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Vasistha NK, Sharma V, Singh S, Kaur R, Kumar A, Ravat VK, Kumar R, Gupta PK. Meta-QTL analysis and identification of candidate genes for multiple-traits associated with spot blotch resistance in bread wheat. Sci Rep 2024; 14:13083. [PMID: 38844568 PMCID: PMC11156910 DOI: 10.1038/s41598-024-63924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
In bread wheat, a literature search gave 228 QTLs for six traits, including resistance against spot blotch and the following five other related traits: (i) stay green; (ii) flag leaf senescence; (iii) green leaf area duration; (iv) green leaf area of the main stem; and (v) black point resistance. These QTLs were used for metaQTL (MQTL) analysis. For this purpose, a consensus map with 72,788 markers was prepared; 69 of the above 228 QTLs, which were suitable for MQTL analysis, were projected on the consensus map. This exercise resulted in the identification of 16 meta-QTLs (MQTLs) located on 11 chromosomes, with the PVE ranging from 5.4% (MQTL7) to 21.8% (MQTL5), and the confidence intervals ranging from 1.5 to 20.7 cM (except five MQTLs with a range of 36.1-57.8 cM). The number of QTLs associated with individual MQTLs ranged from a maximum of 17 in MQTL3 to 8 each in MQTL5 and MQTL8 and 5 each in MQTL7 and MQTL14. The 16 MQTLs, included 12 multi-trait MQTLs; one of the MQTL also overlapped a genomic region carrying the major spot blotch resistance gene Sb1. Of the total 16 MQTLs, 12 MQTLs were also validated through marker-trait associations that were available from earlier genome-wide association studies. The genomic regions associated with MQTLs were also used for the identification of candidate genes (CGs) and led to the identification of 516 CGs encoding 508 proteins; 411 of these proteins are known to be associated with resistance against several biotic stresses. In silico expression analysis of CGs using transcriptome data allowed the identification of 71 differentially expressed CGs, which were examined for further possible studies. The findings of the present study should facilitate fine-mapping and cloning of genes, enabling Marker Assisted Selection.
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Affiliation(s)
- Neeraj Kumar Vasistha
- Department of Genetics and Plant Breeding, Rajiv Gandhi University, Rono Hills, Itanagar, India
- Department of Genetics-Plant Breeding and Biotechnology, Dr K. S. Gill, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, India
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Vaishali Sharma
- Department of Genetics-Plant Breeding and Biotechnology, Dr K. S. Gill, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, India
| | - Sahadev Singh
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
- Meerut Institute of Technology, NH-58 Baral Partapur Bypass Road, Meerut, India
| | - Ramandeep Kaur
- Department of Genetics-Plant Breeding and Biotechnology, Dr K. S. Gill, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, India
| | - Anuj Kumar
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Vikas Kumar Ravat
- Department of Plant Pathology, Rajiv Gandhi University, Rono Hills, Itanagar, India
| | - Rahul Kumar
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Pushpendra K Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
- Murdoch's Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia.
- Borlaug Institute for South Asia (BISA), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India.
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Vishwakarma G, Saini A, Bhardwaj SC, Kumar S, Das BK. Comparative transcriptomics of stem rust resistance in wheat NILs mediated by Sr24 rust resistance gene. PLoS One 2023; 18:e0295202. [PMID: 38079439 PMCID: PMC10712884 DOI: 10.1371/journal.pone.0295202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Stem rust of wheat is a deleterious fungal disease across the globe causing severe yield losses. Although, many stem rust resistance genes (Sr) are being used in wheat breeding programs, new emerging stem rust pathotypes are a challenge to important Sr genes. In recent years, multiple studies on leaf and yellow rust molecular mechanism have been done, however, for stem rust such studies are lacking. Current study investigated stem rust induced response in the susceptible wheat genotype C306 and its Near Isogenic Line (NIL) for Sr24 gene, HW2004, using microarray analysis to understand the transcriptomic differences at different stages of infection. Results showed that HW2004 has higher basal levels of several important genes involved in pathogen detection, defence, and display early activation of multiple defence mechanisms. Further Gene Ontology (GO) and pathway analysis identified important genes responsible for pathogen detection, downstream signalling cascades and transcription factors (TFs) involved in activation and mediation of defence responses. Results suggest that generation of Reactive Oxygen Species (ROS), cytoskeletal rearrangement, activation of multiple hydrolases, and lipid metabolism mediated biosynthesis of certain secondary metabolites are collectively involved in Sr24-mediated defence in HW2004, in response to stem rust infection. Novel and unannotated, but highly responsive genes were also identified, which may also contribute towards resistance phenotype. Furthermore, certain DEGs also mapped close to the Sr24-linked marker on Thinopyrum elongatum translocated fragment on wheat 3E chromosome, which advocate further investigations for better insights of the Sr24-mediated stem rust resistance.
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Affiliation(s)
- Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, India
| | - Ajay Saini
- Homi Bhabha National Institute, Mumbai, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
| | | | - Satish Kumar
- ICAR—Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Bikram Kishore Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, India
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Prasad P, Jain N, Chaudhary J, Thakur RK, Savadi S, Bhardwaj SC, Gangwar OP, Lata C, Adhikari S, Kumar S, Balyan HS, Gupta PK. Candidate effectors for leaf rust resistance gene Lr28 identified through transcriptome and in-silico analysis. Front Microbiol 2023; 14:1143703. [PMID: 37789861 PMCID: PMC10543267 DOI: 10.3389/fmicb.2023.1143703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/31/2023] [Indexed: 10/05/2023] Open
Abstract
Puccinia spp. causing rust diseases in wheat and other cereals secrete several specialized effector proteins into host cells. Characterization of these proteins and their interaction with host's R proteins could greatly help to limit crop losses due to diseases. Prediction of effector proteins by combining the transcriptome analysis and multiple in-silico approaches is gaining importance in revealing the pathogenic mechanism. The present study involved identification of 13 Puccinia triticina (Pt) coding sequences (CDSs), through transcriptome analysis, that were differentially expressed during wheat-leaf rust interaction; and prediction of their effector like features using different in-silico tools. NCBI-BLAST and pathogen-host interaction BLAST (PHI-BLAST) tools were used to annotate and classify these sequences based on their most closely matched counterpart in both the databases. Homology between CDSs and the annotated sequences in the NCBI database ranged from 79 to 94% and with putative effectors of other plant pathogens in PHI-BLAST from 24.46 to 54.35%. Nine of the 13 CDSs had effector-like features according to EffectorP 3.0 (≥0.546 probability of these sequences to be effector). The qRT-PCR expression analysis revealed that the relative expression of all CDSs in compatible interaction (HD2329) was maximum at 11 days post inoculation (dpi) and that in incompatible interactions (HD2329 + Lr28) was maximum at 3 dpi in seven and 9 dpi in five CDSs. These results suggest that six CDSs (>0.8 effector probability as per EffectorP 3.0) could be considered as putative Pt effectors. The molecular docking and MD simulation analysis of these six CDSs suggested that candidate Lr28 protein binds more strongly to candidate effector c14094_g1_i1 to form more stable complex than the remaining five. Further functional characterization of these six candidate effectors should prove useful for a better understanding of wheat-leaf rust interaction. In turn, this should facilitate effector-based leaf rust resistance breeding in wheat.
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Affiliation(s)
- Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Jyoti Chaudhary
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Rajni Kant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | | | | | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Charu Lata
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Sneha Adhikari
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
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Sehgal D, Dhakate P, Ambreen H, Shaik KHB, Rathan ND, Anusha NM, Deshmukh R, Vikram P. Wheat Omics: Advancements and Opportunities. PLANTS (BASEL, SWITZERLAND) 2023; 12:426. [PMID: 36771512 PMCID: PMC9919419 DOI: 10.3390/plants12030426] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco 56237, Mexico
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Priyanka Dhakate
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110076, India
| | - Heena Ambreen
- School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | - Khasim Hussain Baji Shaik
- Faculty of Agriculture Sciences, Georg-August-Universität, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Nagenahalli Dharmegowda Rathan
- Indian Agricultural Research Institute (ICAR-IARI), New Delhi 110012, India
- Corteva Agriscience, Hyderabad 502336, Telangana, India
| | | | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, Haryana, India
| | - Prashant Vikram
- Bioseed Research India Ltd., Hyderabad 5023324, Telangana, India
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Jain N, Shiv A, Sinha N, Singh PK, Prasad P, Balyan HS, Gupta PK. Leaf rust responsive miRNA and their target genes in wheat. Funct Integr Genomics 2022; 23:14. [PMID: 36550370 DOI: 10.1007/s10142-022-00928-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Small RNA sequencing (sRNA-seq) and degradome analysis were used for the identification of miRNAs and their target host genes in a pair of near-isogenic lines (NILs), which differed for the presence of leaf rust resistance gene Lr28. The study led to identification of (i) 506 known and 346 novel miRNAs; and (ii) 5054 target genes including 4557 in silico predicted and 497 degradome-based genes using 105 differentially expressed (DE) miRNAs. A subset of 128 targets (67 in silico + 61 degradome-based) was differentially expressed in RNA-seq data that was generated by us earlier using the same pair of NILs; among these 128 targets, 58 target genes exhibited an inverse relationship with the DE miRNAs (expression of miRNAs and activation/suppression of target genes). Eight miRNAs which belonged to the conserved miRNA families and were known to be induced in response to fungal diseases in plants included the following: miR156, miR158, miR159, miR168, miR169, miR172, miR319, miR396. The target genes belonged to the following classes of genes known to be involved in downstream disease resistance pathways; peroxidases, sugar transporters, auxin response signaling, oxidation-reduction, etc. It was also noticed that although a majority of miRNAs and target genes followed the above classical inverse relationship, there were also examples, where no such relationship was observed. Among the target genes, there were also 51 genes that were not only regulated by miRNAs, but were also differentially methylated at sequences including the following segments: promotors, introns, TSS, exons. The results of the present study suggest a complex interplay among miRNA genes, target genes, and various epigenetic controls, which regulate the expression of genes involved in downstream pathways for disease resistance.
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Affiliation(s)
- Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Aalok Shiv
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - P K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Pramod Prasad
- Regional Station, ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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BS-Seq reveals major role of differential CHH methylation during leaf rust resistance in wheat (Triticum aestivum L.). Mol Genet Genomics 2022; 297:731-749. [PMID: 35305147 DOI: 10.1007/s00438-022-01879-1] [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: 09/13/2021] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
Abstract
Epigenetic regulation of the activity of defense genes during onset of diseases or resistance against diseases in plants is an active area of research. In the present study, a pair of wheat NILs for leaf rust resistance gene Lr28 (R) in the background of an Indian cultivar HD2329 (S) was used for a study of DNA methylation mediated regulation of gene expression. Leaf samples were collected at 0 h before (S0 and R0) and 96 h after inoculation (S96 and R96). The DNA samples were subjected to BS-Seq and sequencing data were used for identification of differentially methylated/demethylated regions/genes (DMRs and DMGs). Following four pairs of comparisons were used for this purpose: S0 vs S96; S0 vs R0; R0 vs R96; S96 vs R96. Major role of CHH methylation relative to that of CG and CHG methylation was observed. Some important observations include the following: (i) abundance of CHH methylation among DMRs; (ii) predominance of DMRs in intergenic region, relative to other genomic regions (promoters, exons, introns, TSS and TTS); (iii) abundance of transposable elements (TEs) in DMRs with CHH context; (iv) demethylation mediated high expression of genes during susceptible reaction (S0 vs S96) and methylation mediated low expression of genes during resistant reaction (R0 vs R96 and S96 vs R96); (v) major genes under regulation encode proteins, which differ from those encoded by genes regulated during susceptible reaction and (vi) ~ 500 DMGs carried differential binding sites for H3K4/K27me3 marks suggesting joint involvement of DNA and H3 methylation. Thus, CHH methylation either alone or in combination with histone methylation plays a major role in regulating the expression of genes involved in wheat-leaf rust interaction.
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Kaur B, Sandhu KS, Kamal R, Kaur K, Singh J, Röder MS, Muqaddasi QH. Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PLANTS 2021; 10:plants10101989. [PMID: 34685799 PMCID: PMC8541486 DOI: 10.3390/plants10101989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.
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Affiliation(s)
- Balwinder Kaur
- Everglades Research and Education Center, University of Florida, 3200 E. Palm Beach Rd., Belle Glade, FL 33430, USA;
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Kawalpreet Kaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
- Correspondence: or
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Transcriptome-based analysis of resistance mechanism to black point caused by Bipolaris sorokiniana in wheat. Sci Rep 2021; 11:6911. [PMID: 33767270 PMCID: PMC7994838 DOI: 10.1038/s41598-021-86303-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/12/2021] [Indexed: 11/23/2022] Open
Abstract
Black point is a cereal disease caused by complex pathogens, of which the pathogenicity of Bipolaris sorokiniana is the most serious in wheat. Resistance to black point is quantitative in nature, and thus the mechanism is poorly understood. We conducted a comparative transcriptome analysis to identify differentially expressed genes (DEGs) in black point-slightly susceptible and -highly susceptible wheat lines at different timepoints following B. sorokiniana inoculation. DEGs associated with photosynthesis were upregulated in black point-slightly susceptible lines. The top Gene Ontology enrichment terms for biological processes were oxidation–reduction, response to cold, salt stress, oxidative stress, and cadmium ion; terms for cellular component genes were mainly involved in plasma membrane and cytoplasmic membrane-bounded vesicle, whereas those for molecular function were heme binding and peroxidase activity. Moreover, activities of antioxidant enzymes superoxide dismutase, catalase, and peroxidase were higher in slightly susceptible lines than those in highly susceptible lines (except peroxidase 12–24 days post-inoculation). Thus, resistance to B. sorokiniana-caused black point in wheat was mainly related to counteracting oxidative stress, although the specific metabolic pathways require further study. This study presents new insights for understanding resistance mechanisms of selected wheat lines to black point.
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Rollar S, Serfling A, Geyer M, Hartl L, Mohler V, Ordon F. QTL mapping of adult plant and seedling resistance to leaf rust (Puccinia triticina Eriks.) in a multiparent advanced generation intercross (MAGIC) wheat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:37-51. [PMID: 33201290 PMCID: PMC7813716 DOI: 10.1007/s00122-020-03657-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/28/2020] [Indexed: 05/22/2023]
Abstract
The Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines was phenotyped for Puccinia triticina resistance in multi-years' field trials at three locations and in a controlled environment seedling test. Simple intervall mapping revealed 19 QTL, corresponding to 11 distinct chromosomal regions. The biotrophic rust fungus Puccinia triticina is one of the most important wheat pathogens with the potential to cause yield losses up to 70%. Growing resistant cultivars is the most cost-effective and environmentally friendly way to encounter this problem. The emergence of leaf rust races being virulent against common resistance genes increases the demand for wheat varieties with novel resistances. In the past decade, the use of complex experimental populations, like multiparent advanced generation intercross (MAGIC) populations, has risen and offers great advantages for mapping resistances. The genetic diversity of multiple parents, which has been recombined over several generations, leads to a broad phenotypic diversity, suitable for high-resolution mapping of quantitative traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for leaf rust resistance in the Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs for adult plant resistance was carried out in field trials at three locations and two years, as well as in a controlled-environment seedling inoculation test. In total, interval mapping revealed 19 QTL, which corresponded to 11 distinct chromosomal regions controlling leaf rust resistance. Six of these regions may represent putative new QTL. Due to the elite parental material, RILs identified to be resistant to leaf rust can be easily introduced in breeding programs.
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Affiliation(s)
- Sandra Rollar
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
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Saripalli G, Singh K, Gautam T, Kumar S, Raghuvanshi S, Prasad P, Jain N, Sharma PK, Balyan HS, Gupta PK. Genome-wide analysis of H3K4me3 and H3K27me3 modifications due to Lr28 for leaf rust resistance in bread wheat (Triticum aestivum). PLANT MOLECULAR BIOLOGY 2020; 104:113-136. [PMID: 32627097 DOI: 10.1007/s11103-020-01029-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Present study revealed a complex relationship among histone H3 methylation (examined using H3K4/K27me3 marks), cytosine DNA methylation and differential gene expression during Lr28 mediated leaf rust resistance in wheat. During the present study, genome-wide histone modifications were examined in a pair of near isogenic lines (NILs) (with and without Lr28 in the background of cv. HD2329). The two histone marks used included H3K4me3 (an activation mark) and H3K27me3 (a repression mark). The results were compared with levels of expression (using RNA-seq) and DNA methylation (MeDIP) data obtained using the same pair of NILs. Some of the salient features of the present study include the following: (i) large scale differential binding sites (DBS) were available for only H3K4me3 in the susceptible cultivar, but for both H3K4me3 and H3K27me3 in its resistant NIL; (ii) DBSs for H3K27me3 mark were more abundant (> 80%) in intergenic regions, whereas DBSs for H3K4me3 were distributed in all genomic regions including exons, introns, intergenic, TTS (transcription termination sites) and promoters; (iii) fourteen (14) genes associated with DBSs showed co-localization for both the marks; (iv) only a small fraction (7% for H3K4me3 and 12% for H3K27me3) of genes associated with DBSs matched with the levels of gene expression inferred from RNA-seq data; (v) validation studies using qRT-PCR were conducted on 26 selected representative genes; results for only 11 genes could be validated. The proteins encoded by important genes involved in promoting infection included domains generally carried by R gene proteins such as Mlo like protein, protein kinases and purple acid phosphatase. Similarly, proteins encoded by genes involved in resistance included those carrying domains for lectin kinase, R gene, aspartyl protease, etc. Overall, the results suggest a very complex network of downstream genes that are expressed during compatible and incompatible interactions; some of the genes identified during the present study may be used in future validation studies involving RNAi/overexpression approaches.
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Affiliation(s)
- Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
| | - Kalpana Singh
- Bioinformatics Infrastructure Facility, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
| | - Santosh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Pramod Prasad
- Regional Station, Indian Institute of Wheat and Barley Research (IIWBR), Flowerdale, Shimla, HP, 171002, India
| | - Neelu Jain
- Division of Genetics and Plant Breeding, ICAR-IARI, Pusa, New Delhi, 110012, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
- Bioinformatics Infrastructure Facility, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India.
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Prasad P, Savadi S, Bhardwaj SC, Gupta PK. The progress of leaf rust research in wheat. Fungal Biol 2020; 124:537-550. [PMID: 32448445 DOI: 10.1016/j.funbio.2020.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/25/2023]
Abstract
Leaf rust (also called brown rust) in wheat, caused by fungal pathogen Puccinia triticina Erikss. (Pt) is one of the major constraints in wheat production worldwide. Pt is widespread with diverse population structure and undergoes rapid evolution to produce new virulent races against resistant cultivars that are regularly developed to provide resistance against the prevailing races of the pathogen. Occasionally, the disease may also take the shape of an epidemic in some wheat-growing areas causing major economic losses. In the recent past, substantial progress has been made in characterizing the sources of leaf rust resistance including non-host resistance (NHR). Progress has also been made in elucidating the population biology of Pt and the mechanisms of wheat-Pt interaction. So far, ∼80 leaf rust resistance genes (Lr genes) have been identified and characterized; some of them have also been used for the development of resistant wheat cultivars. It has also been shown that a gene-for-gene relationship exists between individual wheat Lr genes and the corresponding Pt Avr genes so that no Lr gene can provide resistance unless the prevailing race of the pathogen carries the corresponding Avr gene. Several Lr genes have also been cloned and their products characterized, although no Avr gene corresponding a specific Lr gene has so far been identified. However, several candidate effectors for Pt have been identified and functionally characterized using genome-wide analyses, transcriptomics, RNA sequencing, bimolecular fluorescence complementation (BiFC), virus-induced gene silencing (VIGS), transient expression and other approaches. This review summarizes available information on different aspects of the pathogen Pt, genetics/genomics of leaf rust resistance in wheat including cloning and characterization of Lr genes and epigenetic regulation of disease resistance.
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Affiliation(s)
- Pramod Prasad
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Siddanna Savadi
- ICAR-Directorate of Cashew Research, Puttur, Karnataka, 574202, India
| | - S C Bhardwaj
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India.
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12
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Jain N, Rani S, Sharma C, Sinha N, Singh A, Sharma JB, Prasad P, Saripalli G, Sharma PK, Balyan HS, Gupta PK, Prabhu KV. Large-scale stage-specific regulation of gene expression during host-pathogen interactions in CSP44 bread wheat carrying APR gene Lr48. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:203-225. [PMID: 32007128 DOI: 10.1071/fp18336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Genome-wide transcriptome analysis was undertaken in a leaf-rust resistant bread wheat line CSP44 (selected from Australian cv. Condor) carrying the adult plant resistance (APR) gene Lr48. Two pre-adult plant (P-AP) susceptible stages (S48 and S96) and two adult plant (AP) resistant stages (R48 and R96) were used for RNA-seq. At the susceptible P-AP stage (during S48 to S96), expression increased in 2062 genes, and declined in 130 genes; 1775 of 2062 differentially expressed genes (DEGs) also exhibited high expression during early incompatible stage R48. Comparison of S96 with R96 showed that the expression of 80 genes was enhanced and that of 208 genes declined at the AP stage. At the resistant AP stage (during R48 to R96), expression of mere 25 genes increased and that of 126 genes declined. Apparently, the resistance during late adult stage (R96) is caused by regulation of the expression of relatively fewer genes, although at pre-adult stage (S48 to S96), expression of large number of genes increased; expression of majority of these genes kept on increasing during adult stage at R48 also. These and other results of the present study suggest that APR may mimic some kind of systemic acquired resistance (SAR). The host-specific DEGs belonged to 10 different classes including genes involved in defence, transport, epigenetics, photosynthesis, genes encoding some transcription factors etc. The pathogen (Puccinia triticina) specific DEGs (including three genes encoding known biotrophic effectors) seem to help the pathogen in infection/growth through large-scale stage-specific enhanced expression of host's genes. A putative candidate gene for Lr48 containing protein kinase domain (its ortholog in rice encoding OsWAK8) was also identified.
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Affiliation(s)
- Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sushma Rani
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chanchal Sharma
- Chaudhary Charan Singh University, Meerut 250004, UP, India; and Department of Biotechnology, College of Engineering, Daegu University, Gyeongsan City, Gyeongbook 38453, South Korea
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Anupam Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jai Bhagwan Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Pramod Prasad
- Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla 171002, India
| | | | | | | | | | - Kumble Vinod Prabhu
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; and Protection of Plant Varieties and Farmers' Rights Authority, Govt. of India, Ministry of Agriculture & Farmers Welfare, New Delhi 110012 (India)
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13
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Complex relationship between DNA methylation and gene expression due to Lr28 in wheat-leaf rust pathosystem. Mol Biol Rep 2019; 47:1339-1360. [DOI: 10.1007/s11033-019-05236-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 11/08/2019] [Accepted: 12/07/2019] [Indexed: 11/26/2022]
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Gautam T, Saripalli G, Gahlaut V, Kumar A, Sharma PK, Balyan HS, Gupta PK. Further studies on sugar transporter (SWEET) genes in wheat (Triticum aestivum L.). Mol Biol Rep 2019; 46:2327-2353. [PMID: 30830588 DOI: 10.1007/s11033-019-04691-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/08/2019] [Indexed: 12/20/2022]
Abstract
SWEET proteins represent one of the largest sugar transporter family in the plant kingdom and play crucial roles in plant development and stress responses. In the present study, a total of 108 TaSWEET genes distributed on all the 21 wheat chromosomes were identified using the latest whole genome sequence (as against 59 genes reported in an earlier report). These 108 genes included 14 of the 17 types reported in Arabidopsis and also included three novel types. Tandem duplications (22) and segmental duplications (5) played a significant role in the expansion of TaSWEET family. A number of cis-elements were also identified in the promoter regions of TaSWEET genes, indicating response of TaSWEET genes during development and also during biotic/abiotic stresses. The TaSWEET proteins carried 4-7 trans-membrane helices (TMHs) showing diversity in structure. Phylogenetic analysis using SWEET proteins of wheat and 8 other species gave four well-known clusters. Expression analysis involving both in silico and in planta indicated relatively higher expression of TaSWEET genes in water/heat sensitive and leaf rust resistant genotypes. The results provided insights into the functional role of TaSWEETs in biotic and abiotic stresses, which may further help in planning strategies to develop high yielding wheat varieties tolerant to environmental stresses.
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Affiliation(s)
- Tinku Gautam
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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Sharma C, Kumar S, Saripalli G, Jain N, Raghuvanshi S, Sharma JB, Prabhu KV, Sharma PK, Balyan HS, Gupta PK. H3K4/K9 acetylation and Lr28-mediated expression of six leaf rust responsive genes in wheat (Triticum aestivum). Mol Genet Genomics 2018; 294:227-241. [PMID: 30298213 DOI: 10.1007/s00438-018-1500-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
Abstract
Development of leaf rust-resistant cultivars is a priority during wheat breeding, since leaf rust causes major losses in yield. Resistance against leaf rust due to Lr genes is partly controlled by epigenetic modifications including histone acetylation that is known to respond to biotic/abiotic stresses. In the present study, enrichment of H3K4ac and H3K9ac in promoters of six defense responsive genes (N-acetyltransferase, WRKY 40, WRKY 70, ASR1, Peroxidase 12 and Sarcosine oxidase) was compared with their expression in a pair of near-isogenic lines (NILs) for the gene Lr28 following inoculation with leaf rust pathotype '77-5'; ChIP-qPCR was used for this purpose. The proximal and distal promoters of these genes contained a number of motifs that are known to respond to biotic stresses. The enrichment of two acetylation marks changed with passage of time; changes in expression of two of the six genes (N-acetyltransferase and peroxidase12), largely matched with changes in H3K4/H3K9 acetylation patterns of the two promoter regions. For example, enrichment of both the marks matched with higher expression of N-acetyltransferase gene in susceptible NIL and the deacetylation (H3K4ac) largely matched with reduced gene expression in resistant NIL. In peroxidase12, enrichment of H3K4ac and H3K9ac largely matched with higher expression in both the NILs. In the remaining four genes, changes in H3 acetylation did not always match with gene expression levels. This indicated complexity in the regulation of the expression of these remaining four genes, which may be controlled by other epigenetic/genetic regulatory mechanisms that need further analysis.
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Affiliation(s)
- Chanchal Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.,Department of Biotechnology, College of Engineering, Daegu University, Gyeongsan, Gyeongbuk, 38453, South Korea
| | - Santosh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - J B Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - K V Prabhu
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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