13:853601. [PMID: 35401645 PMCID: PMC8992431 DOI: 10.3389/fpls.2022.853601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Roots are essential for water and nutrient uptake but are rarely the direct target of breeding efforts. To characterize the genetic variability of wheat root architecture, the root and shoot traits of 200 durum and 715 bread wheat varieties were measured at a young stage on a high-throughput phenotyping platform. Heritability of platform traits ranged from 0.40 for root biomass in durum wheat to 0.82 for the number of tillers. Field phenotyping data for yield components and SNP genotyping were already available for all the genotypes. Taking differences in earliness into account, several significant correlations between root traits and field agronomic performances were found, suggesting that plants investing more resources in roots in some stressed environments favored water and nutrient uptake, with improved wheat yield. We identified 100 quantitative trait locus (QTLs) of root traits in the bread wheat panels and 34 in the durum wheat panel. Most colocalized with QTLs of traits measured in field conditions, including yield components and earliness for bread wheat, but only in a few environments. Stress and climatic indicators explained the differential effect of some platform QTLs on yield, which was positive, null, or negative depending on the environmental conditions. Modern breeding has led to deeper rooting but fewer seminal roots in bread wheat. The number of tillers has been increased in bread wheat, but decreased in durum wheat, and while the root-shoot ratio for bread wheat has remained stable, for durum wheat it has been increased. Breeding for root traits or designing ideotypes might help to maintain current yield while adapting to specific drought scenarios.
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Affiliation(s)
- Michel Colombo
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pierre Roumet
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Christophe Salon
- Univ. Bourgogne, Agroecol Lab, Univ. Bourgogne Franche Comte, AgroSup Dijon, INRAE, Dijon, France
| | - Christian Jeudy
- Univ. Bourgogne, Agroecol Lab, Univ. Bourgogne Franche Comte, AgroSup Dijon, INRAE, Dijon, France
| | - Mickael Lamboeuf
- Univ. Bourgogne, Agroecol Lab, Univ. Bourgogne Franche Comte, AgroSup Dijon, INRAE, Dijon, France
| | | | | | | | - Wa Ngo
- INRAE-Universite Clermont-Auvergne, UMR 1095, GDEC, Clermont-Ferrand, France
| | - Brice Derepas
- INRAE-Universite Clermont-Auvergne, UMR 1095, GDEC, Clermont-Ferrand, France
| | | | - Vincent Allard
- INRAE-Universite Clermont-Auvergne, UMR 1095, GDEC, Clermont-Ferrand, France
| | - Jacques Le Gouis
- INRAE-Universite Clermont-Auvergne, UMR 1095, GDEC, Clermont-Ferrand, France
| | - Renaud Rincent
- INRAE-Universite Clermont-Auvergne, UMR 1095, GDEC, Clermont-Ferrand, France
- GQE-Le Moulon, INRAE, Univ. Paris-Sud, CNRS, AgroParisTech, Universite Paris-Saclay, Gif-sur-Yvette, France
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18
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Neuweiler JE, Trini J, Maurer HP, Würschum T. Do lower nitrogen fertilization levels require breeding of different types of cultivars in triticale? TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:993-1009. [PMID: 34958397 PMCID: PMC8942957 DOI: 10.1007/s00122-021-04012-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
The comparably low genotype-by-nitrogen level interaction suggests that selection in early generations can be done under high-input conditions followed by selection under different nitrogen levels to identify genotypes ideally suited for the target environment. Breeding high-yielding, nitrogen-efficient crops is of utmost importance to achieve greater agricultural sustainability. The aim of this study was to evaluate nitrogen use efficiency (NUE) of triticale, investigate long-term genetic trends and the genetic architecture, and develop strategies for NUE improvement by breeding. For this, we evaluated 450 different triticale genotypes under four nitrogen fertilization levels in multi-environment field trials for grain yield, protein content, starch content and derived indices. Analysis of temporal trends revealed that modern cultivars are better in exploiting the available nitrogen. Genome-wide association mapping revealed a complex genetic architecture with many small-effect QTL and a high level of pleiotropy for NUE-related traits, in line with phenotypic correlations. Furthermore, the effect of some QTL was dependent on the nitrogen fertilization level. High correlations of each trait between N levels and the rather low genotype-by-N-level interaction variance showed that generally the same genotypes perform well over different N levels. Nevertheless, the best performing genotype was always a different one. Thus, selection in early generations can be done under high nitrogen fertilizer conditions as these provide a stronger differentiation, but the final selection in later generations should be conducted with a nitrogen fertilization as in the target environment.
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Affiliation(s)
- Jan E Neuweiler
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - Johannes Trini
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - Hans Peter Maurer
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany.
| | - Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
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19
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Touzy G, Lafarge S, Redondo E, Lievin V, Decoopman X, Le Gouis J, Praud S. Identification of QTLs affecting post-anthesis heat stress responses in European bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:947-964. [PMID: 34984510 PMCID: PMC8942932 DOI: 10.1007/s00122-021-04008-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/23/2021] [Indexed: 05/27/2023]
Abstract
The response of a large panel of European elite wheat varieties to post-anthesis heat stress is influenced by 17 QTL linked to grain weight or the stay-green phenotype. Heat stress is a critical abiotic stress for winter bread wheat (Triticum aestivum L.) especially at the flowering and grain filling stages, limiting its growth and productivity in Europe and elsewhere. The breeding of new high-yield and stress-tolerant wheat varieties requires improved understanding of the physiological and genetic bases of heat tolerance. To identify genomic areas associated with plant and grain characteristics under heat stress, a panel of elite European wheat varieties (N = 199) was evaluated under controlled conditions in 2016 and 2017. A split-plot design was used to test the effects of high temperature for ten days after flowering. Flowering time, leaf chlorophyll content, the number of productive spikes, grain number, grain weight and grain size were measured, and the senescence process was modeled. Using genotyping data from a 280 K SNP chip, a genome-wide association study was carried out to test the main effect of each SNP and the effect of SNP × treatment interaction. Genotype × treatment interactions were mainly observed for grain traits measured on the main shoots and tillers. We identified 10 QTLs associated with the main effect of at least one trait and seven QTLs associated with the response to post-anthesis heat stress. Of these, two main QTLs associated with the heat tolerance of thousand-kernel weight were identified on chromosomes 4B and 6B. These QTLs will be useful for breeders to improve grain yield in environments where terminal heat stress is likely to occur.
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Affiliation(s)
- Gaëtan Touzy
- Arvalis-Institut du Végétal, Biopole Clermont Limagne, 63360, Saint-Beauzire, France
- Centre de Recherche de Chappes, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Stéphane Lafarge
- Centre de Recherche de Chappes, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Elise Redondo
- Centre de Recherche de Chappes, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Vincent Lievin
- Centre de Recherche de Chappes, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Xavier Decoopman
- Centre de Recherche de Chappes, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Jacques Le Gouis
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Sébastien Praud
- Centre de Recherche de Chappes, Route d'Ennezat CS90216, 63720, Chappes, France
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20
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Teng W, He X, Tong Y. Genetic Control of Efficient Nitrogen Use for High Yield and Grain Protein Concentration in Wheat: A Review. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040492. [PMID: 35214826 PMCID: PMC8878021 DOI: 10.3390/plants11040492] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 05/12/2023]
Abstract
The increasing global population and the negative effects of nitrogen (N) fertilizers on the environment challenge wheat breeding to maximize yield potential and grain protein concentration (GPC) in an economically and environmentally friendly manner. Understanding the molecular mechanisms for the response of yield components to N availability and assimilates allocation to grains provides the opportunity to increase wheat yield and GPC simultaneously. This review summarized quantitative trait loci/genes which can increase spikes and grain number by enhancing N uptake and assimilation at relative early growth stage, and 1000-grain weight and GPC by increasing post-anthesis N uptake and N allocation to grains.
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Affiliation(s)
- Wan Teng
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (W.T.); (X.H.)
| | - Xue He
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (W.T.); (X.H.)
| | - Yiping Tong
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (W.T.); (X.H.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: ; Tel.: +86-10-64806556
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21
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Colombo M, Montazeaud G, Viader V, Ecarnot M, Prosperi J, David J, Fort F, Violle C, Freville H. A genome‐wide analysis suggests pleiotropic effects of Green Revolution genes on shade avoidance in wheat. Evol Appl 2022; 15:1594-1604. [PMID: 36330302 PMCID: PMC9624089 DOI: 10.1111/eva.13349] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/26/2022] Open
Abstract
A classic example of phenotypic plasticity in plants is the suit of phenotypic responses induced by a change in the ratio of red to far-red light (R∶FR) as a result of shading, also known as the shade avoidance syndrome (SAS). While the adaptive consequences of this syndrome have been extensively discussed in natural ecosystems, how SAS varies within crop populations and how SAS evolved during crop domestication and breeding remain poorly known. In this study, we grew a panel of 180 durum wheat (Triticum turgidum ssp. durum) genotypes spanning diversity from wild, early domesticated, and elite genetic compartments under two light treatments: low R:FR light (shaded treatment) and high R:FR light (unshaded treatment). We first quantified the genetic variability of SAS, here measured as a change in plant height at the seedling stage. We then dissected the genetic basis of this variation through genome-wide association mapping. Genotypes grown in shaded conditions were taller than those grown under unshaded conditions. Interaction between light quality and genotype did not affect plant height. We found six QTLs affecting plant height. Three significantly interacted with light quality among which the well-known Rht1 gene introgressed in elite germplasm during the Green Revolution. Interestingly at three loci, short genotypes systematically expressed reduced SAS, suggesting a positive genetic correlation between plant height and plant height plasticity. Overall, our study sheds light on the evolutionary history of crops and illustrates the relevance of genetic approaches to tackle agricultural challenges.
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Affiliation(s)
- Michel Colombo
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
- CEFE Univ. Montpellier Institut Agro CNRS EPHE, IRD Univ Valéry Montpellier France
| | - Germain Montazeaud
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
- CEFE Univ. Montpellier Institut Agro CNRS EPHE, IRD Univ Valéry Montpellier France
- Department of Ecology and Evolution University of Lausanne 1015 Lausanne Switzerland
| | - Veronique Viader
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
| | - Martin Ecarnot
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
| | | | - Jacques David
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
| | - Florian Fort
- CEFE Univ. Montpellier Institut Agro CNRS EPHE, IRD Univ Valéry Montpellier France
| | - Cyrille Violle
- CEFE Univ. Montpellier CNRS EPHE, IRD Univ Valéry Montpellier France
| | - Helene Freville
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
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22
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Mălinaş A, Vidican R, Rotar I, Mălinaş C, Moldovan CM, Proorocu M. Current Status and Future Prospective for Nitrogen Use Efficiency in Wheat ( Triticum aestivum L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020217. [PMID: 35050105 PMCID: PMC8777959 DOI: 10.3390/plants11020217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 05/11/2023]
Abstract
Although essential for achieving high crop yields required for the growing population worldwide, nitrogen, (N) in large amounts, along with its inefficient use, results in environmental pollution and increased greenhouse gas (GHG) emissions. Therefore, improved nitrogen use efficiency (NUE) has a significant role to play in the development of more sustainable crop production systems. Considering that wheat is one of the major crops cultivated in the world and contributes in high amounts to the large N footprint, designing sustainable wheat crop patterns, briefly defined by us in this review as the 3 Qs (high quantity, good quality and the quintessence of natural environment health) is urgently required. There are numerous indices used to benchmark N management for a specific crop, including wheat, but the misunderstanding of their specific functions could result in an under/overestimation of crop NUE. Thus, a better understanding of N dynamics in relation to wheat N cycling can enhance a higher efficiency of N use. In this sense, the aim of our review is to provide a critical analysis on the current knowledge with respect to wheat NUE. Further, considering the key traits involved in N uptake, assimilation, distribution and utilization efficiency, as well as genetics (G), environment (E) and management (M) interactions, we suggest a series of future perspectives that can enhance a better efficiency of N in wheat.
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Affiliation(s)
- Anamaria Mălinaş
- Department of Plant Culture, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania; (A.M.); (R.V.); (I.R.)
| | - Roxana Vidican
- Department of Plant Culture, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania; (A.M.); (R.V.); (I.R.)
| | - Ioan Rotar
- Department of Plant Culture, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania; (A.M.); (R.V.); (I.R.)
| | - Cristian Mălinaş
- Department of Environmental Protection, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania;
- Correspondence: (C.M.); (C.M.M.)
| | - Cristina Maria Moldovan
- Department of Plant Culture, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania; (A.M.); (R.V.); (I.R.)
- Correspondence: (C.M.); (C.M.M.)
| | - Marian Proorocu
- Department of Environmental Protection, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania;
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23
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Saini DK, Chopra Y, Singh J, Sandhu KS, Kumar A, Bazzer S, Srivastava P. Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:1. [PMID: 37309486 PMCID: PMC10248672 DOI: 10.1007/s11032-021-01272-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.
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Affiliation(s)
- Dinesh K. Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
| | - Anand Kumar
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, 202002 India
| | - Sumandeep Bazzer
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
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24
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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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25
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Nigro D, Fortunato S, Giove SL, Mazzucotelli E, Gadaleta A. Functional Validation of Glutamine synthetase and Glutamate synthase Genes in Durum Wheat near Isogenic Lines with QTL for High GPC. Int J Mol Sci 2020; 21:ijms21239253. [PMID: 33291583 PMCID: PMC7730160 DOI: 10.3390/ijms21239253] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/25/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022] Open
Abstract
Durum wheat (Triticum turgidum L. ssp. durum) is a minor crop grown on about 17 million hectares of land worldwide. Several grain characteristics determine semolina's high end-use quality, such as grain protein content (GPC) which is directly related to the final products' nutritional and technological values. GPC improvement could be pursued by considering a candidate gene approach. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a bottleneck in the first step of nitrogen assimilation. QTL for GPC have been located on all chromosomes, and several major ones have been reported on 2A and 2B chromosomes, where GS2 and Fd-GOGAT genes have been mapped. A useful and efficient method to validate a putative QTL is the constitution of near-isogenic lines (NILs) by using the marker found to be associated to that QTL. Here, we present the development of two distinct sets of heterogeneous inbred family (HIF)- based NILs segregating for GS2 and Fd-GOGAT genes obtained from heterozygous lines at those loci, as well as their genotypic and phenotypic characterizations. The results allow the validation of the previously identified GPC QTL on 2A and 2B chromosomes, along with the role of these key genes in GPC control.
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Affiliation(s)
- Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
- Correspondence: (D.N.); (A.G.); Tel.: +39-0805442997(D.N.); +39-0805442995 (A.G.)
| | | | - Stefania Lucia Giove
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70126 Bari, Italy;
| | | | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70126 Bari, Italy;
- Correspondence: (D.N.); (A.G.); Tel.: +39-0805442997(D.N.); +39-0805442995 (A.G.)
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26
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Yang F, Liu J, Guo Y, He Z, Rasheed A, Wu L, Cao S, Nan H, Xia X. Genome-Wide Association Mapping of Adult-Plant Resistance to Stripe Rust in Common Wheat ( Triticum aestivum). PLANT DISEASE 2020; 104:2174-2180. [PMID: 32452749 DOI: 10.1094/pdis-10-19-2116-re] [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: 06/11/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a globally devastating disease of common wheat (Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated with known resistance genes or quantitative trait loci reported previously, whereas the other six are likely new resistance loci. Annotation of flanking sequences of significantly associated SNPs indicated the presence of three important candidate genes, including E3 ubiquitin-protein ligase, F-box repeat protein, and disease resistance RPP13-like protein. This study increased our knowledge in understanding the genetic architecture for stripe rust resistance and identified wheat varieties with multiple resistance alleles, which are useful for improvement of stripe rust resistance in breeding.
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Affiliation(s)
- Fangping Yang
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Jindong Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Ying Guo
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Ling Wu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
| | - Shiqin Cao
- Institute of Plant Protection, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Hai Nan
- Tianshui Institute of Agricultural Sciences, Tianshui, Gansu 741200, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
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27
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Beral A, Rincent R, Le Gouis J, Girousse C, Allard V. Wheat individual grain-size variance originates from crop development and from specific genetic determinism. PLoS One 2020; 15:e0230689. [PMID: 32214360 PMCID: PMC7098578 DOI: 10.1371/journal.pone.0230689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/05/2020] [Indexed: 11/19/2022] Open
Abstract
Wheat grain yield is usually decomposed in the yield components: number of spikes / m2, number of grains / spike, number of grains / m2 and thousand kernel weight (TKW). These are correlated one with another due to yield component compensation. Under optimal conditions, the number of grains per m2 has been identified as the main determinant of yield. However, with increasing occurrences of post-flowering abiotic stress associated with climate change, TKW may become severely limiting and hence a target for breeding. TKW is usually studied at the plot scale as it represents the average mass of a grain. However, this view disregards the large intra-genotypic variance of individual grain mass and its effect on TKW. The aim of this study is to investigate the determinism of the variance of individual grain size. We measured yield components and individual grain size variances of two large genetic wheat panels grown in two environments. We also carried out a genome-wide association study using a dense SNPs array. We show that the variance of individual grain size partly originates from the pre-flowering components of grain yield; in particular it is driven by canopy structure via its negative correlation with the number of spikes per m2. But the variance of final grain size also has a specific genetic basis. The genome-wide analysis revealed the existence of QTL with strong effects on the variance of individual grain size, independently from the other yield components. Finally, our results reveal some interesting drivers for manipulating individual grain size variance either through canopy structure or through specific chromosomal regions.
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Affiliation(s)
- Aurore Beral
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Renaud Rincent
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jacques Le Gouis
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Christine Girousse
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Vincent Allard
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
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28
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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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29
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Tamisier L, Szadkowski M, Nemouchi G, Lefebvre V, Szadkowski E, Duboscq R, Santoni S, Sarah G, Sauvage C, Palloix A, Moury B. Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding. MOLECULAR PLANT PATHOLOGY 2020; 21:3-16. [PMID: 31605444 PMCID: PMC6913244 DOI: 10.1111/mpp.12874] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.
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Affiliation(s)
- Lucie Tamisier
- GAFLINRA84140MontfavetFrance
- Pathologie VégétaleINRA84140MontfavetFrance
- Present address:
Plant Pathology LaboratoryTERRA‐Gembloux Agro‐Bio TechUniversity of LiègePassage des Déportés, 25030GemblouxBelgium
| | - Marion Szadkowski
- GAFLINRA84140MontfavetFrance
- Pathologie VégétaleINRA84140MontfavetFrance
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30
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Touzy G, Rincent R, Bogard M, Lafarge S, Dubreuil P, Mini A, Deswarte JC, Beauchêne K, Le Gouis J, Praud S. Using environmental clustering to identify specific drought tolerance QTLs in bread wheat (T. aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2859-2880. [PMID: 31324929 DOI: 10.1007/s00122-019-03393-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 07/06/2019] [Indexed: 05/03/2023]
Abstract
Environmental clustering helps to identify QTLs associated with grain yield in different water stress scenarios. These QTLs could be useful for breeders to improve grain yields and increase genetic resilience in marginal environments. Drought is one of the main abiotic stresses limiting winter bread wheat growth and productivity around the world. The acquisition of new high-yielding and stress-tolerant varieties is therefore necessary and requires improved understanding of the physiological and genetic bases of drought resistance. A panel of 210 elite European varieties was evaluated in 35 field trials. Grain yield and its components were scored in each trial. A crop model was then run with detailed climatic data and soil water status to assess the dynamics of water stress in each environment. Varieties were registered from 1992 to 2011, allowing us to test timewise genetic progress. Finally, a genome-wide association study (GWAS) was carried out using genotyping data from a 280 K SNP chip. The crop model simulation allowed us to group the environments into four water stress scenarios: an optimal condition with no water stress, a post-anthesis water stress, a moderate-anthesis water stress and a high pre-anthesis water stress. Compared to the optimal water condition, grain yield losses in the stressed conditions were 3.3%, 12.4% and 31.2%, respectively. This environmental clustering improved understanding of the effect of drought on grain yields and explained 20% of the G × E interaction. The greatest genetic progress was obtained in the optimal condition, mostly represented in France. The GWAS identified several QTLs, some of which were specific of the different water stress patterns. Our results make breeding for improved drought resistance to specific environmental scenarios easier and will facilitate genetic progress in future environments, i.e., water stress environments.
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Affiliation(s)
- Gaëtan Touzy
- Arvalis-Institut du végétal, Biopôle Clermont Limagne, 63360, Saint-Beauzire, France
- Centre de recherche de Chappes, Biogemma, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Renaud Rincent
- INRA, UCA UMR 1095, Génétique, Diversité et Ecophysiologie des Céréales, 24 Avenue des Landais, 63177, Aubière Cedex, France
| | - Matthieu Bogard
- Arvalis-Institut du végétal, 6 Chemin de la côte vieille, 31450, Baziège, France
| | - Stephane Lafarge
- Centre de recherche de Chappes, Biogemma, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Pierre Dubreuil
- Centre de recherche de Chappes, Biogemma, Route d'Ennezat CS90216, 63720, Chappes, France
| | - Agathe Mini
- INRA, UCA UMR 1095, Génétique, Diversité et Ecophysiologie des Céréales, 24 Avenue des Landais, 63177, Aubière Cedex, France
| | - Jean-Charles Deswarte
- Arvalis-Institut du végétal, Route de Châteaufort, ZA des graviers, 91190, Villiers-le-Bâcle, France
| | - Katia Beauchêne
- Arvalis-Institut du végétal, 45 voie Romaine, Ouzouer Le Marché, 41240, Beauce La Romaine, France
| | - Jacques Le Gouis
- INRA, UCA UMR 1095, Génétique, Diversité et Ecophysiologie des Céréales, 24 Avenue des Landais, 63177, Aubière Cedex, France
| | - Sébastien Praud
- Centre de recherche de Chappes, Biogemma, Route d'Ennezat CS90216, 63720, Chappes, France.
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Negro SS, Millet EJ, Madur D, Bauland C, Combes V, Welcker C, Tardieu F, Charcosset A, Nicolas SD. Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies. BMC PLANT BIOLOGY 2019; 19:318. [PMID: 31311506 PMCID: PMC6636005 DOI: 10.1186/s12870-019-1926-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/05/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Single Nucleotide Polymorphism (SNP) array and re-sequencing technologies have different properties (e.g. calling rate, minor allele frequency profile) and drawbacks (e.g. ascertainment bias). This lead us to study their complementarity and the consequences of using them separately or combined in diversity analyses and Genome-Wide Association Studies (GWAS). We performed GWAS on three traits (grain yield, plant height and male flowering time) measured in 22 environments on a panel of 247 F1 hybrids obtained by crossing 247 diverse dent maize inbred lines with a same flint line. The 247 lines were genotyped using three genotyping technologies (Genotyping-By-Sequencing, Illumina Infinium 50 K and Affymetrix Axiom 600 K arrays). RESULTS The effects of ascertainment bias of the 50 K and 600 K arrays were negligible for deciphering global genetic trends of diversity and for estimating relatedness in this panel. We developed an original approach based on linkage disequilibrium (LD) extent in order to determine whether SNPs significantly associated with a trait and that are physically linked should be considered as a single Quantitative Trait Locus (QTL) or several independent QTLs. Using this approach, we showed that the combination of the three technologies, which have different SNP distributions and densities, allowed us to detect more QTLs (gain in power) and potentially refine the localization of the causal polymorphisms (gain in resolution). CONCLUSIONS Conceptually different technologies are complementary for detecting QTLs by tagging different haplotypes in association studies. Considering LD, marker density and the combination of different technologies (SNP-arrays and re-sequencing), the genotypic data available were most likely enough to well represent polymorphisms in the centromeric regions, whereas using more markers would be beneficial for telomeric regions.
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Affiliation(s)
- Sandra S. Negro
- GQE – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Emilie J. Millet
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), UMR759, INRA, SupAgro, 34060 Montpellier, France
- Present address: Biometris, Department of Plant Science, Wageningen University and Research, 6700 AA Wageningen, The Netherlands
| | - Delphine Madur
- GQE – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Cyril Bauland
- GQE – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Valérie Combes
- GQE – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Claude Welcker
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), UMR759, INRA, SupAgro, 34060 Montpellier, France
| | - François Tardieu
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), UMR759, INRA, SupAgro, 34060 Montpellier, France
| | - Alain Charcosset
- GQE – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Stéphane D. Nicolas
- GQE – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
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32
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Hawkesford MJ, Griffiths S. Exploiting genetic variation in nitrogen use efficiency for cereal crop improvement. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:35-42. [PMID: 31176099 PMCID: PMC6692496 DOI: 10.1016/j.pbi.2019.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 05/18/2023]
Abstract
Cereals are the most important sources of calories and nutrition for the human population, and are an essential animal feed. Food security depends on adequate production and demands are predicted to rise as the global population rises. The need for increased yields will have to be coupled to the efficient use of resources including fertilisers such as nitrogen to underpin the sustainability of food production. Although optimally performing crops with high yields require a balanced mineral nutrition, nitrogen fundamentally drives growth and yield as well as requirements for other nutrients. It is estimated that globally only 33% of applied nitrogen fertiliser is recovered in the harvested grain, indicative of a huge waste of resource and potential major pollutant and is thus a major target for crop improvement. Both agronomy and breeding will contribute to improved nitrogen use efficiency (NUE) and an important component of the latter is harnessing germplasm variation. This review will consider the key traits involved in NUE, the potential to exploit genetic variation for these specific traits, and the approaches to be utilised.
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33
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Michel S, Löschenberger F, Ametz C, Pachler B, Sparry E, Bürstmayr H. Simultaneous selection for grain yield and protein content in genomics-assisted wheat breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1745-1760. [PMID: 30810763 PMCID: PMC6531418 DOI: 10.1007/s00122-019-03312-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/15/2019] [Indexed: 05/10/2023]
Abstract
KEY MESSAGE Large genetic improvement can be achieved by simultaneous genomic selection for grain yield and protein content when combining different breeding strategies in the form of selection indices. Genomic selection has been implemented in many national and international breeding programmes in recent years. Numerous studies have shown the potential of this new breeding tool; few have, however, taken the simultaneous selection for multiple traits into account that is though common practice in breeding programmes. The simultaneous improvement in grain yield and protein content is thereby a major challenge in wheat breeding due to a severe negative trade-off. Accordingly, the potential and limits of multi-trait selection for this particular trait complex utilizing the vast phenotypic and genomic data collected in an applied wheat breeding programme were investigated in this study. Two breeding strategies based on various genomic-selection indices were compared, which (1) aimed to select high-protein genotypes with acceptable yield potential and (2) develop high-yielding varieties, while maintaining protein content. The prediction accuracy of preliminary yield trials could be strongly improved when combining phenotypic and genomic information in a genomics-assisted selection approach, which surpassed both genomics-based and classical phenotypic selection methods both for single trait predictions and in genomic index selection across years. The employed genomic selection indices mitigated furthermore the negative trade-off between grain yield and protein content leading to a substantial selection response for protein yield, i.e. total seed nitrogen content, which suggested that it is feasible to develop varieties that combine a superior yield potential with comparably high protein content, thus utilizing available nitrogen resources more efficiently.
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Affiliation(s)
- Sebastian Michel
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
| | | | - Christian Ametz
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Bernadette Pachler
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Ellen Sparry
- C&M Seeds, 6180 5th Line, Palmerston, ON, N0G 2P0, Canada
| | - Hermann Bürstmayr
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
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34
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Scheben A, Verpaalen B, Lawley CT, Chan CKK, Bayer PE, Batley J, Edwards D. CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:142-152. [PMID: 30548723 DOI: 10.1111/tpj.14194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 05/23/2023]
Abstract
Advances in sequencing technology have led to a rapid rise in the genomic data available for plants, driving new insights into the evolution, domestication and improvement of crops. Single nucleotide polymorphisms (SNPs) are a major component of crop genomic diversity, and are invaluable as genetic markers in research and breeding programs. High-throughput SNP arrays, or 'SNP chips', can generate reproducible sets of informative SNP markers and have been broadly adopted. Although there are many public repositories for sequencing data, which are routinely uploaded, there are no formal repositories for crop SNP array data. To make SNP array data more easily accessible, we have developed CropSNPdb (http://snpdb.appliedbioinformatics.com.au), a database for SNP array data produced by the Illumina Infinium™ hexaploid bread wheat (Triticum aestivum) 90K and Brassica 60K arrays. We currently host SNPs from datasets covering 526 Brassica lines and 309 bread wheat lines, and provide search, download and upload utilities for users. CropSNPdb provides a useful repository for these data, which can be applied for a range of genomics and molecular crop-breeding activities.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Brent Verpaalen
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | | | - Chon-Kit K Chan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Australian Genome Research Facility, Melbourne, Vic., 3000, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
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35
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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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36
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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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37
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Lei L, Li G, Zhang H, Powers C, Fang T, Chen Y, Wang S, Zhu X, Carver BF, Yan L. Nitrogen use efficiency is regulated by interacting proteins relevant to development in wheat. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1214-1226. [PMID: 29193541 PMCID: PMC5978868 DOI: 10.1111/pbi.12864] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/01/2017] [Accepted: 11/04/2017] [Indexed: 05/08/2023]
Abstract
Wheat (Triticum aestivum) has low nitrogen use efficiency (NUE). The genetic mechanisms controlling NUE are unknown. Positional cloning of a major quantitative trait locus for N-related agronomic traits showed that the vernalization gene TaVRN-A1 was tightly linked with TaNUE1, the gene shown to influence NUE in wheat. Because of an Ala180 /Val180 substitution, TaVRN-A1a and TaVRN-A1b proteins interact differentially with TaANR1, a protein encoded by a wheat orthologue of Arabidopsis nitrate regulated 1 (ANR1). The transcripts of both TaVRN-A1 and TaANR1 were down-regulated by nitrogen. TaANR1 was functionally characterized in TaANR1::RNAi transgenic wheat, and in a natural mutant with a 23-bp deletion including 10-bp at the 5' end of intron 5 and 13-bp of exon 6 in gDNA sequence in its gDNA sequence, which produced transcript that lacked the full 84-bp exon 6. Both TaANR1 and TaHOX1 bound to the Ala180 /Val180 position of TaVRN-A1. Genetically incorporating favourable alleles from TaVRN-A1, TaANR1 and TaHOX1 increased grain yield from 9.84% to 11.58% in the field. Molecular markers for allelic variation of the genes that regulate nitrogen can be used in breeding programmes aimed at improving NUE and yield in novel wheat cultivars.
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Affiliation(s)
- Lei Lei
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Genqiao Li
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
- Present address:
Wheat, Peanut and Other Field Crops Research UnitUSDA‐ARSStillwaterOKUSA
| | - Hailin Zhang
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Carol Powers
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Tilin Fang
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Yihua Chen
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Shuwen Wang
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
- Present address:
The Land InstituteSalinaKSUSA
| | - Xinkai Zhu
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
- Present address:
Key Laboratory of Crop Genetics and Physiology of Jiangsu ProvinceYangzhou UniversityYangzhouJiangsuChina
| | - Brett F. Carver
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Liuling Yan
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
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Tiwari JK, Plett D, Garnett T, Chakrabarti SK, Singh RK. Integrated genomics, physiology and breeding approaches for improving nitrogen use efficiency in potato: translating knowledge from other crops. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:587-605. [PMID: 32290962 DOI: 10.1071/fp17303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/06/2017] [Indexed: 05/22/2023]
Abstract
Potato plays a key role in global food and nutritional security. Potato is an N fertiliser-responsive crop, producing high tuber yields. However, excessive use of N can result in environmental damage and high production costs, hence improving nitrogen use efficiency (NUE) of potato plants is one of the sustainable options to address these issues and increase yield. Advanced efforts have been undertaken to improve NUE in other plants like Arabidopsis, rice, wheat and maize through molecular and physiological approaches. Conversely, in potato, NUE studies have predominantly focussed on agronomy or soil management, except for a few researchers who have measured gene expression and proteins relevant to N uptake or metabolism. The focus of this review is to adapt knowledge gained from other plants to inform investigation of N metabolism and associated traits in potato with the aim of improving potato NUE using integrated genomics, physiology and breeding methods.
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Affiliation(s)
- Jagesh K Tiwari
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
| | - Darren Plett
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Trevor Garnett
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Swarup K Chakrabarti
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
| | - Rajesh K Singh
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
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Guo J, Shi W, Zhang Z, Cheng J, Sun D, Yu J, Li X, Guo P, Hao C. Association of yield-related traits in founder genotypes and derivatives of common wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2018; 18:38. [PMID: 29458339 PMCID: PMC5819277 DOI: 10.1186/s12870-018-1234-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/14/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Yield improvement is an ever-important objective of wheat breeding. Studying and understanding the phenotypes and genotypes of yield-related traits has potential for genetic improvement of crops. RESULTS The genotypes of 215 wheat cultivars including 11 founder parents and 106 derivatives were analyzed by the 9 K wheat SNP iSelect assay. A total of 4138 polymorphic single nucleotide polymorphism (SNP) loci were detected on 21 chromosomes, of which 3792 were mapped to single chromosome locations. All genotypes were phenotyped for six yield-related traits including plant height (PH), spike length (SL), spikelet number per spike (SNPS), kernel number per spike (KNPS), kernel weight per spike (KWPS), and thousand kernel weight (TKW) in six irrigated environments. Genome-wide association analysis detected 117 significant associations of 76 SNPs on 15 chromosomes with phenotypic explanation rates (R 2 ) ranging from 2.03 to 12.76%. In comparing allelic variation between founder parents and their derivatives (106) and other cultivars (98) using the 76 associated SNPs, we found that the region 116.0-133.2 cM on chromosome 5A in founder parents and derivatives carried alleles positively influencing kernel weight per spike (KWPS), rarely found in other cultivars. CONCLUSION The identified favorable alleles could mark important chromosome regions in derivatives that were inherited from founder parents. Our results unravel the genetic of yield in founder genotypes, and provide tools for marker-assisted selection for yield improvement.
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Affiliation(s)
- Jie Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Weiping Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Zheng Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Jingye Cheng
- College of Agronomy, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Jin Yu
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Xinlei Li
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Pingyi Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Deng Z, Cui Y, Han Q, Fang W, Li J, Tian J. Discovery of Consistent QTLs of Wheat Spike-Related Traits under Nitrogen Treatment at Different Development Stages. FRONTIERS IN PLANT SCIENCE 2017; 8:2120. [PMID: 29326735 PMCID: PMC5737097 DOI: 10.3389/fpls.2017.02120] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/29/2017] [Indexed: 05/24/2023]
Abstract
Spike-related traits such as spike length (Sl), fertile spikelet number (Fsn), sterile spikelet number (Ssn), grain number per spike (Gns), and thousand-kernel weight (Tkw) are important factors influencing wheat yield. However, reliably stable markers that can be used for molecular breeding in different environments have not yet been identified. In this study, a double haploid (DH) population was used for quantitative trait locus (QTL) mapping of five spike-related traits under four different nitrogen (N) supply dates in two locations and years. Seventy additive QTLs with phenotypic variation ranging from 4.12 to 34.74% and 10 major epistatic QTLs were identified. Eight important chromosomal regions on five chromosomes (1B, 2B, 2D, 5D, and 6A) were found. Sixteen stable QTLs were detected for which N application had little effect. Among those stable QTLs, QSl.sdau-2D-1, and QSl.sdau-2D-2, with phenotypic variation explained (PVE) of 10.4 and 24.2%, respectively, were flanked by markers Xwmc112 and Xcfd53 in the same order. The QTLs QSsn.sdau-2B-1, QFsn.sdau-2B-1, and QGns.sdau-2B, with PVE ranging from 4.37 to 28.43%, collocated in the Xwmc179-Xbarc373 marker interval. The consistent kernel wheat QTL (QTkw.sdau-6A) on the long arm of chromosome 6A, flanked by SSR markers Xbarc1055 and Xwmc553, showed PVE of 5.87-15.18%. Among these stable QTLs, the two flanking markers Xwmc112 and Xcfd53 have been validated using different varieties and populations for selecting Sl. Therefore, these results will be of great value for marker-assisted selection (MAS) in breeding programs and will accelerate the understanding of the genetic relationships among spike-related traits at the molecular level.
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Affiliation(s)
- Zhiying Deng
- Group of Wheat Quality Breeding, State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Cooperation Innovation Centre of Efficient Production with High Annual Yield of Wheat and Corn, Agronomy College, Shandong Agricultural University, Tai'an, China
| | - Yong Cui
- Group of Wheat Quality Breeding, State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Cooperation Innovation Centre of Efficient Production with High Annual Yield of Wheat and Corn, Agronomy College, Shandong Agricultural University, Tai'an, China
| | - Qingdian Han
- Horticulture, College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Wenqi Fang
- Group of Wheat Quality Breeding, State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Cooperation Innovation Centre of Efficient Production with High Annual Yield of Wheat and Corn, Agronomy College, Shandong Agricultural University, Tai'an, China
| | - Jifa Li
- Group of Wheat Quality Breeding, State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Cooperation Innovation Centre of Efficient Production with High Annual Yield of Wheat and Corn, Agronomy College, Shandong Agricultural University, Tai'an, China
| | - Jichun Tian
- Group of Wheat Quality Breeding, State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Cooperation Innovation Centre of Efficient Production with High Annual Yield of Wheat and Corn, Agronomy College, Shandong Agricultural University, Tai'an, China
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Liu J, He Z, Rasheed A, Wen W, Yan J, Zhang P, Wan Y, Zhang Y, Xie C, Xia X. Genome-wide association mapping of black point reaction in common wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:220. [PMID: 29169344 PMCID: PMC5701291 DOI: 10.1186/s12870-017-1167-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 11/10/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Black point is a serious threat to wheat production and can be managed by host resistance. Marker-assisted selection (MAS) has the potential to accelerate genetic improvement of black point resistance in wheat breeding. We performed a genome-wide association study (GWAS) using the high-density wheat 90 K and 660 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of black point resistance and identify associated molecular markers. RESULTS Black point reactions were evaluated in 166 elite wheat cultivars in five environments. Twenty-five unique loci were identified on chromosomes 2A, 2B, 3A, 3B (2), 3D, 4B (2), 5A (3), 5B (3), 6A, 6B, 6D, 7A (5), 7B and 7D (2), respectively, explaining phenotypic variation ranging from 7.9 to 18.0%. The highest number of loci was detected in the A genome (11), followed by the B (10) and D (4) genomes. Among these, 13 were identified in two or more environments. Seven loci coincided with known genes or quantitative trait locus (QTL), whereas the other 18 were potentially novel loci. Linear regression showed a clear dependence of black point scores on the number of favorable alleles, suggesting that QTL pyramiding will be an effective approach to increase resistance. In silico analysis of sequences of resistance-associated SNPs identified 6 genes possibly involved in oxidase, signal transduction and stress resistance as candidate genes involved in black point reaction. CONCLUSION SNP markers significantly associated with black point resistance and accessions with a larger number of resistance alleles can be used to further enhance black point resistance in breeding. This study provides new insights into the genetic architecture of black point reaction.
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Affiliation(s)
- Jindong Liu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
- Department of Plant Genetics & Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193 China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Weie Wen
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Jun Yan
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), 38 Huanghe Street, Anyang, Henan 455000 China
| | - Pingzhi Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, Anhui 230001 China
| | - Yingxiu Wan
- Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, Anhui 230001 China
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Chaojie Xie
- Department of Plant Genetics & Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193 China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
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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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Lehnert H, Serfling A, Enders M, Friedt W, Ordon F. Genetics of mycorrhizal symbiosis in winter wheat (Triticum aestivum). THE NEW PHYTOLOGIST 2017; 215:779-791. [PMID: 28517039 DOI: 10.1111/nph.14595] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/30/2017] [Indexed: 05/23/2023]
Abstract
Bread wheat (Triticum aestivum) is a major staple food and therefore of prime importance for feeding the Earth's growing population. Mycorrhiza is known to improve plant growth, but although extensive knowledge concerning the interaction between mycorrhizal fungi and plants is available, genotypic differences concerning the ability of wheat to form mycorrhizal symbiosis and quantitative trait loci (QTLs) involved in mycorrhization are largely unknown. Therefore, a diverse set of 94 bread wheat genotypes was evaluated with regard to root colonization by arbuscular mycorrhizal fungi. In order to identify genomic regions involved in mycorrhization, these genotypes were analyzed using the wheat 90k iSelect chip, resulting in 17 823 polymorphic mapped markers, which were used in a genome-wide association study. Significant genotypic differences (P < 0.0001) were detected in the ability to form symbiosis and 30 significant markers associated with root colonization, representing six QTL regions, were detected on chromosomes 3A, 4A and 7A, and candidate genes located in these QTL regions were proposed. The results reported here provide key insights into the genetics of root colonization by mycorrhizal fungi in wheat.
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Affiliation(s)
- Heike Lehnert
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Albrecht Serfling
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Matthias Enders
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Wolfgang Friedt
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Gießen, Germany
| | - Frank Ordon
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
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Zhang Z, Xiong S, Wei Y, Meng X, Wang X, Ma X. The role of glutamine synthetase isozymes in enhancing nitrogen use efficiency of N-efficient winter wheat. Sci Rep 2017; 7:1000. [PMID: 28428629 PMCID: PMC5430530 DOI: 10.1038/s41598-017-01071-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/27/2017] [Indexed: 11/26/2022] Open
Abstract
Glutamine synthetase (GS) isozymes play critical roles in nitrogen (N) metabolism. However, the exact relationship between GS and nitrogen use efficiency (NUE) remain unclear. We have selected and compared two wheat cultivars, YM49 and XN509, which were identified as the N-efficient and N-inefficient genotypes, respectively. In this study, agronomical, morphological, physiological and biochemical approaches were performed. The results showed that TaGS1 was high expressed post-anthesis, and TaGS2 was highly expressed pre-anthesis in N-efficient genotype compared to N-inefficient genotype. GS1 and GS2 isozymes were also separated by native-PAGE and found that the spatial and temporal distribution of GS isozymes, their expression of gene and protein subunits in source-sink-flow organs during development periods triggered the pool strength and influenced the N flow. According to the physiological role of GS isozymes, we illustrated four metabolic regulation points, by which acting collaboratively in different organs, accelerating the transport of nutrients to the grain. It suggested that the regulation of GS isozymes may promote flow strength and enhance NUE by a complex C-N metabolic mechanism. The relative activity or amount of GS1 and GS2 isozymes could be a potential marker to predict and select wheat genotypes with enhanced NUE.
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Affiliation(s)
- Zhiyong Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Key Laboratory of Physiology, Ecology and Genetic Improvement of Food Crops in HenanProvince, Zhengzhou, 450002, China
| | - Shuping Xiong
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Key Laboratory of Physiology, Ecology and Genetic Improvement of Food Crops in HenanProvince, Zhengzhou, 450002, China
| | - Yihao Wei
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Key Laboratory of Physiology, Ecology and Genetic Improvement of Food Crops in HenanProvince, Zhengzhou, 450002, China
| | - Xiaodan Meng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Key Laboratory of Physiology, Ecology and Genetic Improvement of Food Crops in HenanProvince, Zhengzhou, 450002, China
| | - Xiaochun Wang
- Department of Biochemistry, College of Life Science, Henan Agriculture University, Zhengzhou, 450002, China.
| | - Xinming Ma
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China.
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
- Key Laboratory of Physiology, Ecology and Genetic Improvement of Food Crops in HenanProvince, Zhengzhou, 450002, China.
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Albert E, Segura V, Gricourt J, Bonnefoi J, Derivot L, Causse M. Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6413-6430. [PMID: 27856709 PMCID: PMC5181584 DOI: 10.1093/jxb/erw411] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.
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Affiliation(s)
- Elise Albert
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Vincent Segura
- INRA, UR0588, Amélioration, Génétique et Physiologie Forestières, 2163 Avenue de la Pomme de Pin, Centre de Recherche Val de Loire, CS 40001, Orléans, 45075, France
| | - Justine Gricourt
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | | | | | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
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Bouchet AS, Laperche A, Bissuel-Belaygue C, Baron C, Morice J, Rousseau-Gueutin M, Dheu JE, George P, Pinochet X, Foubert T, Maes O, Dugué D, Guinot F, Nesi N. Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed. BMC Genet 2016; 17:131. [PMID: 27628849 PMCID: PMC5024496 DOI: 10.1186/s12863-016-0432-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/24/2016] [Indexed: 01/13/2023] Open
Abstract
Background Nitrogen use efficiency is an important breeding trait that can be modified to improve the sustainability of many crop species used in agriculture. Rapeseed is a major oil crop with low nitrogen use efficiency, making its production highly dependent on nitrogen input. This complex trait is suspected to be sensitive to genotype × environment interactions, especially genotype × nitrogen interactions. Therefore, phenotyping diverse rapeseed populations under a dense network of trials is a powerful approach to study nitrogen use efficiency in this crop. The present study aimed to determine the quantitative trait loci (QTL) associated with yield in winter oilseed rape and to assess the stability of these regions under contrasting nitrogen conditions for the purpose of increasing nitrogen use efficiency. Results Genome-wide association studies and linkage analyses were performed on two diversity sets and two doubled-haploid populations. These populations were densely genotyped, and yield-related traits were scored in a multi-environment design including seven French locations, six growing seasons (2009 to 2014) and two nitrogen nutrition levels (optimal versus limited). Very few genotype × nitrogen interactions were detected, and a large proportion of the QTL were stable across nitrogen nutrition conditions. In contrast, strong genotype × trial interactions in which most of the QTL were specific to a single trial were found. To obtain further insight into the QTL × environment interactions, genetic analyses of ecovalence were performed to identify the genomic regions contributing to the genotype × nitrogen and genotype × trial interactions. Fifty-one critical genomic regions contributing to the additive genetic control of yield-associated traits were identified, and the structural organization of these regions in the genome was investigated. Conclusions Our results demonstrated that the effect of the trial was greater than the effect of nitrogen nutrition levels on seed yield-related traits under our experimental conditions. Nevertheless, critical genomic regions associated with yield that were stable across environments were identified in rapeseed. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0432-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Anne Laperche
- AGROCAMPUS OUEST, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France.
| | | | - Cécile Baron
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
| | - Jérôme Morice
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
| | | | - Jean-Eric Dheu
- Limagrain Europe, Ferme de l'Etang, 77390, Verneuil-l'Etang, France
| | - Pierre George
- Biogemma, Chemin de Panedautes, 31700, Mondonville, France
| | - Xavier Pinochet
- Terres Inovia, Avenue Lucien Brétignières, 78850, Thiverval Grignon, France
| | - Thomas Foubert
- Euralis, Chemin de Panedautes, 31700, Mondonville, France
| | - Olivier Maes
- Maisadour Semences, Route de Saint Sever, BP27, 40001, Mont de Marsan Cedex, France
| | - Damien Dugué
- RAGT R2n, Rue Emile Singla, BP 3331, 12033, Rodez, France
| | - Florent Guinot
- Syngenta, Chemin de l'Hobit, 31790, Saint-Sauveur, France
| | - Nathalie Nesi
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
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Mahjourimajd S, Taylor J, Rengel Z, Khabaz-Saberi H, Kuchel H, Okamoto M, Langridge P. The Genetic Control of Grain Protein Content under Variable Nitrogen Supply in an Australian Wheat Mapping Population. PLoS One 2016; 11:e0159371. [PMID: 27438012 PMCID: PMC4954668 DOI: 10.1371/journal.pone.0159371] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/03/2016] [Indexed: 11/19/2022] Open
Abstract
Genetic variation has been observed in both protein concentration in wheat grain and total protein content (protein yield). Here we describe the genetic analysis of variation for grain protein in response to nitrogen (N) supply and locate significant genomic regions controlling grain protein components in a spring wheat population. In total, six N use efficiency (NUE) field trials were carried out for the target traits in a sub-population of doubled haploid lines derived from a cross between two Australian varieties, RAC875 and Kukri, in Southern and Western Australia from 2011 to 2013. Twenty-four putative Quantitative Trait Loci (QTL) for protein-related traits were identified at high and low N supply and ten QTL were identified for the response to N for the traits studied. These loci accounted for a significant proportion of the overall effect of N supply. Several of the regions were co-localised with grain yield QTL and are promising targets for further investigation and selection in breeding programs.
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Affiliation(s)
- Saba Mahjourimajd
- Australian Centre for Plant Functional Genomics (ACPFG), The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia
| | - Julian Taylor
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Zed Rengel
- Soil Science and Plant Nutrition M087, School of Earth and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Hossein Khabaz-Saberi
- Soil Science and Plant Nutrition M087, School of Earth and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Haydn Kuchel
- Australian Grain Technologies, PMB1, Glen Osmond, SA 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Mamoru Okamoto
- Australian Centre for Plant Functional Genomics (ACPFG), The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia
- * E-mail: (PL); (MO)
| | - Peter Langridge
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
- * E-mail: (PL); (MO)
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Pascual L, Albert E, Sauvage C, Duangjit J, Bouchet JP, Bitton F, Desplat N, Brunel D, Le Paslier MC, Ranc N, Bruguier L, Chauchard B, Verschave P, Causse M. Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:120-130. [PMID: 26566830 DOI: 10.1016/j.plantsci.2015.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/12/2015] [Accepted: 06/16/2015] [Indexed: 05/21/2023]
Abstract
Quantitative trait loci (QTL) have been identified using traditional linkage mapping and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of the genetic background on QTL effect has been underlined. Genome-wide association studies (GWAs) were proposed to circumvent these limitations. In tomato, we have shown that GWAs is possible, using the admixed nature of cherry tomato genomes that reduces the impact of population structure. Nevertheless, GWAs success might be limited due to the low decay of linkage disequilibrium, which varies along the genome in this species. Multi-parent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage and GWAs by increasing the precision of QTL mapping. We have developed a MAGIC population by crossing eight tomato lines whose genomes were resequenced. We showed the potential of the MAGIC population when coupled with whole genome sequencing to detect candidate single nucleotide polymorphisms (SNPs) underlying the QTLs. QTLs for fruit quality traits were mapped and related to the variations detected at the genome sequence and expression levels. The advantages and limitations of the three types of population, in the context of the available genome sequence and resequencing facilities, are discussed.
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Affiliation(s)
- Laura Pascual
- INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France
| | - Elise Albert
- INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France
| | - Christopher Sauvage
- INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France
| | - Janejira Duangjit
- INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France
| | - Jean-Paul Bouchet
- INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France
| | - Frédérique Bitton
- INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France
| | - Nelly Desplat
- INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France
| | - Dominique Brunel
- INRA, US1279, Etude du Polymorphisme des Génomes végétaux (EPGV), CEA-IG/CNG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Marie-Christine Le Paslier
- INRA, US1279, Etude du Polymorphisme des Génomes végétaux (EPGV), CEA-IG/CNG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Nicolas Ranc
- INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France
| | - Laure Bruguier
- Vilmorin S.A. - Groupe Limagrain, Centre de Recherche de La Costière, Route de Meynes, 30210 Ledenon, France
| | - Betty Chauchard
- Vilmorin S.A. - Groupe Limagrain, Centre de Recherche de La Costière, Route de Meynes, 30210 Ledenon, France
| | - Philippe Verschave
- Vilmorin S.A. - Groupe Limagrain, Centre de Recherche de La Costière, Route de Meynes, 30210 Ledenon, France
| | - Mathilde Causse
- INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France.
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Krapp A. Plant nitrogen assimilation and its regulation: a complex puzzle with missing pieces. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:115-22. [PMID: 26037390 DOI: 10.1016/j.pbi.2015.05.010] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) is an essential element for plants that is available in agricultural soils mainly as macronutrients in the form of nitrate and ammonium. Interplay between high-affinity and low-affinity transporters ensures efficient uptake from the soil even under highly fluctuating N availability. After uptake, N assimilation comprises the reduction of nitrate to ammonium and its subsequent incorporation into amino acids. Amino acids, but also nitrate, are transported from root to shoot and vice versa. Most steps of N transport and assimilation are tightly controlled by a regulatory network acting both cell-autonomously and systemically. N sensors, transcription factors and further regulatory players have been identified during recent years, elucidating parts of the huge puzzle that represents the efficient use of N by plants.
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Affiliation(s)
- Anne Krapp
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France.
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50
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Jordan KW, Wang S, Lun Y, Gardiner LJ, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest KL, Sharpe AG, Sidebottom CH, Hall N, Toomajian C, Close T, Dubcovsky J, Akhunova A, Talbert L, Bansal UK, Bariana HS, Hayden MJ, Pozniak C, Jeddeloh JA, Hall A, Akhunov E. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol 2015; 16:48. [PMID: 25886949 PMCID: PMC4389885 DOI: 10.1186/s13059-015-0606-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/04/2015] [Indexed: 12/21/2022] Open
Abstract
Background Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. Results A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Conclusions Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0606-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine W Jordan
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Shichen Wang
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Yanni Lun
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Ron MacLachlan
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Pierre Hucl
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Krysta Wiebe
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Debbie Wong
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Kerrie L Forrest
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | | | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0 W9, Canada.
| | | | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | | | - Timothy Close
- Department Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA.
| | - Jorge Dubcovsky
- Department Plant Sciences, University of California, Davis, CA, 95616, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Alina Akhunova
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Luther Talbert
- Department Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
| | - Urmil K Bansal
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Harbans S Bariana
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Matthew J Hayden
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Curtis Pozniak
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | | | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Eduard Akhunov
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
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