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Tiwari VK, Saripalli G, Sharma PK, Poland J. Wheat genomics: genomes, pangenomes, and beyond. Trends Genet 2024:S0168-9525(24)00170-7. [PMID: 39191555 DOI: 10.1016/j.tig.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/29/2024]
Abstract
There is an urgent need to improve wheat for upcoming challenges, including biotic and abiotic stresses. Sustainable wheat improvement requires the introduction of new genes and alleles in high-yielding wheat cultivars. Using new approaches, tools, and technologies to identify and introduce new genes in wheat cultivars is critical. High-quality genomes, transcriptomes, and pangenomes provide essential resources and tools to examine wheat closely to identify and manipulate new and targeted genes and alleles. Wheat genomics has improved excellently in the past 5 years, generating multiple genomes, pangenomes, and transcriptomes. Leveraging these resources allows us to accelerate our crop improvement pipelines. This review summarizes the progress made in wheat genomics and trait discovery in the past 5 years.
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Affiliation(s)
- Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA.
| | - Gautam Saripalli
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Department of Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC 29506, USA
| | - Parva K Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Mascher M, Marone MP, Schreiber M, Stein N. Are cereal grasses a single genetic system? NATURE PLANTS 2024; 10:719-731. [PMID: 38605239 DOI: 10.1038/s41477-024-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/17/2024] [Indexed: 04/13/2024]
Abstract
In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Marina Püpke Marone
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mona Schreiber
- University of Marburg, Department of Biology, Marburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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Gao Z, Sun M, Shao C, Chen Y, Xiang L, Wu J, Wang J, Chen X. Genome-wide analysis and characterization of the TaTLP gene family in wheat and functional characterization of the TaTLP44 in response to Rhizoctonia cerealis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108323. [PMID: 38183904 DOI: 10.1016/j.plaphy.2023.108323] [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: 11/08/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/08/2024]
Abstract
Wheat sharp eyespot is a soil-borne disease caused by Rhizoctonia cerealis, which occurs in many countries worldwide and significantly reduces the yield. Thaumatin-like protein (TLP), also known as PR5, is a member of the pathogen response protein family and plays an essential role in plant resistance to pathogen infection. In this study, 131 TaTLP genes were identified from the wheat genome, of which 38 TaTLPs were newly discovered. The TaTLP gene family contains many tandem duplications and fragment duplications, which is a major pathway for gene amplification. Besides, we also analyzed the physicochemical properties, gene structure and promoter cis-acting regulatory elements of all the TaTLP genes. In addition, the expression patterns of nine TaTLPs in response to R. cerealis were analyzed by RT-qPCR. Six TaTLP proteins expressed in vitro had no significant inhibitory effect on R. cerealis, suggesting that these TaTLP proteins may function in other ways. Finally, we performed gene silencing of TaTLP44 in wheat, which increased the expression of some defense-associated genes and improved resistance to R. cerealis. In summary, we systematically analyzed TaTLP family members and demonstrated that TaTLP44 negatively regulates the resistance to R. cerealis by controlling expression of defense-associated genes. These results provide new insights into the functional mechanism of TaTLP proteins.
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Affiliation(s)
- Zhen Gao
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Miao Sun
- College of Agronomy, Henan Institute of Science and Technology, Xinxiang 453003, Henan, China.
| | - Chunyu Shao
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yihua Chen
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Linrun Xiang
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jun Wu
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jun Wang
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xinhong Chen
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Tyagi S, Shumayla, Sharma Y, Madhu, Sharma A, Pandey A, Singh K, Upadhyay SK. TaGPX1-D overexpression provides salinity and osmotic stress tolerance in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 337:111881. [PMID: 37806453 DOI: 10.1016/j.plantsci.2023.111881] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
Glutathione peroxidases (GPXs) are known to play an essential role in guarding cells against oxidative stress by catalyzing the reduction of hydrogen peroxide and organic hydroperoxides. The current study aims functional characterization of the TaGPX1-D gene of bread wheat (Triticum aestivum) for salinity and osmotic stress tolerance. To achieve this, we initially performed the spot assays of TaGPX1-D expressing yeast cells. The growth of recombinant TaGPX1-D expressing yeast cells was notably higher than the control cells under stress conditions. Later, we generated transgenic Arabidopsis plants expressing the TaGPX1-D gene and investigated their tolerance to various stress conditions. The transgenic plants exhibited improved tolerance to both salinity and osmotic stresses compared to the wild-type plants. The higher germination rates, increased antioxidant enzymes activities, improved chlorophyll, carotenoid, proline and relative water contents, and reduced hydrogen peroxide and MDA levels in the transgenic lines supported the stress tolerance mechanism. Overall, this study demonstrated the role of TaGPX1-D in abiotic stress tolerance, and it can be used for improving the tolerance of crops to environmental stressors, such as salinity and osmotic stress in future research.
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Affiliation(s)
- Shivi Tyagi
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Shumayla
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Yashraaj Sharma
- Department of Botany, Panjab University, Chandigarh 160014, India; Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Madhu
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, New Delhi, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
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Chaudhary J, Gautam T, Gahlaut V, Singh K, Kumar S, Batra R, Gupta PK. Identification and characterization of RuvBL DNA helicase genes for tolerance against abiotic stresses in bread wheat (Triticum aestivum L.) and related species. Funct Integr Genomics 2023; 23:255. [PMID: 37498392 DOI: 10.1007/s10142-023-01177-y] [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: 11/02/2022] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023]
Abstract
Recombination UVB (sensitivity) like (RuvBL) helicase genes represent a conserved family of genes, which are known to be involved in providing tolerance against abiotic stresses like heat and drought. We identified nine wheat RuvBL genes, one each on nine different chromosomes, belonging to homoeologous groups 2, 3, and 4. The lengths of genes ranged from 1647 to 2197 bp and exhibited synteny with corresponding genes in related species including Ae. tauschii, Z. mays, O. sativa, H. vulgare, and B. distachyon. The gene sequences were associated with regulatory cis-elements and transposable elements. Two genes, namely TaRuvBL1a-4A and TaRuvBL1a-4B, also carried targets for a widely known miRNA, tae-miR164. Gene ontology revealed that these genes were closely associated with ATP-dependent formation of histone acetyltransferase complex. Analysis of the structure and function of RuvBL proteins revealed that the proteins were localized mainly in the cytoplasm. A representative gene, namely TaRuvBL1a-4A, was also shown to be involved in protein-protein interactions with ten other proteins. On the basis of phylogeny, RuvBL proteins were placed in two sub-divisions, namely RuvBL1 and RuvBL2, which were further classified into clusters and sub-clusters. In silico studies suggested that these genes were differentially expressed under heat/drought. The qRT-PCR analysis confirmed that expression of TaRuvBL genes differed among wheat cultivars, which differed in the level of thermotolerance. The present study advances our understanding of the biological role of wheat RuvBL genes and should help in planning future studies on RuvBL genes in wheat including use of RuvBL genes in breeding thermotolerant wheat cultivars.
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Affiliation(s)
- Jyoti Chaudhary
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Vijay Gahlaut
- Council of Scientific & Industrial Research-Institute of Himalayan Bioresource Technology, Palampur, India
- Department of Biotechnology, University Center for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Kalpana Singh
- Department of Bioinformatics, College of animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Sourabh Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
| | - Ritu Batra
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
- IIMT University, 'O' Pocket, Ganga Nagar, Meerut, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India.
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Kang Y, Choi C, Kim JY, Min KD, Kim C. Optimizing genomic selection of agricultural traits using K-wheat core collection. FRONTIERS IN PLANT SCIENCE 2023; 14:1112297. [PMID: 37389296 PMCID: PMC10303932 DOI: 10.3389/fpls.2023.1112297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/02/2023] [Indexed: 07/01/2023]
Abstract
The agricultural traits that constitute basic plant breeding information are usually quantitative or complex in nature. This quantitative and complex combination of traits complicates the process of selection in breeding. This study examined the potential of genome-wide association studies (GWAS) and genomewide selection (GS) for breeding ten agricultural traits by using genome-wide SNPs. As a first step, a trait-associated candidate marker was identified by GWAS using a genetically diverse 567 Korean (K)-wheat core collection. The accessions were genotyped using an Axiom® 35K wheat DNA chip, and ten agricultural traits were determined (awn color, awn length, culm color, culm length, ear color, ear length, days to heading, days to maturity, leaf length, and leaf width). It is essential to sustain global wheat production by utilizing accessions in wheat breeding. Among the traits associated with awn color and ear color that showed a high positive correlation, a SNP located on chr1B was significantly associated with both traits. Next, GS evaluated the prediction accuracy using six predictive models (G-BLUP, LASSO, BayseA, reproducing kernel Hilbert space, support vector machine (SVM), and random forest) and various training populations (TPs). With the exception of the SVM, all statistical models demonstrated a prediction accuracy of 0.4 or better. For the optimization of the TP, the number of TPs was randomly selected (10%, 30%, 50% and 70%) or divided into three subgroups (CC-sub 1, CC-sub 2 and CC-sub 3) based on the subpopulation structure. Based on subgroup-based TPs, better prediction accuracy was found for awn color, culm color, culm length, ear color, ear length, and leaf width. A variety of Korean wheat cultivars were used for validation to evaluate the prediction ability of populations. Seven out of ten cultivars showed phenotype-consistent results based on genomics-evaluated breeding values (GEBVs) calculated by the reproducing kernel Hilbert space (RKHS) predictive model. Our research provides a basis for improving complex traits in wheat breeding programs through genomics assisted breeding. The results of our research can be used as a basis for improving wheat breeding programs by using genomics-assisted breeding.
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Affiliation(s)
- Yuna Kang
- Department of Crop Science, Chungnam National University, Daejeon, Republic of Korea
| | - Changhyun Choi
- Wheat Research Team, National Institution Crop Sciences, Wanju-gun, Republic of Korea
| | - Jae Yoon Kim
- Department of Plant Resources, Kongju National University, Yesan, Republic of Korea
| | - Kyeong Do Min
- Department of Plant Resources, Kongju National University, Yesan, Republic of Korea
| | - Changsoo Kim
- Department of Crop Science, Chungnam National University, Daejeon, Republic of Korea
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon, Republic of Korea
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Wang Z, Luo Y, Yu J, Kou X, Xie L, Deng P, Li T, Chen C, Ji W, Liu X. Genome-wide identification and characterization of lipoxygenase genes related to the English grain aphid infestation response in wheat. PLANTA 2023; 257:84. [PMID: 36943494 DOI: 10.1007/s00425-023-04114-2] [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: 10/22/2022] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
44 wheat LOX genes were identified by silico genome-wide search method. TaLOX5, 7, 10, 24, 29, 33 were specifically expressed post aphid infestation, indicating their participation in wheat-aphid interaction. In plants, LOX genes play important roles in various biological progresses including seed germination, tuber development, plant vegetative growth and most crucially in plant signal transduction, stress response and plant defense against plant diseases and insects. Although LOX genes have been characterized in many species, the importance of the LOX family in wheat has still not been well understood, hampering further improvement of wheat under stress conditions. Here, we identified 44 LOX genes (TaLOXs) in the whole wheat genome and classified into three subfamilies (9-LOXs, Type I 13-LOXs and Type II 13-LOXs) according to phylogenetic relationships. The TaLOXs belonging to the same subgroup shared similar gene structures and motif organizations. Synteny analysis demonstrated that segmental duplication events mainly contributed to the expansion of the LOX gene family in wheat. The results of protein-protein interaction network (PPI) and miRNA-TaLOXs predictions revealed that three TaLOXs (TaLOX20, 22 and 37) interacted mostly with proteins related to methyl jasmonate (MeJA) signaling pathway. The expression patterns of TaLOXs in different tissues (root, stem, leaf, spike and grain) under diverse abiotic stresses (heat, cold, drought, drought and heat combined treatment, and salt) as well as under diverse biotic stresses (powdery mildew pathogen, Fusarium graminearum and stripe rust pathogen) were systematically analyzed using RNA-seq data. We obtained aphid-responsive candidate genes by RNA-seq data of wheat after the English grain aphid infestation. Aphid-responsive candidate genes, including TaLOX5, 7, 10, 24, 29 and 33, were up-regulated in the wheat aphid-resistant genotype (Lunxuan144), while they were little expressed in the susceptible genotype (Jimai22) during late response (48 h and 72 h) to the English grain aphid infestation. Meanwhile, qRT-PCR analysis was used to validate these aphid-responsive candidate genes. The genetic divergence and diversity of all the TaLOXs in bread wheat and its relative species were investigated by available resequencing data. Finally, the 3D structure of the TaLOX proteins was predicted based on the homology modeling method. This study not only systematically investigated the characteristics and evolutionary relationships of TaLOXs, but also provided potential candidate genes in response to the English grain aphid infestation and laid the foundation to further study the regulatory roles in the English grain aphid infestation of LOX family in wheat and beyond.
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Affiliation(s)
- Zhenyu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yufeng Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jiuyang Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xudan Kou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Lincai Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China.
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Liu J, Cobertera DC, Zemetra RS, Mundt CC. Identification of Quantitative Trait Loci for Resistance to Wheat Sharp Eyespot in the Einstein × Tubbs Recombinant Inbred Line Population. PLANT DISEASE 2023; 107:820-825. [PMID: 35961017 DOI: 10.1094/pdis-05-22-1044-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wheat sharp eyespot (SES), caused by the soilborne pathogen Rhizoctonia cerealis Van der Hoeven (teleomorph: Ceratobasidium cereale), is a common stem disease of wheat globally. The disease caused a severe and extensive epidemic throughout the Willamette Valley of Oregon in 2014 and has remained one of the most important wheat diseases in this region. However, little was known about the genetics of host resistance to this disease. A recombinant inbred line (RIL) population with 257 lines developed from a cross of Einstein × Tubbs was used to study SES resistance of wheat. The phenotyping was conducted at two locations and in 3 years. Genotyping by sequencing was done by using Illumina HiSeq 3000. Low broad-sense heritability across four environments was obtained. The results of analysis of variance demonstrated that disease severity was significantly different among RILs for the data combined over environments and for one of the individual environments. Four SES resistance quantitative trait loci (QTL) were detected, including QSES-1A, QSES-2B, QSES-6A, and QSES-7A, and explained 5.9, 5.9, 8.8, and 8.3%, respectively, of the phenotypic variance. All four QTL overlapped or are in close proximity with one or more plant defense genes, and could lay the foundation for marker-assisted breeding.
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Affiliation(s)
- Jiang Liu
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902
| | - David C Cobertera
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-2821
| | - Robert S Zemetra
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-2821
| | - Christopher C Mundt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902
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Gozzi M, Blandino M, Dall’Asta C, Martinek P, Bruni R, Righetti L. Anthocyanin Content and Fusarium Mycotoxins in Pigmented Wheat ( Triticum aestivum L. spp. aestivum): An Open Field Evaluation. PLANTS (BASEL, SWITZERLAND) 2023; 12:693. [PMID: 36840042 PMCID: PMC9965368 DOI: 10.3390/plants12040693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Twelve Triticum aestivum L. spp. aestivum varieties with pigmented grain, namely one red, six purple, three blue, and two black, were grown in open fields over two consecutive years and screened to investigate their risk to the accumulation of multiple Fusarium-related mycotoxins. Deoxynivalenol (DON) and its modified forms DON3Glc, 3Ac-DON, 15Ac-DON, and T-2, HT-2, ZEN, and Enniatin B were quantified by means of UHPLC-MS/MS, along with 14 different cyanidin, petunidin, delphinidin, pelargonidin, peonidin, and malvidin glycosides. A significant strong influence effect of the harvesting year (p = 0.0002) was noticed for DON content, which was more than doubled between harvesting years growing seasons (mean of 3746 µg kg-1 vs. 1463 µg kg-1). In addition, a striking influence of varieties with different grain colour on DON content (p < 0.0001) emerged in combination with the harvesting year (year×colour, p = 0.0091), with blue grains being more contaminated (mean of 5352 µg kg-1) and red grain being less contaminated (mean of 715 µg kg-1). The trend was maintained between the two harvesting years despite the highly variable absolute mycotoxin content. Varieties accumulating anthocyanins in the pericarp (purple coloration) had significantly lower DON content compared to those in which aleurone was involved (blue coloration).
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Affiliation(s)
- Marco Gozzi
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/a, 43100 Parma, Italy
| | - Massimo Blandino
- Department of Agricultural Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Chiara Dall’Asta
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/a, 43100 Parma, Italy
| | - Petr Martinek
- Agrotest Fyto, Ltd., Havlíčkova 2787/121, 767 01 Kroměříž, Czech Republic
| | - Renato Bruni
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/a, 43100 Parma, Italy
| | - Laura Righetti
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/a, 43100 Parma, Italy
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Gohar S, Sajjad M, Zulfiqar S, Liu J, Wu J, Rahman MU. Domestication of newly evolved hexaploid wheat—A journey of wild grass to cultivated wheat. Front Genet 2022; 13:1022931. [PMID: 36263418 PMCID: PMC9574122 DOI: 10.3389/fgene.2022.1022931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Domestication of wheat started with the dawn of human civilization. Since then, improvement in various traits including resistance to diseases, insect pests, saline and drought stresses, grain yield, and quality were improved through selections by early farmers and then planned hybridization after the discovery of Mendel’s laws. In the 1950s, genetic variability was created using mutagens followed by the selection of superior mutants. Over the last 3 decades, research was focused on developing superior hybrids, initiating marker-assisted selection and targeted breeding, and developing genetically modified wheat to improve the grain yield, tolerance to drought, salinity, terminal heat and herbicide, and nutritive quality. Acceptability of genetically modified wheat by the end-user remained a major hurdle in releasing into the environment. Since the beginning of the 21st century, changing environmental conditions proved detrimental to achieving sustainability in wheat production particularly in developing countries. It is suggested that high-tech phenotyping assays and genomic procedures together with speed breeding procedures will be instrumental in achieving food security beyond 2050.
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Affiliation(s)
- Sasha Gohar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sana Zulfiqar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Jiajun Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China
- *Correspondence: Jiajie Wu, ; Mehboob-ur- Rahman,
| | - Mehboob-ur- Rahman
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
- *Correspondence: Jiajie Wu, ; Mehboob-ur- Rahman,
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11
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Hu Y, Su C, Zhang Y, Li Y, Chen X, Shang H, Hu X. A Puccinia striiformis f. sp. tritici effector inhibits high-temperature seedling-plant resistance in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:249-267. [PMID: 35960661 DOI: 10.1111/tpj.15945] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Resistance to Pseudomonas syringae pv. maculicola 1 (RPM1)-induced protein kinase (RIPK) in Arabidopsis belongs to the receptor-like cytoplasmic kinase (RLCK) family and plays a vital role in immunity. However, the role of RLCKs in the high-temperature seedling-plant (HTSP) resistance of wheat (Triticum aestivum) to Puccinia striiformis f. sp. tritici (Pst), the stripe rust pathogen, remains unclear. Here, we identified a homologous gene of RIPK in wheat, namely TaRIPK. Expression of TaRIPK was induced by Pst inoculation and high temperatures. Silencing of TaRIPK reduced the expression level of TaRPM1, resulting in weaker HTSP resistance. Moreover, TaRIPK interacts with and phosphorylates papain-like cysteine protease 1 (TaPLCP1). Meanwhile, we found that the Pst-secreted protein PSTG_01766 targets TaPLCP1. Transient expression of PSTG_01766 inhibited basal immunity in tobacco (Nicotiana benthamiana) and wheat. The role of PSTG_01766 as an effector involved in HTSP resistance was further supported by host-induced gene silencing and bacterial type three secretion system-mediated delivery into wheat. PSTG_01766 inhibited the TaRIPK-induced phosphorylation of TaPLCP1. Furthermore, PSTG_01766 has the potential to influence the subcellular localization of TaPLCP1. Overall, we suggest that the TaRIPK-TaPLCP1-TaRPM1 module fits the guard model for disease resistance, participating in HTSP resistance. PSTG_01766 decreases HTSP resistance via targeting TaPLCP1. Guarded by wheat and attacked by Pst, TaPLCP1 may serve as a central hub of the defense response. Our findings improve the understanding of the molecular mechanism of wheat HTSP resistance, which may be an important strategy for controlling stripe rust in the face of global warming.
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Affiliation(s)
- Yangshan Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chang Su
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yue Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuxiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xianming Chen
- Agricultural Research Service, United States Department of Agriculture and Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Hongsheng Shang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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12
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Structural and Functional Characterization at the Molecular Level of the MATE Gene Family in Wheat in Silico. CONTRAST MEDIA & MOLECULAR IMAGING 2022. [DOI: 10.1155/2022/9289007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A series of multidrug extransporters known as the multidrug and potentially toxic extrusion (MATE) genes are found in all living things and are crucial for the removal of heavy metal ions, metalloids, exogenous xenobiotics, endogenous secondary metabolites, and other toxic substances from the cells. However, there has only been a small amount of them in silico analysis of the MATE family of genes in plant species. In the current study, the MATE gene family was characterized in silico where two families and seven subfamilies based on their evolutionary relationships were proposed. Plant breeders may use TraesCS1D02G030400, TraesCS4B02G244400, and TraesCS1A02G029900 genes for marker-assisted or transgenic breeding to develop novel cultivars since these genes have been hypothesized from protein-protein interaction study to play a critical role in the transport of toxic chemicals across cells. The exon number varies from 01 to 14. One exon has TraesCS1A02G188100, TraesCS5B02G562500, TraesCS6A02G256400, and TraesCS6D02G384300 genes, while 14 exons have only two genes that are TraesCS6A02G418800 and TraesCS6D02G407900. Biological stress (infestations of disease) affects the expression of most of the MATE genes, with the gene TraesCS5D02G355500 having the highest expression level in the wheat expression browser tool. Using the Grain interpretation search engine tool, it is found that the vast bulk of MATE genes are voiced throughout biotic environmental stresses caused by disease pests, with the genotype TraesCS5B02G326600.1 from family 1 exhibiting the greatest level of expression throughout Fusarium head blight infection by Fusarium graminearum after 4 days of infection. The researchers constructed 39 ternary plots, each with a distinct degree of expression under biotic and abiotic stress settings, and observed that 44% of the triplets have imbalanced outputs (extreme values) due to their higher tissue specificity and increased intensity.
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13
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Gao X, Zou R, Sun H, Liu J, Duan W, Hu Y, Yan Y. Genome-wide identification of wheat ABC1K gene family and functional dissection of TaABC1K3 and TaABC1K6 involved in drought tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:991171. [PMID: 36105699 PMCID: PMC9465391 DOI: 10.3389/fpls.2022.991171] [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: 07/11/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Activity of BC1 complex kinase (ABC1K) serves as an atypical kinase family involved in plant stress resistance. This study identified 44 ABC1K genes in the wheat genome, which contained three clades (I-III). TaABC1K genes generally had similar structural features, but differences were present in motif and exon compositions from different clade members. More type II functional divergence sites were detected between clade I and clade III and no positive selection site were found in TaABC1K family. The three-dimensional structure prediction by Alphafold2 showed that TaABC1K proteins had more α-helixes with a relatively even distribution, and different clade members had differences in the content of secondary structures. The cis-acting element analysis showed that TaABC1K genes contained abundant cis-acting elements related to plant hormones and environmental stress response in the promoter region, and generally displayed a significantly upregulated expression under drought stress. In particular, both TaABC1K3 and TaABC1K6 genes from clade I was highly induced by drought stress, and their overexpression in yeast and Arabidopsis enhanced drought tolerance by suppressing active oxygen burst and reducing photosynthesis impairment. Meanwhile, TaABC1K3 and TaABC1K6 could, respectively, complement the function of Arabidopsis abc1k3 and abc1k6 mutants and reduce photosynthesis damage caused by drought stress.
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Wu B, Xia Y, Zhang G, Wang J, Ma S, Song Y, Yang Z, Dennis ES, Niu N. The Transcription Factors TaTDRL and TaMYB103 Synergistically Activate the Expression of TAA1a in Wheat, Which Positively Regulates the Development of Microspore in Arabidopsis. Int J Mol Sci 2022; 23:ijms23147996. [PMID: 35887343 PMCID: PMC9321142 DOI: 10.3390/ijms23147996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 12/04/2022] Open
Abstract
Pollen fertility plays an important role in the application of heterosis in wheat (Triticum aestivum L.). However, the key genes and mechanisms underlying pollen abortion in K-type male sterility remain unclear. TAA1a is an essential gene for pollen development in wheat. Here, we explored the mechanism involved in its transcriptional regulation during pollen development, focusing on a 1315-bp promoter region. Several cis-acting elements were identified in the TAA1a promoter, including binding motifs for Arabidopsis thaliana AtAMS and AtMYB103 (CANNTG and CCAACC, respectively). Evolutionary analysis indicated that TaTDRL and TaMYB103 were the T. aestivum homologs of AtAMS and AtMYB103, respectively, and encoded nucleus-localized transcription factors containing 557 and 352 amino acids, respectively. TaTDRL and TaMYB103 were specifically expressed in wheat anthers, and their expression levels were highest in the early uninucleate stage; this expression pattern was consistent with that of TAA1a. Meanwhile, we found that TaTDRL and TaMYB03 directly interacted, as evidenced by yeast two-hybrid and bimolecular fluorescence complementation assays, while yeast one-hybrid and dual-luciferase assays revealed that both TaTDRL and TaMYB103 could bind the TAA1a promoter and synergistically increase its transcriptional activity. Furthermore, TaTDRL-EAR and TaMYB103-EAR transgenic Arabidopsis plants displayed abnormal microspore morphology, reduced pollen viability, and lowered seed setting rates. Additionally, the expression of AtMS2, a TAA1a homolog, was significantly lower in the two repressor lines than in the corresponding overexpression lines or WT plants. In summary, we identified a potential transcriptional regulatory mechanism associated with wheat pollen development.
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Affiliation(s)
- Baolin Wu
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China; (B.W.); (Y.X.); (G.Z.); (J.W.); (S.M.); (Y.S.); (Z.Y.)
| | - Yu Xia
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China; (B.W.); (Y.X.); (G.Z.); (J.W.); (S.M.); (Y.S.); (Z.Y.)
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Gaisheng Zhang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China; (B.W.); (Y.X.); (G.Z.); (J.W.); (S.M.); (Y.S.); (Z.Y.)
| | - Junwei Wang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China; (B.W.); (Y.X.); (G.Z.); (J.W.); (S.M.); (Y.S.); (Z.Y.)
| | - Shoucai Ma
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China; (B.W.); (Y.X.); (G.Z.); (J.W.); (S.M.); (Y.S.); (Z.Y.)
| | - Yulong Song
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China; (B.W.); (Y.X.); (G.Z.); (J.W.); (S.M.); (Y.S.); (Z.Y.)
| | - Zhiquan Yang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China; (B.W.); (Y.X.); (G.Z.); (J.W.); (S.M.); (Y.S.); (Z.Y.)
| | - Elizabeth S. Dennis
- Agriculture and Food, Commonwealth Scientifc Industrial Research Organisation, Canberra, ACT 2601, Australia
- Correspondence: (E.S.D.); (N.N.)
| | - Na Niu
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China; (B.W.); (Y.X.); (G.Z.); (J.W.); (S.M.); (Y.S.); (Z.Y.)
- Correspondence: (E.S.D.); (N.N.)
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15
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Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Fusarium graminearum Infection in Wheat. Int J Mol Sci 2022; 23:ijms23147982. [PMID: 35887327 PMCID: PMC9316857 DOI: 10.3390/ijms23147982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/29/2022] [Accepted: 07/14/2022] [Indexed: 12/03/2022] Open
Abstract
RNA/DNA difference (RDD) is a post-transcriptional modification playing a crucial role in regulating diverse biological processes in eukaryotes. Although it has been extensively studied in plant chloroplast and mitochondria genomes, RDDs in plant nuclear genomes are not well studied at present. Here, we investigated the RDDs associated with fusarium head blight (FHB) through a novel method by comparing the RNA-seq data between Fusarium-infected and control samples of four wheat genotypes. A total of 187 high-confidence unique RDDs in 36 genes were identified, representing the first landscape of the FHB-responsive RDD in wheat. The majority (26) of these 36 RDD genes were correlated either positively or negatively with FHB levels. Effects of these RDDs on RNA and protein sequences have been identified, their editing frequency and the expression level of the corresponding genes provided, and the prediction of the effect on the minimum folding free energy of mRNA, miRNA binding, and colocation of RDDs with conserved domains presented. RDDs were predicted to induce modifications in the mRNA and protein structures of the corresponding genes. In two genes, TraesCS1B02G294300 and TraesCS3A02G263900, editing was predicted to enhance their affinity with tae-miR9661-5p and tae-miR9664-3p, respectively. To our knowledge, this study is the first report of the association between RDD and FHB in wheat; this will contribute to a better understanding of the molecular basis underlying FHB resistance, and potentially lead to novel strategies to improve wheat FHB resistance through epigenetic methods.
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16
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Tan YC, Kumar AU, Wong YP, Ling APK. Bioinformatics approaches and applications in plant biotechnology. J Genet Eng Biotechnol 2022; 20:106. [PMID: 35838847 PMCID: PMC9287518 DOI: 10.1186/s43141-022-00394-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 07/05/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND In recent years, major advance in molecular biology and genomic technologies have led to an exponential growth in biological information. As the deluge of genomic information, there is a parallel growth in the demands of tools in the storage and management of data, and the development of software for analysis, visualization, modelling, and prediction of large data set. MAIN BODY Particularly in plant biotechnology, the amount of information has multiplied exponentially with a large number of databases available from many individual plant species. Efficient bioinformatics tools and methodologies are also developed to allow rapid genome sequence and the study of plant genome in the 'omics' approach. This review focuses on the various bioinformatic applications in plant biotechnology, and their advantages in improving the outcome in agriculture. The challenges or limitations faced in plant biotechnology in the aspect of bioinformatics approach that explained the low progression in plant genomics than in animal genomics are also reviewed and assessed. CONCLUSION There is a critical need for effective bioinformatic tools, which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant's genome. The advancement in bioinformatics is not only beneficial to the field of plant biotechnology and agriculture sectors, but will also contribute enormously to the future of humanity.
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Affiliation(s)
- Yung Cheng Tan
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Asqwin Uthaya Kumar
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia
| | - Ying Pei Wong
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Anna Pick Kiong Ling
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.
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Bapela T, Shimelis H, Tsilo TJ, Mathew I. Genetic Improvement of Wheat for Drought Tolerance: Progress, Challenges and Opportunities. PLANTS (BASEL, SWITZERLAND) 2022; 11:1331. [PMID: 35631756 PMCID: PMC9144332 DOI: 10.3390/plants11101331] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/27/2022] [Accepted: 05/04/2022] [Indexed: 06/01/2023]
Abstract
Wheat production and productivity are challenged by recurrent droughts associated with climate change globally. Drought and heat stress resilient cultivars can alleviate yield loss in marginal production agro-ecologies. The ability of some crop genotypes to thrive and yield in drought conditions is attributable to the inherent genetic variation and environmental adaptation, presenting opportunities to develop drought-tolerant varieties. Understanding the underlying genetic, physiological, biochemical, and environmental mechanisms and their interactions is key critical opportunity for drought tolerance improvement. Therefore, the objective of this review is to document the progress, challenges, and opportunities in breeding for drought tolerance in wheat. The paper outlines the following key aspects: (1) challenges associated with breeding for adaptation to drought-prone environments, (2) opportunities such as genetic variation in wheat for drought tolerance, selection methods, the interplay between above-ground phenotypic traits and root attributes in drought adaptation and drought-responsive attributes and (3) approaches, technologies and innovations in drought tolerance breeding. In the end, the paper summarises genetic gains and perspectives in drought tolerance breeding in wheat. The review will serve as baseline information for wheat breeders and agronomists to guide the development and deployment of drought-adapted and high-performing new-generation wheat varieties.
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Affiliation(s)
- Theresa Bapela
- African Centre for Crop Improvement, University of Kwa-Zulu Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa; (H.S.); (I.M.)
- Agricultural Research Council—Small Grain, Bethlehem 9700, South Africa;
| | - Hussein Shimelis
- African Centre for Crop Improvement, University of Kwa-Zulu Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa; (H.S.); (I.M.)
| | - Toi John Tsilo
- Agricultural Research Council—Small Grain, Bethlehem 9700, South Africa;
| | - Isack Mathew
- African Centre for Crop Improvement, University of Kwa-Zulu Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa; (H.S.); (I.M.)
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Komatsu S, Yamaguchi H, Hitachi K, Tsuchida K. Proteomic, Biochemical, and Morphological Analyses of the Effect of Silver Nanoparticles Mixed with Organic and Inorganic Chemicals on Wheat Growth. Cells 2022; 11:1579. [PMID: 35563885 PMCID: PMC9104970 DOI: 10.3390/cells11091579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022] Open
Abstract
Wheat is vulnerable to numerous diseases; on the other hand, silver nanoparticles (AgNPs) exhibit a sterilizing action. To understand the combined effects of AgNPs with nicotinate and potassium nitrate (KNO3) for plant growth and sterilization, a gel- and label-free proteomics was performed. Root weight was promoted by the treatment of AgNPs mixed with nicotinate and KNO3. From a total of 5557 detected proteins, 90 proteins were changed by the mixture of AgNPs, nicotinate, and KNO3; among them, 25 and 65 proteins increased and decreased, respectively. The changed proteins were mainly associated with redox and biotic stress in the functional categorization. By immunoblot analysis, the abundance of glutathione reductase/peroxiredoxin and pathogen-related protein three significantly decreased with the mixture. Furthermore, from the changed proteins, the abundance of starch synthase and lipoxygenase significantly increased and decreased, respectively. Through biochemical analysis, the starch contents increased with the mixture. The application of esculetin, which is a lipoxygenase inhibitor, increased the weight and length of the root. These results suggest that the AgNPs mixed with nicotinate and KNO3 cause positive effects on wheat seedlings by regulating pathogen-related protein and reactive-oxygen species scavenging. Furthermore, increasing starch and decreasing lipoxygenase might improve wheat growth.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Hisateru Yamaguchi
- Department of Medical Technology, Yokkaichi Nursing and Medical Care University, Yokkaichi 512-8045, Japan;
| | - Keisuke Hitachi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (K.T.)
| | - Kunihiro Tsuchida
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (K.T.)
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19
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Zhou M, Li Z. Recent Advances in Minimizing Cadmium Accumulation in Wheat. TOXICS 2022; 10:toxics10040187. [PMID: 35448448 PMCID: PMC9025478 DOI: 10.3390/toxics10040187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 01/14/2023]
Abstract
Cadmium (Cd), a toxic heavy metal, affects the yield and quality of crops. Wheat (Triticum aestivum L.) can accumulate high Cd content in the grain, which poses a major worldwide hazard to human health. Advances in our understanding of Cd toxicity for plants and humans, different parameters influencing Cd uptake and accumulation, as well as phytoremediation technologies to relieve Cd pollution in wheat have been made very recently. In particular, the molecular mechanisms of wheat under Cd stress have been increasingly recognized. In this review, we focus on the recently described omics and functional genes uncovering Cd stress, as well as different mitigation strategies to reduce Cd toxicity in wheat.
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Affiliation(s)
- Min Zhou
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
- Correspondence: (M.Z.); (Z.L.)
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China
- Correspondence: (M.Z.); (Z.L.)
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20
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Kesawat MS, Kherawat BS, Singh A, Dey P, Routray S, Mohapatra C, Saha D, Ram C, Siddique KHM, Kumar A, Gupta R, Chung SM, Kumar M. Genome-Wide Analysis and Characterization of the Proline-Rich Extensin-like Receptor Kinases (PERKs) Gene Family Reveals Their Role in Different Developmental Stages and Stress Conditions in Wheat ( Triticum aestivum L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:496. [PMID: 35214830 PMCID: PMC8880425 DOI: 10.3390/plants11040496] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 05/19/2023]
Abstract
Proline-rich extensin-like receptor kinases (PERKs) are a class of receptor kinases implicated in multiple cellular processes in plants. However, there is a lack of information on the PERK gene family in wheat. Therefore, we identified 37 PERK genes in wheat to understand their role in various developmental processes and stress conditions. Phylogenetic analysis of PERK genes from Arabidopsis thaliana, Oryza sativa, Glycine max, and T. aestivum grouped them into eight well-defined classes. Furthermore, synteny analysis revealed 275 orthologous gene pairs in B. distachyon, Ae. tauschii, T. dicoccoides, O. sativa and A. thaliana. Ka/Ks values showed that most TaPERK genes, except TaPERK1, TaPERK2, TaPERK17, and TaPERK26, underwent strong purifying selection during evolutionary processes. Several cis-acting regulatory elements, essential for plant growth and development and the response to light, phytohormones, and diverse biotic and abiotic stresses, were predicted in the promoter regions of TaPERK genes. In addition, the expression profile of the TaPERK gene family revealed differential expression of TaPERK genes in various tissues and developmental stages. Furthermore, TaPERK gene expression was induced by various biotic and abiotic stresses. The RT-qPCR analysis also revealed similar results with slight variation. Therefore, this study's outcome provides valuable information for elucidating the precise functions of TaPERK in developmental processes and diverse stress conditions in wheat.
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Affiliation(s)
- Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
| | - Bhagwat Singh Kherawat
- Krishi Vigyan Kendra, Bikaner II, Swami Keshwanand Rajasthan Agricultural University, Bikaner 334603, Rajasthan, India;
| | - Anupama Singh
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
| | - Prajjal Dey
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
| | - Snehasish Routray
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (S.R.); (C.M.)
| | - Chinmayee Mohapatra
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (S.R.); (C.M.)
| | - Debanjana Saha
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneshwar 752050, Odisha, India;
| | - Chet Ram
- ICAR-Central Institute for Arid Horticulture, Bikaner 334006, Rajasthan, India;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia;
| | - Ajay Kumar
- Agriculture Research Organization, Volcani Center, Department of Postharvest Science, Rishon Lezzion 50250, Israel;
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Korea;
| | - Sang-Min Chung
- Department of Life Science, Dongguk University, Dong-gu, Ilsan, Seoul 10326, Korea;
| | - Manu Kumar
- Department of Life Science, Dongguk University, Dong-gu, Ilsan, Seoul 10326, Korea;
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21
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Gruet C, Muller D, Moënne-Loccoz Y. Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome. Front Microbiol 2022; 12:782135. [PMID: 35058901 PMCID: PMC8764353 DOI: 10.3389/fmicb.2021.782135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.
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Affiliation(s)
| | | | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
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22
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Evolution of Fusarium Head Blight Management in Wheat: Scientific Perspectives on Biological Control Agents and Crop Genotypes Protocooperation. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11198960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Over the past century, the economically devastating Fusarium Head Blight (FHB) disease has persistently ravished small grain cereal crops worldwide. Annually, losses globally are in the billions of United States dollars (USD), with common bread wheat and durum wheat accounting for a major portion of these losses. Since the unforgettable FHB epidemics of the 1990s and early 2000s in North America, different management strategies have been employed to treat this disease. However, even with some of the best practices including chemical fungicides and innovative breeding technological advances that have given rise to a spectrum of moderately resistant cultivars, FHB still remains an obstinate problem in cereal farms globally. This is in part due to several constraints such as the Fusarium complex of species and the struggle to develop and employ methods that can effectively combat more than one pathogenic line or species simultaneously. This review highlights the last 100 years of major FHB epidemics in the US and Canada, as well as the evolution of different management strategies, and recent progress in resistance and cultivar development. It also takes a look at protocooperation between specific biocontrol agents and cereal genotypes as a promising tool for combatting FHB.
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23
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Kesawat MS, Kherawat BS, Singh A, Dey P, Kabi M, Debnath D, Saha D, Khandual A, Rout S, Manorama, Ali A, Palem RR, Gupta R, Kadam AA, Kim HU, Chung SM, Kumar M. Genome-Wide Identification and Characterization of the Brassinazole-resistant ( BZR) Gene Family and Its Expression in the Various Developmental Stage and Stress Conditions in Wheat ( Triticum aestivum L.). Int J Mol Sci 2021; 22:8743. [PMID: 34445448 PMCID: PMC8395832 DOI: 10.3390/ijms22168743] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
Brassinosteroids (BRs) play crucial roles in various biological processes, including plant developmental processes and response to diverse biotic and abiotic stresses. However, no information is currently available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the BZR gene family in wheat to understand the evolution and their role in diverse developmental processes and under different stress conditions. In this study, we performed the genome-wide analysis of the BZR gene family in the bread wheat and identified 20 TaBZR genes through a homology search and further characterized them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses lead to the classification of TaBZR genes into five different groups or subfamilies, providing evidence of evolutionary relationship with Arabidopsis thaliana, Zea mays, Glycine max, and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, and cis-acting regulatory elements were also examined using various computational approaches. In addition, an analysis of public RNA-seq data also shows that TaBZR genes may be involved in diverse developmental processes and stress tolerance mechanisms. Moreover, qRT-PCR results also showed similar expression with slight variation. Collectively, these results suggest that TaBZR genes might play an important role in plant developmental processes and various stress conditions. Therefore, this work provides valuable information for further elucidate the precise role of BZR family members in wheat.
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Affiliation(s)
- Mahipal Singh Kesawat
- Institute for Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul 08826, Korea;
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Bhagwat Singh Kherawat
- Krishi Vigyan Kendra, Bikaner II, Swami Keshwanand Rajasthan Agricultural University, Bikaner 334603, India;
| | - Anupama Singh
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Prajjal Dey
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Mandakini Kabi
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Debanjana Debnath
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Debanjana Saha
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneshwar 752050, India;
| | - Ansuman Khandual
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Sandeep Rout
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Manorama
- Department of Dairy Microbiology, College of Dairy Science and Food Technology, Raipur 49200, India;
| | - Asjad Ali
- Department of Agriculture and Fisheries, Mareeba, QLD 4880, Australia;
| | - Ramasubba Reddy Palem
- Department of Medical Biotechnology, Biomedical Campus, Dongguk University, Seoul 10326, Korea;
| | - Ravi Gupta
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Avinash Ashok Kadam
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang 10326, Korea;
| | - Hyun-Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea;
| | - Sang-Min Chung
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Goyang 10326, Korea;
| | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Goyang 10326, Korea;
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Genome-Wide Identification and Characterization of PIN-FORMED (PIN) Gene Family Reveals Role in Developmental and Various Stress Conditions in Triticum aestivum L. Int J Mol Sci 2021; 22:ijms22147396. [PMID: 34299014 PMCID: PMC8303626 DOI: 10.3390/ijms22147396] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/17/2022] Open
Abstract
PIN-FORMED (PIN) genes play a crucial role in regulating polar auxin distribution in diverse developmental processes, including tropic responses, embryogenesis, tissue differentiation, and organogenesis. However, the role of PIN-mediated auxin transport in various plant species is poorly understood. Currently, no information is available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the PIN gene family in wheat to understand the evolution of PIN-mediated auxin transport and its role in various developmental processes and under different biotic and abiotic stress conditions. In this study, we performed genome-wide analysis of the PIN gene family in common wheat and identified 44 TaPIN genes through a homology search, further characterizing them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses led to the classification of TaPIN genes into seven different groups, providing evidence of an evolutionary relationship with Arabidopsis thaliana and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, transmembrane domains, and three-dimensional (3D) structure were also examined using various computational approaches. Cis-elements analysis of TaPIN genes showed that TaPIN promoters consist of phytohormone, plant growth and development, and stress-related cis-elements. In addition, expression profile analysis also revealed that the expression patterns of the TaPIN genes were different in different tissues and developmental stages. Several members of the TaPIN family were induced during biotic and abiotic stress. Moreover, the expression patterns of TaPIN genes were verified by qRT-PCR. The qRT-PCR results also show a similar expression with slight variation. Therefore, the outcome of this study provides basic genomic information on the expression of the TaPIN gene family and will pave the way for dissecting the precise role of TaPINs in plant developmental processes and different stress conditions.
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Yang G, Pan W, Zhang R, Pan Y, Guo Q, Song W, Zheng W, Nie X. Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat. BMC Genomics 2021; 22:504. [PMID: 34218810 PMCID: PMC8254967 DOI: 10.1186/s12864-021-07849-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
Background Lignin is one of the main components of the cell wall and is directly associated with plant development and defence mechanisms in plants, especially in response to Fusarium graminearum (Fg) infection. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is the main regulator determining the efficiency of lignin synthesis and composition. Although it has been characterized in many plants, to date, the importance of the CCoAOMT family in wheat is not well understood. Results Here, a total of 21 wheat CCoAOMT genes (TaCCoAOMT) were identified through an in silico genome search method and they were classified into four groups based on phylogenetic analysis, with the members of the same group sharing similar gene structures and conserved motif compositions. Furthermore, the expression patterns and co-expression network in which TaCCoAOMT is involved were comprehensively investigated using 48 RNA-seq samples from Fg infected and mock samples of 4 wheat genotypes. Combined with qRT-PCR validation of 11 Fg-responsive TaCCoAOMT genes, potential candidates involved in the FHB response and their regulation modules were preliminarily suggested. Additionally, we investigated the genetic diversity and main haplotypes of these CCoAOMT genes in bread wheat and its relative populations based on resequencing data. Conclusions This study identified and characterized the CCoAOMT family in wheat, which not only provided potential targets for further functional analysis, but also contributed to uncovering the mechanism of lignin biosynthesis and its role in FHB tolerance in wheat and beyond. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07849-y.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Ruoyu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Yan Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Qifan Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China.,ICARDA-NWSUAF Joint Research Centre, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Weijun Zheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China.
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China. .,ICARDA-NWSUAF Joint Research Centre, Northwest A&F University, 712100, Yangling, Shaanxi, China.
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26
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Zhang G, Yang J, Zhang M, Li Q, Wu Y, Zhao X, Zhang H, Wang Y, Wu J, Wang W. Wheat TaPUB1 Regulates Cd Uptake and Tolerance by Promoting the Degradation of TaIRT1 and TaIAA17. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5818-5829. [PMID: 34018722 DOI: 10.1021/acs.jafc.0c08042] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cadmium (Cd) accumulation in agricultural soils is an increasingly serious problem, as plants absorb Cd, which inhibits their growth and development. Nonetheless, the molecular mechanisms underlying Cd detoxification and accumulation in wheat (Triticum aestivum L.) are unclear. Here, we isolated the U-box E3 ligase TaPUB1 from wheat and reported the functional characterization of TaPUB1 in Cd uptake and tolerance in wheat. Under Cd stress, TaPUB1 overexpression lines displayed higher photosynthetic rates than the wild type; opposite results were observed in the TaPUB1-RNAi lines. In addition, TaPUB1 overexpression lines showed reduced Cd uptake and accumulation, whereas RNAi plants exhibited a significant increase in Cd accumulation after Cd treatment. We further found that TaPUB1 enhanced the resistance of wheat to Cd stress in three ways. First, TaPUB1 interacts with and ubiquitinates TaIRT1, resulting in the inhibition of Cd uptake. Second, TaPUB1 interacts directly with and ubiquitinates TaIAA17, facilitates its degradation, and results in primary root elongation by activating the Aux signaling pathway under Cd stress. Moreover, TaPUB1 decreases ROS accumulation by regulating antioxidant-related gene expression and antioxidant enzyme activity under Cd stress. Thus, a molecular mechanism by which TaPUB1 regulates Cd uptake and tolerance by modulating the stability of TaIRT1 and TaIAA17 proteins was revealed.
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Affiliation(s)
- Guangqiang Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, P. R. China
- College of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, P. R. China
| | - Junjiao Yang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, P. R. China
| | - Meng Zhang
- Collaborative Innovation Center, Jining Medical University, Jining, Shandong 272067, P. R. China
| | - Qinxue Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, P. R. China
| | - Yunzhen Wu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, P. R. China
| | - Xiaoyu Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, P. R. China
| | - Huifei Zhang
- College of Agricultural, Shandong Agricultural University, Tai'an, Shandong 271018, P. R. China
| | - Yong Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, P. R. China
| | - Jiajie Wu
- College of Agricultural, Shandong Agricultural University, Tai'an, Shandong 271018, P. R. China
| | - Wei Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an, Shandong 271018, P. R. China
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Lai DL, Yan J, Fan Y, Li Y, Ruan JJ, Wang JZ, Fan Y, Cheng XB, Cheng JP. Genome-wide identification and phylogenetic relationships of the Hsp70 gene family of Aegilops tauschii, wild emmer wheat ( Triticum dicoccoides) and bread wheat ( Triticum aestivum). 3 Biotech 2021; 11:301. [PMID: 34194894 DOI: 10.1007/s13205-021-02639-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/03/2021] [Indexed: 12/22/2022] Open
Abstract
Heat shock protein 70 (Hsp70) plays an important role in plant development. It is closely related to the physiological process of cell development and the response to abiotic and biological stress. However, the classification and evolution of Hsp70 genes in bread wheat, wild emmer wheat and Aegilops tauschii are still unclear. Therefore, this study conducted a comprehensive bioinformatics analysis of Hsp70 gene in three species. Among these three species, 113, 79 and 36 Hsp70 genes were identified. They are divided into six subfamilies. Group vi-1 is different from Arabidopsis thaliana. It may be the result of early evolutionary segregation. The number of exons in different subfamilies (from 1 to 13) was different, but the distribution patterns of exons / introns in the same subfamily were similar. The results of Hsp70 promoter region analysis showed that the cis-regulatory elements of A. tauschii and wild emmer wheat were different from those of wheat. In addition, CpG island proportion of wild emmer Hsp70 was higher than that of wheat, which may be the molecular basis of heat resistance of wild wheat relative to cultivated wheat. Further comprehensive analysis of chromosome location and repeat events of Hsp70 gene showed that whole-genome duplication and tandem duplication events contributed to the evolution and expansion of Hsp70 gene in wheat. The results of non-synonymous substitution and synonymous substitution analysis showed that Hsp70 genes of three species had undergone purification selection. The expression profile analysis showed that Hsp70 gene was highly expressed in the roots during the vegetative growth period. In addition, TaHsp70 gene was highly expressed under various stress. The identification, classification and evolution of Hsp70 in wheat and its relatives provided a basis for further research on its evolution and its molecular mechanism in response to stress. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02639-5.
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Affiliation(s)
- Di-Li Lai
- College of Agriculture, Guizhou University, Guiyang, 550025 People's Republic of China
| | - Jun Yan
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106 People's Republic of China
| | - Yu Fan
- College of Agriculture, Guizhou University, Guiyang, 550025 People's Republic of China
| | - Yao Li
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137 People's Republic of China
| | - Jing-Jun Ruan
- College of Agriculture, Guizhou University, Guiyang, 550025 People's Republic of China
| | - Jun-Zhen Wang
- Research Station of Alpine Crops, Xichang Institute of Agricultural Sciences, Liangshan, 616150 People's Republic of China
| | - Yue Fan
- College of Agriculture, Guizhou University, Guiyang, 550025 People's Republic of China
| | - Xiao-Bin Cheng
- Department of Environmental and Life Sciences, Sichuan MinZu College, Kangding, 626001 People's Republic of China
| | - Jian-Ping Cheng
- College of Agriculture, Guizhou University, Guiyang, 550025 People's Republic of China
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EMS Derived Wheat Mutant BIG8-1 ( Triticum aestivum L.)-A New Drought Tolerant Mutant Wheat Line. Int J Mol Sci 2021; 22:ijms22105314. [PMID: 34070033 PMCID: PMC8158095 DOI: 10.3390/ijms22105314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
Drought response in wheat is considered a highly complex process, since it is a multigenic trait; nevertheless, breeding programs are continuously searching for new wheat varieties with characteristics for drought tolerance. In a previous study, we demonstrated the effectiveness of a mutant known as RYNO3936 that could survive 14 days without water. In this study, we reveal another mutant known as BIG8-1 that can endure severe water deficit stress (21 days without water) with superior drought response characteristics. Phenotypically, the mutant plants had broader leaves, including a densely packed fibrous root architecture that was not visible in the WT parent plants. During mild (day 7) drought stress, the mutant could maintain its relative water content, chlorophyll content, maximum quantum yield of PSII (Fv/Fm) and stomatal conductance, with no phenotypic symptoms such as wilting or senescence despite a decrease in soil moisture content. It was only during moderate (day 14) and severe (day 21) water deficit stress that a decline in those variables was evident. Furthermore, the mutant plants also displayed a unique preservation of metabolic activity, which was confirmed by assessing the accumulation of free amino acids and increase of antioxidative enzymes (peroxidases and glutathione S-transferase). Proteome reshuffling was also observed, allowing slow degradation of essential proteins such as RuBisCO during water deficit stress. The LC-MS/MS data revealed a high abundance of proteins involved in energy and photosynthesis under well-watered conditions, particularly Serpin-Z2A and Z2B, SGT1 and Calnexin-like protein. However, after 21 days of water stress, the mutants expressed ABC transporter permeases and xylanase inhibitor protein, which are involved in the transport of amino acids and protecting cells, respectively. This study characterizes a new mutant BIG8-1 with drought-tolerant characteristics suited for breeding programs.
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Rani S, Kumari P, Poddar R, Chattopadhyay S. Study of lipase producing gene in wheat - an in silico approach. J Genet Eng Biotechnol 2021; 19:73. [PMID: 33999287 PMCID: PMC8128969 DOI: 10.1186/s43141-021-00150-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/18/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Lipases (EC 3.1.1.3) catalyze the hydrolysis of oil into free fatty acids and glycerol forming the 3rd largest group of commercialized enzymes. Plant lipases grab attention recently because of their specificity, less production and purified cost, and easy availability. In silico approach is the first step to identify different genes coding for lipase in a most common indigenous plant, wheat, to explore the possibility of this plant as an alternative source for commercial lipase production. As the hierarchy organization of genes reflects an ancient process of gene duplication and divergence, many of the theoretical and analytical tools of the phylogenetic systematics can be utilized for comparative genomic studies. Also, in addition to experimental identification and characterization of genes, for computational genomic analysis, Arabidopsis has become a popular strategy to identify crop genes which are economically important, as Arabidopsis genes had been well identified and characterized for lipase. A number of articles had been reported in which genes of wheat have shown strong homology with Arabidopsis. The complete genome sequences of rice and Arabidopsis constitute a valuable resource for comparative genome analysis as they are representatives of the two major evolutionary lineages within the angiosperms. Here, in this in silico approach, Arabidopsis and Oryza sativa serve as models for dicotyledonous and monocotyledonous species, respectively, and the genomic sequence data available was used to identify the lipase genes in wheat. RESULTS In this present study, Ensembl Plants database was explored for lipase producing gene present in wheat genome and 21 genes were screened down as they contain specific domain and motif for lipase (GXSXG). According to the evolutionary analysis, it was found that the gene TraesCS5B02G157100, located in 5B chromosome, has 58.35% sequence similarity with the reported lipase gene of Arabidopsis thaliana and gene TraesCS3A02G463500 located in the 3A chromosome has 51.74% sequence similarity with the reported lipase gene of Oryza sativa. Homology modeling was performed using protein sequences coded by aforementioned genes and optimized by molecular dynamic simulations. Further with the help of molecular docking of modeled structures with tributyrin, binding efficiency was checked, and the difference in energies (DE) was -9.83 kcal/mol and -6.67 kcal/mol, respectively. CONCLUSIONS The present work provides a basic understanding of the gene-encoding lipase in wheat, which could be easily accessible and used as a potent industrial enzyme. The study enlightens another direction which can be used further to explore plant lipases.
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Affiliation(s)
- Shradha Rani
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, India
| | - Priya Kumari
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, India
| | - Raju Poddar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, India
| | - Soham Chattopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, India.
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Konstantinov DK, Zubairova US, Ermakov AA, Doroshkov AV. Comparative transcriptome profiling of a resistant vs susceptible bread wheat ( Triticum aestivum L.) cultivar in response to water deficit and cold stress. PeerJ 2021; 9:e11428. [PMID: 34026365 PMCID: PMC8123233 DOI: 10.7717/peerj.11428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/19/2021] [Indexed: 11/28/2022] Open
Abstract
Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars.
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Affiliation(s)
- Dmitrii K Konstantinov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Ulyana S Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Anton A Ermakov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexey V Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
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Genome-wide identification of PYL gene family in wheat: Evolution, expression and 3D structure analysis. Genomics 2020; 113:854-866. [PMID: 33321205 DOI: 10.1016/j.ygeno.2020.12.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/26/2020] [Accepted: 12/10/2020] [Indexed: 11/23/2022]
Abstract
Here, 38 wheat PYL genes (TaPYLs) belonging to 13 homoeologous groups were identified using the genome-search method, with 26 and 12 PYL genes identified in Triticum dicoccoides and Aegilops tauschii, respectively. Phylogenetic relationship, conserved domain and molecular evolution analysis revealed that PYL genes showed highly conservative between wheat and theprogenitors. Interaction network and miRNA target prediction found that TaPYLs could interact with the important components of ABA signaling pathway and Tae-miR966b-3p might be a hub regulator mediating wheat ABA signal network. Furthermore, the tissue-specific and stress-responsive TaPYLs were detected through RNA-seq analysis. Expressions of 10 TaPYLs were validated by QPCR analysis and the homoeologous genes showed significantly differential expression, suggesting subfunctionalization of them has occurred. Finally, 3D structures of the TaPYL proteins were predicted by homology modeling. This study lays the foundation for further functional study of PYL genes for development and stress tolerance improvement in wheat and beyond.
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Deblieck M, Fatiukha A, Grundman N, Merchuk-Ovnat L, Saranga Y, Krugman T, Pillen K, Serfling A, Makalowski W, Ordon F, Perovic D. GenoTypeMapper: graphical genotyping on genetic and sequence-based maps. PLANT METHODS 2020; 16:123. [PMID: 32944061 PMCID: PMC7488165 DOI: 10.1186/s13007-020-00665-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable. RESULTS We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time. CONCLUSIONS In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.
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Affiliation(s)
- Mathieu Deblieck
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Andrii Fatiukha
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Abba Khoushy Ave 199, 3498838 Haifa, Israel
| | - Norbert Grundman
- Faculty of Medicine, Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Niels-Stensen Strasse 14, 48149 Münster, Germany
| | - Lianne Merchuk-Ovnat
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel
| | - Yehoshua Saranga
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel
| | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Abba Khoushy Ave 199, 3498838 Haifa, Israel
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Department of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Wojciech Makalowski
- Faculty of Medicine, Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Niels-Stensen Strasse 14, 48149 Münster, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
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Placido DF, Sandhu J, Sato SJ, Nersesian N, Quach T, Clemente TE, Staswick PE, Walia H. The LATERAL ROOT DENSITY gene regulates root growth during water stress in wheat. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1955-1968. [PMID: 32031318 PMCID: PMC7415784 DOI: 10.1111/pbi.13355] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/21/2020] [Accepted: 01/26/2020] [Indexed: 05/10/2023]
Abstract
Drought stress is the major limiting factor in agriculture. Wheat, which is the most widely grown crop in the world, is predominantly cultivated in drought-prone rainfed environments. Since roots play a critical role in water uptake, root response to water limitations is an important component for enhancing wheat adaptation. In an effort to discover novel genetic sources for improving wheat adaptation, we characterized a wheat translocation line with a chromosomal segment from Agropyron elongatum, a wild relative of wheat, which unlike common wheat maintains root growth under limited-water conditions. By exploring the root transcriptome data, we found that reduced transcript level of LATERAL ROOT DENSITY (LRD) gene under limited water in the Agropyron translocation line confers it the ability to maintain root growth. The Agropyron allele of LRD is down-regulated in response to water limitation in contrast with the wheat LRD allele, which is up-regulated by water deficit stress. Suppression of LRD expression in wheat RNAi plants confers the ability to maintain root growth under water limitation. We show that exogenous gibberellic acid (GA) promotes lateral root growth and present evidence for the role of GA in mediating the differential regulation of LRD between the common wheat and the Agropyron alleles under water stress. Suppression of LRD also had a positive pleiotropic effect on grain size and number under optimal growth conditions. Collectively, our findings suggest that LRD can be potentially useful for improving wheat response to water stress and altering yield components.
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Affiliation(s)
- Dante F. Placido
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
- Bioproducts Research UnitWestern Regional Research CenterAgricultural Research ServiceUnited States Department of AgricultureAlbanyCAUSA
| | - Jaspreet Sandhu
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
| | - Shirley J. Sato
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
- Center for BiotechnologyUniversity of NebraskaLincolnNEUSA
| | - Natalya Nersesian
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
- Center for BiotechnologyUniversity of NebraskaLincolnNEUSA
| | - Truyen Quach
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
- Center for BiotechnologyUniversity of NebraskaLincolnNEUSA
| | - Thomas E. Clemente
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
- Center for BiotechnologyUniversity of NebraskaLincolnNEUSA
| | - Paul E. Staswick
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
| | - Harkamal Walia
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
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Tian R, Yang Y, Chen M. Genome-wide survey of the amino acid transporter gene family in wheat (Triticum aestivum L.): Identification, expression analysis and response to abiotic stress. Int J Biol Macromol 2020; 162:1372-1387. [PMID: 32781128 DOI: 10.1016/j.ijbiomac.2020.07.302] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/30/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022]
Abstract
Amino acid transporters (AATs), which transport amino acids across cell membranes, play important roles in alleviating plant damage under stresses and in plant growth. To data, little is known about the AAT genes in wheat because of its complex genome. In this study, a total of 296 AAT genes were identified from the latest wheat genome sequence (IWGSC v1.1) and classified into 12 distinct subfamilies based upon their sequence composition and phylogenetic relationship. The expansion of the wheat AAT family was mainly the results of whole-genome duplication (WGD) and tandem events. The unequal expansion of different subfamilies brought new features to TaAATs. TaAATs were highly expressed and exhibited distinct expression patterns in different tissues. On the basis of homology and expression pattern analysis, we identified several wheat AAT family members that may affect grain quality. In addition, TaAAP3, TaATLa2 and TaATLb13 exhibited sustained expression in response to drought and high-temperature stress. These genes are involved in the response of wheat to abiotic stress by regulating the transport and distribution of amino acids. Overall, our results help to understand the complexity of TaAATs and provide a theoretical basis for further identification and utilization of AATs in wheat and other crop species.
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Affiliation(s)
- Ruizheng Tian
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, Yangling 712100, China
| | - Yang Yang
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Yangling 712100, China
| | - Maohua Chen
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, Yangling 712100, China.
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Derakhshani B, Ayalew H, Mishina K, Tanaka T, Kawahara Y, Jafary H, Oono Y. Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat. PLANTS 2020; 9:plants9050596. [PMID: 32392904 PMCID: PMC7284651 DOI: 10.3390/plants9050596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/15/2020] [Accepted: 05/03/2020] [Indexed: 11/16/2022]
Abstract
Crop cultivars with larger root systems have an increased ability to absorb water and nutrients under conditions of water deficit. To unravel the molecular mechanism of water-stress tolerance in wheat, we performed RNA-seq analysis on the two genotypes, Colotana 296-52 (Colotana) and Tincurrin, contrasting the root growth under polyethylene-glycol-induced water-stress treatment. Out of a total of 35,047 differentially expressed genes, 3692 were specifically upregulated in drought-tolerant Colotana under water stress. Transcription factors, pyrroline-5-carboxylate reductase and late-embryogenesis-abundant proteins were among upregulated genes in Colotana. Variant calling between Colotana and Tincurrin detected 15,207 SNPs and Indels, which may affect protein function and mediate the contrasting root length phenotype. Finally, the expression patterns of five triads in response to water, high-salinity, heat, and cold stresses were analyzed using qRT-PCR to see if there were differences in homoeologous gene expression in response to those conditions. The five examined triads showed variation in the contribution of homoeologous genes to water, high-salinity, heat, and cold stresses in the two genotypes. The variation of homoeologous gene expression in response to environmental stresses may enable plants to better cope with stresses in their natural environments.
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Affiliation(s)
- Behnam Derakhshani
- Department of Agronomy & Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38791, Iran;
- Breeding Material Development Unit, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8518, Japan
| | - Habtamu Ayalew
- Small Grains Breeding Laboratory, Noble Research Institute LLC, Ardmore, OK 73401, USA;
| | - Kohei Mishina
- Plant Genome Research Unit, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan;
| | - Tsuyoshi Tanaka
- Breeding Informatics Research Unit, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan; (T.T.); (Y.K.)
- Bioinformatics Team, Advanced Analysis Center, NARO, Tsukuba 305-8518, Japan
| | - Yoshihiro Kawahara
- Breeding Informatics Research Unit, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan; (T.T.); (Y.K.)
- Bioinformatics Team, Advanced Analysis Center, NARO, Tsukuba 305-8518, Japan
| | - Hossein Jafary
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran 19395-1454, Iran;
| | - Youko Oono
- Breeding Material Development Unit, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8518, Japan
- Correspondence: ; Tel.: +81-29-838-7443
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Cyclin-Dependent Kinase Inhibitor Gene TaICK1 acts as a Potential Contributor to Wheat Male Sterility induced by a Chemical Hybridizing Agent. Int J Mol Sci 2020; 21:ijms21072468. [PMID: 32252420 PMCID: PMC7177297 DOI: 10.3390/ijms21072468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 02/05/2023] Open
Abstract
Heterosis has been widely accepted as an effective strategy to increase yields in plant breeding. Notably, the chemical hybridization agent SQ-1 induces male sterility in wheat, representing a critical potential tool in hybrid seed production. However, the mechanisms underlying the male sterility induced by SQ-1 still remain poorly understood. In this study, a cyclin-dependent kinase inhibitor gene, TaICK1, which encodes a 229 amino acid protein, was identified as a potential contributor to male sterility in common wheat. The expression of TaICK1 was upregulated during the development of anthers in Xinong1376 wheat treated with SQ-1. Meanwhile, the seed setting rate was found to be significantly decreased in TaICK1 transgenic rice. Furthermore, we identified two cyclin proteins, TaCYCD2;1 and TaCYCD6;1, as interactors through yeast two-hybrid screening using TaICK1 as the bait, which were validated using bimolecular fluorescence complementation. Subcellular localization revealed that the proteins encoded by TaICK1, TaCYCD2;1, and TaCYCD6;1 were localized in the cell nucleus. The expression levels of TaCYCD2;1 and TaCYCD6;1 were lower in Xinong1376 treated with SQ-1. A further analysis demonstrated that the expression levels of OsCYCD2;1 and OsCYCD6;1 were lower in transgenic TaICK1 rice lines as well. Taken together, these results suggest that the upregulation of TaICK1, induced by SQ-1, may subsequently suppress the expression of TaCYCD2;1 and TaCYCD6;1 in anthers, resulting in male sterility. This study provides new insights into the understanding of SQ-1-induced wheat male sterility, as well as the developmental mechanisms of anthers.
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Liu Y, Zhang S, Zhou Q, Li S, Zhang J, Zhang L, Jiang S, Zhang Q, Zhou X, Wu C, Gu Q, Qian ZY. Subchronic feeding toxicity studies of drought-tolerant transgenic wheat MGX11-10 in Wistar Han RCC rats. Food Chem Toxicol 2020; 137:111129. [PMID: 31935424 DOI: 10.1016/j.fct.2020.111129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/18/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022]
Abstract
A subchronic toxicity study were conducted in Wistar Han RCC rats to evaluate the potential health effects of genetically modified (GM), drought-tolerant wheat MGX11-10. Rats were fed a rodent diet formulated with MGX11-10 and were compared with rats fed a diet formulated with its corresponding non-transgenic control Jimai22 and rats fed a basal diet. MGX11-10 and Jimai22 were ground into flour and formulated into diets at concentrations of 16.25, 32.5, or 65%, w/w% and fed to rats (10/sex/group) for 13 weeks. Compared with rats fed Jimai22 and the basal-diet group, no biologically relevant differences were observed in rats fed the GM diet with respect to body weight/gain, food consumption/efficiency, clinical signs, mortality, ophthalmology, clinical pathology (hematology, prothrombin time, urinalysis, clinical chemistry), organ weights, and gross and microscopic pathology. Under the conditions of this study, the MGX11-10 diets did not cause any treatment-related effects in rats following at least 90 days of dietary administration as compared with rats fed diets with the corresponding non-transgenic control diet and the basal-diet group. The MGX11-10 diets are considered equivalent to the diets prepared from conventional comparators. The results demonstrated that MGX11-10 wheat is as safe and wholesome as the corresponding non-transgenic control wheat.
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Affiliation(s)
- Yinghua Liu
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Shujing Zhang
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Qinghong Zhou
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Shufei Li
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Jing Zhang
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Li Zhang
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Shuqing Jiang
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Qian Zhang
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Xiaoli Zhou
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Chao Wu
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Qing Gu
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China.
| | - Zhi Yong Qian
- Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China.
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Moradi Tarnabi Z, Iranbakhsh A, Mehregan I, Ahmadvand R. Impact of arbuscular mycorrhizal fungi (AMF) on gene expression of some cell wall and membrane elements of wheat ( Triticum aestivum L.) under water deficit using transcriptome analysis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:143-162. [PMID: 32153322 PMCID: PMC7036378 DOI: 10.1007/s12298-019-00727-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/30/2019] [Accepted: 10/18/2019] [Indexed: 05/26/2023]
Abstract
Mycorrhizal symbiotic relationship is one of the most common collaborations between plant roots and the arbuscular mycorrhizal fungi (AMF). The first barrier for establishing this symbiosis is plant cell wall which strongly provides protection against biotic and abiotic stresses. The aim of this study was to investigate the gene expression changes in cell wall of wheat root cv. Chamran after inoculation with AMF, Funneliformis mosseae under two different irrigation regimes. To carry out this investigation, total RNA was extracted from the roots of mycorrhizal and non-mycorrhizal plants, and analyzed using RNA-Seq in an Illumina Next-Seq 500 platform. The results showed that symbiotic association between wheat and AMF and irrigation not only affect transcription profile of the plant growth, but also cell wall and membrane components. Of the 114428 genes expressed in wheat roots, the most differentially expressed genes were related to symbiotic plants under water stress. The most differentially expressed genes were observed in carbohydrate metabolic process, lipid metabolic process, cellulose synthase activity, membrane transports, nitrogen compound metabolic process and chitinase activity related genes. Our results indicated alteration in cell wall and membrane composition due to mycorrhization and irrigation regimes might have a noteworthy effect on the plant tolerance to water deficit.
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Affiliation(s)
- Zahra Moradi Tarnabi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Alireza Iranbakhsh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Iraj Mehregan
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Rahim Ahmadvand
- Vegetable Research Department, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
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Xu L, Wang D, Liu S, Fang Z, Su S, Guo C, Zhao C, Tang Y. Comprehensive Atlas of Wheat ( Triticum aestivum L.) AUXIN RESPONSE FACTOR Expression During Male Reproductive Development and Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:586144. [PMID: 33101350 PMCID: PMC7554351 DOI: 10.3389/fpls.2020.586144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/14/2020] [Indexed: 05/13/2023]
Abstract
AUXIN RESPONSE FACTOR (ARF) proteins regulate a wide range of signaling pathways, from general plant growth to abiotic stress responses. Here, we performed a genome-wide survey in wheat (Triticum aestivum) and identified 69 TaARF members that formed 24 homoeologous groups. Phylogenetic analysis clustered TaARF genes into three clades, similar to ARF genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Structural characterization suggested that ARF gene structure and domain composition are well conserved between plant species. Expression profiling revealed diverse patterns of TaARF transcript levels across a range of developmental stages, tissues, and abiotic stresses. A number of TaARF genes shared similar expression patterns and were preferentially expressed in anthers. Moreover, our systematic analysis identified three anther-specific TaARF genes (TaARF8, TaARF9, and TaARF21) whose expression was significantly altered by low temperature in thermosensitive genic male-sterile (TGMS) wheat; these TaARF genes are candidates to participate in the cold-induced male sterility pathway, and offer potential applications in TGMS wheat breeding and hybrid seed production. Moreover, we identified putative functions for a set of TaARFs involved in responses to abscisic acid and abiotic stress. Overall, this study characterized the wheat ARF gene family and generated several hypotheses for future investigation of ARF function during anther development and abiotic stress.
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Affiliation(s)
- Lei Xu
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Dezhou Wang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shan Liu
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zhaofeng Fang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shichao Su
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunman Guo
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Changping Zhao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Changping Zhao, ; Yimiao Tang,
| | - Yimiao Tang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Changping Zhao, ; Yimiao Tang,
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Du H, Zhang H, Wei L, Li C, Duan Y, Wang H. A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.). BMC PLANT BIOLOGY 2019; 19:588. [PMID: 31881840 PMCID: PMC6935206 DOI: 10.1186/s12870-019-2172-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/28/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. RESULTS The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. CONCLUSIONS This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.
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Affiliation(s)
- Hua Du
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Huili Wang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
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Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 2019; 20:284. [PMID: 31849336 DOI: 10.1101/631648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/25/2019] [Indexed: 05/29/2023] Open
Abstract
Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
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Affiliation(s)
- Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Thomas Lux
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Heidrun Gundlach
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jennifer Ens
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Chengdao Li
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Center for Grain Industry/School of Agriculture, Yangtze University, Jingzhou, China
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics & Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Alan H Schulman
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Robbie Waugh
- The James Hutton Institute, Dundee, UK
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Klaus F X Mayer
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Manuel Spannagl
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 2019; 20:284. [PMID: 31849336 PMCID: PMC6918601 DOI: 10.1186/s13059-019-1899-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/25/2019] [Indexed: 11/24/2022] Open
Abstract
Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
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Affiliation(s)
- Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Thomas Lux
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Heidrun Gundlach
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jennifer Ens
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Chengdao Li
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Center for Grain Industry/School of Agriculture, Yangtze University, Jingzhou, China
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics & Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Alan H Schulman
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Robbie Waugh
- The James Hutton Institute, Dundee, UK
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Klaus F X Mayer
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Manuel Spannagl
- PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Tufan HA, Taşkin BG, Maccormack R, Boyd LA, Kaya Z, Türet M. The utility of NBS-profiling for characterization of yellow rust resistance in an F 6 durum wheat population. J Genet 2019; 98:98. [PMID: 31767816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Seedling and adult plant (field) resistance to yellow rust in the durum wheat (Triticum turgidum ssp. durum) cross Kunduru-1149 x Cham-1 was characterized using a functionally-targeted DNA marker system, NBS-profiling. Chi-squared analysis indicated a four gene model conferring seedling yellow rust resistance against Puccinia striiformis f. sp. tritici isolate WYR85/22 (virulent on Yr2, Yr6, Yr7 and Yr9). Interval mapping located two QTL for yellow rust resistance on the long arm of chromosome 1B, while Kruskal-Wallis single marker regression identified a number of additional marker loci associated with seedling and/or adult plant, field resistance to yellow rust. These results suggested that much of the yellow rust resistance seen in the field may be due to seedling expressed resistance (R) genes. Characterization of the DNA sequence of three NBS marker loci indicated that all showed significant homology to functionally-characterized R-genes and resistance gene analogues (RGAs), with the greatest homology being NBS-LRR-type R-genes and RGAs from cereal species.
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Affiliation(s)
- Hale A Tufan
- Department of Molecular Biology and Genetics, Bogazici University, 34342 Bebek, Istanbul, Turkey.
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44
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The utility of NBS-profiling for characterization of yellow rust resistance in an F6 durum wheat population. J Genet 2019. [DOI: 10.1007/s12041-019-1143-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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45
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Comparative profiling of roots small RNA expression and corresponding gene ontology and pathway analyses for low- and high-cadmium-accumulating genotypes of wheat in response to cadmium stress. Funct Integr Genomics 2019; 20:177-190. [PMID: 31435847 DOI: 10.1007/s10142-019-00710-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
MicroRNAs (miRNAs) participate in multiple biological processes in plant. Cd accumulation ability differs among varieties in wheat, but little is known about miRNAs and their function in Cd accumulation of wheat under Cd stress. Therefore, the present study detected small RNAs responsible for differential Cd accumulation between two contrasting wheat genotypes (low-Cd accumulation one L17 and high-Cd accumulation one H17) to identify novel targets to further study Cd stress in wheat. Under normal conditions, 139 miRNAs were differentially expressed between L17 and H17, while this value reached 142 after Cd exposure. For Cd-induced DEMs, total 25 miRNAs were differentially expressed in L17 after Cd treatment, while, 70 Cd-induced DEMs were found in H17. Moreover, GO analysis revealed that target genes of DEMs related to lipid biosynthetic process and chlorophyll binding are uniquely enriched in L17, target genes of DEMs related to ribosome biogenesis and sucrose alpha-glucosidase activity are uniquely enriched in H17. By pathway analysis, target genes of DEMs related to PI3K-Akt signaling pathway was specifically enriched in L17, target genes of DEMs related to carbohydrate digestion and absorption pathway was uniquely enriched in H17. In addition, miRNA-gene co-expression showed that tae-miR9774 was uniquely expressed between L17Cd and L17CK, while tae-miR398 was specially expressed between H17Cd and H17CK. Our results suggested that Cd-accumulating ability of L17 and H17 varied from the expression of induced unique miRNA, such as expression of tae-miR-9774 and tae-miR-398. Our study not only provide the foundation for further exploring the miRNAs-induced molecular mechanisms of Cd accumulation in wheat but also supply novel strategies for improving phytoremediation ability of food plants through genetic engineering.
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46
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Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology. PLANTS 2019; 8:plants8080270. [PMID: 31390788 PMCID: PMC6724115 DOI: 10.3390/plants8080270] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/29/2019] [Accepted: 08/04/2019] [Indexed: 12/19/2022]
Abstract
The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.
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47
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Zhou M, Zheng S, Liu R, Lu L, Zhang C, Zhang L, Yant L, Wu Y. The genome-wide impact of cadmium on microRNA and mRNA expression in contrasting Cd responsive wheat genotypes. BMC Genomics 2019; 20:615. [PMID: 31357934 PMCID: PMC6664702 DOI: 10.1186/s12864-019-5939-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 06/26/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Heavy metal ATPases (HMAs) are responsible for Cd translocation and play a primary role in Cd detoxification in various plant species. However, the characteristics of HMAs and the regulatory mechanisms between HMAs and microRNAs in wheat (Triticum aestivum L) remain unknown. RESULTS By comparative microRNA and transcriptome analysis, a total three known and 19 novel differentially expressed microRNAs (DEMs) and 1561 differentially expressed genes (DEGs) were found in L17 after Cd treatment. In H17, by contrast, 12 known and 57 novel DEMs, and only 297 Cd-induced DEGs were found. Functional enrichments of DEMs and DEGs indicate how genotype-specific biological processes responded to Cd stress. Processes found to be involved in microRNAs-associated Cd response include: ubiquitin mediated proteolysis, tyrosine metabolism, and carbon fixation pathways and thiamine metabolism. For the mRNA response, categories including terpenoid backbone biosynthesis and phenylalanine metabolism, and photosynthesis - antenna proteins and ABC transporters were enriched. Moreover, we identified 32 TaHMA genes in wheat. Phylogenetic trees, chromosomal locations, conserved motifs and expression levels in different tissues and roots under Cd stress are presented. Finally, we infer a microRNA-TaHMAs expression network, indicating that miRNAs can regulate TaHMAs. CONCLUSION Our findings suggest that microRNAs play important role in wheat under Cd stress through regulation of targets such as TaHMA2;1. Identification of these targets will be useful for screening and breeding low-Cd accumulation wheat lines.
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Affiliation(s)
- Min Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Shigang Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Rong Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lu Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Chihong Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Lei Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan China
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48
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Different Roles of Heat Shock Proteins (70 kDa) During Abiotic Stresses in Barley ( Hordeum vulgare) Genotypes. PLANTS 2019; 8:plants8080248. [PMID: 31357401 PMCID: PMC6724185 DOI: 10.3390/plants8080248] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
In this work, the involvement of heat shock proteins (HSP70) in barley (Hordeum vulgare) has been studied in response to drought and salinity. Thus, 3 barley genotypes usually cultivated and/or selected in Italy, 3 Middle East/North Africa landraces and genotypes and 1 improved genotype from ICARDA have been studied to identify those varieties showing the best stress response. Preliminarily, a bioinformatic characterization of the HSP70s protein family in barley has been made by using annotated Arabidopsis protein sequences. This study identified 20 putative HSP70s orthologs in the barley genome. The construction of un-rooted phylogenetic trees showed the partition into four main branches, and multiple subcellular localizations. The enhanced HSP70s presence upon salt and drought stress was investigated by both immunoblotting and expression analyses. It is worth noting the Northern Africa landraces showed peculiar tolerance behavior versus drought and salt stresses. The drought and salinity conditions indicated the involvement of specific HSP70s to counteract abiotic stress. Particularly, the expression of cytosolic MLOC_67581, mitochondrial MLOC_50972, and encoding for HSP70 isoforms showed different expressions and occurrence upon stress. Therefore, genotypes originated in the semi-arid area of the Mediterranean area can represent an important genetic source for the improvement of commonly cultivated high-yielding varieties.
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Wang H, Wang S, Chang X, Hao C, Sun D, Jing R. Identification of TaPPH-7A haplotypes and development of a molecular marker associated with important agronomic traits in common wheat. BMC PLANT BIOLOGY 2019; 19:296. [PMID: 31286893 PMCID: PMC6615193 DOI: 10.1186/s12870-019-1901-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/20/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Premature senescence of flag leaf severely affects wheat yield and quality. Chlorophyll (Chl) degradation is the most obvious symptom during leaf senescence and catalyzed by a series of enzymes. Pheophytin pheophorbide hydrolase (Pheophytinase, PPH) gene encodes a Chl degradation hydrolase. RESULTS In this study, the coding, genomic and promoter sequences of wheat TaPPH-A gene were cloned. The corresponding lengths were 1467 bp, 4479 bp and 3666 bp, respectively. Sequence structure analysis showed that TaPPH-A contained five exons and four introns. After the multiple sequences alignment of TaPPH-A genome from 36 accessions in a wheat diversity panel, four SNPs and one 2-bp InDel were observed, which formed two haplotypes, TaPPH-7A-1 and TaPPH-7A-2. Based on the SNP at 1299 bp (A/G), a molecular marker TaPPH-7A-dCAPS was developed to distinguish allelic variation (A/G). Using the molecular markers, 13 SSR, and 116 SNP markers, a linkage map of chromosome 7A were integrated. TaPPH-A was mapped on the chromosome region flanked by Xwmc9 (0.94 cM) and AX-95634545 (1.04 cM) on 7A in a DH population. Association analysis between TaPPH-7A allelic variation and agronomic traits found that TaPPH-7A was associated with TGW in 11 of 12 environments and Chl content at grain-filling stage under drought stress using Population 1 consisted of 323 accessions. The accessions possessed TaPPH-7A-1 (A) had higher TGW and Chl content than those possessed TaPPH-7A-2 (G), thus TaPPH-7A-1 (A) was a favorable allelic variation. By analyzing the frequency of favorable allelic variation TaPPH-7A-1 (A) in Population 2 with 157 landraces and Population 3 with 348 modern cultivars, we found it increased from pre-1950 (0) to 1960s (54.5%), then maintained a relatively stable level about 56% from 1960s to 1990s. CONCLUSION These results suggested the favorable allelic variation TaPPH-7A-1 (A) should be valuable in enhancing grain yield by improving the source (chlorophyll content) and sink (the developing grain) simultaneously. Furthermore, the newly developed molecular marker TaPPH-7A-dCAPS could be integrated into a breeding kit of screening high TGW wheat for marker-assisted selection.
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Affiliation(s)
- Huiyan Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801 China
| | - Shuguang Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801 China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chenyang Hao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801 China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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50
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Casartelli A, Melino VJ, Baumann U, Riboni M, Suchecki R, Jayasinghe NS, Mendis H, Watanabe M, Erban A, Zuther E, Hoefgen R, Roessner U, Okamoto M, Heuer S. Opposite fates of the purine metabolite allantoin under water and nitrogen limitations in bread wheat. PLANT MOLECULAR BIOLOGY 2019; 99:477-497. [PMID: 30721380 DOI: 10.1007/s11103-019-00831-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/24/2019] [Indexed: 05/06/2023]
Abstract
Degradation of nitrogen-rich purines is tightly and oppositely regulated under drought and low nitrogen supply in bread wheat. Allantoin is a key target metabolite for improving nitrogen homeostasis under stress. The metabolite allantoin is an intermediate of the catabolism of purines (components of nucleotides) and is known for its housekeeping role in nitrogen (N) recycling and also for its function in N transport and storage in nodulated legumes. Allantoin was also shown to differentially accumulate upon abiotic stress in a range of plant species but little is known about its role in cereals. To address this, purine catabolic pathway genes were identified in hexaploid bread wheat and their chromosomal location was experimentally validated. A comparative study of two Australian bread wheat genotypes revealed a highly significant increase of allantoin (up to 29-fold) under drought. In contrast, allantoin significantly decreased (up to 22-fold) in response to N deficiency. The observed changes were accompanied by transcriptional adjustment of key purine catabolic genes, suggesting that the recycling of purine-derived N is tightly regulated under stress. We propose opposite fates of allantoin in plants under stress: the accumulation of allantoin under drought circumvents its degradation to ammonium (NH4+) thereby preventing N losses. On the other hand, under N deficiency, increasing the NH4+ liberated via allantoin catabolism contributes towards the maintenance of N homeostasis.
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Affiliation(s)
- Alberto Casartelli
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
- Strube Research GmbH & Co. KG, 38387, Söllingen, Germany
| | - Vanessa J Melino
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
- School of Agriculture and Food, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ute Baumann
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Matteo Riboni
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Radoslaw Suchecki
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Nirupama S Jayasinghe
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Himasha Mendis
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Mutsumi Watanabe
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Alexander Erban
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Ellen Zuther
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Rainer Hoefgen
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Ute Roessner
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Mamoru Okamoto
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Sigrid Heuer
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia.
- Rothamsted Research, Plant Science Department, Harpenden, Hertfordshire, AL5 2JQ, UK.
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