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Goyal E, Singh AK, Mahajan MM, Kanika K. Comparative transcriptome profiling of contrasting finger millet (Eleusine coracana (L.) Gaertn) genotypes under heat stress. Mol Biol Rep 2024; 51:283. [PMID: 38324135 DOI: 10.1007/s11033-024-09233-x] [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: 08/15/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Eleusine coracana (L.) Gaertn is a crucial C4 species renowned for its stress robustness and nutritional significance. Because of its adaptability traits, finger millet (ragi) is a storehouse of critical genomic resources for crop improvement. However, more knowledge about this crop's molecular responses to heat stress needs to be gained. METHODS AND RESULTS In the present study, a comparative RNA sequencing analysis was done in the leaf tissue of the finger millet, between the heat-sensitive (KJNS-46) and heat-tolerant (PES-110) cultivars of Ragi, in response to high temperatures. On average, each sample generated about 24 million reads. Interestingly, a comparison of transcriptomic profiling identified 684 transcripts which were significantly differentially expressed genes (DEGs) examined between the heat-stressed samples of both genotypes. The heat-induced change in the transcriptome was confirmed by qRT-PCR using a set of randomly selected genes. Pathway analysis and functional annotation analysis revealed the activation of various genes involved in response to stress specifically heat, oxidation-reduction process, water deprivation, and changes in heat shock protein (HSP) and transcription factors, calcium signaling, and kinase signaling. The basal regulatory genes, such as bZIP, were involved in response to heat stress, indicating that heat stress activates genes involved in housekeeping or related to basal regulatory processes. A substantial percentage of the DEGs belonged to proteins of unknown functions (PUFs), i.e., not yet characterized. CONCLUSION These findings highlight the importance of candidate genes, such as HSPs and pathways that can confer tolerance towards heat stress in ragi. These results will provide valuable information to improve the heat tolerance in heat-susceptible agronomically important varieties of ragi and other crops.
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Affiliation(s)
- Etika Goyal
- Biotechnology and Climate Change Laboratory, National Institute for Plant Biotechnology, New Delhi, India
| | - Amit Kumar Singh
- Biotechnology and Climate Change Laboratory, National Institute for Plant Biotechnology, New Delhi, India
| | - Mahesh Mohanrao Mahajan
- Biotechnology and Climate Change Laboratory, National Institute for Plant Biotechnology, New Delhi, India
| | - Kumar Kanika
- Biotechnology and Climate Change Laboratory, National Institute for Plant Biotechnology, New Delhi, India.
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Chen J, Zhang L, Liu Y, Shen X, Guo Y, Ma X, Zhang X, Li X, Cheng T, Wen H, Qiao L, Chang Z. RNA-Seq-Based WGCNA and Association Analysis Reveal the Key Regulatory Module and Genes Responding to Salt Stress in Wheat Roots. PLANTS (BASEL, SWITZERLAND) 2024; 13:274. [PMID: 38256827 PMCID: PMC10818790 DOI: 10.3390/plants13020274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Soil salinization is the main abiotic stressor faced by crops. An improved understanding of the transcriptional response to salt stress in roots, the organ directly exposed to a high salinity environment, can inform breeding strategies to enhance tolerance and increase crop yield. Here, RNA-sequencing was performed on the roots of salt-tolerant wheat breeding line CH7034 at 0, 1, 6, 24, and 48 h after NaCl treatment. Based on transcriptome data, a weighted gene co-expression network analysis (WGCNA) was constructed, and five gene co-expression modules were obtained, of which the blue module was correlated with the time course of salt stress at 1 and 48 h. Two GO terms containing 249 differentially expressed genes (DEGs) related to osmotic stress response and salt-stress response were enriched in the blue module. These DEGs were subsequently used for association analysis with a set of wheat germplasm resources, and the results showed that four genes, namely a Walls Are Thin 1-related gene (TaWAT), an aquaporin gene (TaAQP), a glutathione S-transfer gene (TaGST), and a zinc finger gene (TaZFP), were associated with the root salt-tolerance phenotype. Using the four candidate genes as hub genes, a co-expression network was constructed with another 20 DEGs with edge weights greater than 0.6. The network showed that TaWAT and TaAQP were mainly co-expressed with fifteen interacting DEGs 1 h after salt treatment, while TaGST and TaZFP were mainly co-expressed with five interacting DEGs 48 h after salt treatment. This study provides key modules and candidate genes for understanding the salt-stress response mechanism in wheat roots.
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Affiliation(s)
- Jiating Chen
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Lei Zhang
- Department of Biology, Taiyuan Normal University, Taiyuan 030031, China;
| | - Yingxi Liu
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Xinyao Shen
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Yujing Guo
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Xiaofei Ma
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China
| | - Xiaojun Zhang
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Xin Li
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Tianling Cheng
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Huiqin Wen
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Linyi Qiao
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Zhijian Chang
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
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Yang R, Yang Z, Peng Z, He F, Shi L, Dong Y, Ren M, Zhang Q, Geng G, Zhang S. Integrated transcriptomic and proteomic analysis of Tritipyrum provides insights into the molecular basis of salt tolerance. PeerJ 2022; 9:e12683. [PMID: 35036157 PMCID: PMC8710252 DOI: 10.7717/peerj.12683] [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: 06/22/2021] [Accepted: 12/02/2021] [Indexed: 12/21/2022] Open
Abstract
Background Soil salinity is a major environmental stress that restricts crop growth and yield. Methods Here, crucial proteins and biological pathways were investigated under salt-stress and recovery conditions in Tritipyrum ‘Y1805’ using the data-independent acquisition proteomics techniques to explore its salt-tolerance mechanism. Results In total, 44 and 102 differentially expressed proteins (DEPs) were identified in ‘Y1805’ under salt-stress and recovery conditions, respectively. A proteome-transcriptome-associated analysis revealed that the expression patterns of 13 and 25 DEPs were the same under salt-stress and recovery conditions, respectively. ‘Response to stimulus’, ‘antioxidant activity’, ‘carbohydrate metabolism’, ‘amino acid metabolism’, ‘signal transduction’, ‘transport and catabolism’ and ‘biosynthesis of other secondary metabolites’ were present under both conditions in ‘Y1805’. In addition, ‘energy metabolism’ and ‘lipid metabolism’ were recovery-specific pathways, while ‘antioxidant activity’, and ‘molecular function regulator’ under salt-stress conditions, and ‘virion’ and ‘virion part’ during recovery, were ‘Y1805’-specific compared with the salt-sensitive wheat ‘Chinese Spring’. ‘Y1805’ contained eight specific DEPs related to salt-stress responses. The strong salt tolerance of ‘Y1805’ could be attributed to the strengthened cell walls, reactive oxygen species scavenging, osmoregulation, phytohormone regulation, transient growth arrest, enhanced respiration, transcriptional regulation and error information processing. These data will facilitate an understanding of the molecular mechanisms of salt tolerance and aid in the breeding of salt-tolerant wheat.
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Affiliation(s)
- Rui Yang
- Guizhou University, Guiyang, China
| | | | - Ze Peng
- Guizhou University, Guiyang, China
| | - Fang He
- Guizhou University, Guiyang, China
| | - Luxi Shi
- Guizhou University, Guiyang, China
| | | | - Mingjian Ren
- Guizhou University, Guiyang, China.,Guizhou Subcenter of National Wheat Improvement Center, Guiyang, China
| | | | | | - Suqin Zhang
- Guizhou University, Guiyang, China.,Guizhou Subcenter of National Wheat Improvement Center, Guiyang, China
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Zhang X, Han C, Liang Y, Yang Y, Liu Y, Cao Y. Combined full-length transcriptomic and metabolomic analysis reveals the regulatory mechanisms of adaptation to salt stress in asparagus. FRONTIERS IN PLANT SCIENCE 2022; 13:1050840. [PMID: 36388563 PMCID: PMC9648818 DOI: 10.3389/fpls.2022.1050840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/14/2022] [Indexed: 05/10/2023]
Abstract
Soil salinity is a very serious abiotic stressor that affects plant growth and threatens crop yield. Thus, it is important to explore the mechanisms of salt tolerance of plant and then to stabilize and improve crop yield. Asparagus is an important cash crop, but its salt tolerance mechanisms are largely unknown. Full-length transcriptomic and metabolomic analyses were performed on two asparagus genotypes: 'jx1502' (a salt-tolerant genotype) and 'gold crown' (a salt-sensitive genotype). Compared with the distilled water treatment (control), 877 and 1610 differentially expressed genes (DEGs) were identified in 'jx1502' and 'gold crown' under salt stress treatment, respectively, and 135 and 73 differentially accumulated metabolites (DAMs) were identified in 'jx1502' and 'gold crown' under salt stress treatment, respectively. DEGs related to ion transport, plant hormone response, and cell division and growth presented differential expression profiles between 'jx1502' and 'gold crown.' In 'jx1502,' 11 ion transport-related DEGs, 8 plant hormone response-related DEGs, and 12 cell division and growth-related DEGs were upregulated, while 7 ion transport-related DEGs, 4 plant hormone response-related DEGs, and 2 cell division and growth-related DEGs were downregulated. Interestingly, in 'gold crown,' 14 ion transport-related DEGs, 2 plant hormone response-related DEGs, and 6 cell division and growth-related DEGs were upregulated, while 45 ion transport-related DEGs, 13 plant hormone response-related DEGs, and 16 cell division and growth-related DEGs were downregulated. Genotype 'jx1502' can modulate K+/Na+ and water homeostasis and maintain a more constant transport system for nutrient uptake and distribution than 'gold crown' under salt stress. Genotype 'jx1502' strengthened the response to auxin (IAA), as well as cell division and growth for root remodeling and thus salt tolerance. Therefore, the integration analysis of transcriptomic and metabolomic indicated that 'jx1502' enhanced sugar and amino acid metabolism for energy supply and osmotic regulatory substance accumulation to meet the demands of protective mechanisms against salt stress. This work contributed to reveal the underlying salt tolerance mechanism of asparagus at transcription and metabolism level and proposed new directions for asparagus variety improvement.
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Affiliation(s)
- Xuhong Zhang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
- Landscape Management and Protection Center, Shijiazhuang Bureau of Landscape Architecture, Shijiazhuang, China
| | - Changzhi Han
- College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Yuqin Liang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yang Yang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yun Liu
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yanpo Cao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
- *Correspondence: Yanpo Cao,
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Sivalingam PN, Mahajan MM, Satheesh V, Chauhan S, Changal H, Gurjar K, Singh D, Bhan C, Sivalingam A, Marathe A, Ram C, Dokka N, More TA, Padaria JC, Bhat KV, Mohapatra T. Distinct morpho-physiological and biochemical features of arid and hyper-arid ecotypes of Ziziphus nummularia under drought suggest its higher tolerance compared with semi-arid ecotype. TREE PHYSIOLOGY 2021; 41:2063-2081. [PMID: 33929534 DOI: 10.1093/treephys/tpab058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Tree species in the arid and semi-arid regions use various strategies to combat drought stress. Ziziphus nummularia (Burm. f.) Wight et Arn., native to the Thar Desert in India, is highly drought-tolerant. To identify the most drought-tolerant ecotype of Z. nummularia, one ecotype each from semi-arid (Godhra, annual rainfall >750 mm), arid (Bikaner, 250-350 mm) and hyper-arid (Jaisalmer, <150 mm) regions was selected along with two other Ziziphus species, Ziziphus mauritiana Lamk. and Ziziphus rotundifolia Lamk., and screened for parameters contributing to drought tolerance. Among these, Z. nummularia (Jaisalmer) (CIAHZN-J) was the most drought - tolerant. The tolerance nature of CIAHZN-J was associated with increased membrane stability, root length and number, length of hairs and thorns, root dry/fresh weight ratio, seed germination (at -0.5 MPa), proline content (31-fold), catalase and sugar content (two- to three-fold). Apart from these characteristics, it also exhibited the longest duration to reach highest cumulative drought stress rating, maintained higher relative water content for a longer period of time with reduced leaf size, leaf rolling and falling of older leaves, and displayed sustained shoot growth during drought stress. To determine drought tolerance in Ziziphus, we developed a morphological symptom-based screening technique in this study. Additionally, transcriptome profiling of CIAHZN-J in response to drought revealed the up-regulation of genes involved in sugar metabolism and transport, abscisic acid biosynthesis, osmoregulation, reactive oxygen species homeostasis and maintaining water potential. Expression profiles and semi-quantitative reverse transcription PCR results further correlated with the physiological and biochemical mechanisms. In conclusion, CIAHZN-J is an excellent genetic stock for the identification of drought-responsive genes and can also be deployed in crop improvement programs for drought tolerance.
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Affiliation(s)
- P N Sivalingam
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, Chhattisgarh 493225, India
| | - Mahesh M Mahajan
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, Chhattisgarh 493225, India
| | - Viswanathan Satheesh
- ICAR-National Institute for Plant Biotechnology (Previously: National Research Centre on Plant Biotechnology), IARI Campus, PUSA, New Delhi, 110012, India
| | - Sarita Chauhan
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Harish Changal
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Karun Gurjar
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Dhurendra Singh
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Chander Bhan
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Anandhan Sivalingam
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, Maharashtra 410 505, India
| | - Ashish Marathe
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, Chhattisgarh 493225, India
| | - Chet Ram
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - Narasimham Dokka
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, Chhattisgarh 493225, India
| | - T A More
- ICAR-Central Institute for Arid Horticulture, NH-15 Sri Ganganagar Road, Beechwal, Bikaner, Rajasthan 334 006, India
| | - J C Padaria
- ICAR-National Institute for Plant Biotechnology (Previously: National Research Centre on Plant Biotechnology), IARI Campus, PUSA, New Delhi, 110012, India
| | - K V Bhat
- ICAR-National Bureau of Plant Genetic Resources, IARI Campus, PUSA, New Delhi 110012, India
| | - T Mohapatra
- ICAR-National Institute for Plant Biotechnology (Previously: National Research Centre on Plant Biotechnology), IARI Campus, PUSA, New Delhi, 110012, India
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Amirbakhtiar N, Ismaili A, Ghaffari MR, Mirdar Mansuri R, Sanjari S, Shobbar ZS. Transcriptome analysis of bread wheat leaves in response to salt stress. PLoS One 2021; 16:e0254189. [PMID: 34242309 PMCID: PMC8270127 DOI: 10.1371/journal.pone.0254189] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/21/2021] [Indexed: 11/18/2022] Open
Abstract
Salinity is one of the main abiotic stresses limiting crop productivity. In the current study, the transcriptome of wheat leaves in an Iranian salt-tolerant cultivar (Arg) was investigated in response to salinity stress to identify salinity stress-responsive genes and mechanisms. More than 114 million reads were generated from leaf tissues by the Illumina HiSeq 2500 platform. An amount of 81.9% to 85.7% of reads could be mapped to the wheat reference genome for different samples. The data analysis led to the identification of 98819 genes, including 26700 novel transcripts. A total of 4290 differentially expressed genes (DEGs) were recognized, comprising 2346 up-regulated genes and 1944 down-regulated genes. Clustering of the DEGs utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that transcripts associated with phenylpropanoid biosynthesis, transporters, transcription factors, hormone signal transduction, glycosyltransferases, exosome, and MAPK signaling might be involved in salt tolerance. The expression patterns of nine DEGs were investigated by quantitative real-time PCR in Arg and Moghan3 as the salt-tolerant and susceptible cultivars, respectively. The obtained results were consistent with changes in transcript abundance found by RNA-sequencing in the tolerant cultivar. The results presented here could be utilized for salt tolerance enhancement in wheat through genetic engineering or molecular breeding.
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Affiliation(s)
- Nazanin Amirbakhtiar
- Plant Production and Genetic Engineering Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
- National Plant Gene Bank of Iran, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ahmad Ismaili
- Plant Production and Genetic Engineering Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Mohammad-Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Raheleh Mirdar Mansuri
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Sepideh Sanjari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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Kumar D, Kumar A, Chhokar V, Gangwar OP, Bhardwaj SC, Sivasamy M, Prasad SVS, Prakasha TL, Khan H, Singh R, Sharma P, Sheoran S, Iquebal MA, Jaiswal S, Angadi UB, Singh G, Rai A, Singh GP, Kumar D, Tiwari R. Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:748. [PMID: 32582265 PMCID: PMC7286347 DOI: 10.3389/fpls.2020.00748] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/12/2020] [Indexed: 05/20/2023]
Abstract
Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.
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Affiliation(s)
- Deepender Kumar
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Animesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Vinod Chhokar
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | | | - M. Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, India
| | - S. V. Sai Prasad
- ICAR-Indian Agricultural Research Institute, Regional Station, Indore, India
| | - T. L. Prakasha
- ICAR-Indian Agricultural Research Institute, Regional Station, Indore, India
| | - Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Mir Asif Iquebal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ulavappa B. Angadi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dinesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
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