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Amouzoune M, Rehman S, Benkirane R, Udupa S, Mamidi S, Kehel Z, Al-Jaboobi M, Amri A. Genome wide association study of seedling and adult plant leaf rust resistance in two subsets of barley genetic resources. Sci Rep 2024; 14:15428. [PMID: 38965257 PMCID: PMC11224298 DOI: 10.1038/s41598-024-53149-2] [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: 05/31/2023] [Accepted: 01/29/2024] [Indexed: 07/06/2024] Open
Abstract
Leaf rust (LR) caused by Puccinia hordei is a serious disease of barley worldwide, causing significant yield losses and reduced grain quality. Discovery and incorporation of new sources of resistance from gene bank accessions into barley breeding programs is essential for the development of leaf rust resistant varieties. To identify Quantitative Trait Loci (QTL) conferring LR resistance in the two barley subsets, the Generation Challenge Program (GCP) reference set of 142 accessions and the leaf rust subset constructed using the Focused Identification of Germplasm Strategy (FIGS) of 76 barley accessions, were genotyped to conduct a genome-wide association study (GWAS). The results revealed a total of 59 QTL in the 218 accessions phenotyped against barley leaf rust at the seedling stage using two P. hordei isolates (ISO-SAT and ISO-MRC), and at the adult plant stage in four environments in Morocco. Out of these 59 QTL, 10 QTL were associated with the seedling resistance (SR) and 49 QTL were associated with the adult plant resistance (APR). Four QTL showed stable effects in at least two environments for APR, whereas two common QTL associated with SR and APR were detected on chromosomes 2H and 7H. Furthermore, 39 QTL identified in this study were potentially novel. Interestingly, the sequences of 27 SNP markers encoded the candidate genes (CGs) with predicted protein functions in plant disease resistance. These results will provide new perspectives on the diversity of leaf rust resistance loci for fine mapping, isolation of resistance genes, and for marker-assisted selection for the LR resistance in barley breeding programs worldwide.
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Affiliation(s)
- Mariam Amouzoune
- Faculty of Sciences, University Ibn Tofail, 14000, Kenitra, Morocco.
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco.
| | - Sajid Rehman
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco
- Field Crop Development Center, The Olds College, Lacombe, AB, T4L 1W8, Canada
| | - Rachid Benkirane
- Faculty of Sciences, University Ibn Tofail, 14000, Kenitra, Morocco
| | - Sripada Udupa
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco
| | - Sujan Mamidi
- Hudson Alpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Zakaria Kehel
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco
| | - Muamer Al-Jaboobi
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco
| | - Ahmed Amri
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), 10100, Rabat, Morocco
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Basak P, Gurjar MS, Kumar TPJ, Kashyap N, Singh D, Jha SK, Saharan MS. Transcriptome analysis of Bipolaris sorokiniana - Hordeum vulgare provides insights into mechanisms of host-pathogen interaction. Front Microbiol 2024; 15:1360571. [PMID: 38577688 PMCID: PMC10993733 DOI: 10.3389/fmicb.2024.1360571] [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: 12/23/2023] [Accepted: 03/01/2024] [Indexed: 04/06/2024] Open
Abstract
Spot blotch disease incited by Bipolaris sorokiniana severely affects the cultivation of barley. The resistance to B. sorokiniana is quantitative in nature and its interaction with the host is highly complex which necessitates in-depth molecular analysis. Thus, the study aimed to conduct the transcriptome analysis to decipher the mechanisms and pathways involved in interactions between barley and B. sorokiniana in both the resistant (EC0328964) and susceptible (EC0578292) genotypes using the RNA Seq approach. In the resistant genotype, 6,283 genes of Hordeum vulgare were differentially expressed out of which 5,567 genes were upregulated and 716 genes were downregulated. 1,158 genes of Hordeum vulgare were differentially expressed in the susceptible genotype, out of which 654 genes were upregulated and 504 genes were downregulated. Several defense-related genes like resistant gene analogs (RGAs), disease resistance protein RPM1, pathogenesis-related protein PRB1-2-like, pathogenesis-related protein 1, thaumatin-like protein PWIR2 and defensin Tm-AMP-D1.2 were highly expressed exclusively in resistant genotype only. The pathways involved in the metabolism and biosynthesis of secondary metabolites were the most prominently represented pathways in both the resistant and susceptible genotypes. However, pathways involved in MAPK signaling, plant-pathogen interaction, and plant hormone signal transduction were highly enriched in resistant genotype. Further, a higher number of pathogenicity genes of B. sorokiniana was found in response to the susceptible genotype. The pathways encoding for metabolism, biosynthesis of secondary metabolites, ABC transporters, and ubiquitin-mediated proteolysis were highly expressed in susceptible genotype in response to the pathogen. 14 and 11 genes of B. sorokiniana were identified as candidate effectors from susceptible and resistant host backgrounds, respectively. This investigation will offer valuable insights in unraveling the complex mechanisms involved in barley- B. sorokiniana interaction.
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Affiliation(s)
- Poulami Basak
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Malkhan Singh Gurjar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Natasha Kashyap
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Dinesh Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra Kumar Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mahender Singh Saharan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Taliei F, Sabouri H, Kazerani B, Ghasemi S. Finding stable and closely linked QTLs against spot blotch in different planting dates during the adult stage in barley. Sci Rep 2024; 14:818. [PMID: 38191625 PMCID: PMC10774436 DOI: 10.1038/s41598-024-51358-3] [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: 07/14/2023] [Accepted: 01/03/2024] [Indexed: 01/10/2024] Open
Abstract
The common resistance to Spot Blotch (SB) and drought stress in barley was studied using a RILs population caused Kavir × Badia cross. These lines were inoculated with Cochliobolus sativus Gonbad isolate during the adult stage and were evaluated for three crop seasons in different planting dates. The different osmotic potentials during the flowering were regulated by changing the planting dates. In total, 43 lines had resistant to SB and drought. The high-density linkage map covered 1045 cM of barley genome. A total of five stable and closely linked QTLs to SB resistance were mapped on chromosomes 2H, 3H, 4H and 7H using genome-wide composite interval mapping. Moreover, four stable and closely linked QTLs to SB susceptibility were located on chromosomes 3H, 4H, 5H and 7H. Additionally, the ISJ19-A, SCoT7-C, ISJ17-B, Bmac0144k, iPBS2415-1, Bmac0282b and EBmatc0016 markers can be used for positive screening of resistant cultivars. However, ISJ3-C, UMB310, ISJ9-B, UMB706, D03-D and iPBS2257-A markers can be used for negative screening of susceptible cultivars in marker-assisted selection. The bioinformatics studies showed that QRCsa-2H (ISJ19-A region), QRCsa-2H (SCoT7-C-ISJ17-B region), QRCsa-3H (Bmac0144k region), QRCsa-4H (iPBS2415-1 region) and QRCsa-7H (Bmac0282b-EBmatc0016 region) are involved in the carboxypeptidase, Glycosyltransferase, transcription factors, kinase and AP2/ERF, respectively.
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Affiliation(s)
- Fakhtak Taliei
- Department of Plant Production, College of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous, Iran.
| | - Hossein Sabouri
- Department of Plant Production, College of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous, Iran
| | - Borzo Kazerani
- Department of Plant Breeding and Biotechnology, Faculty of Plant Production, Gorgan University of Agricultural Science and Natural Resources, Gorgan, Iran
| | - Shahram Ghasemi
- Department of Plant Production, College of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous, Iran
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Bouhlal O, Visioni A, Verma RPS, Kandil M, Gyawali S, Capettini F, Sanchez-Garcia M. CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world. FRONTIERS IN PLANT SCIENCE 2022; 13:1034322. [PMID: 36452106 PMCID: PMC9702823 DOI: 10.3389/fpls.2022.1034322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Breeding programs in developing countries still cannot afford the new genotyping technologies, hindering their research. We aimed to assemble an Association Mapping panel to serve as CGIAR Barley Breeding Toolbox (CBBT), especially for the Developing World. The germplasm had to be representative of the one grown in the Developing World; with high genetic variability and be of public domain. For it, we genotyped with the Infinium iSelect 50K chip, a Global Barley Panel (GBP) of 530 genotypes representing a wide range of row-types, end-uses, growth habits, geographical origins and environments. 40,342 markers were polymorphic with an average polymorphism information content of 0.35 and 66% of them exceeding 0.25. The analysis of the population structure identified 8 subpopulations mostly linked to geographical origin, four of them with significant ICARDA origin. The 16 allele combinations at 4 major flowering genes (HvVRN-H3, HvPPD-H1, HvVRN-H1 and HvCEN) explained 11.07% genetic variation and were linked to the geographic origins of the lines. ICARDA material showed the widest diversity as revealed by the highest number of polymorphic loci (99.76% of all polymorphic SNPs in GBP), number of private alleles and the fact that ICARDA lines were present in all 8 subpopulations and carried all 16 allelic combinations. Due to their genetic diversity and their representativity of the germplasm adapted to the Developing World, ICARDA-derived lines and cultivated landraces were pre-selected to form the CBBT. Using the Mean of Transformed Kinships method, we assembled a panel capturing most of the allelic diversity in the GBP. The CBBT (N=250) preserves good balance between row-types and good representation of both phenology allelic combinations and subpopulations of the GBP. The CBBT and its genotypic data is available to researchers worldwide as a collaborative tool to underpin the genetic mechanisms of traits of interest for barley cultivation.
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Affiliation(s)
- Outmane Bouhlal
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, El-Jadida, Morocco
| | - Andrea Visioni
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | | | - Mostafa Kandil
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, El-Jadida, Morocco
| | | | | | - Miguel Sanchez-Garcia
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
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Gangurde SS, Xavier A, Naik YD, Jha UC, Rangari SK, Kumar R, Reddy MSS, Channale S, Elango D, Mir RR, Zwart R, Laxuman C, Sudini HK, Pandey MK, Punnuri S, Mendu V, Reddy UK, Guo B, Gangarao NVPR, Sharma VK, Wang X, Zhao C, Thudi M. Two decades of association mapping: Insights on disease resistance in major crops. FRONTIERS IN PLANT SCIENCE 2022; 13:1064059. [PMID: 37082513 PMCID: PMC10112529 DOI: 10.3389/fpls.2022.1064059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/10/2022] [Indexed: 05/03/2023]
Abstract
Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.
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Affiliation(s)
- Sunil S. Gangurde
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Alencar Xavier
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | | | - Uday Chand Jha
- Indian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | | | - Raj Kumar
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - M. S. Sai Reddy
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Sonal Channale
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - Dinakaran Elango
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Reyazul Rouf Mir
- Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Sopore, India
| | - Rebecca Zwart
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - C. Laxuman
- Zonal Agricultural Research Station (ZARS), Kalaburagi, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Manish K. Pandey
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Somashekhar Punnuri
- College of Agriculture, Family Sciences and Technology, Dr. Fort Valley State University, Fort Valley, GA, United States
| | - Venugopal Mendu
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, United States
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, West Virginia, WV, United States
| | - Baozhu Guo
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
| | | | - Vinay K. Sharma
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
- *Correspondence: Mahendar Thudi, ; Chuanzhi Zhao,
| | - Mahendar Thudi
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
- *Correspondence: Mahendar Thudi, ; Chuanzhi Zhao,
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Sweeney DW, Rooney TE, Sorrells ME. Gain from genomic selection for a selection index in two-row spring barley. THE PLANT GENOME 2021; 14:e20138. [PMID: 34482639 DOI: 10.1002/tpg2.20138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
New breeding programs are faced with many challenges including evaluation of unknown germplasm, initiation of breeding populations that will satisfy short- and long-term breeding goals, and implementation of efficient phenotyping strategies for multiple traits. Genomic selection (GS) is a potentially valuable tool for recently established breeding programs to quickly accelerate genetic gain. Genomic selection on selection index (SI) values may increase gain over phenotypic selection but empirical studies remain limited. We compared gain in overall SI value for height, heading date, preharvest sprouting (PHS) resistance, and spot blotch resistance and component traits in two cycles of GS with one round of phenotypic selection (PS) in two-row spring malting barley (Hordeum vulgare L.). Higher realized gain for SI value, height, and PHS was observed with GS compared with PS but GS did not result in significant gain for heading date and spot blotch. Genetic variances for height and heading date, which had small index weights, were not reduced with GS but variances were substantially reduced for heavily weighted PHS and correlated seed germination traits. Inbreeding was increased by GS compared with PS but restricted mating of high breeding value individuals limited potential inbreeding. Our results indicate GS is a useful method to improve selection on index values with different weights.
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Affiliation(s)
- Daniel W Sweeney
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Travis E Rooney
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
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