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Roth L, Binder M, Kirchgessner N, Tschurr F, Yates S, Hund A, Kronenberg L, Walter A. From Neglecting to Including Cultivar-Specific Per Se Temperature Responses: Extending the Concept of Thermal Time in Field Crops. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0185. [PMID: 38827955 PMCID: PMC11142864 DOI: 10.34133/plantphenomics.0185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/08/2024] [Indexed: 06/05/2024]
Abstract
Predicting plant development, a longstanding goal in plant physiology, involves 2 interwoven components: continuous growth and the progression of growth stages (phenology). Current models for winter wheat and soybean assume species-level growth responses to temperature. We challenge this assumption, suggesting that cultivar-specific temperature responses substantially affect phenology. To investigate, we collected field-based growth and phenology data in winter wheat and soybean over multiple years. We used diverse models, from linear to neural networks, to assess growth responses to temperature at various trait and covariate levels. Cultivar-specific nonlinear models best explained phenology-related cultivar-environment interactions. With cultivar-specific models, additional relations to other stressors than temperature were found. The availability of the presented field phenotyping tools allows incorporating cultivar-specific temperature response functions in future plant physiology studies, which will deepen our understanding of key factors that influence plant development. Consequently, this work has implications for crop breeding and cultivation under adverse climatic conditions.
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Affiliation(s)
- Lukas Roth
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Martina Binder
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Norbert Kirchgessner
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Flavian Tschurr
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Steven Yates
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Andreas Hund
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zürich, Switzerland
| | | | - Achim Walter
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zürich, Switzerland
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2
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Roth L, Kronenberg L, Aasen H, Walter A, Hartung J, van Eeuwijk F, Piepho HP, Hund A. High-throughput field phenotyping reveals that selection in breeding has affected the phenology and temperature response of wheat in the stem elongation phase. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2084-2099. [PMID: 38134290 DOI: 10.1093/jxb/erad481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/19/2023] [Indexed: 12/24/2023]
Abstract
Crop growth and phenology are driven by seasonal changes in environmental variables, with temperature as one important factor. However, knowledge about genotype-specific temperature response and its influence on phenology is limited. Such information is fundamental to improve crop models and adapt selection strategies. We measured the increase in height of 352 European winter wheat varieties in 4 years to quantify phenology, and fitted an asymptotic temperature response model. The model used hourly fluctuations in temperature to parameterize the base temperature (Tmin), the temperature optimum (rmax), and the steepness (lrc) of growth responses. Our results show that higher Tmin and lrc relate to an earlier start and end of stem elongation. A higher rmax relates to an increased final height. Both final height and rmax decreased for varieties originating from the continental east of Europe towards the maritime west. A genome-wide association study (GWAS) indicated a quantitative inheritance and a large degree of independence among loci. Nevertheless, genomic prediction accuracies (GBLUPs) for Tmin and lrc were low (r≤0.32) compared with other traits (r≥0.59). As well as known, major genes related to vernalization, photoperiod, or dwarfing, the GWAS indicated additional, as yet unknown loci that dominate the temperature response.
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Affiliation(s)
- Lukas Roth
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Lukas Kronenberg
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Helge Aasen
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zurich, Switzerland
- Agroscope, Earth Observation of Agroecosystems Team, Division Agroecology and Environment, Reckenholzstrasse 191, 8046 Zurich, Switzerland
| | - Achim Walter
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Jens Hartung
- University of Hohenheim, Institute for Crop Science, Biostatistics Unit, Fruwirthstrasse 23, D-70593 Stuttgart, Germany
| | - Fred van Eeuwijk
- Wageningen University and Research, Biometris, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Hans-Peter Piepho
- University of Hohenheim, Institute for Crop Science, Biostatistics Unit, Fruwirthstrasse 23, D-70593 Stuttgart, Germany
| | - Andreas Hund
- ETH Zurich, Institute of Agricultural Sciences, Universitätstrasse 2, 8092 Zurich, Switzerland
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Mao H, Jiang C, Tang C, Nie X, Du L, Liu Y, Cheng P, Wu Y, Liu H, Kang Z, Wang X. Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement. MOLECULAR PLANT 2023; 16:1564-1589. [PMID: 37671604 DOI: 10.1016/j.molp.2023.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/19/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023]
Abstract
Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.
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Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuling Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Mroz T, Dieseth JA, Lillemo M. Grain yield and adaptation of spring wheat to Norwegian growing conditions is driven by allele frequency changes at key adaptive loci discovered by genome-wide association mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:191. [PMID: 37589760 PMCID: PMC10435424 DOI: 10.1007/s00122-023-04424-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/24/2023] [Indexed: 08/18/2023]
Abstract
KEY MESSAGE Adaptation to the Norwegian environment is associated with polymorphisms in the Vrn-A1 locus. Historical selection for grain yield in Nordic wheat is associated with TaGS5-3A and TaCol-5 loci. Grain yields in Norwegian spring wheat increased by 18 kg ha-1 per year between 1972 and 2019 due to introduction of new varieties. These gains were associated with increments in the number of grains per spike and extended length of the vegetative period. However, little is known about the genetic background of this progress. To fill this gap, we conducted genome-wide association study on a panel consisting of both adapted (historical and current varieties and lines in the Nordics) and important not adapted accessions used as parents in the Norwegian wheat breeding program. The study concerned grain yield, plant height, and heading and maturity dates, and detected 12 associated loci, later validated using independent sets of recent breeding lines. Adaptation to the Norwegian cropping conditions was found to be associated with the Vrn-A1 locus, and a previously undescribed locus on chromosome 1B associated with heading date. Two loci associated with grain yield, corresponding to the TaGS5-3A and TaCol-5 loci, indicated historical selection pressure for high grain yield. A locus on chromosome 2A explained the tallness of the oldest accessions. We investigated the origins of the beneficial alleles associated with the wheat breeding progress in the Norwegian material, tracing them back to crosses with Swedish, German, or CIMMYT lines. This study contributes to the understanding of wheat adaptation to the Norwegian growing conditions, sheds light on the genetic basis of historical wheat improvement and aids future breeding efforts by discovering loci associated with important agronomic traits in wheat.
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Affiliation(s)
- Tomasz Mroz
- Department of Plant Sciences, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jon Arne Dieseth
- Graminor, AS, Bjørke Gård, Hommelstadvegen 60, 2322, Ridabu, Norway
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, 1432, Ås, Norway.
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Mizuno N, Matsunaka H, Yanaka M, Ishikawa G, Kobayashi F, Nakamura K. Natural variations of wheat EARLY FLOWERING 3 highlight their contributions to local adaptation through fine-tuning of heading time. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:139. [PMID: 37233781 DOI: 10.1007/s00122-023-04386-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE We identified a large chromosomal deletion containing TaELF-B3 that confers early flowering in wheat. This allele has been preferred in recent wheat breeding in Japan to adapt to the environment. Heading at the appropriate time in each cultivation region can greatly contribute to stabilizing and maximizing yield. Vrn-1 and Ppd-1 are known as the major genes for vernalization requirement and photoperiod sensitivity in wheat. Genotype combinations of Vrn-1 and Ppd-1 can explain the variation in heading time. However, the genes that can explain the remaining variations in heading time are largely unknown. In this study, we aimed to identify the genes conferring early heading using doubled haploid lines derived from Japanese wheat varieties. Quantitative trait locus (QTL) analysis revealed a significant QTL on the long arm of chromosome 1B in multiple growing seasons. Genome sequencing using Illumina short reads and Pacbio HiFi reads revealed a large deletion of a ~ 500 kb region containing TaELF-B3, an orthologue of Arabidopsis clock gene EARLY FLOWERING 3 (ELF3). Plants with the deleted allele of TaELF-B3 (ΔTaELF-B3 allele) headed earlier only under short-day vernalization conditions. Higher expression levels of clock- and clock-output genes, such as Ppd-1 and TaGI, were observed in plants with the ΔTaELF-B3 allele. These results suggest that the deletion of TaELF-B3 causes early heading. Of the TaELF-3 homoeoalleles conferring early heading, the ΔTaELF-B3 allele showed the greatest effect on the early heading phenotype in Japan. The higher allele frequency of the ΔTaELF-B3 allele in western Japan suggests that the ΔTaELF-B3 allele was preferred during recent breeding to adapt to the environment. TaELF-3 homoeologs will help to expand the cultivated area by fine-tuning the optimal timing of heading in each environment.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Hitoshi Matsunaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-Minami, Memuro, Kasai, Hokkaido, 082-0081, Japan
| | - Mikiko Yanaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazuhiro Nakamura
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
- Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8517, Japan
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Alvarez MA, Li C, Lin H, Joe A, Padilla M, Woods DP, Dubcovsky J. EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time. PLoS Genet 2023; 19:e1010655. [PMID: 37163495 PMCID: PMC10171656 DOI: 10.1371/journal.pgen.1010655] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/04/2023] [Indexed: 05/12/2023] Open
Abstract
The photoperiodic response is critical for plants to adjust their reproductive phase to the most favorable season. Wheat heads earlier under long days (LD) than under short days (SD) and this difference is mainly regulated by the PHOTOPERIOD1 (PPD1) gene. Tetraploid wheat plants carrying the Ppd-A1a allele with a large deletion in the promoter head earlier under SD than plants carrying the wildtype Ppd-A1b allele with an intact promoter. Phytochromes PHYB and PHYC are necessary for the light activation of PPD1, and mutations in either of these genes result in the downregulation of PPD1 and very late heading time. We show here that both effects are reverted when the phyB mutant is combined with loss-of-function mutations in EARLY FLOWERING 3 (ELF3), a component of the Evening Complex (EC) in the circadian clock. We also show that the wheat ELF3 protein interacts with PHYB and PHYC, is rapidly modified by light, and binds to the PPD1 promoter in planta (likely as part of the EC). Deletion of the ELF3 binding region in the Ppd-A1a promoter results in PPD1 upregulation at dawn, similar to PPD1 alleles with intact promoters in the elf3 mutant background. The upregulation of PPD1 is correlated with the upregulation of the florigen gene FLOWERING LOCUS T1 (FT1) and early heading time. Loss-of-function mutations in PPD1 result in the downregulation of FT1 and delayed heading, even when combined with the elf3 mutation. Taken together, these results indicate that ELF3 operates downstream of PHYB as a direct transcriptional repressor of PPD1, and that this repression is relaxed both by light and by the deletion of the ELF3 binding region in the Ppd-A1a promoter. In summary, the regulation of the light mediated activation of PPD1 by ELF3 is critical for the photoperiodic regulation of wheat heading time.
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Affiliation(s)
- Maria Alejandra Alvarez
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Chengxia Li
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Huiqiong Lin
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Anna Joe
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Mariana Padilla
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Daniel P Woods
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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Kopecká R, Kameniarová M, Černý M, Brzobohatý B, Novák J. Abiotic Stress in Crop Production. Int J Mol Sci 2023; 24:ijms24076603. [PMID: 37047573 PMCID: PMC10095105 DOI: 10.3390/ijms24076603] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
The vast majority of agricultural land undergoes abiotic stress that can significantly reduce agricultural yields. Understanding the mechanisms of plant defenses against stresses and putting this knowledge into practice is, therefore, an integral part of sustainable agriculture. In this review, we focus on current findings in plant resistance to four cardinal abiotic stressors—drought, heat, salinity, and low temperatures. Apart from the description of the newly discovered mechanisms of signaling and resistance to abiotic stress, this review also focuses on the importance of primary and secondary metabolites, including carbohydrates, amino acids, phenolics, and phytohormones. A meta-analysis of transcriptomic studies concerning the model plant Arabidopsis demonstrates the long-observed phenomenon that abiotic stressors induce different signals and effects at the level of gene expression, but genes whose regulation is similar under most stressors can still be traced. The analysis further reveals the transcriptional modulation of Golgi-targeted proteins in response to heat stress. Our analysis also highlights several genes that are similarly regulated under all stress conditions. These genes support the central role of phytohormones in the abiotic stress response, and the importance of some of these in plant resistance has not yet been studied. Finally, this review provides information about the response to abiotic stress in major European crop plants—wheat, sugar beet, maize, potatoes, barley, sunflowers, grapes, rapeseed, tomatoes, and apples.
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Affiliation(s)
- Romana Kopecká
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Michaela Kameniarová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Jan Novák
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
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Wittern L, Steed G, Taylor LJ, Ramirez DC, Pingarron-Cardenas G, Gardner K, Greenland A, Hannah MA, Webb AAR. Wheat EARLY FLOWERING 3 affects heading date without disrupting circadian oscillations. PLANT PHYSIOLOGY 2023; 191:1383-1403. [PMID: 36454669 PMCID: PMC9922389 DOI: 10.1093/plphys/kiac544] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 09/23/2022] [Accepted: 11/29/2022] [Indexed: 05/26/2023]
Abstract
Plant breeders have indirectly selected for variation at circadian-associated loci in many of the world's major crops, when breeding to increase yield and improve crop performance. Using an eight-parent Multiparent Advanced Generation Inter-Cross (MAGIC) population, we investigated how variation in circadian clock-associated genes contributes to the regulation of heading date in UK and European winter wheat (Triticum aestivum) varieties. We identified homoeologues of EARLY FLOWERING 3 (ELF3) as candidates for the Earliness per se (Eps) D1 and B1 loci under field conditions. We then confirmed a single-nucleotide polymorphism within the coding region of TaELF3-B1 as a candidate polymorphism underlying the Eps-B1 locus. We found that a reported deletion at the Eps-D1 locus encompassing TaELF3-D1 is, instead, an allele that lies within an introgression region containing an inversion relative to the Chinese Spring D genome. Using Triticum turgidum cv. Kronos carrying loss-of-function alleles of TtELF3, we showed that ELF3 regulates heading, with loss of a single ELF3 homoeologue sufficient to alter heading date. These studies demonstrated that ELF3 forms part of the circadian oscillator; however, the loss of all homoeologues was required to affect circadian rhythms. Similarly, loss of functional LUX ARRHYTHMO (LUX) in T. aestivum, an orthologue of a protein partner of Arabidopsis (Arabidopsis thaliana) ELF3, severely disrupted circadian rhythms. ELF3 and LUX transcripts are not co-expressed at dusk, suggesting that the structure of the wheat circadian oscillator might differ from that of Arabidopsis. Our demonstration that alterations to ELF3 homoeologues can affect heading date separately from effects on the circadian oscillator suggests a role for ELF3 in cereal photoperiodic responses that could be selected for without pleiotropic deleterious alterations to circadian rhythms.
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9
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Benaouda S, Stöcker T, Schoof H, Léon J, Ballvora A. Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat. BMC PLANT BIOLOGY 2023; 23:25. [PMID: 36631761 PMCID: PMC9835304 DOI: 10.1186/s12870-022-03986-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The transition from vegetative to floral phase is the result of complex crosstalk of exogenous and endogenous floral integrators. This critical physiological event is the response to environmental interaction, which causes biochemical cascades of reactions at different internal tissues, organs, and releases signals that make the plant moves from vegetative status to a reproductive phase. This network controlling flowering time is not deciphered largely in bread wheat. In this study, a comparative transcriptome analysis at a transition time in combination with genetic mapping was used to identify responsible genes in a stage and tissue-specific manner. For this reason, two winter cultivars that have been bred in Germany showing contrasting and stable heading time in different environments were selected for the analysis. RESULTS In total, 670 and 1075 differentially expressed genes in the shoot apical meristem and leaf tissue, respectively, could be identified in 23 QTL intervals for the heading date. In the transition apex, Histone methylation H3-K36 and regulation of circadian rhythm are both controlled by the same homoeolog genes mapped in QTL TaHd112, TaHd124, and TaHd137. TaAGL14 gene that identifies the floral meristem was mapped in TaHd054 in the double ridge. In the same stage, the homoeolog located on chromosome 7D of FLOWERING TIME LOCUS T mapped on chr 7B, which evolved an antagonist function and acts as a flowering repressor was uncovered. The wheat orthologue of transcription factor ASYMMETRIC LEAVES 1 (AS1) was identified in the late reproductive stage and was mapped in TaHd102, which is strongly associated with heading date. Deletion of eight nucleotides in the AS1 promoter could be identified in the binding site of the SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 (SOC1) gene in the late flowering cultivar. Both proteins AS1 and SOC1 are inducing flowering time in response to gibberellin biosynthesis. CONCLUSION The global transcriptomic at the transition phase uncovered stage and tissue-specific genes mapped in QTL of heading date in winter wheat. In response to Gibberellin signaling, wheat orthologous transcription factor AS1 is expressed in the late reproductive phase of the floral transition. The locus harboring this gene is the strongest QTL associated with the heading date trait in the German cultivars. Consequently, we conclude that this is another indication of the Gibberellin biosynthesis as the mechanism behind the heading variation in wheat.
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Affiliation(s)
- Salma Benaouda
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Tyll Stöcker
- Institute for Crop Science and Resource Conservation, Chair of Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- Institute for Crop Science and Resource Conservation, Chair of Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Jens Léon
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
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10
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Rees H, Rusholme-Pilcher R, Bailey P, Colmer J, White B, Reynolds C, Ward SJ, Coombes B, Graham CA, de Barros Dantas LL, Dodd AN, Hall A. Circadian regulation of the transcriptome in a complex polyploid crop. PLoS Biol 2022; 20:e3001802. [PMID: 36227835 PMCID: PMC9560141 DOI: 10.1371/journal.pbio.3001802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/18/2022] [Indexed: 11/07/2022] Open
Abstract
The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.
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Affiliation(s)
- Hannah Rees
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Paul Bailey
- Royal Botanic Gardens Kew, Richmond, Surrey, United Kingdom
| | - Joshua Colmer
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Benjamen White
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Connor Reynolds
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Benedict Coombes
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Calum A. Graham
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Antony N. Dodd
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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Maeda AE, Nakamichi N. Plant clock modifications for adapting flowering time to local environments. PLANT PHYSIOLOGY 2022; 190:952-967. [PMID: 35266545 PMCID: PMC9516756 DOI: 10.1093/plphys/kiac107] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/09/2022] [Indexed: 05/25/2023]
Abstract
During and after the domestication of crops from ancestral wild plants, humans selected cultivars that could change their flowering time in response to seasonal daylength. Continuous selection of this trait eventually allowed the introduction of crops into higher or lower latitudes and different climates from the original regions where domestication initiated. In the past two decades, numerous studies have found the causal genes or alleles that change flowering time and have assisted in adapting crop species such as barley (Hordeum vulgare), wheat (Triticum aestivum L.), rice (Oryza sativa L.), pea (Pisum sativum L.), maize (Zea mays spp. mays), and soybean (Glycine max (L.) Merr.) to new environments. This updated review summarizes the genes or alleles that contributed to crop adaptation in different climatic areas. Many of these genes are putative orthologs of Arabidopsis (Arabidopsis thaliana) core clock genes. We also discuss how knowledge of the clock's molecular functioning can facilitate molecular breeding in the future.
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Affiliation(s)
- Akari E Maeda
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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12
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Benaouda S, Dadshani S, Koua P, Léon J, Ballvora A. Identification of QTLs for wheat heading time across multiple-environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2833-2848. [PMID: 35776141 PMCID: PMC9325850 DOI: 10.1007/s00122-022-04152-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The genetic response to changing climatic factors selects consistent across the tested environments and location-specific thermo-sensitive and photoperiod susceptible alleles in lower and higher altitudes, respectively, for starting flowering in winter wheat. Wheat breeders select heading date to match the most favorable conditions for their target environments and this is favored by the extensive genetic variation for this trait that has the potential to be further explored. In this study, we used a germplasm with broad geographic distribution and tested it in multi-location field trials across Germany over three years. The genotypic response to the variation in the climatic parameters depending on location and year uncovered the effect of photoperiod and spring temperatures in accelerating heading date in higher and lower latitudes, respectively. Spring temperature dominates other factors in inducing heading, whereas the higher amount of solar radiation delays it. A genome-wide scan of marker-trait associations with heading date detected two QTL: an adapted allele at locus TaHd102 on chromosome 5A that has a consistent effect on HD in German cultivars in multiple environments and a non-adapted allele at locus TaHd044 on chromosome 3A that accelerates flowering by 5.6 days. TaHd102 and TaHd044 explain 13.8% and 33% of the genetic variance, respectively. The interplay of the climatic variables led to the detection of environment specific association responding to temperature in lower latitudes and photoperiod in higher ones. Another locus TaHd098 on chromosome 5A showed epistatic interactions with 15 known regulators of flowering time when non-adapted cultivars from outside Germany were included in the analysis.
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Affiliation(s)
- Salma Benaouda
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, Rheinische Friedrich-Wilhelms-University, Katzenburgweg 5, 53115, Bonn, Germany
| | - Said Dadshani
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, Rheinische Friedrich-Wilhelms-University, Katzenburgweg 5, 53115, Bonn, Germany
| | - Patrice Koua
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, Rheinische Friedrich-Wilhelms-University, Katzenburgweg 5, 53115, Bonn, Germany
| | - Jens Léon
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, Rheinische Friedrich-Wilhelms-University, Katzenburgweg 5, 53115, Bonn, Germany
- Field Lab Campus Klein-Altendorf, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Agim Ballvora
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, Rheinische Friedrich-Wilhelms-University, Katzenburgweg 5, 53115, Bonn, Germany.
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13
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Bhati PK, Juliana P, Singh RP, Joshi AK, Vishwakarma MK, Poland J, Govindan V, Shrestha S, Crespo-Herrera L, Mondal S, Huerta-Espino J, Kumar U. Dissecting the Genetic Architecture of Phenology Affecting Adaptation of Spring Bread Wheat Genotypes to the Major Wheat-Producing Zones in India. FRONTIERS IN PLANT SCIENCE 2022; 13:920682. [PMID: 35873987 PMCID: PMC9298574 DOI: 10.3389/fpls.2022.920682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Spring bread wheat adaptation to diverse environments is supported by various traits such as phenology and plant architecture. A large-scale genome-wide association study (GWAS) was designed to investigate and dissect the genetic architecture of phenology affecting adaptation. It used 48 datasets from 4,680 spring wheat lines. For 8 years (2014-2021), these lines were evaluated for days to heading (DH) and maturity (DM) at three sites: Jabalpur, Ludhiana, and Samastipur (Pusa), which represent the three major Indian wheat-producing zones: the Central Zone (CZ), North-Western Plain Zone (NWPZ), and North-Eastern Plain Zone (NEPZ), respectively. Ludhiana had the highest mean DH of 103.8 days and DM of 148.6 days, whereas Jabalpur had the lowest mean DH of 77.7 days and DM of 121.6 days. We identified 119 markers significantly associated with DH and DM on chromosomes 5B (76), 2B (18), 7D (10), 4D (8), 5A (1), 6B (4), 7B (1), and 3D (1). Our results clearly indicated the importance of the photoperiod-associated gene (Ppd-B1) for adaptation to the NWPZ and the Vrn-B1 gene for adaptation to the NEPZ and CZ. A maximum variation of 21.1 and 14% was explained by markers 2B_56134146 and 5B_574145576 linked to the Ppd-B1 and Vrn-B1 genes, respectively, indicating their significant role in regulating DH and DM. The results provide important insights into the genomic regions associated with the two phenological traits that influence adaptation to the major wheat-producing zones in India.
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Affiliation(s)
- Pradeep Kumar Bhati
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Philomin Juliana
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Arun Kumar Joshi
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Manish Kumar Vishwakarma
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Sandesh Shrestha
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | | | - Suchismita Mondal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México-INIFAP, Carretera los Reyes-Texcoco, Texcoco, Mexico
| | - Uttam Kumar
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
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14
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Yield-Related QTL Clusters and the Potential Candidate Genes in Two Wheat DH Populations. Int J Mol Sci 2021; 22:ijms222111934. [PMID: 34769361 PMCID: PMC8585063 DOI: 10.3390/ijms222111934] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9–16.5 Mb), 2B.3, 3B (68.9–214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1–613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3–672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0–56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding.
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15
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Steed G, Ramirez DC, Hannah MA, Webb AAR. Chronoculture, harnessing the circadian clock to improve crop yield and sustainability. Science 2021; 372:372/6541/eabc9141. [PMID: 33926926 DOI: 10.1126/science.abc9141] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human health is dependent on a plentiful and nutritious supply of food, primarily derived from crop plants. Rhythmic supply of light as a result of the day and night cycle led to the evolution of circadian clocks that modulate most plant physiology, photosynthesis, metabolism, and development. To regulate crop traits and adaptation, breeders have indirectly selected for variation at circadian genes. The pervasive impact of the circadian system on crops suggests that future food production might be improved by modifying circadian rhythms, engineering the timing of transgene expression, and applying agricultural treatments at the most effective time of day. We describe the applied research required to take advantage of circadian biology in agriculture to increase production and reduce inputs.
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Affiliation(s)
- Gareth Steed
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Dora Cano Ramirez
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Matthew A Hannah
- BASF, BBCC-Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
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16
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Martinez AF, Lister C, Freeman S, Ma J, Berry S, Wingen L, Griffiths S. Resolving a QTL complex for height, heading, and grain yield on chromosome 3A in bread wheat. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2965-2978. [PMID: 33578415 PMCID: PMC8023219 DOI: 10.1093/jxb/erab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 02/11/2021] [Indexed: 05/28/2023]
Abstract
Crop height (Ht), heading date (Hd), and grain yield (GY) are inter-related in wheat. Independent manipulation of each is important for adaptation and performance. Validated quantitative trait loci (QTLs) for all three co-locate on chromosome 3A in the Avalon×Cadenza population, with increased Ht, Hd, and GY contributed by Cadenza. We asked if these are linked or pleiotropic effects using recombinant lines, and showed that Ht and Hd effects are independent. The Chinese Spring equivalent to the newly defined Ht interval contained a gene cluster involved in cell wall growth and displaying high levels of differential transcript expression. The Hd locus is larger and rearranged compared with the reference genome, but FT2 (Flowering Locus T2) is of particular interest. The Hd effect acted independently of photoperiod and vernalization, but did exhibit seasonal genotype×environment interaction. Recombinants were phenotyped for GY in replicated field experiments. GY was most associated with Cadenza alleles for later Hd, supporting physiological studies using the same lines proposing that 'late' alleles at this locus increase spike fertility and grain number (GN). The work has uncoupled height from heading and yield, and shown that one of very few validated GY QTLs in wheat is probably mediated by phenological variation.
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Affiliation(s)
| | - Clare Lister
- John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Sue Freeman
- John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Simon Berry
- Limagrain UK, Woolpit Business Park, Woolpit, Bury St Edmunds, Suffolk,UK
| | - Luzie Wingen
- John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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17
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Wheat Developmental Traits as Affected by the Interaction between Eps-7D and Temperature under Contrasting Photoperiods with Insensitive Ppd-D1 Background. PLANTS 2021; 10:plants10030547. [PMID: 33805828 PMCID: PMC7999118 DOI: 10.3390/plants10030547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 01/14/2023]
Abstract
Earliness per se (Eps) genes are important to fine tune adaptation, and studying their probable pleiotropic effect on wheat yield traits is worthwhile. In addition, it has been shown that some Eps genes interact with temperature and therefore determining the likely Eps × temperature interaction is needed for each newly identified Eps gene. We studied two NILs differing in the newly identified Eps-7D (carrying insensitive Ppd-D1 in the background) under three temperature regimes (9, 15 and 18 °C) and two photoperiods (12 and 24 h). Eps-7D affected time to anthesis as expected and the Eps-7D-late allele extended both the period before and after terminal spikelet. The interaction effect of Eps-7D × temperature was significant but not cross-over: the magnitude and level of significance of the difference between NILs with the late or early allele was affected by the growing temperature (i.e., difference was least at 18 °C and largest at 9 °C), and the differences caused due to temperature sensitivity were influenced by photoperiod. The rate of leaf initiation was faster in NIL with Eps-7D-early than with the late allele which compensated for the shorter duration of leaf initiation resulting in similar final leaf number between two NILs. Eps-7D-late consistently increased spike fertility through improving floret primordia survival as a consequence of extending the late reproductive phase.
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18
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Basavaraddi PA, Savin R, Bencivenga S, Griffiths S, Slafer GA. Phenology and Floret Development as Affected by the Interaction between Eps-7D and Ppd-D1. PLANTS 2021; 10:plants10030533. [PMID: 33809009 PMCID: PMC8001856 DOI: 10.3390/plants10030533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022]
Abstract
Earliness per se (Eps) genes may play a critical role in further improving wheat adaptation and fine-tuning wheat development to cope with climate change. There are only few studies on the detailed effect of Eps on wheat development and fewer on the interaction of Eps with the environment and other genes determining time to anthesis. Furthermore, it seems relevant to study every newly discovered Eps gene and its probable interactions as the mechanisms and detailed effects of each Eps may be quite different. In the present study, we evaluated NILs differing in the recently identified Eps-7D as well as in Ppd-D1 at three temperature regimes (9, 15 and 18 °C) under short day. The effect of Eps-7D on time to anthesis as well as on its component phases varied both qualitatively and quantitatively depending on the allelic status of Ppd-D1 and temperature, being larger in a photoperiod-sensitive background. A more noticeable effect of Eps-7D (when combined with Ppd-D1b) was realised during the late reproductive phase. Consequently, the final leaf number was not clearly altered by Eps-7D, while floret development of the labile florets (florets 2 and 3 in this case, depending on the particular spikelet) was favoured by the action of the Eps-7D-late allele, increasing the likelihood of particular florets to become fertile, and consequently, improving spike fertility when combined with Ppd-D1b.
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Affiliation(s)
- Priyanka A. Basavaraddi
- Department of Crop and Forest Sciences-AGROTECNIO CERCA Center, University of Lleida, Av. R. Roure 191, 25198 Lleida, Spain; (P.A.B.); (R.S.)
| | - Roxana Savin
- Department of Crop and Forest Sciences-AGROTECNIO CERCA Center, University of Lleida, Av. R. Roure 191, 25198 Lleida, Spain; (P.A.B.); (R.S.)
| | - Stefano Bencivenga
- John Innes Centre, Norwich Research Park, Colney Ln, Norwich NR4 7UH, UK; (S.B.); (S.G.)
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Ln, Norwich NR4 7UH, UK; (S.B.); (S.G.)
| | - Gustavo A. Slafer
- Department of Crop and Forest Sciences-AGROTECNIO CERCA Center, University of Lleida, Av. R. Roure 191, 25198 Lleida, Spain; (P.A.B.); (R.S.)
- ICREA, Catalonian Institution for Research and Advanced Studies, 23, 08010 Barcelona, Spain
- Correspondence:
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19
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Bogard M, Hourcade D, Piquemal B, Gouache D, Deswartes JC, Throude M, Cohan JP. Marker-based crop model-assisted ideotype design to improve avoidance of abiotic stress in bread wheat. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1085-1103. [PMID: 33068400 DOI: 10.1093/jxb/eraa477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/12/2020] [Indexed: 05/22/2023]
Abstract
Wheat phenology allows escape from seasonal abiotic stresses including frosts and high temperatures, the latter being forecast to increase with climate change. The use of marker-based crop models to identify ideotypes has been proposed to select genotypes adapted to specific weather and management conditions and anticipate climate change. In this study, a marker-based crop model for wheat phenology was calibrated and tested. Climate analysis of 30 years of historical weather data in 72 locations representing the main wheat production areas in France was performed. We carried out marker-based crop model simulations for 1019 wheat cultivars and three sowing dates, which allowed calculation of genotypic stress avoidance frequencies of frost and heat stress and identification of ideotypes. The phenology marker-based crop model allowed prediction of large genotypic variations for the beginning of stem elongation (GS30) and heading date (GS55). Prediction accuracy was assessed using untested genotypes and environments, and showed median genotype prediction errors of 8.5 and 4.2 days for GS30 and GS55, respectively. Climate analysis allowed the definition of a low risk period for each location based on the distribution of the last frost and first heat days. Clustering of locations showed three groups with contrasting levels of frost and heat risks. Marker-based crop model simulations showed the need to optimize the genotype depending on sowing date, particularly in high risk environments. An empirical validation of the approach showed that it holds good promises to improve frost and heat stress avoidance.
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Affiliation(s)
- Matthieu Bogard
- Arvalis - Institut du Végétal, 6 Chemin de la côte vieille, Baziège, France
| | - Delphine Hourcade
- Arvalis - Institut du Végétal, 6 Chemin de la côte vieille, Baziège, France
| | - Benoit Piquemal
- Arvalis - Institut du Végétal, station expérimentale, Boigneville, France
| | | | - Jean-Charles Deswartes
- Arvalis - Institut du Végétal, Route de Châteaufort ZA des graviers, Villiers-le-Bâcle, France
| | - Mickael Throude
- Biogemma: Centre de Recherche de Chappes, Route d'Ennezat, CS, Chappes, France
| | - Jean-Pierre Cohan
- Arvalis - Institut du Végétal, Station expérimentale de La Jaillière, La Chapelle Saint-Sauveur, Loireauxence, France
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20
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Kronenberg L, Yates S, Boer MP, Kirchgessner N, Walter A, Hund A. Temperature response of wheat affects final height and the timing of stem elongation under field conditions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:700-717. [PMID: 33057698 PMCID: PMC7853599 DOI: 10.1093/jxb/eraa471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/10/2020] [Indexed: 05/18/2023]
Abstract
In wheat, temperature affects the timing and intensity of stem elongation. Genetic variation for this process is therefore important for adaptation. This study investigates the genetic response to temperature fluctuations during stem elongation and its relationship to phenology and height. Canopy height of 315 wheat genotypes (GABI wheat panel) was scanned twice weekly in the field phenotyping platform (FIP) of ETH Zurich using a LIDAR. Temperature response was modelled using linear regressions between stem elongation and mean temperature in each measurement interval. This led to a temperature-responsive (slope) and a temperature-irresponsive (intercept) component. The temperature response was highly heritable (H2=0.81) and positively related to a later start and end of stem elongation as well as final height. Genome-wide association mapping revealed three temperature-responsive and four temperature-irresponsive quantitative trait loci (QTLs). Furthermore, putative candidate genes for temperature-responsive QTLs were frequently related to the flowering pathway in Arabidopsis thaliana, whereas temperature-irresponsive QTLs corresponded to growth and reduced height genes. In combination with Rht and Ppd alleles, these loci, together with the loci for the timing of stem elongation, accounted for 71% of the variability in height. This demonstrates how high-throughput field phenotyping combined with environmental covariates can contribute to a smarter selection of climate-resilient crops.
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Affiliation(s)
- Lukas Kronenberg
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Martin P Boer
- Biometris, Wageningen University & Research, PB Wageningen, The Netherlands
| | - Norbert Kirchgessner
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Achim Walter
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Andreas Hund
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
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21
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Kronenberg L, Yates S, Boer MP, Kirchgessner N, Walter A, Hund A. Temperature response of wheat affects final height and the timing of stem elongation under field conditions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:700-717. [PMID: 33057698 DOI: 10.1101/756700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/10/2020] [Indexed: 05/29/2023]
Abstract
In wheat, temperature affects the timing and intensity of stem elongation. Genetic variation for this process is therefore important for adaptation. This study investigates the genetic response to temperature fluctuations during stem elongation and its relationship to phenology and height. Canopy height of 315 wheat genotypes (GABI wheat panel) was scanned twice weekly in the field phenotyping platform (FIP) of ETH Zurich using a LIDAR. Temperature response was modelled using linear regressions between stem elongation and mean temperature in each measurement interval. This led to a temperature-responsive (slope) and a temperature-irresponsive (intercept) component. The temperature response was highly heritable (H2=0.81) and positively related to a later start and end of stem elongation as well as final height. Genome-wide association mapping revealed three temperature-responsive and four temperature-irresponsive quantitative trait loci (QTLs). Furthermore, putative candidate genes for temperature-responsive QTLs were frequently related to the flowering pathway in Arabidopsis thaliana, whereas temperature-irresponsive QTLs corresponded to growth and reduced height genes. In combination with Rht and Ppd alleles, these loci, together with the loci for the timing of stem elongation, accounted for 71% of the variability in height. This demonstrates how high-throughput field phenotyping combined with environmental covariates can contribute to a smarter selection of climate-resilient crops.
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Affiliation(s)
- Lukas Kronenberg
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Martin P Boer
- Biometris, Wageningen University & Research, PB Wageningen, The Netherlands
| | - Norbert Kirchgessner
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Achim Walter
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Andreas Hund
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
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22
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Basavaraddi PA, Savin R, Wingen LU, Bencivenga S, Przewieslik-Allen AM, Griffiths S, Slafer GA. Interactions between two QTLs for time to anthesis on spike development and fertility in wheat. Sci Rep 2021; 11:2451. [PMID: 33510240 PMCID: PMC7843729 DOI: 10.1038/s41598-021-81857-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
Earliness per se (Eps) genes are reported to be important in fine-tuning flowering time in wheat independently of photoperiod (Ppd) and vernalisation (Vrn). Unlike Ppd and Vrn genes, Eps have relatively small effects and their physiological effect along with chromosomal position are not well defined. We evaluated eight lines derived from crossing two vernalisation insensitive lines, Paragon and Baj (late and early flowering respectively), to study the detailed effects of two newly identified QTLs, Eps-7D and Eps-2B and their interactions under field conditions. The effect of both QTLs was minor and was affected by the allelic status of the other. While the magnitude of effect of these QTLs on anthesis was similar, they are associated with very different profiles of pre-anthesis development which also depends on their interaction. Eps-7D affected both duration before and after terminal spikelet while not affecting final leaf number (FLN) so Eps-7D-early had a faster rate of leaf appearance. Eps-2B acted more specifically in the early reproductive phase and slightly altered FLN without affecting the leaf appearance rate. Both QTLs affected the spike fertility by altering the rate of floret development and mortality. The effect of Eps-2B was very small but consistent in that -late allele tended to produce more fertile florets.
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Affiliation(s)
- Priyanka A. Basavaraddi
- grid.15043.330000 0001 2163 1432Department of Crop and Forest Sciences, University of Lleida-AGROTECNIO Center, Av. R. Roure 191, 25198 Lleida, Spain
| | - Roxana Savin
- grid.15043.330000 0001 2163 1432Department of Crop and Forest Sciences, University of Lleida-AGROTECNIO Center, Av. R. Roure 191, 25198 Lleida, Spain
| | - Luzie U. Wingen
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Stefano Bencivenga
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | - Simon Griffiths
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Gustavo A. Slafer
- grid.15043.330000 0001 2163 1432Department of Crop and Forest Sciences, University of Lleida-AGROTECNIO Center, Av. R. Roure 191, 25198 Lleida, Spain ,grid.425902.80000 0000 9601 989XICREA, Catalonian Institution for Research and Advanced Studies, Barcelona, Spain
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DEFECTIVE ENDOSPERM-D1 (Dee-D1) is crucial for endosperm development in hexaploid wheat. Commun Biol 2020; 3:791. [PMID: 33361776 PMCID: PMC7758331 DOI: 10.1038/s42003-020-01509-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
Hexaploid wheat (Triticum aestivum L.) is a natural allopolyploid and provides a usable model system to better understand the genetic mechanisms that underlie allopolyploid speciation through the hybrid genome doubling. Here we aimed to identify the contribution of chromosome 1D in the development and evolution of hexaploid wheat. We identified and mapped a novel DEFECTIVE ENDOSPERM–D1 (Dee-D1) locus on 1DL that is involved in the genetic control of endosperm development. The absence of Dee-D1 leads to non-viable grains in distant crosses and alters grain shape, which negatively affects grain number and thousand-grain weight. Dee-D1 can be classified as speciation locus with a positive effect on the function of genes which are involved in endosperm development in hybrid genomes. The presence of Dee-D1 is necessary for the normal development of endosperm, and thus play an important role in the evolution and improvement of grain yield in hexaploid wheat. Natalia Tikhenko et al. investigate the genetic contribution of the wheat chromosome 1D to its development and evolution. They find a novel locus, DEFECTIVE ENDOSPERM-D1, on the long arm of 1D that is required for normal endosperm development as its absence leads to non-viable grains and altered grain shape.
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Jacott CN, Boden SA. Feeling the heat: developmental and molecular responses of wheat and barley to high ambient temperatures. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5740-5751. [PMID: 32667992 PMCID: PMC7540836 DOI: 10.1093/jxb/eraa326] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/10/2020] [Indexed: 05/22/2023]
Abstract
The increasing demand for global food security in the face of a warming climate is leading researchers to investigate the physiological and molecular responses of cereals to rising ambient temperatures. Wheat and barley are temperate cereals whose yields are adversely affected by high ambient temperatures, with each 1 °C increase above optimum temperatures reducing productivity by 5-6%. Reproductive development is vulnerable to high-temperature stress, which reduces yields by decreasing grain number and/or size and weight. In recent years, analysis of early inflorescence development and genetic pathways that control the vegetative to floral transition have elucidated molecular processes that respond to rising temperatures, including those involved in the vernalization- and photoperiod-dependent control of flowering. In comparison, our understanding of genes that underpin thermal responses during later developmental stages remains poor, thus highlighting a key area for future research. This review outlines the responses of developmental genes to warmer conditions and summarizes our knowledge of the reproductive traits of wheat and barley influenced by high temperatures. We explore ways in which recent advances in wheat and barley research capabilities could help identify genes that underpin responses to rising temperatures, and how improved knowledge of the genetic regulation of reproduction and plant architecture could be used to develop thermally resilient cultivars.
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Affiliation(s)
- Catherine N Jacott
- Department of Crop Genetics, John Innes Centre, Colney Lane, Norwich, UK
| | - Scott A Boden
- Department of Crop Genetics, John Innes Centre, Colney Lane, Norwich, UK
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia
- Correspondence:
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25
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Phenology and related traits for wheat adaptation. Heredity (Edinb) 2020; 125:417-430. [PMID: 32457509 PMCID: PMC7784700 DOI: 10.1038/s41437-020-0320-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
Wheat is a major food crop, with around 765 million tonnes produced globally. The largest wheat producers include the European Union, China, India, Russia, United States, Canada, Pakistan, Australia, Ukraine and Argentina. Cultivation of wheat across such diverse global environments with variation in climate, biotic and abiotic stresses, requires cultivars adapted to a range of growing conditions. One intrinsic way that wheat achieves adaptation is through variation in phenology (seasonal timing of the lifecycle) and related traits (e.g., those affecting plant architecture). It is important to understand the genes that underlie this variation, and how they interact with each other, other traits and the growing environment. This review summarises the current understanding of phenology and developmental traits that adapt wheat to different environments. Examples are provided to illustrate how different combinations of alleles can facilitate breeding of wheat varieties with optimal crop performance for different growing regions or farming systems.
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26
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Prieto P, Ochagavía H, Griffiths S, Slafer GA. Earliness per se×temperature interaction: consequences on leaf, spikelet, and floret development in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1956-1968. [PMID: 31875911 PMCID: PMC7242086 DOI: 10.1093/jxb/erz568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 12/20/2019] [Indexed: 05/28/2023]
Abstract
Wheat adaptation can be fine-tuned by earliness per se (Eps) genes. Although the effects of Eps genes are often assumed to act independently of the environment, previous studies have shown that they exhibit temperature sensitivity. The number of leaves and phyllochron are considered determinants of flowering time and the numerical components of yield include spikelets per spike and fertile floret number within spikelets. We studied the dynamics of leaf, spikelet, and floret development in near isogenic lines with either late or early alleles of Eps-D1 under seven temperature regimes. Leaf appearance dynamics were modulated by temperature, and Eps alleles had a greater effect on the period from flag leaf to heading than phyllochron. In addition, the effects of the Eps alleles on spikelets per spike were minor, and more related to spikelet plastochron than the duration of the early reproductive phase. However, fertile floret number was affected by the interaction between Eps alleles and temperature. So, at 9 °C, Eps-early alleles had more fertile florets than Eps-late alleles, at intermediate temperatures there was no significant difference, and at 18 °C (the highest temperature) the effect was reversed, with lines carrying the late allele producing more fertile florets. These effects were mediated through changes in floret survival; there were no clear effects on the maximum number of floret primordia.
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Affiliation(s)
- Paula Prieto
- Department of Crop and Forest Sciences, University of Lleida - AGROTECNIO Center, Lleida, Spain
| | - Helga Ochagavía
- Department of Crop and Forest Sciences, University of Lleida - AGROTECNIO Center, Lleida, Spain
| | | | - Gustavo A Slafer
- Department of Crop and Forest Sciences, University of Lleida - AGROTECNIO Center, Lleida, Spain
- ICREA, Catalonian Institution for Research and Advanced Studies, Spain
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27
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Xie Y, Wang C, Yang W, Feng M, Qiao X, Song J. Canopy hyperspectral characteristics and yield estimation of winter wheat (Triticum aestivum) under low temperature injury. Sci Rep 2020; 10:244. [PMID: 31937859 PMCID: PMC6959340 DOI: 10.1038/s41598-019-57100-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 12/22/2019] [Indexed: 12/04/2022] Open
Abstract
To evaluate the effect of low-temperature stress in winter wheat during the early growth stages, the response regularity of the canopy spectral reflectance was evaluated. Besides, winter wheat yield during the maturation stage and the relationship between yield and canopy spectral reflectance were also analyzed. Two multivariate methods, namely, the successive projections algorithm (SPA) and multiple linear regression (MLR), were combined to explore the relationship between the spectral reflectance and yield. Our results showed that the green peak and red valley in visible wavelengths altered obviously and the red edge gradually moved towards blue wavebands. The canopy spectral reflectance in the near-infrared wavebands increased with an increase in low-temperature stress intensity. Moreover, the reflectance proved that the red edge region under low-temperature stress is related to winter wheat yield, and approximately 38% of extracted wavebands were concentrated in the red edge region (680-780 nm). Compared with the predictive MLR models, the model calibrated during the flowering period of winter wheat (25 days post low-temperature treatment) had better performance in predicting crop yield. Whole-spectrum predictive models based on the principle component regression (PCR) method and Normalized Difference Vegetation Index (NDVI) models based on MLR were also established. Moreover, the performance of three kinds of calibration methods and the validation result of the field test were compared to select the optimal monitoring stage and technique to estimate the yield in the early growth stage of winter wheat under low-temperature stress. This study could provide a theoretical basis and practical reference for hyperspectral assessment of yield in winter wheat during low-temperature stress.
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Affiliation(s)
- Yongkai Xie
- Institute of Dry Farming Engineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Chao Wang
- Institute of Dry Farming Engineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Wude Yang
- Institute of Dry Farming Engineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Meichen Feng
- Institute of Dry Farming Engineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Xingxing Qiao
- Institute of Dry Farming Engineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Jinyao Song
- Institute of Dry Farming Engineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
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28
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Farooq MU, Zhu J. The paradox in accumulation behavior of cadmium and selenium at different planting times in rice. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:22421-22430. [PMID: 31154647 DOI: 10.1007/s11356-019-05467-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
The synergistic effects of trace elements selenium (Se) and cadmium (Cd) are well known. But the reasons for the trending accumulation behavior in both trace elements are under debate in the scientific community. The present investigation was conducted to evaluate the impact of heat units on the accumulation behavior in two environments. Se and Cd were applied in three groups (T0; 0:0, T1; 0.4:1, T2; 1:2) mg kg-1. As the time of planting and heat units consumed by the crop to attain its physiological maturity appears to be different. The sunlight may contribute as an important manipulating factor for the accumulation of heavy metals in the plant. The results of the present study indicated that the behavior in the accumulation pattern of both elements appears to be distinct in the same material. The increased fertilizer treatment in soil bulk linearly increased the metal contents in rice grain. The studies between different plant parts disclosed panicle as the primary reservoir for Se and Cd accumulation. The plant sown earlier accumulates more Se than Cd while the plants uptake more Cd when sown 1 month later. The plant completes the critical developmental phases (tillering, heading, and flowering) within 20-30 days interval depending on the variety. But the late-sown plants complete these transitional phases within 9-10 days interval ultimately result in less utilization of heat units. These quick transitional changes may lead to the uptake of an ample amount of Cd contents in rice grain even at a low level of Cd stress (1 and 2 mg kg-1), making rice unsafe for edible purposes. The proper time of planting could be effective in timely acclimatization of Se and Cd sequestration and translocation in rice various components. Graphical Abstract.
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Affiliation(s)
- Muhammad Umer Farooq
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jianqing Zhu
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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