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Wang W, Zheng M, Shen Z, Meng H, Chen L, Li T, Lin F, Hong L, Lin Z, Ye T, Guo Y, He E. Tolerance enhancement of Dendrobium officinale by salicylic acid family-related metabolic pathways under unfavorable temperature. BMC PLANT BIOLOGY 2024; 24:770. [PMID: 39135170 PMCID: PMC11320864 DOI: 10.1186/s12870-024-05499-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
BACKGROUND Unfavorable temperatures significantly constrain the quality formation of Dendrobium officinale, severely limiting its food demand. Salicylic acid (SA) enhances the resistance of D. officinale to stress and possesses various analogs. The impact and mechanism of the SA family on improving the quality of D. officinale under adverse temperature conditions remains unclear. RESULTS Combined with molecular docking analysis, chlorophyll fluorescence and metabolic analysis after treatments with SA analogues or extreme temperatures are performed in this study. The results demonstrate that both heat and cold treatments impede several main parameters of chlorophyll fluorescence of D. officinale, including the ΦPSII parameter, a sensitive growth indicator. However, this inhibition is mitigated by SA or its chemically similar compounds. Comprehensive branch imaging of ΦPSII values revealed position-dependent improvement of tolerance. Molecular docking analysis using a crystal structure model of NPR4 protein reveals that the therapeutic effects of SA analogs are determined by their binding energy and the contact of certain residues. Metabolome analysis identifies 17 compounds are considered participating in the temperature-related SA signaling pathway. Moreover, several natural SA analogs such as 2-hydroxycinnamic acid, benzamide, 2-(formylamino) benzoic acid and 3-o-methylgallic acid, are further found to have high binding ability to NPR4 protein and probably enhance the tolerance of D. officinale against unfavorable temperatures through flavone and guanosine monophosphate degradation pathways. CONCLUSIONS These results reveal that the SA family with a high binding capability of NPR4 could improve the tolerance of D. officinale upon extreme temperature challenges. This study also highlights the collaborative role of SA-related natural compounds present in D. officinale in the mechanism of temperature resistance and offers a potential way to develop protective agents for the cultivation of D. officinale.
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Affiliation(s)
- Wenhua Wang
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Mingqiong Zheng
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Zhijun Shen
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Hongyan Meng
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Lianghua Chen
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Tiantian Li
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Fucong Lin
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Liping Hong
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Zhikai Lin
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Ting Ye
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Ying Guo
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China
| | - Enming He
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, Fujian, China.
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Liu J, Wang X, Wu H, Zhu Y, Ahmad I, Dong G, Zhou G, Wu Y. Association between Reactive Oxygen Species, Transcription Factors, and Candidate Genes in Drought-Resistant Sorghum. Int J Mol Sci 2024; 25:6464. [PMID: 38928168 PMCID: PMC11203540 DOI: 10.3390/ijms25126464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/04/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
Drought stress is one of the most severe natural disasters in terms of its frequency, length, impact intensity, and associated losses, making it a significant threat to agricultural productivity. Sorghum (Sorghum bicolor), a C4 plant, shows a wide range of morphological, physiological, and biochemical adaptations in response to drought stress, paving the way for it to endure harsh environments. In arid environments, sorghum exhibits enhanced water uptake and reduced dissipation through its morphological activity, allowing it to withstand drought stress. Sorghum exhibits physiological and biochemical resistance to drought, primarily by adjusting its osmotic potential, scavenging reactive oxygen species, and changing the activities of its antioxidant enzymes. In addition, certain sorghum genes exhibit downregulation capabilities in response to drought stress. Therefore, in the current review, we explore drought tolerance in sorghum, encompassing its morphological characteristics and physiological mechanisms and the identification and selection of its functional genes. The use of modern biotechnological and molecular biological approaches to improving sorghum resistance is critical for selecting and breeding drought-tolerant sorghum varieties.
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Affiliation(s)
- Jiao Liu
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Xin Wang
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Hao Wu
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Yiming Zhu
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Irshad Ahmad
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Guichun Dong
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Guisheng Zhou
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Yanqing Wu
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
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Gimode DM, Ochieng G, Deshpande S, Manyasa EO, Kondombo CP, Mikwa EO, Avosa MO, Kunguni JS, Ngugi K, Sheunda P, Jumbo MB, Odeny DA. Validation of sorghum quality control (QC) markers across African breeding lines. THE PLANT GENOME 2024; 17:e20438. [PMID: 38409578 DOI: 10.1002/tpg2.20438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] is a cereal crop of critical importance in the semi-arid tropics, particularly in Africa where it is second only to maize (Zea mays L.) by area of cultivation. The International Crops Research Institute for the Semi-Arid Tropics sorghum breeding program for Eastern and Southern Africa is the largest in the region and develops improved varieties for target agro-ecologies. Varietal purity and correct confirmation of new crosses are essential for the integrity and efficiency of a breeding program. We used 49 quality control (QC) kompetitive allele-specific PCR single nucleotide polymorphism (SNP) markers to genotype 716 breeding lines. Note that 46 SNPs were polymorphic with the top 10 most informative revealing polymorphism information content (PIC), minor allele frequency (MAF), and observed heterozygosity (Ho) of 0.37, 0.43, and 0.02, respectively, and explaining 45% of genetic variance within the first two principal components (PC). Thirty-nine markers were highly informative across 16 Burkina Faso breeding lines, out of which the top 10 revealed average PIC, MAF, and Ho of 0.36, 0.39, and 0.05, respectively. Discriminant analysis of principal components done using top 30 markers separated the breeding lines into five major clusters, three of which were distinct. Six of the top 10 most informative markers successfully confirmed hybridization of crosses between genotypes IESV240, KARIMTAMA1, F6YQ212, and FRAMIDA. A set of 10, 20, and 30 most informative markers are recommended for routine QC applications. Future effort should focus on the deployment of these markers in breeding programs for enhanced genetic gain.
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Affiliation(s)
- Davis M Gimode
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Grace Ochieng
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-arid Tropics-Patancheru, Patancheru, Telangana, India
| | - Eric O Manyasa
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Clarisse P Kondombo
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Erick O Mikwa
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Millicent O Avosa
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | | | - Kahiu Ngugi
- Department of Plant Science & Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Patrick Sheunda
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
- The Kenya Seed Company Limited, Kitale Branch, Kitale, Kenya
| | - McDonald Bright Jumbo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako, Mali
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
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Agnew E, Ziegler G, Lee S, Lizárraga C, Fahlgren N, Baxter I, Mockler TC, Shakoor N. Longitudinal genome-wide association study reveals early QTL that predict biomass accumulation under cold stress in sorghum. FRONTIERS IN PLANT SCIENCE 2024; 15:1278802. [PMID: 38807776 PMCID: PMC11130433 DOI: 10.3389/fpls.2024.1278802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/24/2024] [Indexed: 05/30/2024]
Abstract
Introduction Sorghum bicolor is a promising cellulosic feedstock crop for bioenergy due to its high biomass yields. However, early growth phases of sorghum are sensitive to cold stress, limiting its planting in temperate environments. Cold adaptability is crucial for cultivating bioenergy and grain sorghum at higher latitudes and elevations, or for extending the growing season. Identifying genes and alleles that enhance biomass accumulation under early cold stress can lead to improved sorghum varieties through breeding or genetic engineering. Methods We conducted image-based phenotyping on 369 accessions from the sorghum Bioenergy Association Panel (BAP) in a controlled environment with early cold treatment. The BAP includes diverse accessions with dense genotyping and varied racial, geographical, and phenotypic backgrounds. Daily, non-destructive imaging allowed temporal analysis of growth-related traits and water use efficiency (WUE). A genome-wide association study (GWAS) was performed to identify genomic intervals and genes associated with cold stress response. Results The GWAS identified transient quantitative trait loci (QTL) strongly associated with growth-related traits, enabling an exploration of the genetic basis of cold stress response at different developmental stages. This analysis of daily growth traits, rather than endpoint traits, revealed early transient QTL predictive of final phenotypes. The study identified both known and novel candidate genes associated with growth-related traits and temporal responses to cold stress. Discussion The identified QTL and candidate genes contribute to understanding the genetic mechanisms underlying sorghum's response to cold stress. These findings can inform breeding and genetic engineering strategies to develop sorghum varieties with improved biomass yields and resilience to cold, facilitating earlier planting, extended growing seasons, and cultivation at higher latitudes and elevations.
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Affiliation(s)
| | | | | | | | | | | | | | - Nadia Shakoor
- Donald Danforth Plant Science Center, Saint Louis, MO, United States
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5
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González-Espíndola LÁ, Pedroza-Sandoval A, Trejo-Calzada R, Jacobo-Salcedo MDR, García de los Santos G, Quezada-Rivera JJ. Relative Water Content, Chlorophyll Index, and Photosynthetic Pigments on Lotus corniculatus L. in Response to Water Deficit. PLANTS (BASEL, SWITZERLAND) 2024; 13:961. [PMID: 38611490 PMCID: PMC11013262 DOI: 10.3390/plants13070961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/18/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
This study aimed to evaluate different L. corniculatus L. ecotypes under water-deficit conditions to identify changes in relative water content and photosynthetic pigments as indicators of physiological responses during different years' seasons. The experiment was conducted in a randomized block design with three replicates. Ten treatments were performed as a factorial of 2 × 5, where the first variation factor was the soil water content-no water deficit (NDW) with 100% field capacity (FC), and water deficit (DW) corresponding to 85.4% of the FC-and the second variation factor comprised four ecotypes and one variety of L. corniculatus. A significant effect was identified on the concentration of photosynthetic pigments, mainly total chlorophyll, with chlorophyll a in the 255301 ecotype with records of 187.8, 167.5, and 194.6 mg g-1 FW in WD, corresponding to an increase of 86.0%, 172.6%, and 16.6%, respectively, in relation the lower values obtained in the ecotype 202700 under NWD. In carotenoids, higher concentrations were observed in the 255301 and 202700 ecotypes and the Estanzuela Ganador variety under WD in most seasonal periods, except summer; a similar response was found in the 202700 ecotype and the Estanzuela Ganador variety during the winter season, also in WD. The results showed that the first two principal components accounted for 71.8% of the total variation, with PC1 representing chlorophyll a, chlorophyll b, and total chlorophyll, and PC2 representing carotenoids, temperature, relative chlorophyll index, and relative water content. The observations were grouped based on soil moisture content, with the optimal moisture group exhibiting higher chlorophyll and carotenoid concentrations. The findings suggest that soil moisture content significantly affects the performance of L. corniculatus ecotypes, and the plant shows seasonal variations in response to water-deficit conditions. This research contributes to understanding the physiological responses of L. corniculatus and its potential as a water-efficient forage crop for promoting sustainable agriculture and enhancing food security.
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Affiliation(s)
- Luis Ángel González-Espíndola
- Universidad Autónoma Chapingo, Unidad Regional Universitaria de Zonas Áridas, Km 40 Carretera Gómez Palacio—Chihuahua, Bermejillo C.P. 35230, Durango, Mexico; (L.Á.G.-E.); (R.T.-C.); (M.d.R.J.-S.)
| | - Aurelio Pedroza-Sandoval
- Universidad Autónoma Chapingo, Unidad Regional Universitaria de Zonas Áridas, Km 40 Carretera Gómez Palacio—Chihuahua, Bermejillo C.P. 35230, Durango, Mexico; (L.Á.G.-E.); (R.T.-C.); (M.d.R.J.-S.)
| | - Ricardo Trejo-Calzada
- Universidad Autónoma Chapingo, Unidad Regional Universitaria de Zonas Áridas, Km 40 Carretera Gómez Palacio—Chihuahua, Bermejillo C.P. 35230, Durango, Mexico; (L.Á.G.-E.); (R.T.-C.); (M.d.R.J.-S.)
| | - María del Rosario Jacobo-Salcedo
- Universidad Autónoma Chapingo, Unidad Regional Universitaria de Zonas Áridas, Km 40 Carretera Gómez Palacio—Chihuahua, Bermejillo C.P. 35230, Durango, Mexico; (L.Á.G.-E.); (R.T.-C.); (M.d.R.J.-S.)
| | - Gabino García de los Santos
- Colegio de Postgraduados, Campus Montecillo, Km 36.5 Carretera México-Texcoco, Montecillo C.P. 56230, Texcoco, Mexico;
| | - Jesús Josafath Quezada-Rivera
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fraccionamiento Filadelfia, Gómez Palacio, Durango C.P. 35010, Mexico;
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Schuh A, Felderhoff TJ, Marla S, Morris GP. Precise colocalization of sorghum's major chilling tolerance locus with Tannin1 due to tight linkage drag rather than antagonistic pleiotropy. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:42. [PMID: 38308687 PMCID: PMC10838249 DOI: 10.1007/s00122-023-04534-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/19/2023] [Indexed: 02/05/2024]
Abstract
Chilling tolerance in crops can increase resilience through longer growing seasons, drought escape, and nitrogen use efficiency. In sorghum (Sorghum bicolor [L.] Moench), breeding for chilling tolerance has been stymied by coinheritance of the largest-effect chilling tolerance locus, qSbCT04.62, with the major gene underlying undesirable grain proanthocyanidins, WD40 transcriptional regulator Tannin1. To test if this coinheritance is due to antagonistic pleiotropy of Tannin1, we developed and studied near-isogenic lines (NILs) carrying chilling tolerant haplotypes at qCT04.62. Whole-genome sequencing of the NILs revealed introgressions spanning part of the qCT04.62 confidence interval, including the Tannin1 gene and an ortholog of Arabidopsis cold regulator CBF/DREB1G. Segregation pattern of grain tannin in NILs confirmed the presence of wildtype Tannin1 and the reconstitution of a functional MYB-bHLH-WD40 regulatory complex. Low-temperature germination did not differ between NILs, suggesting that Tannin1 does not modulate this component of chilling tolerance. Similarly, NILs did not differ in seedling growth rate under either of two contrasting controlled environment chilling scenarios. Finally, while the chilling tolerant parent line had notably different photosynthetic responses from the susceptible parent line - including greater non-photochemical quenching before, during, and after chilling - the NIL responses match the susceptible parent. Thus, our findings suggest that tight linkage drag, not pleiotropy, underlies the precise colocalization of Tan1 with qCT04.62 and the qCT04.62 quantitative trait nucleotide lies outside the NIL introgressions. Breaking linkage at this locus should advance chilling tolerance breeding in sorghum and the identification of a novel chilling tolerance regulator.
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Affiliation(s)
- Anthony Schuh
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, 80526, USA
| | - Terry J Felderhoff
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Sandeep Marla
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Geoffrey P Morris
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, 80526, USA.
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Honda S, Imamura A, Seki Y, Chigira K, Iwasa M, Hayami K, Nomura T, Ohkubo S, Ookawa T, Nagano AJ, Matsuoka M, Tanaka Y, Adachi S. Genome-wide association study of leaf photosynthesis using a high-throughput gas exchange system in rice. PHOTOSYNTHESIS RESEARCH 2024; 159:17-28. [PMID: 38112862 DOI: 10.1007/s11120-023-01065-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023]
Abstract
Enhancing leaf photosynthetic capacity is essential for improving the yield of rice (Oryza sativa L.). Although the exploitation of natural genetic resources is considered a promising approach to enhance photosynthetic capacity, genomic factors related to the genetic diversity of leaf photosynthetic capacity have yet to be fully elucidated due to the limitation of measurement efficiency. In this study, we aimed to identify novel genomic regions for the net CO2 assimilation rate (A) by combining genome-wide association study (GWAS) and the newly developed rapid closed gas exchange system MIC-100. Using three MIC-100 systems in the field at the vegetative stage, we measured A of 168 temperate japonica rice varieties with six replicates for three years. We found that the modern varieties exhibited higher A than the landraces, while there was no significant relationship between the release year and A among the modern varieties. Our GWAS scan revealed two major peaks located on chromosomes 4 and 8, which were repeatedly detected in the different experiments and in the generalized linear modelling approach. We suggest that high-throughput gas exchange measurements combined with GWAS is a reliable approach for understanding the genetic mechanisms underlying photosynthetic diversities in crop species.
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Affiliation(s)
- Sotaro Honda
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Ayumu Imamura
- Graduate School of Agriculture, Ibaraki University, Ibaraki, 300-0393, Japan
| | - Yoshiaki Seki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Koki Chigira
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Marina Iwasa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Kentaro Hayami
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Tomohiro Nomura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Satoshi Ohkubo
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, Yamagata, 997-0017, Japan
| | - Makoto Matsuoka
- Faculty of Food and Agricultural Sciences, Institute of Fermentation Sciences, Fukushima University, Fukushima, 960-1296, Japan
| | - Yu Tanaka
- Graduate School of Environment and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan.
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Guo J, Beemster GTS, Liu F, Wang Z, Li X. Abscisic Acid Regulates Carbohydrate Metabolism, Redox Homeostasis and Hormonal Regulation to Enhance Cold Tolerance in Spring Barley. Int J Mol Sci 2023; 24:11348. [PMID: 37511108 PMCID: PMC10379442 DOI: 10.3390/ijms241411348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/02/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Abscisic acid (ABA) plays a vital role in the induction of low temperature tolerance in plants. To understand the molecular basis of this phenomenon, we performed a proteomic analysis on an ABA-deficit mutant barley (Az34) and its wild type (cv Steptoe) under control conditions (25/18 °C) and after exposure to 0 °C for 24 h. Most of the differentially abundant proteins were involved in the processes of photosynthesis and metabolisms of starch, sucrose, carbon, and glutathione. The chloroplasts in Az34 leaves were more severely damaged, and the decrease in Fv/Fm was larger in Az34 plants compared with WT under low temperature. Under low temperature, Az34 plants possessed significantly higher activities of ADP-glucose pyrophosphorylase, fructokinase, monodehydroascorbate reductase, and three invertases, but lower UDP-glucose pyrophosphorylase activity than WT. In addition, concentrations of proline and soluble protein were lower, while concentration of H2O2 was higher in Az34 plants compared to WT under low temperature. Collectively, the results indicated that ABA deficiency induced modifications in starch and sucrose biosynthesis and sucrolytic pathway and overaccumulation of reactive oxygen species were the main reason for depressed low temperature tolerance in barley, which provide novel insights to the response of barley to low temperature under future climate change.
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Affiliation(s)
- Junhong Guo
- Key Laboratory of Black Soil Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Fulai Liu
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark
| | - Zongming Wang
- Key Laboratory of Black Soil Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xiangnan Li
- Key Laboratory of Black Soil Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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10
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Guo J, Wang Z, Wei Q, Li G, Yang H, Lu D. Response of waxy maize ( Zea mays L. var. ceratina Kulesh) leaf photosynthesis to low temperature during the grain-filling stage. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:335-346. [PMID: 36894514 DOI: 10.1071/fp22252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Low temperature (LT) during the grain-filling stage is an important factor that affects the source-sink relationship and leads to yield loss in maize (Zea mays L). In this study, field and pot trials were conducted to investigate the effects of LT during the grain-filling stage on leaf photosynthesis, antioxidant system, hormones, and grain yield of waxy maize cultivars Suyunuo 5 (S5) and Yunuo 7 (Y7). The results showed that LT treatment inhibited the chlorophyll biosynthesis and reduced the photosynthetic pigment levels during grain-filling stage. Ribulose-1,5-bisphosphate carboxylase and phosphoenolpyruvate carboxylase activities, photosynthetic rate, transpiration rate, and stomatal conductance decreased under LT treatment during the grain-filling stage. Furthermore, LT treatment increased the contents of malondialdehyde and reactive oxygen species, and decreased the activities of catalase, superoxide dismutase, peroxidase, and ascorbate peroxidase in the ear leaves, which accelerated the oxidative damage of leaf. The LT treatment also raised abscisic acid content and reduced indole acetic acid content in the ear leaves during grain-filling stage. The results of field and pot trials were verified by each other, but the field effect was greater than that of pot. Overall, LT treatment reduced the waxy maize dry matter accumulation after silking by affecting the physiological and biochemical processes of leaves, and ultimately decreased grain yield.
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Affiliation(s)
- Jian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College, Yangzhou University, Yangzhou 225009, P. R. China; and Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, P. R. China
| | - Zitao Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College, Yangzhou University, Yangzhou 225009, P. R. China
| | - Qi Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College, Yangzhou University, Yangzhou 225009, P. R. China
| | - Guanghao Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College, Yangzhou University, Yangzhou 225009, P. R. China; and Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, P. R. China
| | - Huan Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College, Yangzhou University, Yangzhou 225009, P. R. China; and Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, P. R. China
| | - Dalei Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College, Yangzhou University, Yangzhou 225009, P. R. China; and Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, P. R. China; and Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, P. R. China
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11
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Jalili I, Ebadi A, Askari MA, KalatehJari S, Aazami MA. Foliar application of putrescine, salicylic acid, and ascorbic acid mitigates frost stress damage in Vitis vinifera cv. ̒Giziluzum̕. BMC PLANT BIOLOGY 2023; 23:135. [PMID: 36899321 PMCID: PMC10155332 DOI: 10.1186/s12870-023-04126-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/15/2023] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cold stress is an effective factor in reducing production and injuring fruit trees. Various materials, such as salicylic acid, ascorbic acid, and putrescine, are used to alleviate the damage of abiotic stress. RESULTS The effect of different treatments of putrescine, salicylic acid, and ascorbic acid on alleviating the damage of frost stress (- 3 °C) to grapes 'Giziluzum' was investigated. Frost stress increased the amount of H2O2, MDA, proline, and MSI. On the other hand, it decreased the concentration of chlorophyll and carotenoids in the leaves. Putrescine, salicylic acid and ascorbic acid significantly increased the activities of catalase, guaiacol peroxidase, ascorbate peroxidase, and superoxide dismutase under frost stress. Following frost stress, the grapes treated with putrescine, salicylic acid, and ascorbic acid showed higher levels of DHA, AsA, and AsA/DHA than the untreated grapes. Our results showed that the treatment with ascorbic acid outperformed the other treatments in adjusting frost stress damages. CONCLUSION The use of compounds, such as ascorbic ac id, salicylic acid, and putrescine, modulates the effects of frost stress, thereby increasing the antioxidant defense system of cells, reducing its damage, and stabilizing stable cell conditions, so it can be used to reduce frost damage to different grape cultivars.
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Affiliation(s)
- Ilnaz Jalili
- Department of Horticulture and Agronomy, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ali Ebadi
- Department of Horticulture, College of Agriculture, University of Tehran, Tehran, Iran.
| | - Mohammad Ali Askari
- Department of Horticulture and Agronomy, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Sepideh KalatehJari
- Department of Horticulture and Agronomy, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Ali Aazami
- Department of Horticulture, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
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12
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Vera Hernández PF, Mendoza Onofre LE, Rosas Cárdenas FDF. Responses of sorghum to cold stress: A review focused on molecular breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1124335. [PMID: 36909409 PMCID: PMC9996117 DOI: 10.3389/fpls.2023.1124335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Climate change has led to the search for strategies to acclimatize plants to various abiotic stressors to ensure the production and quality of crops of commercial interest. Sorghum is the fifth most important cereal crop, providing several uses including human food, animal feed, bioenergy, or industrial applications. The crop has an excellent adaptation potential to different types of abiotic stresses, such as drought, high salinity, and high temperatures. However, it is susceptible to low temperatures compared with other monocotyledonous species. Here, we have reviewed and discussed some of the research results and advances that focused on the physiological, metabolic, and molecular mechanisms that determine sorghum cold tolerance to improve our understanding of the nature of such trait. Questions and opportunities for a comprehensive approach to clarify sorghum cold tolerance or susceptibility are also discussed.
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Affiliation(s)
- Pedro Fernando Vera Hernández
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla, Tlaxcala, Mexico
| | | | - Flor de Fátima Rosas Cárdenas
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla, Tlaxcala, Mexico
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13
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Voelker WG, Krishnan K, Chougule K, Alexander LC, Lu Z, Olson A, Ware D, Songsomboon K, Ponce C, Brenton ZW, Boatwright JL, Cooper EA. Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes. FRONTIERS IN PLANT SCIENCE 2023; 13:1040909. [PMID: 36684744 PMCID: PMC9846640 DOI: 10.3389/fpls.2022.1040909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Introduction Sorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations. Methods Expanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs). Results We show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes. Discussion These resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.
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Affiliation(s)
- William G. Voelker
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Krittika Krishnan
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Kapeel Chougule
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
| | - Louie C. Alexander
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Zhenyuan Lu
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
| | - Andrew Olson
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
- United States Department of Agriculture - Agricultural Research Service in the North Atlantic Area (USDA-ARS NAA), Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Kittikun Songsomboon
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Cristian Ponce
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Zachary W. Brenton
- Carolina Seed Systems, Darlington, SC, United States
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - J. Lucas Boatwright
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Dept. of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Elizabeth A. Cooper
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
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14
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Rosado-Souza L, Yokoyama R, Sonnewald U, Fernie AR. Understanding source-sink interactions: Progress in model plants and translational research to crops. MOLECULAR PLANT 2023; 16:96-121. [PMID: 36447435 DOI: 10.1016/j.molp.2022.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/25/2022] [Indexed: 06/16/2023]
Abstract
Agriculture is facing a massive increase in demand per hectare as a result of an ever-expanding population and environmental deterioration. While we have learned much about how environmental conditions and diseases impact crop yield, until recently considerably less was known concerning endogenous factors, including within-plant nutrient allocation. In this review, we discuss studies of source-sink interactions covering both fundamental research in model systems under controlled growth conditions and how the findings are being translated to crop plants in the field. In this respect we detail efforts aimed at improving and/or combining C3, C4, and CAM modes of photosynthesis, altering the chloroplastic electron transport chain, modulating photorespiration, adopting bacterial/algal carbon-concentrating mechanisms, and enhancing nitrogen- and water-use efficiencies. Moreover, we discuss how modulating TCA cycle activities and primary metabolism can result in increased rates of photosynthesis and outline the opportunities that evaluating natural variation in photosynthesis may afford. Although source, transport, and sink functions are all covered in this review, we focus on discussing source functions because the majority of research has been conducted in this field. Nevertheless, considerable recent evidence, alongside the evidence from classical studies, demonstrates that both transport and sink functions are also incredibly important determinants of yield. We thus describe recent evidence supporting this notion and suggest that future strategies for yield improvement should focus on combining improvements in each of these steps to approach yield optimization.
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Affiliation(s)
- Laise Rosado-Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Ryo Yokoyama
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Uwe Sonnewald
- Department of Biochemistry, University of Erlangen-Nuremberg, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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15
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Garassino F, Wijfjes RY, Boesten R, Reyes Marquez F, Becker FFM, Clapero V, van den Hatert I, Holmer R, Schranz ME, Harbinson J, de Ridder D, Smit S, Aarts MGM. The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1298-1315. [PMID: 36239071 PMCID: PMC10100226 DOI: 10.1111/tpj.16005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C3 plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light-use efficiency at high irradiance as identified in a small number of exceptional C3 species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light-use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light-saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light-use efficiency and enhancing photosynthetic rates in crop species.
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Affiliation(s)
| | - Raúl Y. Wijfjes
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
- Present address:
Faculty of BiologyLudwig Maximilian University of MunichMunichGermany
| | - René Boesten
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
| | | | - Frank F. M. Becker
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
| | - Vittoria Clapero
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
- Present address:
Max Planck Institute for Molecular Plant PhysiologyGolmGermany
| | | | - Rens Holmer
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
| | - M. Eric Schranz
- Biosystematics GroupWageningen University & ResearchWageningenNetherlands
| | - Jeremy Harbinson
- Laboratory of BiophysicsWageningen University & ResearchWageningenNetherlands
| | - Dick de Ridder
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
| | - Sandra Smit
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
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16
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Improving
C
3
photosynthesis by exploiting natural genetic variation:
Hirschfeldia incana
as a model species. Food Energy Secur 2022. [DOI: 10.1002/fes3.420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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17
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Theeuwen TPJM, Logie LL, Harbinson J, Aarts MGM. Genetics as a key to improving crop photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3122-3137. [PMID: 35235648 PMCID: PMC9126732 DOI: 10.1093/jxb/erac076] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/23/2022] [Indexed: 05/02/2023]
Abstract
Since the basic biochemical mechanisms of photosynthesis are remarkably conserved among plant species, genetic modification approaches have so far been the main route to improve the photosynthetic performance of crops. Yet, phenotypic variation observed in wild species and between varieties of crop species implies there is standing natural genetic variation for photosynthesis, offering a largely unexplored resource to use for breeding crops with improved photosynthesis and higher yields. The reason this has not yet been explored is that the variation probably involves thousands of genes, each contributing only a little to photosynthesis, making them hard to identify without proper phenotyping and genetic tools. This is changing, though, and increasingly studies report on quantitative trait loci for photosynthetic phenotypes. So far, hardly any of these quantitative trait loci have been used in marker assisted breeding or genomic selection approaches to improve crop photosynthesis and yield, and hardly ever have the underlying causal genes been identified. We propose to take the genetics of photosynthesis to a higher level, and identify the genes and alleles nature has used for millions of years to tune photosynthesis to be in line with local environmental conditions. We will need to determine the physiological function of the genes and alleles, and design novel strategies to use this knowledge to improve crop photosynthesis through conventional plant breeding, based on readily available crop plant germplasm. In this work, we present and discuss the genetic methods needed to reveal natural genetic variation, and elaborate on how to apply this to improve crop photosynthesis.
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Affiliation(s)
- Tom P J M Theeuwen
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
- Correspondence:
| | - Louise L Logie
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - Jeremy Harbinson
- Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
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18
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Simpson CJC, Reeves G, Tripathi A, Singh P, Hibberd JM. Using breeding and quantitative genetics to understand the C4 pathway. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3072-3084. [PMID: 34747993 PMCID: PMC9126733 DOI: 10.1093/jxb/erab486] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/03/2021] [Indexed: 05/09/2023]
Abstract
Reducing photorespiration in C3 crops could significantly increase rates of photosynthesis and yield. One method to achieve this would be to integrate C4 photosynthesis into C3 species. This objective is challenging as it involves engineering incompletely understood traits into C3 leaves, including complex changes to their biochemistry, cell biology, and anatomy. Quantitative genetics and selective breeding offer underexplored routes to identify regulators of these processes. We first review examples of natural intraspecific variation in C4 photosynthesis as well as the potential for hybridization between C3 and C4 species. We then discuss how quantitative genetic approaches including artificial selection and genome-wide association could be used to better understand the C4 syndrome and in so doing guide the engineering of the C4 pathway into C3 crops.
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Affiliation(s)
- Conor J C Simpson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Gregory Reeves
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Anoop Tripathi
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Pallavi Singh
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Correspondence:
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19
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Sharwood RE, Quick WP, Sargent D, Estavillo GM, Silva-Perez V, Furbank RT. Mining for allelic gold: finding genetic variation in photosynthetic traits in crops and wild relatives. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3085-3108. [PMID: 35274686 DOI: 10.1093/jxb/erac081] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Improvement of photosynthetic traits in crops to increase yield potential and crop resilience has recently become a major breeding target. Synthetic biology and genetic technologies offer unparalleled opportunities to create new genetics for photosynthetic traits driven by existing fundamental knowledge. However, large 'gene bank' collections of germplasm comprising historical collections of crop species and their relatives offer a wealth of opportunities to find novel allelic variation in the key steps of photosynthesis, to identify new mechanisms and to accelerate genetic progress in crop breeding programmes. Here we explore the available genetic resources in food and fibre crops, strategies to selectively target allelic variation in genes underpinning key photosynthetic processes, and deployment of this variation via gene editing in modern elite material.
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Affiliation(s)
- Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - W Paul Quick
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Demi Sargent
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | | | | | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
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20
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Ortiz D, Salas-Fernandez MG. Dissecting the genetic control of natural variation in sorghum photosynthetic response to drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3251-3267. [PMID: 34791180 PMCID: PMC9126735 DOI: 10.1093/jxb/erab502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Drought stress causes crop yield losses worldwide. Sorghum is a C4 species tolerant to moderate drought stress, and its extensive natural variation for photosynthetic traits under water-limiting conditions can be exploited for developing cultivars with enhanced stress tolerance. The objective of this study was to discover genes/genomic regions that control the sorghum photosynthetic capacity under pre-anthesis water-limiting conditions. We performed a genome-wide association study for seven photosynthetic gas exchange and chlorophyll fluorescence traits during three periods of contrasting soil volumetric water content (VWC): control (30% VWC), drought (15% VWC), and recovery (30% VWC). Water stress was imposed with an automated irrigation system that generated a controlled dry-down period for all plants, to perform an unbiased genotypic comparison. A total of 60 genomic regions were associated with natural variation in one or more photosynthetic traits in a particular treatment or with derived variables. We identified 33 promising candidate genes with predicted functions related to stress signaling, oxidative stress protection, hormonal response to stress, and dehydration protection. Our results provide new knowledge about the natural variation and genetic control of sorghum photosynthetic response to drought with the ultimate goal of improving its adaptation and productivity under water stress scenarios.
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Affiliation(s)
- Diego Ortiz
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
- Instituto Nacional de Tecnologia Agropecuaria, Manfredi, Cordoba 5988, Argentina
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21
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Boatwright JL, Sapkota S, Myers M, Kumar N, Cox A, Jordan KE, Kresovich S. Dissecting the Genetic Architecture of Carbon Partitioning in Sorghum Using Multiscale Phenotypes. FRONTIERS IN PLANT SCIENCE 2022; 13:790005. [PMID: 35665170 PMCID: PMC9159972 DOI: 10.3389/fpls.2022.790005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Carbon partitioning in plants may be viewed as a dynamic process composed of the many interactions between sources and sinks. The accumulation and distribution of fixed carbon is not dictated simply by the sink strength and number but is dependent upon the source, pathways, and interactions of the system. As such, the study of carbon partitioning through perturbations to the system or through focus on individual traits may fail to produce actionable developments or a comprehensive understanding of the mechanisms underlying this complex process. Using the recently published sorghum carbon-partitioning panel, we collected both macroscale phenotypic characteristics such as plant height, above-ground biomass, and dry weight along with microscale compositional traits to deconvolute the carbon-partitioning pathways in this multipurpose crop. Multivariate analyses of traits resulted in the identification of numerous loci associated with several distinct carbon-partitioning traits, which putatively regulate sugar content, manganese homeostasis, and nitrate transportation. Using a multivariate adaptive shrinkage approach, we identified several loci associated with multiple traits suggesting that pleiotropic and/or interactive effects may positively influence multiple carbon-partitioning traits, or these overlaps may represent molecular switches mediating basal carbon allocating or partitioning networks. Conversely, we also identify a carbon tradeoff where reduced lignin content is associated with increased sugar content. The results presented here support previous studies demonstrating the convoluted nature of carbon partitioning in sorghum and emphasize the importance of taking a holistic approach to the study of carbon partitioning by utilizing multiscale phenotypes.
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Affiliation(s)
- J. Lucas Boatwright
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Sirjan Sapkota
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - Matthew Myers
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - Neeraj Kumar
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Alex Cox
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - Kathleen E. Jordan
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - Stephen Kresovich
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Feed the Future Innovation Lab for Crop Improvement, Cornell University, Ithaca, NY, United States
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22
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Cui H, Chen J, Liu M, Zhang H, Zhang S, Liu D, Chen S. Genome-Wide Analysis of C2H2 Zinc Finger Gene Family and Its Response to Cold and Drought Stress in Sorghum [ Sorghum bicolor (L.) Moench]. Int J Mol Sci 2022; 23:ijms23105571. [PMID: 35628380 PMCID: PMC9146226 DOI: 10.3390/ijms23105571] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
C2H2 zinc finger protein (C2H2-ZFP) is one of the most important transcription factor families in higher plants. In this study, a total of 145 C2H2-ZFPs was identified in Sorghum bicolor and randomly distributed on 10 chromosomes. Based on the phylogenetic tree, these zinc finger gene family members were divided into 11 clades, and the gene structure and motif composition of SbC2H2-ZFPs in the same clade were similar. SbC2H2-ZFP members located in the same clade contained similar intron/exon and motif patterns. Thirty-three tandem duplicated SbC2H2-ZFPs and 24 pairs of segmental duplicated genes were identified. Moreover, synteny analysis showed that sorghum had more collinear regions with monocotyledonous plants such as maize and rice than did dicotyledons such as soybean and Arabidopsis. Furthermore, we used quantitative RT-PCR (qRT-PCR) to analyze the expression of C2H2-ZFPs in different organs and demonstrated that the genes responded to cold and drought. For example, Sobic.008G088842 might be activated by cold but is inhibited in drought in the stems and leaves. This work not only revealed an important expanded C2H2-ZFP gene family in Sorghum bicolor but also provides a research basis for determining the role of C2H2-ZFPs in sorghum development and abiotic stress resistance.
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Affiliation(s)
- Huiying Cui
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
- Correspondence: (H.C.); (S.C.)
| | - Jiaqi Chen
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
| | - Mengjiao Liu
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
| | - Hongzhi Zhang
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
| | - Shuangxi Zhang
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
| | - Dan Liu
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
| | - Shaolin Chen
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
- Correspondence: (H.C.); (S.C.)
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23
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Pandian BA, Sexton-Bowser S, Prasad PV, Jugulam M. Current status and prospects of herbicide-resistant grain sorghum (Sorghum bicolor). PEST MANAGEMENT SCIENCE 2022; 78:409-415. [PMID: 34532972 DOI: 10.1002/ps.6644] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Grain sorghum is a versatile crop, which can thrive under limited water and other inputs. However, crop loss from weed infestation continues to be a major constraint in grain sorghum production. Particularly, post-emergence grass weed control is a great challenge in grain sorghum due to the lack of herbicide options. Unlike in other major crops, such as maize or soybean, herbicide-resistant sorghum technology that can facilitate weed control throughout crop growing season is not available to growers yet. The development of herbicide-resistant sorghum can have potential to improve weed management, including post-emergence grass weed control. One of the major concerns in the development of such technology in sorghum is escape of resistance traits into weedy relatives of sorghum (e.g. shattercane and johnsongrass). This review focuses on sources of herbicide resistance in sorghum, the status of the development of herbicide-resistant sorghum technologies, overview of breeding methods, and limitations in the development of such sorghum technology as well as economic benefits for sorghum growers. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Balaji A Pandian
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | | | - Pv Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, USA
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
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24
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Chiluwal A, Perumal R, Poudel HP, Muleta K, Ostmeyer T, Fedenia L, Pokharel M, Bean SR, Sebela D, Bheemanahalli R, Oumarou H, Klein P, Rooney WL, Jagadish SVK. Genetic control of source-sink relationships in grain sorghum. PLANTA 2022; 255:40. [PMID: 35038036 DOI: 10.1007/s00425-022-03822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
QTL hotspots identified for selected source-sink-related traits provide the opportunity for pyramiding favorable alleles for improving sorghum productivity under diverse environments. A sorghum bi-parental mapping population was evaluated under six different environments at Hays and Manhattan, Kansas, USA, in 2016 and 2017, to identify genomic regions controlling source-sink relationships. The population consisted of 210 recombinant inbred lines developed from US elite post-flowering drought susceptible (RTx430) and a known post-flowering drought tolerant cultivar (SC35). Selected physiological traits related to source (effective quantum yield of photosystem II and chlorophyll index), sink (grain yield per panicle) and panicle neck diameter were recorded during grain filling. The results showed strong phenotypic and genotypic association between panicle neck diameter and grain yield per panicle during mid-grain filling and at maturity. Multiple QTL model revealed 5-12 including 2-5 major QTL for each trait. Among them 3, 7 and 8 QTL for quantum yield, panicle neck diameter and chlorophyll index, respectively, have not been identified previously in sorghum. Phenotypic variation explained by QTL identified across target traits ranged between 5.5 and 25.4%. Panicle neck diameter and grain yield per panicle were positively associated, indicating the possibility of targeting common co-localized QTL to improve both traits simultaneously through marker-assisted selection. Three major QTL hotspots, controlling multiple traits were identified on chromosome 1 (52.23-61.18 Mb), 2 (2.52-11.43 Mb) and 3 (1.32-3.95 Mb). The identified genomic regions and underlying candidate genes can be utilized in pyramiding favorable alleles for improving source-sink relationships in sorghum under diverse environments.
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Affiliation(s)
- Anuj Chiluwal
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, 67601, USA
| | - Hari P Poudel
- Agriculture and Agri-Food Canada, 5403 First Ave. South, Lethbridge, AB, T1J 4B1, Canada
| | - Kebede Muleta
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Troy Ostmeyer
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Lauren Fedenia
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Meghnath Pokharel
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, CGAHR, USDA-ARS, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - David Sebela
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Raju Bheemanahalli
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Halilou Oumarou
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Patricia Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - William L Rooney
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - S V Krishna Jagadish
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA.
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25
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Chaudhry S, Sidhu GPS. Climate change regulated abiotic stress mechanisms in plants: a comprehensive review. PLANT CELL REPORTS 2022; 41:1-31. [PMID: 34351488 DOI: 10.1007/s00299-021-02759-5] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/18/2021] [Indexed: 05/20/2023]
Abstract
Global climate change is identified as a major threat to survival of natural ecosystems. Climate change is a dynamic, multifaceted system of alterations in environmental conditions that affect abiotic and biotic components of the world. It results in alteration in environmental conditions such as heat waves, intensity of rainfall, CO2 concentration and temperature that lead to rise in new pests, weeds and pathogens. Climate change is one of the major constraints limiting plant growth and development worldwide. It impairs growth, disturbs photosynthesis, and reduces physiological responses in plants. The variations in global climate have gained the attention of researchers worldwide, as these changes negatively affect the agriculture by reducing crop productivity and food security. With this background, this review focuses on the effects of elevated atmospheric CO2 concentration, temperature, drought and salinity on the morphology, physiology and biochemistry of plants. Furthermore, this paper outlines an overview on the reactive oxygen species (ROS) production and their impact on the biochemical and molecular status of plants with increased climatic variations. Also additionally, different tolerance strategies adopted by plants to combat environmental adversities have been discussed.
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Affiliation(s)
- Smita Chaudhry
- Institute of Environmental Studies, Kurukshetra University, Kurukshetra, Haryana, 136119, India
- Centre for Applied Biology in Environment Sciences, Kurukshetra University, Kurukshetra, Haryana, 136119, India
| | - Gagan Preet Singh Sidhu
- Centre for Applied Biology in Environment Sciences, Kurukshetra University, Kurukshetra, Haryana, 136119, India.
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26
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Pignon CP, Fernandes SB, Valluru R, Bandillo N, Lozano R, Buckler E, Gore MA, Long SP, Brown PJ, Leakey ADB. Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes. PLANT PHYSIOLOGY 2021; 187:2544-2562. [PMID: 34618072 PMCID: PMC8644692 DOI: 10.1093/plphys/kiab395] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/26/2021] [Indexed: 05/07/2023]
Abstract
Stomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential for maintaining water-use efficiency (WUE). However, a little is known about the genetic basis for natural variation in stomatal movement, especially in C4 crops. This is partly because the stomatal response to a change in light intensity is difficult to measure at the scale required for association studies. Here, we used high-throughput thermal imaging to bypass the phenotyping bottleneck and assess 10 traits describing stomatal conductance (gs) before, during and after a stepwise decrease in light intensity for a diversity panel of 659 sorghum (Sorghum bicolor) accessions. Results from thermal imaging significantly correlated with photosynthetic gas exchange measurements. gs traits varied substantially across the population and were moderately heritable (h2 up to 0.72). An integrated genome-wide and transcriptome-wide association study identified candidate genes putatively driving variation in stomatal conductance traits. Of the 239 unique candidate genes identified with the greatest confidence, 77 were putative orthologs of Arabidopsis (Arabidopsis thaliana) genes related to functions implicated in WUE, including stomatal opening/closing (24 genes), stomatal/epidermal cell development (35 genes), leaf/vasculature development (12 genes), or chlorophyll metabolism/photosynthesis (8 genes). These findings demonstrate an approach to finding genotype-to-phenotype relationships for a challenging trait as well as candidate genes for further investigation of the genetic basis of WUE in a model C4 grass for bioenergy, food, and forage production.
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Affiliation(s)
- Charles P Pignon
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Samuel B Fernandes
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Lincoln Institute for Agri-Food Technology, University of Lincoln, Lincoln LN1 3QE, UK
| | - Nonoy Bandillo
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Edward Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Stephen P Long
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Lancaster Environment Centre, University of Lancaster, Lancaster LA1 1YX, UK
| | - Patrick J Brown
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Andrew D B Leakey
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Author for communication:
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27
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Quero G, Bonnecarrère V, Simondi S, Santos J, Fernández S, Gutierrez L, Garaycochea S, Borsani O. Genetic architecture of photosynthesis energy partitioning as revealed by a genome-wide association approach. PHOTOSYNTHESIS RESEARCH 2021; 150:97-115. [PMID: 32072456 DOI: 10.1007/s11120-020-00721-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
The photosynthesis process is determined by the intensity level and spectral quality of the light; therefore, leaves need to adapt to a changing environment. The incident energy absorbed can exceed the sink capability of the photosystems, and, in this context, photoinhibition may occur in both photosystem II (PSII) and photosystem I (PSI). Quantum yield parameters analyses reveal how the energy is managed. These parameters are genotype-dependent, and this genotypic variability is a good opportunity to apply mapping association strategies to identify genomic regions associated with photosynthesis energy partitioning. An experimental and mathematical approach is proposed for the determination of an index which estimates the energy per photon flux for each spectral bandwidth (Δλ) of the light incident (QI index). Based on the QI, the spectral quality of the plant growth, environmental lighting, and the actinic light of PAM were quantitatively very similar which allowed an accurate phenotyping strategy of a rice population. A total of 143 genomic single regions associated with at least one trait of chlorophyll fluorescence were identified. Moreover, chromosome 5 gathers most of these regions indicating the importance of this chromosome in the genetic regulation of the photochemistry process. Through a GWAS strategy, 32 genes of rice genome associated with the main parameters of the photochemistry process of photosynthesis in rice were identified. Association between light-harvesting complexes and the potential quantum yield of PSII, as well as the relationship between coding regions for PSI-linked proteins in energy distribution during the photochemical process of photosynthesis is analyzed.
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Affiliation(s)
- Gastón Quero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 809, Montevideo, Uruguay.
| | - Victoria Bonnecarrère
- Unidad de Biotecnología, Estación Experimental Wilson Ferreira Aldunate, Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 48, Km 10, Rincón del Colorado, 90200, Canelones, Uruguay
| | - Sebastián Simondi
- Área de Matemática, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (FCEN-UNCuyo), Padre Contreras 1300, Mendoza, Argentina
| | - Jorge Santos
- Área de Física, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (FCEN-UNCuyo), Padre Contreras 1300, Mendoza, Argentina
| | - Sebastián Fernández
- Facultad de Ingeniería, Instituto de Ingeniería Eléctrica, Universidad de La República, Julio Herrera y Reissig 565, Montevideo, Uruguay
| | - Lucía Gutierrez
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr., Madison, WI, 53706, USA
- Departamento de Biometría, Estadística y Cómputos, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo, Uruguay
| | - Silvia Garaycochea
- Unidad de Biotecnología, Estación Experimental Wilson Ferreira Aldunate, Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 48, Km 10, Rincón del Colorado, 90200, Canelones, Uruguay
| | - Omar Borsani
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 809, Montevideo, Uruguay
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28
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Ferguson JN, Fernandes SB, Monier B, Miller ND, Allen D, Dmitrieva A, Schmuker P, Lozano R, Valluru R, Buckler ES, Gore MA, Brown PJ, Spalding EP, Leakey ADB. Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. PLANT PHYSIOLOGY 2021; 187:1481-1500. [PMID: 34618065 PMCID: PMC9040483 DOI: 10.1093/plphys/kiab346] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/29/2021] [Indexed: 05/04/2023]
Abstract
Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.
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Affiliation(s)
- John N Ferguson
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Samuel B Fernandes
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Brandon Monier
- Institute for Genomic Diversity, Cornell University, Ithaca, New
York 14853, USA
| | - Nathan D Miller
- Department of Botany, University of Wisconsin, Madison, Wisconsin
53706, USA
| | - Dylan Allen
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Anna Dmitrieva
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Peter Schmuker
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, New York 14853, USA
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, New
York 14853, USA
- Present address: Lincoln Institute for Agri-Food Technology,
University of Lincoln, Lincoln LN2 2LG, UK
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New
York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, New York 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, New York 14853, USA
| | - Patrick J Brown
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Present address: Section of Agricultural Plant Biology,
Department of Plant Sciences, University of California Davis, California 95616,
USA
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin
53706, USA
| | - Andrew D B Leakey
- Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Crop Sciences, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Plant Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61901, USA
- Author for communication: ,
Present address: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA,
UK
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29
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Ferguson JN, Fernandes SB, Monier B, Miller ND, Allen D, Dmitrieva A, Schmuker P, Lozano R, Valluru R, Buckler ES, Gore MA, Brown PJ, Spalding EP, Leakey ADB. Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. PLANT PHYSIOLOGY 2021; 187:1481-1500. [PMID: 34618065 DOI: 10.1093/plphys/kiab34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/29/2021] [Indexed: 05/27/2023]
Abstract
Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.
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Affiliation(s)
- John N Ferguson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Samuel B Fernandes
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Brandon Monier
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Nathan D Miller
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Dylan Allen
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Anna Dmitrieva
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Peter Schmuker
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Patrick J Brown
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Andrew D B Leakey
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61901, USA
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Transcriptome Profiling of Maize ( Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage. Genes (Basel) 2021; 12:genes12101638. [PMID: 34681032 PMCID: PMC8535276 DOI: 10.3390/genes12101638] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/27/2021] [Accepted: 10/11/2021] [Indexed: 01/22/2023] Open
Abstract
Cold tolerance is a complex trait that requires a critical perspective to understand its underpinning mechanism. To unravel the molecular framework underlying maize (Zea mays L.) cold stress tolerance, we conducted a comparative transcriptome profiling of 24 cold-tolerant and 22 cold-sensitive inbred lines affected by cold stress at the seedling stage. Using the RNA-seq method, we identified 2237 differentially expressed genes (DEGs), namely 1656 and 581 annotated and unannotated DEGs, respectively. Further analysis of the 1656 annotated DEGs mined out two critical sets of cold-responsive DEGs, namely 779 and 877 DEGs, which were significantly enhanced in the tolerant and sensitive lines, respectively. Functional analysis of the 1656 DEGs highlighted the enrichment of signaling, carotenoid, lipid metabolism, transcription factors (TFs), peroxisome, and amino acid metabolism. A total of 147 TFs belonging to 32 families, including MYB, ERF, NAC, WRKY, bHLH, MIKC MADS, and C2H2, were strongly altered by cold stress. Moreover, the tolerant lines’ 779 enhanced DEGs were predominantly associated with carotenoid, ABC transporter, glutathione, lipid metabolism, and amino acid metabolism. In comparison, the cold-sensitive lines’ 877 enhanced DEGs were significantly enriched for MAPK signaling, peroxisome, ribosome, and carbon metabolism pathways. The biggest proportion of the unannotated DEGs was implicated in the roles of long non-coding RNAs (lncRNAs). Taken together, this study provides valuable insights that offer a deeper understanding of the molecular mechanisms underlying maize response to cold stress at the seedling stage, thus opening up possibilities for a breeding program of maize tolerance to cold stress.
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Sales CRG, Wang Y, Evers JB, Kromdijk J. Improving C4 photosynthesis to increase productivity under optimal and suboptimal conditions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5942-5960. [PMID: 34268575 PMCID: PMC8411859 DOI: 10.1093/jxb/erab327] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/09/2021] [Indexed: 05/05/2023]
Abstract
Although improving photosynthetic efficiency is widely recognized as an underutilized strategy to increase crop yields, research in this area is strongly biased towards species with C3 photosynthesis relative to C4 species. Here, we outline potential strategies for improving C4 photosynthesis to increase yields in crops by reviewing the major bottlenecks limiting the C4 NADP-malic enzyme pathway under optimal and suboptimal conditions. Recent experimental results demonstrate that steady-state C4 photosynthesis under non-stressed conditions can be enhanced by increasing Rubisco content or electron transport capacity, both of which may also stimulate CO2 assimilation at supraoptimal temperatures. Several additional putative bottlenecks for photosynthetic performance under drought, heat, or chilling stress or during photosynthetic induction await further experimental verification. Based on source-sink interactions in maize, sugarcane, and sorghum, alleviating these photosynthetic bottlenecks during establishment and growth of the harvestable parts are likely to improve yield. The expected benefits are also shown to be augmented by the increasing trend in planting density, which increases the impact of photosynthetic source limitation on crop yields.
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Affiliation(s)
- Cristina R G Sales
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Yu Wang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jochem B Evers
- Centre for Crops Systems Analysis (WUR), Wageningen University, Wageningen, The Netherlands
| | - Johannes Kromdijk
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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32
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Bheemanahalli R, Wang C, Bashir E, Chiluwal A, Pokharel M, Perumal R, Moghimi N, Ostmeyer T, Caragea D, Jagadish SK. Classical phenotyping and deep learning concur on genetic control of stomatal density and area in sorghum. PLANT PHYSIOLOGY 2021; 186:1562-1579. [PMID: 33856488 PMCID: PMC8260133 DOI: 10.1093/plphys/kiab174] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/28/2021] [Indexed: 05/18/2023]
Abstract
Stomatal density (SD) and stomatal complex area (SCA) are important traits that regulate gas exchange and abiotic stress response in plants. Despite sorghum (Sorghum bicolor) adaptation to arid conditions, the genetic potential of stomata-related traits remains unexplored due to challenges in available phenotyping methods. Hence, identifying loci that control stomatal traits is fundamental to designing strategies to breed sorghum with optimized stomatal regulation. We implemented both classical and deep learning methods to characterize genetic diversity in 311 grain sorghum accessions for stomatal traits at two different field environments. Nearly 12,000 images collected from abaxial (Ab) and adaxial (Ad) leaf surfaces revealed substantial variation in stomatal traits. Our study demonstrated significant accuracy between manual and deep learning methods in predicting SD and SCA. In sorghum, SD was 32%-39% greater on the Ab versus the Ad surface, while SCA on the Ab surface was 2%-5% smaller than on the Ad surface. Genome-Wide Association Study identified 71 genetic loci (38 were environment-specific) with significant genotype to phenotype associations for stomatal traits. Putative causal genes underlying the phenotypic variation were identified. Accessions with similar SCA but carrying contrasting haplotypes for SD were tested for stomatal conductance and carbon assimilation under field conditions. Our findings provide a foundation for further studies on the genetic and molecular mechanisms controlling stomata patterning and regulation in sorghum. An integrated physiological, deep learning, and genomic approach allowed us to unravel the genetic control of natural variation in stomata traits in sorghum, which can be applied to other plants.
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Affiliation(s)
- Raju Bheemanahalli
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Chaoxin Wang
- Department of Computer Science, Kansas State University, Manhattan, Kansas 66506, USA
| | - Elfadil Bashir
- Agricultural Research Center, Kansas State University, Hays, Kansas 67601, USA
| | - Anuj Chiluwal
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Meghnath Pokharel
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, Kansas 67601, USA
| | - Naghmeh Moghimi
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Troy Ostmeyer
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Doina Caragea
- Department of Computer Science, Kansas State University, Manhattan, Kansas 66506, USA
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Hao H, Li Z, Leng C, Lu C, Luo H, Liu Y, Wu X, Liu Z, Shang L, Jing HC. Sorghum breeding in the genomic era: opportunities and challenges. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1899-1924. [PMID: 33655424 PMCID: PMC7924314 DOI: 10.1007/s00122-021-03789-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/05/2021] [Indexed: 05/04/2023]
Abstract
The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.
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Affiliation(s)
- Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chuanyuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Cheng Lu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiquan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- Engineering Laboratory for Grass-based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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34
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Mural RV, Grzybowski M, Miao C, Damke A, Sapkota S, Boyles RE, Salas Fernandez MG, Schnable PS, Sigmon B, Kresovich S, Schnable JC. Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum. Genetics 2021; 218:6294935. [PMID: 34100945 PMCID: PMC9335936 DOI: 10.1093/genetics/iyab087] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/07/2021] [Indexed: 01/03/2023] Open
Abstract
Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome wide association studies conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.
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Affiliation(s)
- Ravi V Mural
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Marcin Grzybowski
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Chenyong Miao
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Alyssa Damke
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Sirjan Sapkota
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634 USA.,Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA
| | - Richard E Boyles
- Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA.,Pee Dee Research and Education Center, Clemson University, Florence, SC 29532 USA
| | | | | | - Brandi Sigmon
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Stephen Kresovich
- Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA.,Feed the Future Innovation Lab for Crop Improvement Cornell University, Ithaca, NY 14850 USA
| | - James C Schnable
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
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35
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Emendack Y, Sanchez J, Hayes C, Nesbitt M, Laza H, Burke J. Seed-to-seed early-season cold resiliency in sorghum. Sci Rep 2021; 11:7801. [PMID: 33833364 PMCID: PMC8032771 DOI: 10.1038/s41598-021-87450-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 11/14/2022] Open
Abstract
Early planted sorghum usually experiences cooler day/night temperatures, which may result in delayed growth, floral initiation, and infertile pollen, limiting productivity in high altitudes and temperate regions. Genetic variability for cold tolerance in sorghum has been evaluated by characterizing germination, emergence, vigor, and seedling growth under sub-optimal temperatures. However, the compounded effect of early season cold on plant growth and development and subsequent variability in potential grain yield losses has not been evaluated. Agro-morphological and physiological responses of sorghum grown under early-, mid-, and standard planting dates in West Texas were characterized from seed-to-seed. A set of diverse lines and hybrids with two major sources of tolerance, and previously selected for seedling cold tolerance were used. These were evaluated with a standard commercial hybrid known for its seedling cold tolerance and some cold susceptible breeding lines as checks. Variabilities in assessed parameters at seedling, early vegetative, and maturity stages were observed across planting dates for genotypes and sources of cold tolerance. Panicle initiation was delayed, and panicle size reduced, resulting in decreased grain yields under early and mid-planting dates. Coupled with final germination percent, panicle width and area were significant unique predictors of yield under early and mid-planting dates. Significant variability in performance was observed not only between cold tolerant and susceptible checks, but noticeably between sources of cold tolerance, with the Ethiopian highland sources having lesser yield penalties than their Chinese counterparts. Thus, screening for cold tolerance should not be limited to early seedling characterization but should also consider agronomic traits that may affect yield penalties depending on the sources of tolerance.
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Affiliation(s)
- Yves Emendack
- Cropping Systems Research Laboratory, USDA-ARS, 3810 4th Street, Lubbock, TX, USA.
| | - Jacobo Sanchez
- Cropping Systems Research Laboratory, USDA-ARS, 3810 4th Street, Lubbock, TX, USA
| | - Chad Hayes
- Cropping Systems Research Laboratory, USDA-ARS, 3810 4th Street, Lubbock, TX, USA
| | - Matthew Nesbitt
- Cropping Systems Research Laboratory, USDA-ARS, 3810 4th Street, Lubbock, TX, USA
| | - Haydee Laza
- Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX, USA
| | - John Burke
- Cropping Systems Research Laboratory, USDA-ARS, 3810 4th Street, Lubbock, TX, USA
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Amini S, Maali-Amiri R, Kazemi-Shahandashti SS, López-Gómez M, Sadeghzadeh B, Sobhani-Najafabadi A, Kariman K. Effect of cold stress on polyamine metabolism and antioxidant responses in chickpea. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153387. [PMID: 33636556 DOI: 10.1016/j.jplph.2021.153387] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/04/2023]
Abstract
Metabolic and genomic characteristics of polyamines (PAs) may be associated with the induction of cold tolerance (CT) responses in plants. Characteristics of PAs encoding genes in chickpea (Cicer arietinum L.) and their function under cold stress (CS) are currently unknown. In this study, the potential role of PAs along with the antioxidative defense systems were assessed in two chickpea genotypes (Sel96th11439, cold-tolerant and ILC533, cold-sensitive) under CS conditions. Six days after exposure to CS, the leaf H2O2 content and electrolyte leakage index increased in the sensitive genotype by 47.7 and 59 %, respectively, while these values decreased or remained unchanged, respectively, in the tolerant genotype. In tolerant genotype, the enhanced activity of superoxide dismutase (SOD) (by 50 %) was accompanied by unchanged activities of ascorbate peroxidase (APX), guaiacol peroxidase (GPX) and catalase (CAT) as well as the accumulation of glutathione (GSH) (by 43 %) on the sixth day of CS. Higher levels of putrescine (Put) (322 %), spermidine (Spd) (45 %), spermine (Spm) (69 %) and the highest ratio of Put/(Spd + Spm) were observed in tolerant genotype compared to the sensitive one on the sixth day of CS. Gamma-aminobutyric acid (GABA) accumulation was 74 % higher in tolerant genotype compared to the sensitive one on the sixth day of CS. During CS, the activity of diamine oxidase (DAO) and polyamine oxidase (PAO) increased in tolerant (by 3.02- and 2.46-fold) and sensitive (by 2.51- and 2.8-fold) genotypes, respectively, in comparison with the respective non-stressed plants (normal conditions). The highest activity of DAO and PAO in the tolerant genotype was accompanied by PAs decomposition and a peak in GABA content on the sixth day of CS. The analysis of chickpea genome revealed the presence of five PAs biosynthetic genes, their chromosomal locations, and cis-regulatory elements. A significant increase in transcript levels of arginine decarboxylase (ADC) (24.26- and 7.96-fold), spermidine synthase 1 (SPDS1) (3.03- and 1.53-fold), SPDS2 (5.5- and 1.62-fold) and spermine synthase (SPMS) (3.92- and 1.65-fold) genes was detected in tolerant and sensitive genotypes, respectively, whereas the expression of ornithine decarboxylase (ODC) genes decreased significantly under CS conditions in both genotypes. Leaf chlorophyll and carotenoid contents exhibited declining trends in the sensitive genotype, while these photosynthetic pigments were stable in the tolerant genotype due to the superior performance of defensive processes under CS conditions. Overall, these results suggested the specific roles of putative PAs genes and PAs metabolism in development of effective CT responses in chickpea.
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Affiliation(s)
- Saeed Amini
- Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, 31587-77871, Karaj, Iran
| | - Reza Maali-Amiri
- Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, 31587-77871, Karaj, Iran.
| | - Seyyedeh-Sanam Kazemi-Shahandashti
- Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, 31587-77871, Karaj, Iran
| | - Miguel López-Gómez
- Departamento de Fisiología Vegetal, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain
| | - Behzad Sadeghzadeh
- Dryland Agricultural Research Institute, Ministry of Jihad-e-Agriculture Research and Education Organization, Maraghe, Iran
| | - Ahmad Sobhani-Najafabadi
- Agricultural Biotechnology Research Institute of Iran, Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Iran
| | - Khalil Kariman
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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Pandian BA, Varanasi A, Vennapusa AR, Sathishraj R, Lin G, Zhao M, Tunnell M, Tesso T, Liu S, Prasad PVV, Jugulam M. Characterization, Genetic Analyses, and Identification of QTLs Conferring Metabolic Resistance to a 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor in Sorghum ( Sorghum bicolor). FRONTIERS IN PLANT SCIENCE 2020; 11:596581. [PMID: 33362828 PMCID: PMC7756693 DOI: 10.3389/fpls.2020.596581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/09/2020] [Indexed: 05/24/2023]
Abstract
Postemergence grass weed control continues to be a major challenge in grain sorghum [Sorghum bicolor (L.) Moench], primarily due to lack of herbicide options registered for use in this crop. The development of herbicide-resistant sorghum technology to facilitate broad-spectrum postemergence weed control can be an economical and viable solution. The 4-hydroxyphenylpyruvate dioxygenase-inhibitor herbicides (e.g., mesotrione or tembotrione) can control a broad spectrum of weeds including grasses, which, however, are not registered for postemergence application in sorghum due to crop injury. In this study, we identified two tembotrione-resistant sorghum genotypes (G-200, G-350) and one susceptible genotype (S-1) by screening 317 sorghum lines from a sorghum association panel (SAP). These tembotrione-resistant and tembotrione-susceptible genotypes were evaluated in a tembotrione dose-response [0, 5.75, 11.5, 23, 46, 92 (label recommended dose), 184, 368, and 736 g ai ha-1] assay. Compared with S-1, the genotypes G-200 and G-350 exhibited 10- and seven fold more resistance to tembotrione, respectively. To understand the inheritance of tembotrione-resistant trait, crosses were performed using S-1 and G-200 or G-350 to generate F1 and F2 progeny. The F1 and F2 progeny were assessed for their response to tembotrione treatment. Genetic analyses of the F1 and F2 progeny demonstrated that the tembotrione resistance in G-200 and G-350 is a partially dominant polygenic trait. Furthermore, cytochrome P450 (CYP)-inhibitor assay using malathion and piperonyl butoxide suggested possible CYP-mediated metabolism of tembotrione in G-200 and G-350. Genotype-by-sequencing based quantitative trait loci (QTL) mapping revealed QTLs associated with tembotrione resistance in G-200 and G-350 genotypes. Overall, the genotypes G-200 and G-350 confer a high level of metabolic resistance to tembotrione and controlled by a polygenic trait. There is an enormous potential to introgress the tembotrione resistance into breeding lines to develop agronomically desirable sorghum hybrids.
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Affiliation(s)
| | | | | | | | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Mingxia Zhao
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Madison Tunnell
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - P. V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, United States
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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Mantilla-Perez MB, Bao Y, Tang L, Schnable PS, Salas-Fernandez MG. Toward "Smart Canopy" Sorghum: Discovery of the Genetic Control of Leaf Angle Across Layers. PLANT PHYSIOLOGY 2020; 184:1927-1940. [PMID: 33093232 PMCID: PMC7723111 DOI: 10.1104/pp.20.00632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/09/2020] [Indexed: 05/15/2023]
Abstract
A "smart canopy" ideotype has been proposed with leaves being upright at the top and more horizontal toward the bottom of the plant to maximize light interception and conversion efficiencies, and thus increasing yield. The genetic control of leaf angle has, to date, been studied on one or two leaves, or data have been merged from multiple leaves to generate average values. This approach has limited our understanding of the diversity of leaf angles across layers and their genetic control. Genome-wide association studies and quantitative trait loci mapping studies in sorghum (Sorghum bicolor) were performed using layer-specific angle data collected manually and via high-throughput phenotyping strategies. The observed distribution of angles in indoor and field settings is opposite to the ideotype. Several genomic regions were associated with leaf angle within layers or across the canopy. The expression of the brassinosteroid-related transcription factor BZR1/BES1 and the auxin-transporter Dwarf3 were found to be highly correlated with the distribution of angles at different layers. The application of a brassinosteroid biosynthesis inhibitor could not revert the undesirable overall angle distribution. These discoveries demonstrate that the exploitation of layer-specific quantitative trait loci/genes will be instrumental to reversing the natural angle distribution in sorghum according to the "smart canopy" ideotype.
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Affiliation(s)
| | - Yin Bao
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa 50011
| | - Lie Tang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa 50011
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Baslam M, Mitsui T, Hodges M, Priesack E, Herritt MT, Aranjuelo I, Sanz-Sáez Á. Photosynthesis in a Changing Global Climate: Scaling Up and Scaling Down in Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:882. [PMID: 32733499 PMCID: PMC7357547 DOI: 10.3389/fpls.2020.00882] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/29/2020] [Indexed: 05/06/2023]
Abstract
Photosynthesis is the major process leading to primary production in the Biosphere. There is a total of 7000bn tons of CO2 in the atmosphere and photosynthesis fixes more than 100bn tons annually. The CO2 assimilated by the photosynthetic apparatus is the basis of crop production and, therefore, of animal and human food. This has led to a renewed interest in photosynthesis as a target to increase plant production and there is now increasing evidence showing that the strategy of improving photosynthetic traits can increase plant yield. However, photosynthesis and the photosynthetic apparatus are both conditioned by environmental variables such as water availability, temperature, [CO2], salinity, and ozone. The "omics" revolution has allowed a better understanding of the genetic mechanisms regulating stress responses including the identification of genes and proteins involved in the regulation, acclimation, and adaptation of processes that impact photosynthesis. The development of novel non-destructive high-throughput phenotyping techniques has been important to monitor crop photosynthetic responses to changing environmental conditions. This wealth of data is being incorporated into new modeling algorithms to predict plant growth and development under specific environmental constraints. This review gives a multi-perspective description of the impact of changing environmental conditions on photosynthetic performance and consequently plant growth by briefly highlighting how major technological advances including omics, high-throughput photosynthetic measurements, metabolic engineering, and whole plant photosynthetic modeling have helped to improve our understanding of how the photosynthetic machinery can be modified by different abiotic stresses and thus impact crop production.
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Affiliation(s)
- Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Michael Hodges
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Saclay, Université Evry, Université Paris Diderot, Paris, France
| | - Eckart Priesack
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthew T. Herritt
- USDA-ARS Plant Physiology and Genetics Research, US Arid-Land Agricultural Research Center, Maricopa, AZ, United States
| | - Iker Aranjuelo
- Agrobiotechnology Institute (IdAB-CSIC), Consejo Superior de Investigaciones Científicas-Gobierno de Navarra, Mutilva, Spain
| | - Álvaro Sanz-Sáez
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
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Ritonga FN, Chen S. Physiological and Molecular Mechanism Involved in Cold Stress Tolerance in Plants. PLANTS (BASEL, SWITZERLAND) 2020; 9:E560. [PMID: 32353940 PMCID: PMC7284489 DOI: 10.3390/plants9050560] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/18/2020] [Accepted: 04/21/2020] [Indexed: 01/26/2023]
Abstract
Previous studies have reported that low temperature (LT) constrains plant growth and restricts productivity in temperate regions. However, the underlying mechanisms are complex and not well understood. Over the past ten years, research on the process of adaptation and tolerance of plants during cold stress has been carried out. In molecular terms, researchers prioritize research into the field of the ICE-CBF-COR signaling pathway which is believed to be the important key to the cold acclimation process. Inducer of CBF Expression (ICE) is a pioneer of cold acclimation and plays a central role in C-repeat binding (CBF) cold induction. CBFs activate the expression of COR genes via binding to cis-elements in the promoter of COR genes. An ICE-CBF-COR signaling pathway activates the appropriate expression of downstream genes, which encodes osmoregulation substances. In this review, we summarize the recent progress of cold stress tolerance in plants from molecular and physiological perspectives and other factors, such as hormones, light, and circadian clock. Understanding the process of cold stress tolerance and the genes involved in the signaling network for cold stress is essential for improving plants, especially crops.
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Affiliation(s)
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China;
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Du T, Meng P, Huang J, Peng S, Xiong D. Fast photosynthesis measurements for phenotyping photosynthetic capacity of rice. PLANT METHODS 2020; 16:6. [PMID: 31998402 PMCID: PMC6979334 DOI: 10.1186/s13007-020-0553-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Over the past decades, the structural and functional genomics of rice have been deeply studied, and high density of molecular genetic markers have been developed. However, the genetic variation in leaf photosynthesis, the most important trait for rice yield improvement, was rarely studied. The lack of photosynthesis phenotyping tools is one of the bottlenecks, as traditional direct photosynthesis measurements are very low-throughput, and recently developed high-throughput methods are indirect measurements. Hence, there is an urgent need for a fast, accurate and direct measurement approach. RESULT We reported a fast photosynthesis measurement (FPM) method for phenotyping photosynthetic capacity of rice, which measures photosynthesis of excised tillers in environment-controlled lab conditions. The light response curves measured using FPM approach coped well with that the curves measured using traditional gas exchange approach. Importantly, the FPM technique achieved an average throughput of 5.4 light response curves per hour, which was 3 times faster than the 1.8 light response curves per hour using the traditional method. Tillers sampled at early morning had the highest photosynthesis, stomatal conductance and the lowest variability. In addition, even 12 h after sampling, there was no significant difference of photosynthesis rate between excised tillers and in situ. We finally investigated the genetic variations of photosynthetic traits across 568 F2 lines using the FPM technique and discussed the logistics of screening several hundred samples per day per instrumental unit using FPM to generate a wealth of photosynthetic phenotypic data, which might help to improve the selection power in large populations of rice with the ultimate aim of improving yield through improved photosynthesis. CONCLUSIONS Here we developed a high-throughput method that can measure the rice leaf photosynthetic capacity approximately 10 times faster than traditional gas exchange approaches. Importantly, this method can overcome measurement errors caused by environmental heterogeneity under field conditions, and it is possible to measure 12 or more hours per day under lab conditions.
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Affiliation(s)
- Tingting Du
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Ping Meng
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Jianliang Huang
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Shaobing Peng
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Dongliang Xiong
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 Hubei China
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Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population. G3-GENES GENOMES GENETICS 2019; 9:4045-4057. [PMID: 31611346 PMCID: PMC6893202 DOI: 10.1534/g3.119.400353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dissecting the genetic architecture of stress tolerance in crops is critical to understand and improve adaptation. In temperate climates, early planting of chilling-tolerant varieties could provide longer growing seasons and drought escape, but chilling tolerance (<15°) is generally lacking in tropical-origin crops. Here we developed a nested association mapping (NAM) population to dissect the genetic architecture of early-season chilling tolerance in the tropical-origin cereal sorghum (Sorghum bicolor [L.] Moench). The NAM resource, developed from reference line BTx623 and three chilling-tolerant Chinese lines, is comprised of 771 recombinant inbred lines genotyped by sequencing at 43,320 single nucleotide polymorphisms. We phenotyped the NAM population for emergence, seedling vigor, and agronomic traits (>75,000 data points from ∼16,000 plots) in multi-environment field trials in Kansas under natural chilling stress (sown 30-45 days early) and normal growing conditions. Joint linkage mapping with early-planted field phenotypes revealed an oligogenic architecture, with 5-10 chilling tolerance loci explaining 20-41% of variation. Surprisingly, several of the major chilling tolerance loci co-localize precisely with the classical grain tannin (Tan1 and Tan2) and dwarfing genes (Dw1 and Dw3) that were under strong directional selection in the US during the 20th century. These findings suggest that chilling sensitivity was inadvertently selected due to coinheritance with desired nontannin and dwarfing alleles. The characterization of genetic architecture with NAM reveals why past chilling tolerance breeding was stymied and provides a path for genomics-enabled breeding of chilling tolerance.
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Sorghum as a Novel Crop for Central Europe: Using a Broad Diversity Set to Dissect Temperate-Adaptation. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9090535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sorghum (Sorghum bicolor L. Moench) is a promising novel crop for Central Europe. However, enhancements in cold tolerance and early maturity are essential for a successful adaptation to cooler climates. We scored a broad sorghum diversity set (n = 338) for early chilling tolerance, high-latitude adaptation, and bioenergy related agronomical traits in multi-environment trials. Our results show a high phenotypic variation and medium to high heritabilities for most traits, indicating that a robust breeding progress is feasible. Several public accessions with a good adaptation to cooler climates were identified, which can serve as valuable base material for sorghum breeding in temperate areas. Genome-wide association studies reveal a polygenic (quantitative) character for most of the traits, confirming previous studies. Hence, for practical breeding, it will be difficult to conduct efficient marker-assisted selection for temperate-adaptation traits in genetically diverse material.
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Kromdijk J, Głowacka K, Long SP. Predicting light-induced stomatal movements based on the redox state of plastoquinone: theory and validation. PHOTOSYNTHESIS RESEARCH 2019; 141:83-97. [PMID: 30891661 PMCID: PMC6612513 DOI: 10.1007/s11120-019-00632-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 02/25/2019] [Indexed: 05/23/2023]
Abstract
Prediction of stomatal conductance is a key element to relate and scale up leaf-level gas exchange processes to canopy, ecosystem and land surface models. The empirical models that are typically employed for this purpose are simple and elegant formulations which relate stomatal conductance on a leaf area basis to the net rate of CO2 assimilation, humidity and CO2 concentration. Although light intensity is not directly modelled as a stomatal opening cue, it is well-known that stomata respond strongly to light. One response mode depends specifically on the blue-light part of the light spectrum, whereas the quantitative or 'red' light response is less spectrally defined and relies more on the quantity of incident light. Here, we present a modification of an empirical stomatal conductance model which explicitly accounts for the stomatal red-light response, based on a mesophyll-derived signal putatively initiated by the chloroplastic plastoquinone redox state. The modified model showed similar prediction accuracy compared to models using a relationship between stomatal conductance and net assimilation rate. However, fitted parameter values with the modified model varied much less across different measurement conditions, lessening the need for frequent re-parameterization to different conditions required of the current model. We also present a simple and easy to parameterize extension to the widely used Farquhar-Von Caemmerer-Berry photosynthesis model to facilitate coupling with the modified stomatal conductance model, which should enable use of the new stomatal conductance model to simulate ecosystem water vapour exchange in terrestrial biosphere models.
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Affiliation(s)
- Johannes Kromdijk
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA.
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB23EA, UK.
| | - Katarzyna Głowacka
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland
- Department of Biochemistry, University of Nebraska-Lincoln, N246 Beadle Center, 1901 Vine Street, Lincoln, NE, USA
| | - Stephen P Long
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
- Lancaster Environment Centre, University of Lancaster, Bailrigg, LA1 1YX, UK
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Moghimi N, Desai JS, Bheemanahalli R, Impa SM, Vennapusa AR, Sebela D, Perumal R, Doherty CJ, Jagadish SVK. New candidate loci and marker genes on chromosome 7 for improved chilling tolerance in sorghum. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3357-3371. [PMID: 30949711 DOI: 10.1093/jxb/erz143] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Sorghum is often exposed to suboptimal low temperature stress under field conditions, particularly at the seedling establishment stage. Enhancing chilling tolerance will facilitate earlier planting and so minimize the negative impacts of other stresses experienced at later growth stages. Genome-wide association mapping was performed on a sorghum association panel grown under control (30/20 °C; day/night) and chilling (20/10 °C) conditions. Genomic regions on chromosome 7, controlling the emergence index and seedling (root and shoot) vigor, were associated with increased chilling tolerance but they did not co-localize with undesirable tannin content quantitative trait loci (QTLs). Shoot and root samples from highly contrasting haplotype pairs expressing differential responses to chilling stress were used to identify candidate genes. Three candidate genes (an alpha/beta hydrolase domain protein, a DnaJ/Hsp40 motif-containing protein, and a YTH domain-containing RNA-binding protein) were expressed at significantly higher levels under chilling stress in the tolerant haplotype compared with the sensitive haplotype and BTx623. Moreover, two CBF/DREB1A transcription factors on chromosome 2 showed a divergent response to chilling in the contrasting haplotypes. These studies identify haplotype differences on chromosome 7 that modulate chilling tolerance by either regulating CBF or feeding back into this signaling pathway. We have identified new candidate genes that will be useful markers in ongoing efforts to develop tannin-free chilling-tolerant sorghum hybrids.
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Affiliation(s)
- Naghmeh Moghimi
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Jigar S Desai
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | | | - Somayanda M Impa
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | | | - David Sebela
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, USA
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
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Hamdani S, Wang H, Zheng G, Perveen S, Qu M, Khan N, Khan W, Jiang J, Li M, Liu X, Zhu X, Chu C, Zhu XG. Genome-wide association study identifies variation of glucosidase being linked to natural variation of the maximal quantum yield of photosystem II. PHYSIOLOGIA PLANTARUM 2019; 166:105-119. [PMID: 30834537 DOI: 10.1111/ppl.12957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/06/2019] [Accepted: 03/01/2019] [Indexed: 06/09/2023]
Abstract
The maximum quantum yield of photosystem II (as reflected by variable to maximum chlorophyll a fluorescence, Fv /Fm ) is regarded as one of the most important photosynthetic parameters. The genetic basis underlying natural variation in Fv /Fm , which shows low level of variations in plants under non-stress conditions, is not easy to be exploited using the conventional gene cloning approaches. Thus, in order to answer this question, we have followed another strategy: we used genome-wide association study (GWAS) and transgenic analysis in a rice mini-core collection. We report here that four single-nucleotide polymorphisms, located in the promoter region of β-glucosidase 5 (BGlu-5), are associated with observed variation in Fv /Fm . Indeed, our transgenic analysis showed a good correlation between BGlu-5 and Fv /Fm . Thus, our work demonstrates the feasibility of using GWAS to study natural variation in Fv /Fm , suggesting that cis-element polymorphism, affecting the BGlu-5 expression level, may, indirectly, contribute to Fv /Fm variation in rice through the gibberellin signaling pathway. Further research is needed to understand the mechanism of our novel observation.
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Affiliation(s)
- Saber Hamdani
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hongru Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangyong Zheng
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shahnaz Perveen
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mingnan Qu
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Naveed Khan
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Waqasuddin Khan
- Jamil-ur-Rahman Center for Genome Research, DR. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Jianjun Jiang
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ming Li
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xinyu Liu
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiaocen Zhu
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin-Guang Zhu
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
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van Bezouw RFHM, Keurentjes JJB, Harbinson J, Aarts MGM. Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:112-133. [PMID: 30548574 PMCID: PMC6850172 DOI: 10.1111/tpj.14190] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 05/18/2023]
Abstract
In recent years developments in plant phenomic approaches and facilities have gradually caught up with genomic approaches. An opportunity lies ahead to dissect complex, quantitative traits when both genotype and phenotype can be assessed at a high level of detail. This is especially true for the study of natural variation in photosynthetic efficiency, for which forward genetics studies have yielded only a little progress in our understanding of the genetic layout of the trait. High-throughput phenotyping, primarily from chlorophyll fluorescence imaging, should help to dissect the genetics of photosynthesis at the different levels of both plant physiology and development. Specific emphasis should be directed towards understanding the acclimation of the photosynthetic machinery in fluctuating environments, which may be crucial for the identification of genetic variation for relevant traits in food crops. Facilities should preferably be designed to accommodate phenotyping of photosynthesis-related traits in such environments. The use of forward genetics to study the genetic architecture of photosynthesis is likely to lead to the discovery of novel traits and/or genes that may be targeted in breeding or bio-engineering approaches to improve crop photosynthetic efficiency. In the near future, big data approaches will play a pivotal role in data processing and streamlining the phenotype-to-gene identification pipeline.
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Affiliation(s)
- Roel F. H. M. van Bezouw
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
| | - Joost J. B. Keurentjes
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
| | - Jeremy Harbinson
- Horticulture and Product PhysiologyWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
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Luo D, Wu Y, Liu J, Zhou Q, Liu W, Wang Y, Yang Q, Wang Z, Liu Z. Comparative Transcriptomic and Physiological Analyses of Medicago sativa L. Indicates that Multiple Regulatory Networks Are Activated during Continuous ABA Treatment. Int J Mol Sci 2018; 20:E47. [PMID: 30583536 PMCID: PMC6337461 DOI: 10.3390/ijms20010047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022] Open
Abstract
Alfalfa is the most extensively cultivated forage legume worldwide. However, the molecular mechanisms underlying alfalfa responses to exogenous abscisic acid (ABA) are still unknown. In this study, the first global transcriptome profiles of alfalfa roots under ABA treatments for 1, 3 and 12 h (three biological replicates for each time point, including the control group) were constructed using a BGISEQ-500 sequencing platform. A total of 50,742 isoforms with a mean length of 2541 bp were generated, and 4944 differentially expressed isoforms (DEIs) were identified after ABA deposition. Metabolic analyses revealed that these DEIs were involved in plant hormone signal transduction, transcriptional regulation, antioxidative defense and pathogen immunity. Notably, several well characterized hormone signaling pathways, for example, the core ABA signaling pathway, was activated, while salicylic acid, jasmonate and ethylene signaling pathways were mainly suppressed by exogenous ABA. Moreover, the physiological work showed that catalase and peroxidase activity and glutathione and proline content were increased after ABA deposition, which is in accordance with the dynamic transcript profiles of the relevant genes in antioxidative defense system. These results indicate that ABA has the potential to improve abiotic stress tolerance, but that it may negatively regulate pathogen resistance in alfalfa.
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Affiliation(s)
- Dong Luo
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Yuguo Wu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Jie Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Qiang Zhou
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China.
| | - Zengyu Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
- Core Research & Transformation, Noble Research Institute, Ardmore, OK 73401, USA.
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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49
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Dreyer A, Dietz KJ. Reactive Oxygen Species and the Redox-Regulatory Network in Cold Stress Acclimation. Antioxidants (Basel) 2018; 7:E169. [PMID: 30469375 PMCID: PMC6262571 DOI: 10.3390/antiox7110169] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 01/08/2023] Open
Abstract
Cold temperatures restrict plant growth, geographical extension of plant species, and agricultural practices. This review deals with cold stress above freezing temperatures often defined as chilling stress. It focuses on the redox regulatory network of the cell under cold temperature conditions. Reactive oxygen species (ROS) function as the final electron sink in this network which consists of redox input elements, transmitters, targets, and sensors. Following an introduction to the critical network components which include nicotinamide adenine dinucleotide phosphate (NADPH)-dependent thioredoxin reductases, thioredoxins, and peroxiredoxins, typical laboratory experiments for cold stress investigations will be described. Short term transcriptome and metabolome analyses allow for dissecting the early responses of network components and complement the vast data sets dealing with changes in the antioxidant system and ROS. This review gives examples of how such information may be integrated to advance our knowledge on the response and function of the redox regulatory network in cold stress acclimation. It will be exemplarily shown that targeting the redox network might be beneficial and supportive to improve cold stress acclimation and plant yield in cold climate.
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Affiliation(s)
- Anna Dreyer
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, 33615 Bielefeld, Germany.
| | - Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, 33615 Bielefeld, Germany.
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Zhou Q, Luo D, Chai X, Wu Y, Wang Y, Nan Z, Yang Q, Liu W, Liu Z. Multiple Regulatory Networks Are Activated during Cold Stress in Medicago sativa L. Int J Mol Sci 2018; 19:ijms19103169. [PMID: 30326607 PMCID: PMC6214131 DOI: 10.3390/ijms19103169] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 12/18/2022] Open
Abstract
Cultivated alfalfa (Medicago sativa L.) is one of the most important perennial legume forages in the world, and it has considerable potential as a valuable forage crop for livestock. However, the molecular mechanisms underlying alfalfa responses to cold stress are largely unknown. In this study, the transcriptome changes in alfalfa under cold stress at 4 °C for 2, 6, 24, and 48 h (three replicates for each time point) were analyzed using the high-throughput sequencing platform, BGISEQ-500, resulting in the identification of 50,809 annotated unigenes and 5283 differentially expressed genes (DEGs). Metabolic pathway enrichment analysis demonstrated that the DEGs were involved in carbohydrate metabolism, photosynthesis, plant hormone signal transduction, and the biosynthesis of amino acids. Moreover, the physiological changes of glutathione and proline content, catalase, and peroxidase activity were in accordance with dynamic transcript profiles of the relevant genes. Additionally, some transcription factors might play important roles in the alfalfa response to cold stress, as determined by the expression pattern of the related genes during 48 h of cold stress treatment. These findings provide valuable information for identifying and characterizing important components in the cold signaling network in alfalfa and enhancing the understanding of the molecular mechanisms underlying alfalfa responses to cold stress.
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Affiliation(s)
- Qiang Zhou
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Dong Luo
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Xutian Chai
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yuguo Wu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhibiao Nan
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China.
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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