1
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.)
| |
Collapse
|
2
|
Esposito S, Vitale P, Taranto F, Saia S, Pecorella I, D'Agostino N, Rodriguez M, Natoli V, De Vita P. Simultaneous improvement of grain yield and grain protein concentration in durum wheat by using association tests and weighted GBLUP. Theor Appl Genet 2023; 136:242. [PMID: 37947927 DOI: 10.1007/s00122-023-04487-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
KEY MESSAGE Simultaneous improvement for GY and GPC by using GWAS and GBLUP suggested a significant application in durum wheat breeding. Despite the importance of grain protein concentration (GPC) in determining wheat quality, its negative correlation with grain yield (GY) is still one of the major challenges for breeders. Here, a durum wheat panel of 200 genotypes was evaluated for GY, GPC, and their derived indices (GPD and GYD), under eight different agronomic conditions. The plant material was genotyped with the Illumina 25 k iSelect array, and a genome-wide association study was performed. Two statistical models revealed dozens of marker-trait associations (MTAs), each explaining up to 30%. phenotypic variance. Two markers on chromosomes 2A and 6B were consistently identified by both models and were found to be significantly associated with GY and GPC. MTAs identified for phenological traits co-mapped to well-known genes (i.e., Ppd-1, Vrn-1). The significance values (p-values) that measure the strength of the association of each single nucleotide polymorphism marker with the target traits were used to perform genomic prediction by using a weighted genomic best linear unbiased prediction model. The trained models were ultimately used to predict the agronomic performances of an independent durum wheat panel, confirming the utility of genomic prediction, although environmental conditions and genetic backgrounds may still be a challenge to overcome. The results generated through our study confirmed the utility of GPD and GYD to mitigate the inverse GY and GPC relationship in wheat, provided novel markers for marker-assisted selection and opened new ways to develop cultivars through genomic prediction approaches.
Collapse
Affiliation(s)
- Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy
| | - Paolo Vitale
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122, Foggia, Italy
| | - Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), Via Amendola 165/A, 70126, Bari, Italy
| | - Sergio Saia
- Department of Veterinary Sciences, University of Pisa, 56129, Pisa, Italy
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy
| | - Vincenzo Natoli
- Genetic Services SRL, Contrada Catenaccio, snc, 71026, Deliceto, FG, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy.
| |
Collapse
|
3
|
Valladares García AP, Desiderio F, Simeone R, Ravaglia S, Ciorba R, Fricano A, Guerra D, Blanco A, Cattivelli L, Mazzucotelli E. QTL mapping for kernel-related traits in a durum wheat x T. dicoccum segregating population. Front Plant Sci 2023; 14:1253385. [PMID: 37849841 PMCID: PMC10577384 DOI: 10.3389/fpls.2023.1253385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/28/2023] [Indexed: 10/19/2023]
Abstract
Durum wheat breeding relies on grain yield improvement to meet its upcoming demand while coping with climate change. Kernel size and shape are the determinants of thousand kernel weight (TKW), which is a key component of grain yield, and the understanding of the genetic control behind these traits supports the progress in yield potential. The present study aimed to dissect the genetic network responsible for kernel size components (length, width, perimeter, and area) and kernel shape traits (width-to-length ratio and formcoefficient) as well as their relationships with kernel weight, plant height, and heading date in durum wheat. Quantitative Trait Locus (QTL) mapping was performed on a segregating population of 110 recombinant inbred lines, derived from a cross between the domesticated emmer wheat accession MG5323 and the durum wheat cv. Latino, evaluated in four different environments. A total of 24 QTLs stable across environments were found and further grouped in nine clusters on chromosomes 2A, 2B, 3A, 3B, 4B, 6B, and 7A. Among them, a QTL cluster on chromosome 4B was associated with kernel size traits and TKW, where the parental MG5323 contributed the favorable alleles, highlighting its potential to improve durum wheat germplasm. The physical positions of the clusters, defined by the projection on the T. durum reference genome, overlapped with already known genes (i.e., BIG GRAIN PROTEIN 1 on chromosome 4B). These results might provide genome-based guidance for the efficient exploitation of emmer wheat diversity in wheat breeding, possibly through yield-related molecular markers.
Collapse
Affiliation(s)
- Ana Paola Valladares García
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, Valencia, Spain
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | | | - Roberto Ciorba
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Rome, Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| |
Collapse
|
4
|
Krishnappa G, Khan H, Krishna H, Devate NB, Kumar S, Mishra CN, Parkash O, Kumar S, Kumar M, Mamrutha HM, Singh GP, Singh G. Genome-Wide Association Study for Grain Protein, Thousand Kernel Weight, and Normalized Difference Vegetation Index in Bread Wheat (Triticum aestivum L.). Genes (Basel) 2023; 14:637. [PMID: 36980909 PMCID: PMC10048783 DOI: 10.3390/genes14030637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Genomic regions governing grain protein content (GPC), 1000 kernel weight (TKW), and normalized difference vegetation index (NDVI) were studied in a set of 280 bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using a 35K Axiom array and phenotyped in three environments. A total of 26 marker-trait associations (MTAs) were detected on 18 chromosomes covering the A, B, and D subgenomes of bread wheat. The GPC showed the maximum MTAs (16), followed by NDVI (6), and TKW (4). A maximum of 10 MTAs was located on the B subgenome, whereas, 8 MTAs each were mapped on the A and D subgenomes. In silico analysis suggest that the SNPs were located on important putative candidate genes such as NAC domain superfamily, zinc finger RING-H2-type, aspartic peptidase domain, folylpolyglutamate synthase, serine/threonine-protein kinase LRK10, pentatricopeptide repeat, protein kinase-like domain superfamily, cytochrome P450, and expansin. These candidate genes were found to have different roles including regulation of stress tolerance, nutrient remobilization, protein accumulation, nitrogen utilization, photosynthesis, grain filling, mitochondrial function, and kernel development. The effects of newly identified MTAs will be validated in different genetic backgrounds for further utilization in marker-aided breeding.
Collapse
|
5
|
Pascual L, Solé-Medina A, Faci I, Giraldo P, Ruiz M, Benavente E. Development and marker-trait relationships of functional markers for glutamine synthetase GS1 and GS2 homoeogenes in bread wheat. Mol Breed 2023; 43:8. [PMID: 37309364 PMCID: PMC10248667 DOI: 10.1007/s11032-022-01354-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/28/2022] [Indexed: 06/14/2023]
Abstract
GS1 and GS2 genes encode, respectively, the main cytosolic and the plastidic isoforms of glutamine synthetase (GS). In the present study, the wheat GS1 and GS2 homoeogenes located in the A, B and D genome chromosomes have been sequenced in a group of 15 bread wheat varieties including landraces, old commercial varieties and modern cultivars. Phenotypic characterization by multi-environment field trials detected significant effects of specific GS homoeogenes on three of the seven agronomic and grain quality traits analyzed. Based on the gene sequence polymorphisms found, biallelic molecular markers that could facilitate marker-assisted breeding were developed for genes GS1A, GS2A and GS2D. The remaining genes encoding main wheat GS were excluded because of being monomorphic (GS1D) or too polymorphic (GS1B and GS2B) in the sequencing panel varieties. A collection of 187 Spanish bread wheat landraces was genotyped for these gene-based molecular markers. Data analyses conducted with phenotypic records reported for this germplasm collection in López-Fernández et al. (Plants-Basel 10: 620, 2021) have revealed the beneficial influence of some individual alleles on thousand-kernel weight (TKW), kernels per spike (KS) and grain protein content. Furthermore, genetic interactions between GS1A, a cytosolic GS isoform coding gene, and GS2A or GS2D, plastidic GS enzyme coding genes, were found to affect TKW and KS. The finding that some alleles at one locus may mask the effect of positive alleles at hypostatic GS loci should be kept in mind if gene pyramiding strategies are attempted for the improvement of N-use efficiency-related traits. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01354-0.
Collapse
Affiliation(s)
- Laura Pascual
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Aida Solé-Medina
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- Department of Forest Ecology & Genetics, Forest Research Centre (INIA, CSIC), Ctra. de La Coruña Km 7.5, 28040 Madrid, Spain
| | - Isabel Faci
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- John Innes Centre, Norwich Research Park, Colney, NR4 7UH UK
| | - Patricia Giraldo
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Magdalena Ruiz
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), CSIC, Autovía A2, Km. 36.2, Finca La Canaleja, Alcalá de Henares, Madrid, 28805 Spain
| | - Elena Benavente
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| |
Collapse
|
6
|
Jadon V, Sharma S, Krishna H, Krishnappa G, Gajghate R, Devate NB, Panda KK, Jain N, Singh PK, Singh GP. Molecular Mapping of Biofortification Traits in Bread Wheat (Triticum aestivum L.) Using a High-Density SNP Based Linkage Map. Genes (Basel) 2023; 14. [PMID: 36672962 DOI: 10.3390/genes14010221] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
A set of 188 recombinant inbred lines (RILs) derived from a cross between a high-yielding Indian bread wheat cultivar HD2932 and a synthetic hexaploid wheat (SHW) Synthetic 46 derived from tetraploid Triticum turgidum (AA, BB 2n = 28) and diploid Triticum tauschii (DD, 2n = 14) was used to identify novel genomic regions associated in the expression of grain iron concentration (GFeC), grain zinc concentration (GZnC), grain protein content (GPC) and thousand kernel weight (TKW). The RIL population was genotyped using SNPs from 35K Axiom® Wheat Breeder's Array and 34 SSRs and phenotyped in two environments. A total of nine QTLs including five for GPC (QGpc.iari_1B, QGpc.iari_4A, QGpc.iari_4B, QGpc.iari_5D, and QGpc.iari_6B), two for GFeC (QGfec.iari_5B and QGfec.iari_6B), and one each for GZnC (QGznc.iari_7A) and TKW (QTkw.iari_4B) were identified. A total of two stable and co-localized QTLs (QGpc.iari_4B and QTkw.iari_4B) were identified on the 4B chromosome between the flanking region of Xgwm149-AX-94559916. In silico analysis revealed that the key putative candidate genes such as P-loop containing nucleoside triphosphatehydrolase, Nodulin-like protein, NAC domain, Purine permease, Zinc-binding ribosomal protein, Cytochrome P450, Protein phosphatase 2A, Zinc finger CCCH-type, and Kinesin motor domain were located within the identified QTL regions and these putative genes are involved in the regulation of iron homeostasis, zinc transportation, Fe, Zn, and protein remobilization to the developing grain, regulation of grain size and shape, and increased nitrogen use efficiency. The identified novel QTLs, particularly stable and co-localized QTLs are useful for subsequent use in marker-assisted selection (MAS).
Collapse
|
7
|
Subedi M, Ghimire B, Bagwell JW, Buck JW, Mergoum M. Wheat end-use quality: State of art, genetics, genomics-assisted improvement, future challenges, and opportunities. Front Genet 2023; 13:1032601. [PMID: 36685944 PMCID: PMC9849398 DOI: 10.3389/fgene.2022.1032601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Wheat is the most important source of food, feed, and nutrition for humans and livestock around the world. The expanding population has increasing demands for various wheat products with different quality attributes requiring the development of wheat cultivars that fulfills specific demands of end-users including millers and bakers in the international market. Therefore, wheat breeding programs continually strive to meet these quality standards by screening their improved breeding lines every year. However, the direct measurement of various end-use quality traits such as milling and baking qualities requires a large quantity of grain, traits-specific expensive instruments, time, and an expert workforce which limits the screening process. With the advancement of sequencing technologies, the study of the entire plant genome is possible, and genetic mapping techniques such as quantitative trait locus mapping and genome-wide association studies have enabled researchers to identify loci/genes associated with various end-use quality traits in wheat. Modern breeding techniques such as marker-assisted selection and genomic selection allow the utilization of these genomic resources for the prediction of quality attributes with high accuracy and efficiency which speeds up crop improvement and cultivar development endeavors. In addition, the candidate gene approach through functional as well as comparative genomics has facilitated the translation of the genomic information from several crop species including wild relatives to wheat. This review discusses the various end-use quality traits of wheat, their genetic control mechanisms, the use of genetics and genomics approaches for their improvement, and future challenges and opportunities for wheat breeding.
Collapse
Affiliation(s)
- Madhav Subedi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Bikash Ghimire
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - John White Bagwell
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - James W. Buck
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Mohamed Mergoum
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, United States,*Correspondence: Mohamed Mergoum,
| |
Collapse
|
8
|
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. Theor Appl Genet 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
9
|
Mu H, Wang B, Yuan F. Bioinformatics in Plant Breeding and Research on Disease Resistance. Plants (Basel) 2022; 11:3118. [PMID: 36432847 PMCID: PMC9696050 DOI: 10.3390/plants11223118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/04/2022] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
In the context of plant breeding, bioinformatics can empower genetic and genomic selection to determine the optimal combination of genotypes that will produce a desired phenotype and help expedite the isolation of these new varieties. Bioinformatics is also instrumental in collecting and processing plant phenotypes, which facilitates plant breeding. Robots that use automated and digital technologies to collect and analyze different types of information to monitor the environment in which plants grow, analyze the environmental stresses they face, and promptly optimize suboptimal and adverse growth conditions accordingly, have helped plant research and saved human resources. In this paper, we describe the use of various bioinformatics databases and algorithms and explore their potential applications in plant breeding and for research on plant disease resistance.
Collapse
|
10
|
Zia MAB, Yousaf MF, Asim A, Naeem M. An overview of genome-wide association mapping studies in Poaceae species (model crops: wheat and rice). Mol Biol Rep 2022; 49:12077-12090. [DOI: 10.1007/s11033-022-08036-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
|
11
|
Chen Y, Wang K, Chen H, Yang H, Zheng T, Huang X, Fan G. Simultaneously genetic selection of wheat yield and grain protein quality in rice-wheat and soybean-wheat cropping systems through critical nitrogen efficiency-related traits. Front Plant Sci 2022; 13:899387. [PMID: 36247613 PMCID: PMC9558111 DOI: 10.3389/fpls.2022.899387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Analyzing the contribution of nitrogen (N) uptake and its utilization in grain yield and protein quality-related traits in rice-wheat (RW) and soybean-wheat (SW) cropping systems is essential for simultaneous improvements in the two target traits. A field experiment with nine wheat genotypes was conducted in 2018-19 and 2019-20 cropping years to investigate N uptake and utilization-related traits associated with high wheat yield and good protein quality. Results showed that N uptake efficiency (NUpE) in the RW cropping system and N utilization efficiency (NUtE) in the SW cropping system explained 77.6 and 65.2% of yield variation, respectively, due to the contribution of fertile spikes and grain number per spike to grain yield varied depending on soil water and N availability in the two rotation systems. Lower grain protein content in the RW cropping system in comparison to the SW cropping system was mainly related to lower individual N accumulation at maturity, resulting from higher fertile spikes, rather than N harvest index (NHI). However, NHI in the SW cropping system accounted for greater variation in grain protein content. Both gluten index and post-anthesis N uptake were mainly affected by genotype, and low gluten index caused by high post-anthesis N uptake may be related to the simultaneous increase in kernel weight. N remobilization process associated with gluten quality was driven by increased sink N demand resulting from high grain number per unit area in the RW cropping system; confinement of low sink N demand and source capability resulted in low grain number per spike and water deficit limiting photosynthesis of flag leaf in the SW cropping system. CY-25 obtained high yield and wet gluten content at the expense of gluten index in the two wheat cropping systems, due to low plant height and high post-anthesis N uptake and kernel weight. From these results, we concluded that plant height, kernel weight, and post-anthesis N uptake were the critically agronomic and NUE-related traits for simultaneous selection of grain yield and protein quality. Our research results provided useful guidelines for improving both grain yield and protein quality by identifying desirable N-efficient genotypes in the two rotation systems.
Collapse
Affiliation(s)
- Yufeng Chen
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Kun Wang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Haolan Chen
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hongkun Yang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Ministry of Science and Technology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Eco-Physiology and Farming System in Southwest China, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu, China
| | - Ting Zheng
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Ministry of Science and Technology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Eco-Physiology and Farming System in Southwest China, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu, China
| | - Xiulan Huang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Ministry of Science and Technology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Eco-Physiology and Farming System in Southwest China, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu, China
| | - Gaoqiong Fan
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Ministry of Science and Technology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Eco-Physiology and Farming System in Southwest China, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
12
|
Geyer M, Mohler V, Hartl L. Genetics of the Inverse Relationship between Grain Yield and Grain Protein Content in Common Wheat. Plants 2022; 11:plants11162146. [PMID: 36015449 PMCID: PMC9413592 DOI: 10.3390/plants11162146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022]
Abstract
Grain protein content (GPC) is one of the most important criteria to determine the quality of common wheat (Triticum aestivum). One of the major obstacles for bread wheat production is the negative correlation between GPC and grain yield (GY). Previous studies demonstrated that the deviation from this inverse relationship is highly heritable. However, little is known about the genetics controlling these deviations in common wheat. To fill this gap, we performed quantitative trait locus (QTL) analysis for GY, GPC, and four derived GY-GPC indices using an eight-way multiparent advanced generation intercross population comprising 394 lines. Interval mapping was conducted using phenotypic data from up to nine environments and genotypic data from a 20k single-nucleotide polymorphism array. The four indices were highly heritable (0.76–0.88) and showed distinct correlations to GY and GPC. Interval mapping revealed that GY, GPC, and GY-GPC indices were controlled by 6, 12, and 12 unique QTL, of which each explained only a small amount of phenotypic variance (R2 ≤ 10%). Ten of the 12 index QTL were independent of loci affecting GY and GPC. QTL regions harboured several candidate genes, including Rht-1, WAPO-A1, TaTEF-7A, and NRT2.6-7A. The study confirmed the usefulness of indices to mitigate the inverse GY-GPC relationship in breeding, though the selection method should reflect their polygenic inheritance.
Collapse
|
13
|
Gupta OP, Singh AK, Singh A, Singh GP, Bansal KC, Datta SK. Wheat Biofortification: Utilizing Natural Genetic Diversity, Genome-Wide Association Mapping, Genomic Selection, and Genome Editing Technologies. Front Nutr 2022; 9:826131. [PMID: 35938135 PMCID: PMC9348810 DOI: 10.3389/fnut.2022.826131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/06/2022] [Indexed: 01/11/2023] Open
Abstract
Alleviating micronutrients associated problems in children below five years and women of childbearing age, remains a significant challenge, especially in resource-poor nations. One of the most important staple food crops, wheat attracts the highest global research priority for micronutrient (Fe, Zn, Se, and Ca) biofortification. Wild relatives and cultivated species of wheat possess significant natural genetic variability for these micronutrients, which has successfully been utilized for breeding micronutrient dense wheat varieties. This has enabled the release of 40 biofortified wheat cultivars for commercial cultivation in different countries, including India, Bangladesh, Pakistan, Bolivia, Mexico and Nepal. In this review, we have systematically analyzed the current understanding of availability and utilization of natural genetic variations for grain micronutrients among cultivated and wild relatives, QTLs/genes and different genomic regions regulating the accumulation of micronutrients, and the status of micronutrient biofortified wheat varieties released for commercial cultivation across the globe. In addition, we have also discussed the potential implications of emerging technologies such as genome editing to improve the micronutrient content and their bioavailability in wheat.
Collapse
Affiliation(s)
- Om Prakash Gupta
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | | | | | - Swapan K. Datta
- Department of Botany, University of Calcutta, Kolkata, India
| |
Collapse
|
14
|
Yang F, Zhang J, Zhao Y, Liu Q, Islam S, Yang W, Ma W. Wheat glutamine synthetase TaGSr-4B is a candidate gene for a QTL of thousand grain weight on chromosome 4B. Theor Appl Genet 2022; 135:2369-2384. [PMID: 35588016 PMCID: PMC9271121 DOI: 10.1007/s00122-022-04118-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Glutamine synthetase TaGSr-4B is a candidate gene for a QTL of thousand grain weight on 4B, and the gene marker is ready for wheat breeding. A QTL for thousand grain weight (TGW) in wheat was previously mapped on chromosome 4B in a DH population of Westonia × Kauz. For identifying the candidate genes of the QTL, wheat 90 K SNP array was used to saturate the existing linkage map, and four field trials plus one glasshouse experiment over five locations were conducted to refine the QTL. Three nitrogen levels were applied to two of those field trials, resulting in a TGW phenotype data set from nine environments. A robust TGW QTL cluster including 773 genes was detected in six environments with the highest LOD value of 13.4. Based on differentiate gene expression within the QTL cluster in an RNAseq data of Westonia and Kauz during grain filling, a glutamine synthesis gene (GS: TaGSr-4B) was selected as a potential candidate gene for the QTL. A SNP on the promoter region between Westonia and Kauz was used to develop a cleaved amplified polymorphic marker for TaGSr-4B gene mapping and QTL reanalysing. As results, TGW QTL appeared in seven environments, and in four out of seven environments, the TGW QTL were localized on the TaGSr-4B locus and showed significant contributions to the phenotype. Based on the marker, two allele groups of Westonia and Kauz formed showed significant differences on TGW in eight environments. In agreement with the roles of GS genes on nitrogen and carbon remobilizations, TaGSr-4B is likely the candidate gene of the TGW QTL on 4B and the TaGSr-4B gene marker is ready for wheat breeding.
Collapse
Affiliation(s)
- Fan Yang
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Chengdu, 610066, China
| | - Jingjuan Zhang
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.
| | - Yun Zhao
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- College of Agronomy, Qingdao Agriculture University, Qingdao, 266109, China
| | - Qier Liu
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Shahidul Islam
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Chengdu, 610066, China
| | - Wujun Ma
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.
- College of Agronomy, Qingdao Agriculture University, Qingdao, 266109, China.
| |
Collapse
|
15
|
Oszvald M, Hassall KL, Hughes D, Torres-Ballesteros A, Clark I, Riche AB, Heuer S. Genetic Diversity in Nitrogen Fertiliser Responses and N Gas Emission in Modern Wheat. Front Plant Sci 2022; 13:816475. [PMID: 35646002 PMCID: PMC9137425 DOI: 10.3389/fpls.2022.816475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/20/2022] [Indexed: 06/08/2023]
Abstract
Crops assimilate nitrogen (N) as ammonium via the glutamine synthetase/glutamate synthase (GS/GOGAT) pathway which is of central importance for N uptake and potentially represents a bottle neck for N fertiliser-use efficiency. The aim of this study was to assess whether genetic diversity for N-assimilation capacity exists in wheat and could be exploited for breeding. Wheat plants rapidly, within 6 h, responded to N application with an increase in GS activity. This was not accompanied by an increase in GS gene transcript abundance and a comparison of GS1 and GS2 protein models revealed a high degree of sequence conservation. N responsiveness amongst ten wheat varieties was assessed by measuring GS enzyme activity, leaf tissue ammonium, and by a leaf-disc assay as a proxy for apoplastic ammonia. Based on these data, a high-GS group showing an overall positive response to N could be distinguished from an inefficient, low-GS group. Subsequent gas emission measurements confirmed plant ammonia emission in response to N application and also revealed emission of N2O when N was provided as nitrate, which is in agreement with our current understanding that N2O is a by-product of nitrate reduction. Taken together, the data suggest that there is scope for improving N assimilation capacity in wheat and that further investigations into the regulation and role of GS-GOGAT in NH3 emission is justified. Likewise, emission of the climate gas N2O needs to be reduced, and future research should focus on assessing the nitrate reductase pathway in wheat and explore fertiliser management options.
Collapse
Affiliation(s)
- Maria Oszvald
- Plant Science Department, Rothamsted Research, Harpenden, United Kingdom
| | - Kirsty L. Hassall
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - David Hughes
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom
| | | | - Ian Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Andrew B. Riche
- Plant Science Department, Rothamsted Research, Harpenden, United Kingdom
| | - Sigrid Heuer
- Plant Science Department, Rothamsted Research, Harpenden, United Kingdom
- Department of Crop Improvement and Resilience, NIAB, Cambridge, United Kingdom
| |
Collapse
|
16
|
Zhou Z, Geng S, Guan H, Liu C, Qin M, Li W, Shi X, Dai Z, Yao W, Lei Z, Wu Z, Hou J. Dissection of the Genetic Architecture for Quantities of Gliadins Fractions in Wheat ( Triticum aestivum L.). Front Plant Sci 2022; 13:826909. [PMID: 35401644 PMCID: PMC8988047 DOI: 10.3389/fpls.2022.826909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Gliadin is a group of grain storage proteins that confers extensibility/viscosity to the dough and are vital to end-use quality in wheat. Moreover, gliadins are one of the important components for nutritional quality because they contain the nutritional unprofitable epitopes that cause chronic immune-mediated intestinal disorder in genetically susceptible individuals designated celiac disease (CD). The main genetic loci encoding the gliadins were revealed by previous studies; however, the genes related to the content of gliadins and their fractions were less elucidated. To illustrate the genetic basis of the content of gliadins and their fractions comprehensively, a recombinant inbred line (RIL) population that consisted of 196 lines was constructed from the two parents, Luozhen No.1 and Zhengyumai 9987. Quantitative trait loci (QTL) controlling the content of total gliadins and their fractions (ω-, α-, and γ-gliadin) were screened genome-widely under four environments across 2 years. Totally, thirty QTL which explained 1.97-12.83% of the phenotypic variation were detected to be distributed on 17 chromosomes and they were gathered into 12 clusters. One hundred and one pairs of epistatic QTL (E-QTL) were revealed, among which five were involved with the total gliadins and its fractions content QTL located on chromosome 1AS, 1DS, 4DS, 1DL, and 6AS. Three Kompetitive Allele-Specific PCR (KASP) markers were developed from three major QTL clusters located on chromosomes 6A, 6D, and 7D, respectively. The present research not only dissects the genetic loci for improving the content of gliadins and their three fractions, but may also contribute to marker-assisted selection of varieties with appropriate gliadin fractions content for end-use quality and health benefit at the early developmental stages and early breeding generations.
Collapse
Affiliation(s)
- Zhengfu Zhou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Shenghui Geng
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Huiyue Guan
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Congcong Liu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Maomao Qin
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenxu Li
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xia Shi
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Ziju Dai
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zhensheng Lei
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zhengqing Wu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jinna Hou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| |
Collapse
|
17
|
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) 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
18
|
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. Mol Breed 2022; 42:1. [PMID: 37309486 PMCID: PMC10248672 DOI: 10.1007/s11032-021-01272-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
19
|
Melino VJ, Tester MA, Okamoto M. Strategies for engineering improved nitrogen use efficiency in crop plants via redistribution and recycling of organic nitrogen. Curr Opin Biotechnol 2021; 73:263-269. [PMID: 34560475 DOI: 10.1016/j.copbio.2021.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/29/2021] [Accepted: 09/03/2021] [Indexed: 12/17/2022]
Abstract
Global use of nitrogen (N) fertilizers has increased sevenfold from 1960 to 1995 but much of the N applied is lost to the environment. Modifying the temporal and spatial distribution of organic N within the plant can lead to improved grain yield and/or grain protein content for the same or reduced N fertilizer inputs. Biotechnological approaches to modify whole plant distribution of amino acids and ureides has proven successful in several crop species. Manipulating selective autophagy pathways in crops has also improved N remobilization efficiency to sink tissues whilst the contribution of ribophagy, RNA and purine catabolism to N recycling in crops is still too early to foretell. Improved recycling and remobilization of N must exploit N-stress responsive transcriptional regulators, N-sensing or phloem-localized promotors and genetic variation for N-responsive traits.
Collapse
Affiliation(s)
- Vanessa J Melino
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Mark A Tester
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Mamoru Okamoto
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, 5064, Australia
| |
Collapse
|
20
|
Colasuonno P, Marcotuli I, Gadaleta A, Soriano JM. From Genetic Maps to QTL Cloning: An Overview for Durum Wheat. Plants (Basel) 2021; 10:315. [PMID: 33562160 PMCID: PMC7914919 DOI: 10.3390/plants10020315] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022]
Abstract
Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.
Collapse
Affiliation(s)
- Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
| |
Collapse
|
21
|
Mangini G, Blanco A, Nigro D, Signorile MA, Simeone R. Candidate Genes and Quantitative Trait Loci for Grain Yield and Seed Size in Durum Wheat. Plants (Basel) 2021; 10:plants10020312. [PMID: 33562879 PMCID: PMC7916090 DOI: 10.3390/plants10020312] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 11/22/2022]
Abstract
Grain yield (YLD) is affected by thousand kernel weight (TKW) which reflects the combination of grain length (GL), grain width (GW) and grain area (AREA). Grain weight is also influenced by heading time (HT) and plant height (PH). To detect candidate genes and quantitative trait loci (QTL) of yield components, a durum wheat recombinant inbred line (RIL) population was evaluated in three field trials. The RIL was genotyped with a 90K single nucleotide polymorphism (SNP) array and a high-density genetic linkage map with 5134 markers was obtained. A total of 30 QTL were detected including 23 QTL grouped in clusters on 1B, 2A, 3A, 4B and 6B chromosomes. A QTL cluster on 2A chromosome included a major QTL for HT co-located with QTL for YLD, TKW, GL, GW and AREA, respectively. The photoperiod sensitivity (Ppd-A1) gene was found in the physical position of this cluster. Serine carboxypeptidase, Big grain 1 and β-fructofuranosidase candidate genes were mapped in clusters containing QTL for seed size. This study showed that yield components and phenological traits had higher inheritances than grain yield, allowing an accurate QTL cluster detection. This was a requisite to physically map QTL on durum genome and to identify candidate genes affecting grain yield.
Collapse
Affiliation(s)
- Giacomo Mangini
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (A.B.); (D.N.); (M.A.S.); (R.S.)
- Correspondence:
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (A.B.); (D.N.); (M.A.S.); (R.S.)
| | - Domenica Nigro
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (A.B.); (D.N.); (M.A.S.); (R.S.)
| | - Massimo Antonio Signorile
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (A.B.); (D.N.); (M.A.S.); (R.S.)
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (A.B.); (D.N.); (M.A.S.); (R.S.)
| |
Collapse
|
22
|
Ngoot-Chin T, Zulkifli MA, van de Weg E, Zaki NM, Serdari NM, Mustaffa S, Zainol Abidin MI, Sanusi NSNM, Smulders MJM, Low ETL, Ithnin M, Singh R. Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers. Planta 2021; 253:63. [PMID: 33544231 DOI: 10.1007/s00425-021-03567-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/04/2021] [Indexed: 05/14/2023]
Abstract
Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts. Oil palm produces a quarter of the world's total vegetable oil. In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts of sequence information, allowing SNP discovery. High-capacity SNP genotyping platforms have been widely used for marker-trait association studies in oil palm. Besides genotyping, a SNP array is also an attractive tool for understanding aberrations in chromosome inheritance. Exploiting this, the present study utilized chromosome-wide SNP allelic distributions to determine the ploidy composition of over 1,000 oil palms from a commercial F1 family, including 197 derived from twin-embryo seeds. Our method consisted of an inspection of the allelic intensity ratio using SNP markers. For palms with a shifted or abnormal distribution ratio, the SNP allelic frequencies were plotted along the pseudo-chromosomes. This method proved to be efficient in identifying whole genome duplication (triploids) and aneuploidy. We also detected several loss of heterozygosity regions which may indicate small chromosomal deletions and/or inheritance of identical by descent regions from both parents. The SNP analysis was validated by flow cytometry and chromosome counts. The triploids were all derived from twin-embryo seeds. This is the first report on the efficiency and reliability of SNP array data for karyotyping oil palm chromosomes, as an alternative to the conventional cytogenetic technique. Information on the ploidy composition and chromosomal structural variation can help to better understand the genetic makeup of samples and lead to a more robust interpretation of the genomic data in marker-trait association analyses.
Collapse
Affiliation(s)
- Ting Ngoot-Chin
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Muhammad Azwan Zulkifli
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Noorhariza Mohd Zaki
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Norhalida Mohamed Serdari
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Suzana Mustaffa
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Isa Zainol Abidin
- Plant Breeding and Services Department, KULIM Plantations Berhad, 81900, Kota Tinggi, Johor, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | - Eng Ti Leslie Low
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Maizura Ithnin
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| |
Collapse
|
23
|
Islam S, Zhang J, Zhao Y, She M, Ma W. Genetic regulation of the traits contributing to wheat nitrogen use efficiency. Plant Sci 2021; 303:110759. [PMID: 33487345 DOI: 10.1016/j.plantsci.2020.110759] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/14/2020] [Accepted: 11/11/2020] [Indexed: 05/25/2023]
Abstract
High nitrogen application aimed at increasing crop yield is offset by higher production costs and negative environmental consequences. For wheat, only one third of the applied nitrogen is utilized, which indicates there is scope for increasing Nitrogen Use Efficiency (NUE). However, achieving greater NUE is challenged by the complexity of the trait, which comprises processes associated with nitrogen uptake, transport, reduction, assimilation, translocation and remobilization. Thus, knowledge of the genetic regulation of these processes is critical in increasing NUE. Although primary nitrogen uptake and metabolism-related genes have been well studied, the relative influence of each towards NUE is not fully understood. Recent attention has focused on engineering transcription factors and identification of miRNAs acting on expression of specific genes related to NUE. Knowledge obtained from model species needs to be translated into wheat using recently-released whole genome sequences, and by exploring genetic variations of NUE-related traits in wild relatives and ancient germplasm. Recent findings indicate the genetic basis of NUE is complex. Pyramiding various genes will be the most effective approach to achieve a satisfactory level of NUE in the field.
Collapse
Affiliation(s)
- Shahidul Islam
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Jingjuan Zhang
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Yun Zhao
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Maoyun She
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Wujun Ma
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia.
| |
Collapse
|
24
|
Ruan Y, Yu B, Knox RE, Zhang W, Singh AK, Cuthbert R, Fobert P, DePauw R, Berraies S, Sharpe A, Fu BX, Sangha J. Conditional Mapping Identified Quantitative Trait Loci for Grain Protein Concentration Expressing Independently of Grain Yield in Canadian Durum Wheat. Front Plant Sci 2021; 12:642955. [PMID: 33841470 PMCID: PMC8024689 DOI: 10.3389/fpls.2021.642955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/26/2021] [Indexed: 05/22/2023]
Abstract
Grain protein concentration (GPC) is an important trait in durum cultivar development as a major determinant of the nutritional value of grain and end-use product quality. However, it is challenging to simultaneously select both GPC and grain yield (GY) due to the negative correlation between them. To characterize quantitative trait loci (QTL) for GPC and understand the genetic relationship between GPC and GY in Canadian durum wheat, we performed both traditional and conditional QTL mapping using a doubled haploid (DH) population of 162 lines derived from Pelissier × Strongfield. The population was grown in the field over 5 years and GPC was measured. QTL contributing to GPC were detected on chromosome 1B, 2B, 3A, 5B, 7A, and 7B using traditional mapping. One major QTL on 3A (QGpc.spa-3A.3) was consistently detected over 3 years accounting for 9.4-18.1% of the phenotypic variance, with the favorable allele derived from Pelissier. Another major QTL on 7A (QGpc.spa-7A) detected in 3 years explained 6.9-14.8% of the phenotypic variance, with the beneficial allele derived from Strongfield. Comparison of the QTL described here with the results previously reported led to the identification of one novel major QTL on 3A (QGpc.spa-3A.3) and five novel minor QTL on 1B, 2B and 3A. Four QTL were common between traditional and conditional mapping, with QGpc.spa-3A.3 and QGpc.spa-7A detected in multiple environments. The QTL identified by conditional mapping were independent or partially independent of GY, making them of great importance for development of high GPC and high yielding durum.
Collapse
Affiliation(s)
- Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
- Yuefeng Ruan
| | - Bianyun Yu
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
- *Correspondence: Bianyun Yu
| | - Ron E. Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Wentao Zhang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Asheesh K. Singh
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Pierre Fobert
- Aquatic and Crop Resource Development, National Research Council Canada, Ottawa, ON, Canada
| | - Ron DePauw
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Samia Berraies
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Andrew Sharpe
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Bin Xiao Fu
- Grain Research Laboratory, Canadian Grain Commission, Winnipeg, MB, Canada
| | - Jatinder Sangha
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| |
Collapse
|
25
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.)
| |
Collapse
|
26
|
Singh RK, Prasad A, Muthamilarasan M, Parida SK, Prasad M. Breeding and biotechnological interventions for trait improvement: status and prospects. Planta 2020; 252:54. [PMID: 32948920 PMCID: PMC7500504 DOI: 10.1007/s00425-020-03465-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/12/2020] [Indexed: 05/06/2023]
Abstract
Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.
Collapse
Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
27
|
Mosleth EF, Lillehammer M, Pellny TK, Wood AJ, Riche AB, Hussain A, Griffiths S, Hawkesford MJ, Shewry PR. Genetic variation and heritability of grain protein deviation in European wheat genotypes. Field Crops Res 2020; 255:107896. [PMID: 32943810 PMCID: PMC7397848 DOI: 10.1016/j.fcr.2020.107896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
There is a well-established negative relationship between the yield and the concentration of protein in the mature wheat grain. However, some wheat genotypes consistently deviate from this relationship, a phenomenon known as Grain Protein Deviation (GPD). Positive GPD is therefore of considerable interest in relation to reducing the requirement for nitrogen fertilization for producing wheat for breadmaking. We have carried out two sets of field experiments on multiple sites in South East England. The first set comprised 11 field trials of 6 cultivars grown over three years (2008-2011) and the second comprised 9 field trials of 40 genotypes grown over two years (2015-2017) and 5 field trials of 30 genotypes grown in a single year (2017-2018). All trials comprised three replicate randomized plots of each genotype and nutrient regime. These studies showed strong genetic variation in GPD, which also differed in stability between genotypes, with cultivars bred in the UK generally having higher GPD and higher stability than those bred in other European countries. The heritability of GPD was estimated as 0.44, based on data from the field trials of 30 and 40 genotypes. The largest component contributing to the genetic variance was genotype (0.30), with a smaller contribution of the interaction between genotype and year/site (0.11) and a small (but statistically significant) contribution of nitrogen level. These studies suggest that selection for GPD is a viable target for breeders.
Collapse
Affiliation(s)
| | | | - Till K Pellny
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | | | | | - Abrar Hussain
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Punjab 57000, Pakistan
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | | | - Peter R. Shewry
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
- Corresponding author.
| |
Collapse
|
28
|
Muqaddasi QH, Brassac J, Ebmeyer E, Kollers S, Korzun V, Argillier O, Stiewe G, Plieske J, Ganal MW, Röder MS. Prospects of GWAS and predictive breeding for European winter wheat's grain protein content, grain starch content, and grain hardness. Sci Rep 2020; 10:12541. [PMID: 32719416 PMCID: PMC7385145 DOI: 10.1038/s41598-020-69381-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023] Open
Abstract
Grain quality traits determine the classification of registered wheat (Triticum aestivum L.) varieties. Although environmental factors and crop management practices exert a considerable influence on wheat quality traits, a significant proportion of the variance is attributed to the genetic factors. To identify the underlying genetic factors of wheat quality parameters viz., grain protein content (GPC), grain starch content (GSC), and grain hardness (GH), we evaluated 372 diverse European wheat varieties in replicated field trials in up to eight environments. We observed that all of the investigated traits hold a wide and significant genetic variation, and a significant negative correlation exists between GPC and GSC plus grain yield. Our association analyses based on 26,694 high-quality single nucleotide polymorphic markers revealed a strong quantitative genetic nature of GPC and GSC with associations on groups 2, 3, and 6 chromosomes. The identification of known Puroindoline-b gene for GH provided a positive analytic proof for our studies. We report that a locus QGpc.ipk-6A controls both GPC and GSC with opposite allelic effects. Based on wheat's reference and pan-genome sequences, the physical characterization of two loci viz., QGpc.ipk-2B and QGpc.ipk-6A facilitated the identification of the candidate genes for GPC. Furthermore, by exploiting additive and epistatic interactions of loci, we evaluated the prospects of predictive breeding for the investigated traits that suggested its efficient use in the breeding programs.
Collapse
Affiliation(s)
- Quddoos H Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany.
- European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany.
| | - Jonathan Brassac
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | | | | | | | | | - Gunther Stiewe
- Syngenta Seeds GmbH, 32107, Bad Salzuflen, Germany
- SaKa Beteiligungsgesellschaft mbH, Albert-Einstein-Ring 5, 22761, Hamburg, Germany
| | - Jörg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| |
Collapse
|
29
|
Abstract
Plant nitrogen (N), acquired mainly in the form of nitrate and ammonium from soil, dominates growth and development, and high-yield crop production relies heavily on N fertilization. The mechanisms of root adaptation to altered supply of N forms and concentrations have been well characterized and reviewed, while reports concerning the effects of N on the architecture of vegetative and reproductive organs are limited and are widely dispersed in the literature. In this review, we summarize the nitrate and amino acid regulation of shoot branching, flowering, and panicle development, as well as the N regulation of cell division and expansion in shaping plant architecture, mainly in cereal crops. The basic regulatory steps involving the control of plant architecture by the N supply are auxin-, cytokinin-, and strigolactone-controlled cell division in shoot apical meristem and gibberellin-controlled inverse regulation of shoot height and tillering. In addition, transport of amino acids has been shown to be involved in the control of shoot branching. The N supply may alter the timing and duration of the transition from the vegetative to the reproductive growth phase, which in turn may affect cereal crop architecture, particularly the structure of panicles for grain yield. Thus, proper manipulation of N-regulated architecture can increase crop yield and N use efficiency.
Collapse
Affiliation(s)
- Le Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- China MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
| | - Yali Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- China MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- China MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
- Correspondence:
| |
Collapse
|
30
|
Taranto F, D'Agostino N, Rodriguez M, Pavan S, Minervini AP, Pecchioni N, Papa R, De Vita P. Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm. Front Genet 2020; 11:217. [PMID: 32373150 PMCID: PMC7187681 DOI: 10.3389/fgene.2020.00217] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/24/2020] [Indexed: 01/31/2023] Open
Abstract
The first breeding program in the world for durum wheat was conceived in Italy in the early 1900s. Over the decades, pressure exerted by natural and artificial selection could have progressively reduced the genetic diversity of the durum wheat germplasm. In the present study, a large panel of Italian durum wheat accessions that includes landraces, old and modern cultivars was subjected to genotyping using the Illumina iSelect 15K wheat SNP array. The aim was to assess the impact that selection has in shaping Italian durum wheat genetic diversity and to exploit the patterns of genetic diversity between populations to identify molecular signatures of divergence and selection. Relatively small differences in genetic diversity have been observed among accessions, which have been selected and cultivated in Italy over the past 150 years. Indeed, directional selection combined with that operated by farmers/breeders resulted in the increase of linkage disequilibrium (LD) and in changes of the allelic frequencies in DNA regions that control important agronomic traits. Results from this study also show that major well-known genes and/or QTLs affecting plant height (RHT), earliness (VRN, PPD) and grain quality (GLU, PSY, PSD, LYC, PPO, LOX3) co-localized with outlier SNP loci. Interestingly, many of these SNPs fall in genomic regions where genes involved in nitrogen metabolism are. This finding highlights the key role these genes have played in the transition from landraces to modern cultivars. Finally, our study remarks on the need to fully exploit the genetic diversity of Italian landraces by intense pre-breeding activities aimed at introducing a new source of adaptability and resistance in the genetic background of modern cultivars, to contrast the effect of climate change. The list of divergent loci and loci under selection associated with useful agronomic traits represents an invaluable resource to detect new allelic variants for target genes and for guiding new genomic selection programs in durum wheat.
Collapse
Affiliation(s)
- Francesca Taranto
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, Sassari, Italy.,CBV - Interdepartmental Centre for Plant Biodiversity Conservation and Enhancement Sassari University, Alghero, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Anna P Minervini
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| |
Collapse
|
31
|
Astorkia M, Hernandez M, Bocs S, Lopez de Armentia E, Herran A, Ponce K, León O, Morales S, Quezada N, Orellana F, Wendra F, Sembiring Z, Asmono D, Ritter E. Association Mapping Between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids. Plants (Basel) 2019; 8:plants8100377. [PMID: 31561627 PMCID: PMC6843369 DOI: 10.3390/plants8100377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 01/07/2023]
Abstract
Oil palm production is gaining importance in Central and South America. However, the main species Elaeis guineensis (Eg) is suffering severely from bud rod disease, restricting the potential cultivation areas. Therefore, breeding companies have started to work with interspecific Elaeis oleifera × Eg (Eo × Eg) hybrids which are tolerant to this disease. We performed association studies between candidate gene (CG) single nucleotide polymorphisms (SNP) and six production and 19 oil quality traits in 198 accessions of interspecific oil palm hybrids from five different origins. For this purpose, barcoded amplicons of initially 167 CG were produced from each genotype and sequenced with Ion Torrent. After sequence cleaning 115 SNP remained targeting 62 CG. The influence of the origins on the different traits was analyzed and a genetic diversity study was performed. Two generalized linear models (GLM) with principle component analysis (PCA) or structure (Q) matrixes as covariates and two mixed linear models (MLM) which included in addition a Kinship (K) matrix were applied for association mapping using GAPIT. False discovery rate (FDR) multiple testing corrections were applied in order to avoid Type I errors. However, with FDR adjusted p values no significant associations between SNP and traits were detected. If using unadjusted p values below 0.05, seven of the studied CG showed potential associations with production traits, while 23 CG may influence different quality traits. Under these conditions the current approach and the detected candidate genes could be exploited for selecting genotypes with superior CG alleles in Marker Assisted Selection systems.
Collapse
Affiliation(s)
- Maider Astorkia
- NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain; (M.H.); (E.L.d.A.); (A.H.); (E.R.)
- Correspondence:
| | - Mónica Hernandez
- NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain; (M.H.); (E.L.d.A.); (A.H.); (E.R.)
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, F-34398 Montpellier, France;
- AGAP, CIRAD, Univ Montpellier, INRA, Montpellier SupAgro, F-34398 Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, F-34398 Montpellier, France
| | - Emma Lopez de Armentia
- NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain; (M.H.); (E.L.d.A.); (A.H.); (E.R.)
| | - Ana Herran
- NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain; (M.H.); (E.L.d.A.); (A.H.); (E.R.)
| | - Kevin Ponce
- La Fabril SA, km 5.5 via Manta–Montecristi, Avenida 113, 130902 Manta, Ecuador; (K.P.); (S.M.); (N.Q.)
| | - Olga León
- Energy & Palma SA, Av. Atahualpa E3-49 y Juan Gonzales, Ed. Fundación Pérez Pallarez, Officina 4ª, Quito 170507, Ecuador; (O.L.); (F.O.)
| | - Shone Morales
- La Fabril SA, km 5.5 via Manta–Montecristi, Avenida 113, 130902 Manta, Ecuador; (K.P.); (S.M.); (N.Q.)
| | - Nathalie Quezada
- La Fabril SA, km 5.5 via Manta–Montecristi, Avenida 113, 130902 Manta, Ecuador; (K.P.); (S.M.); (N.Q.)
| | - Francisco Orellana
- Energy & Palma SA, Av. Atahualpa E3-49 y Juan Gonzales, Ed. Fundación Pérez Pallarez, Officina 4ª, Quito 170507, Ecuador; (O.L.); (F.O.)
| | - Fahmi Wendra
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788 Palembang 30127, Indonesia; (F.W.); (Z.S.); (D.A.)
| | - Zulhermana Sembiring
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788 Palembang 30127, Indonesia; (F.W.); (Z.S.); (D.A.)
| | - Dwi Asmono
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788 Palembang 30127, Indonesia; (F.W.); (Z.S.); (D.A.)
| | - Enrique Ritter
- NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain; (M.H.); (E.L.d.A.); (A.H.); (E.R.)
| |
Collapse
|
32
|
Giancaspro A, Giove SL, Zacheo SA, Blanco A, Gadaleta A. Genetic Variation for Protein Content and Yield-Related Traits in a Durum Population Derived From an Inter-Specific Cross Between Hexaploid and Tetraploid Wheat Cultivars. Front Plant Sci 2019; 10:1509. [PMID: 31824537 PMCID: PMC6883369 DOI: 10.3389/fpls.2019.01509] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/30/2019] [Indexed: 05/18/2023]
Abstract
Wheat grain protein content (GPC) and yield components are complex quantitative traits influenced by a multi-factorial system consisting of both genetic and environmental factors. Although seed storage proteins represent less than 15% of mature kernels, they are crucial in determining end-use properties of wheat, as well as the nutritional value of derived products. Yield and GPC are negatively correlated, and this hampers breeding programs of commercially valuable wheat varieties. The goal of this work was the evaluation of genetic variability for quantity and composition of seed storage proteins, together with yield components [grain yield per spike (GYS) and thousand-kernel weight (TKW)] in a durum wheat population obtained by an inter-specific cross between a common wheat accession and the durum cv. Saragolla. Quantitative trait loci (QTL) analysis was conducted and closely associated markers identified on a genetic map composed of 4,366 SNP markers previously obtained in the same durum population genotyped with the 90K iSelect SNP assay. A total of 22 QTL were detected for traits related to durum wheat quality. Six genomic regions responsible for GPC control were mapped on chromosomes 2B, 3A, 4A, 4B, 5B, and 7B, with major QTL on chromosomes 2B, 4A, and 5B. Nine loci were detected for GYS: two on chromosome 5B and 7A and one on chromosomes 2A, 2B, 4A, 4B, 7B, with the strongest QTL on 2B. Eight QTL were identified for TKW, three of which located on chromosome 3A, two on 1B and one on 4B, 5A, and 5B. Only small overlapping was found among QTL for GYS, TKW, and GPC, and increasing alleles coming from both parents on different chromosomes. Good candidate genes were identified in the QTL confidence intervals for GYS and TKW.
Collapse
|