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Vasquez-Teuber P, Rouxel T, Mason AS, Soyer JL. Breeding and management of major resistance genes to stem canker/blackleg in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:192. [PMID: 39052130 PMCID: PMC11272824 DOI: 10.1007/s00122-024-04641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/29/2024] [Indexed: 07/27/2024]
Abstract
Blackleg (also known as Phoma or stem canker) is a major, worldwide disease of Brassica crop species, notably B. napus (rapeseed, canola), caused by the ascomycete fungus Leptosphaeria maculans. The outbreak and severity of this disease depend on environmental conditions and management practices, as well as a complex interaction between the pathogen and its hosts. Genetic resistance is a major method to control the disease (and the only control method in some parts of the world, such as continental Europe), but efficient use of genetic resistance is faced with many difficulties: (i) the scarcity of germplasm/genetic resources available, (ii) the different history of use of resistance genes in different parts of the world and the different populations of the fungus the resistance genes are exposed to, (iii) the complexity of the interactions between the plant and the pathogen that expand beyond typical gene-for-gene interactions, (iv) the incredible evolutionary potential of the pathogen and the importance of knowing the molecular processes set up by the fungus to "breakdown' resistances, so that we may design high-throughput diagnostic tools for population surveys, and (v) the different strategies and options to build up the best resistances and to manage them so that they are durable. In this paper, we aim to provide a comprehensive overview of these different points, stressing the differences between the different continents and the current prospects to generate new and durable resistances to blackleg disease.
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Affiliation(s)
- Paula Vasquez-Teuber
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
- Department of Plant Production, Faculty of Agronomy, University of Concepción, Av. Vicente Méndez 595, Chillán, Chile
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France.
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Fondevilla S, Calderón-González Á, Rojas-Panadero B, Cruz V, Matías J. Genome-wide association study, combined with bulk segregant analysis, identify plant receptors and defense related genes as candidate genes for downy mildew resistance in quinoa. BMC PLANT BIOLOGY 2024; 24:594. [PMID: 38910245 PMCID: PMC11194881 DOI: 10.1186/s12870-024-05302-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
BACKGROUND Downy mildew is the most relevant disease of quinoa and the most widespread. Though, little is known about the genetics of resistance to this disease. The objective of this study was to identify the genomic regions controlling downy mildew resistance in quinoa and candidate genes for this trait. With this aim we carried out a GWAS analysis in a collection formed by 211 quinoa accessions from different origins. This approach was combined with inheritance studies and Bulk Segregant Analysis (BSA) in a segregating population. RESULTS GWAS analysis identified 26 genomic regions associated with the trait. Inheritance studies in a F2 population segregating for resistance revealed the existence of a major single dominant gene controlling downy mildew complete resistance in quinoa accession PI614911. Through BSA, this gene was found to be located in chromosome 4, in a region also identified by GWAS. Furthermore, several plant receptors and resistance genes were found to be located into the genomic regions identified by GWAS and are postulated as candidate genes for resistance. CONCLUSIONS Until now, little was known about the genetic control of downy mildew resistance in quinoa. A previous inheritance study suggested that resistance to this disease was a quantitative polygenic trait and previous GWAS analyses were unable to identify accurate markers for this disease. In our study we demonstrate the existence of, at least, one major gene conferring resistance to this disease, identify the genomic regions involved in the trait and provide plausible candidate genes involved in defense. Therefore, this study significantly increases our knowledge about the genetics of downy mildew resistance and provides relevant information for breeding for this important trait.
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Affiliation(s)
- Sara Fondevilla
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Avd. Menéndez Pidal s/n, Córdoba, 14004, Spain.
| | - Álvaro Calderón-González
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Avd. Menéndez Pidal s/n, Córdoba, 14004, Spain
| | - Borja Rojas-Panadero
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Avd. Menéndez Pidal s/n, Córdoba, 14004, Spain
| | - Verónica Cruz
- Agrarian Research Institute "La Orden-Valdesequera" of Extremadura, Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), Autovía A-5, km 372 - 06187, Guadajira, Badajoz, 06187, Spain
| | - Javier Matías
- Agrarian Research Institute "La Orden-Valdesequera" of Extremadura, Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), Autovía A-5, km 372 - 06187, Guadajira, Badajoz, 06187, Spain
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Goettelmann F, Chen Y, Knorst V, Yates S, Copetti D, Studer B, Kölliker R. High-resolution bulked segregant analysis enables candidate gene identification for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1516-1527. [PMID: 38412295 DOI: 10.1111/tpj.16693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 02/29/2024]
Abstract
Bacterial wilt, caused by Xanthomonas translucens pv. graminis (Xtg), is a serious disease of economically important forage grasses, including Italian ryegrass (Lolium multiflorum Lam.). A major QTL for resistance to Xtg was previously identified, but the precise location as well as the genetic factors underlying the resistance are yet to be determined. To this end, we applied a bulked segregant analysis (BSA) approach, using whole-genome deep sequencing of pools of the most resistant and most susceptible individuals of a large (n = 7484) biparental F2 population segregating for resistance to Xtg. Using chromosome-level genome assemblies as references, we were able to define a ~300 kb region highly associated with resistance on pseudo-chromosome 4. Further investigation of this region revealed multiple genes with a known role in disease resistance, including genes encoding for Pik2-like disease resistance proteins, cysteine-rich kinases, and RGA4- and RGA5-like disease resistance proteins. Investigation of allele frequencies in the pools and comparative genome analysis in the grandparents of the F2 population revealed that some of these genes contain variants with allele frequencies that correspond to the expected heterozygosity in the resistant grandparent. This study emphasizes the efficacy of combining BSA studies in very large populations with whole genome deep sequencing and high-quality genome assemblies to pinpoint regions associated with a binary trait of interest and accurately define a small set of candidate genes. Furthermore, markers identified in this region hold significant potential for marker-assisted breeding strategies to breed resistance to Xtg in Italian ryegrass cultivars more efficiently.
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Affiliation(s)
- Florian Goettelmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Yutang Chen
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Verena Knorst
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Dario Copetti
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Arizona Genomics Institute, The University of Arizona, Tucson, AZ, USA
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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Mo C, Wang H, Wei M, Zeng Q, Zhang X, Fei Z, Zhang Y, Kong Q. Complete genome assembly provides a high-quality skeleton for pan-NLRome construction in melon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2249-2268. [PMID: 38430487 DOI: 10.1111/tpj.16705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Melon (Cucumis melo L.), being under intensive domestication and selective breeding, displays an abundant phenotypic diversity. Wild germplasm with tolerance to stress represents an untapped genetic resource for discovery of disease-resistance genes. To comprehensively characterize resistance genes in melon, we generate a telomere-to-telomere (T2T) and gap-free genome of wild melon accession PI511890 (C. melo var. chito) with a total length of 375.0 Mb and a contig N50 of 31.24 Mb. The complete genome allows us to dissect genome architecture and identify resistance gene analogs. We construct a pan-NLRome using seven melon genomes, which include 208 variable and 18 core nucleotide-binding leucine-rich repeat receptors (NLRs). Multiple disease-related transcriptome analyses indicate that most up-regulated NLRs induced by pathogens are shell or cloud NLRs. The T2T gap-free assembly and the pan-NLRome not only serve as essential resources for genomic studies and molecular breeding of melon but also provide insights into the genome architecture and NLR diversity.
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Affiliation(s)
- Changjuan Mo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyan Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minghua Wei
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingguo Zeng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuejun Zhang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | | | - Yongbing Zhang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Qiusheng Kong
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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Singh K, Huff M, Liu J, Park JW, Rickman T, Keremane M, Krueger RR, Kunta M, Roose ML, Dardick C, Staton M, Ramadugu C. Chromosome-Scale, De Novo, Phased Genome Assemblies of Three Australian Limes: Citrus australasica, C. inodora, and C. glauca. PLANTS (BASEL, SWITZERLAND) 2024; 13:1460. [PMID: 38891269 PMCID: PMC11174732 DOI: 10.3390/plants13111460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024]
Abstract
Huanglongbing (HLB) is a severe citrus disease worldwide. Wild Australian limes like Citrus australasica, C. inodora, and C. glauca possess beneficial HLB resistance traits. Individual trees of the three taxa were extensively used in a breeding program for over a decade to introgress resistance traits into commercial-quality citrus germplasm. We generated high-quality, phased, de novo genome assemblies of the three Australian limes using PacBio long-read sequencing. The genome assembly sizes of the primary and alternate haplotypes were determined for C. australasica (337 Mb/335 Mb), C. inodora (304 Mb/299 Mb), and C. glauca (376 Mb/379 Mb). The nine chromosome-scale scaffolds included 86-91% of the genome sequences generated. The integrity and completeness of the assembled genomes were estimated to be at 97.2-98.8%. Gene annotation studies identified 25,461 genes in C. australasica, 27,665 in C. inodora, and 30,067 in C. glauca. Genes belonging to 118 orthogroups were specific to Australian lime genomes compared to other citrus genomes analyzed. Significantly fewer canonical resistance (R) genes were found in C. inodora and C. glauca (319 and 449, respectively) compared to C. australasica (576), C. clementina (579), and C. sinensis (651). Similar patterns were observed for other gene families associated with potential HLB resistance, including Phloem protein 2 (PP2) and Callose synthase (CalS) genes predicted in the Australian lime genomes. The genomic information on Australian limes developed in the present study will help understand the genetic basis of HLB resistance.
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Affiliation(s)
- Khushwant Singh
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (K.S.); (M.L.R.)
| | - Matthew Huff
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (M.H.); (T.R.); (M.S.)
| | - Jianyang Liu
- Innovative Fruit Production, Improvement, and Protection, Appalachian Fruit Research Station, USDA-ARS, Kearneysville, WV 25430, USA; (J.L.); (C.D.)
| | - Jong-Won Park
- Citrus Center, Texas A&M University-Kingsville, Weslaco, TX 78599, USA; (J.-W.P.); (M.K.)
| | - Tara Rickman
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (M.H.); (T.R.); (M.S.)
| | - Manjunath Keremane
- National Clonal Germplasm Repository for Citrus and Dates, USDA-ARS, Riverside, CA 92507, USA; (M.K.); (R.R.K.)
| | - Robert R. Krueger
- National Clonal Germplasm Repository for Citrus and Dates, USDA-ARS, Riverside, CA 92507, USA; (M.K.); (R.R.K.)
| | - Madhurababu Kunta
- Citrus Center, Texas A&M University-Kingsville, Weslaco, TX 78599, USA; (J.-W.P.); (M.K.)
| | - Mikeal L. Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (K.S.); (M.L.R.)
| | - Chris Dardick
- Innovative Fruit Production, Improvement, and Protection, Appalachian Fruit Research Station, USDA-ARS, Kearneysville, WV 25430, USA; (J.L.); (C.D.)
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (M.H.); (T.R.); (M.S.)
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (K.S.); (M.L.R.)
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Hohenfeld CS, de Oliveira SAS, Ferreira CF, Mello VH, Margarido GRA, Passos AR, de Oliveira EJ. Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance. Sci Rep 2024; 14:10587. [PMID: 38719851 PMCID: PMC11078935 DOI: 10.1038/s41598-024-60847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Cassava root-rot incited by soil-borne pathogens is one of the major diseases that reduces root yield. Although the use of resistant cultivars is the most effective method of management, the genetic basis for root-rot resistance remains poorly understood. Therefore, our work analyzed the transcriptome of two contrasting genotypes (BRS Kiriris/resistant and BGM-1345/susceptible) using RNA-Seq to understand the molecular response and identify candidate genes for resistance. Cassava seedlings (resistant and susceptible to root-rot) were both planted in infested and sterilized soil and samples from Initial-time and Final-time periods, pooled. Two controls were used: (i) seedlings collected before planting in infested soil (absolute control) and, (ii) plants grown in sterilized soil (mock treatments). For the differentially expressed genes (DEGs) analysis 23.912 were expressed in the resistant genotype, where 10.307 were differentially expressed in the control treatment, 15 DEGs in the Initial Time-period and 366 DEGs in the Final Time-period. Eighteen candidate genes from the resistant genotype were related to plant defense, such as the MLP-like protein 31 and the peroxidase A2-like gene. This is the first model of resistance at the transcriptional level proposed for the cassava × root-rot pathosystem. Gene validation will contribute to screening for resistance of germplasm, segregating populations and/or use in gene editing in the pursuit to develop most promising cassava clones with resistance to root-rot.
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Affiliation(s)
- Camila Santiago Hohenfeld
- Universidade Estadual de Feira de Santana, Av. Transnordestina, S/N - 44036-900, Novo Horizonte, Feira de Santana, BA, Brazil
| | | | - Claudia Fortes Ferreira
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, Cruz das Almas, BA, 44380-000, Brazil
| | - Victor Hugo Mello
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Adriana Rodrigues Passos
- Universidade Estadual de Feira de Santana, Av. Transnordestina, S/N - 44036-900, Novo Horizonte, Feira de Santana, BA, Brazil
| | - Eder Jorge de Oliveira
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, Cruz das Almas, BA, 44380-000, Brazil.
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Alam P, Albalawi T. Insights into cucumber ( Cucumis sativus) genetics: Genome-wide discovery and computational analysis of the Calreticulin Domain-Encoding gene (CDEG) family. Saudi J Biol Sci 2024; 31:103959. [PMID: 38404540 PMCID: PMC10883824 DOI: 10.1016/j.sjbs.2024.103959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
Cucumber is an essential vegetable crop throughout the world. Cucumber development is vital for accomplishing both quality and productivity requirements. Meanwhile, numerous factors have resulted in substantial cucumber losses. However, the calreticulin domain-encoding genes (CDEGs) in cucumber were not well-characterized and had little function. In the genome-wide association study (GWAS), we recognized and characterized the CDEGs in Cucumis sativus (cucumber). Through a comprehensive study of C. sativus, our research has unveiled the presence of three unique genes, denoted as CsCRTb, CsCRT3, and CsCNX1, unevenly distributed on three chromosomes in the genome of C. sativus. In accordance to the phylogenetic investigation, these genes may be categorized into three subfamilies. Based on the resemblance with AtCDE genes, we reorganized the all CsCDE genes in accordance with international nomenclature. The expression analysis and cis-acting components revealed that each of CsCDE gene promoter region enclosed number of cis-elements connected with hormone and stress response. According to subcellular localization studies demonstrated that, they were found in deferent locations of the cell such as endoplasmic reticulum, plasma membrane, golgi apparatus, and vacuole, according to subcellular localization studies. Chromosomal distribution analysis and synteny analysis demonstrated the probability of segmental or tandem duplications within the cucumber CDEG gene family. Additionally, miRNAs displayed diverse modes of action, including mRNA cleavage and translational inhibition. We used the RNA seq data to analyze the expression of CDEG genes in response to cold stress and also improved cold tolerance, which was brought on by treating cucumber plants to an exogenous chitosan oligosaccharide spray. Our investigation revealed that these genes responded to this stress in a variety of ways, demonstrating that they may adapt quickly to environmental changes in cucumber plants. This study provides a base for further understanding in reference to CDE gene family and reveals that genes play significant functions in cucumber stress responses.
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Affiliation(s)
- Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Thamer Albalawi
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia
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Gupta S, Petrov V, Garg V, Mueller-Roeber B, Fernie AR, Nikoloski Z, Gechev T. The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments. Cell Mol Life Sci 2024; 81:117. [PMID: 38443747 PMCID: PMC10914886 DOI: 10.1007/s00018-024-05140-3] [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: 08/12/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 03/07/2024]
Abstract
Haberlea rhodopensis, a resurrection species, is the only plant known to be able to survive multiple extreme environments, including desiccation, freezing temperatures, and long-term darkness. However, the molecular mechanisms underlying tolerance to these stresses are poorly studied. Here, we present a high-quality genome of Haberlea and found that ~ 23.55% of the 44,306 genes are orphan. Comparative genomics analysis identified 89 significantly expanded gene families, of which 25 were specific to Haberlea. Moreover, we demonstrated that Haberlea preserves its resurrection potential even in prolonged complete darkness. Transcriptome profiling of plants subjected to desiccation, darkness, and low temperatures revealed both common and specific footprints of these stresses, and their combinations. For example, PROTEIN PHOSPHATASE 2C (PP2C) genes were substantially induced in all stress combinations, while PHYTOCHROME INTERACTING FACTOR 1 (PIF1) and GROWTH RESPONSE FACTOR 4 (GRF4) were induced only in darkness. Additionally, 733 genes with unknown functions and three genes encoding transcription factors specific to Haberlea were specifically induced/repressed upon combination of stresses, rendering them attractive targets for future functional studies. The study provides a comprehensive understanding of the genomic architecture and reports details of the mechanisms of multi-stress tolerance of this resurrection species that will aid in developing strategies that allow crops to survive extreme and multiple abiotic stresses.
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Affiliation(s)
- Saurabh Gupta
- Intercellular Macromolecular Transport, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Curtin Medical School, Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, WA, 6102, Australia.
| | - Veselin Petrov
- Center of Plant Systems Biology and Biotechnology, 14 Knyaz Boris I Pokrastitel Str., 4023, Plovdiv, Bulgaria
- Department of Plant Physiology, Biochemistry and Genetics, Agricultural University Plovdiv, 12 Mendeleev Str., 4000, Plovdiv, Bulgaria
| | - Vanika Garg
- Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Bernd Mueller-Roeber
- Center of Plant Systems Biology and Biotechnology, 14 Knyaz Boris I Pokrastitel Str., 4023, Plovdiv, Bulgaria
- Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
- Plant Signalling, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, 14 Knyaz Boris I Pokrastitel Str., 4023, Plovdiv, Bulgaria
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Center of Plant Systems Biology and Biotechnology, 14 Knyaz Boris I Pokrastitel Str., 4023, Plovdiv, Bulgaria
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Tsanko Gechev
- Center of Plant Systems Biology and Biotechnology, 14 Knyaz Boris I Pokrastitel Str., 4023, Plovdiv, Bulgaria.
- Department of Plant Physiology and Molecular Biology, Plovdiv University, 24 Tsar Assen Str., 4000, Plovdiv, Bulgaria.
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Septiani P, Pramesti Y, Ningsih DU, Pancaningtyas S, Meitha K. Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease. Sci Rep 2024; 14:3272. [PMID: 38332251 PMCID: PMC10853554 DOI: 10.1038/s41598-024-53685-x] [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: 07/24/2023] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Cacao (Theobroma cacao) is a highly valuable crop with growing demand in the global market. However, cacao farmers often face challenges posed by black pod disease caused by Phytophthora spp., with P. palmivora being the most dominant. Regulations of various gene expressions influence plant resistance to pathogens. One mechanism involves targeting the mRNA of virulence genes in the invading pathogens, suppressing their infection. However, resistance also could be suppressed by plant-derived miRNAs that target their own defence genes. The objective of this study is to identify differentially expressed miRNAs in black pod-resistant and susceptible cacao varieties and to predict their targets in T. cacao and P. palmivora transcripts. Extracted miRNA from resistant and susceptible varieties of T. Cacao was sequenced, identified, and matched to host and pathogen mRNA. In total, 54 known miRNAs from 40 miRNA families and 67 novel miRNAs were identified. Seventeen miRNAs were differentially expressed in susceptible variety compared to resistant one, with 9 miRNAs upregulated and 8 miRNAs downregulated. In T. cacao transcripts, the upregulated miRNAs were predicted to target several genes, including defence genes. The suppression of these defense genes can lead to a reduction in plant resistance against pathogen infection. In P. palmivora transcripts, the upregulated miRNAs were predicted to target several genes, including P. palmivora effector genes. In the future, limiting expression of miRNAs that target T. cacao's defence genes and applying miRNAs that target P. palmivora effector genes hold promise for enhancing cacao plant resistance against P. palmivora infection.
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Affiliation(s)
- Popi Septiani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Yonadita Pramesti
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Devi Ulfa Ningsih
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Sulistyani Pancaningtyas
- Indonesian Coffee and Cocoa Research Institute (ICCRI), Jl. PB. Sudirman 90, Jember, 68118, Indonesia
| | - Karlia Meitha
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia.
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10
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Fu R, Zhao L, Chen C, Wang J, Lu D. Conjunctive Analysis of BSA-Seq and SSR Markers Unveil the Candidate Genes for Resistance to Rice False Smut. Biomolecules 2024; 14:79. [PMID: 38254679 PMCID: PMC10813778 DOI: 10.3390/biom14010079] [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: 11/12/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Rice false smut (RFS) caused by the fungus Ustilaginoidea virens (Cook) leads to serious yield losses in rice. Identification of the gene or quantitative trait loci (QTLs) is crucial to resistance breeding and mitigation of RFS damage. In this study, we crossed a resistant variety, IR77298-14-1-2::IRGC117374-1, with a susceptible indica cultivar, 9311, and evaluated recombinant inbred lines in a greenhouse. The genetic analysis showed that the RFS resistance of IR77298-14-1-2::IRGC117374-1 was controlled by multiple recessive loci. We identified a novel QTL, qRFS12.01, for RFS resistance in IR77298-14-1-2::IRGC117374-1 by combining bulked segregant analysis with whole genome resequencing (BSA-seq) and simple sequence repeat (SSR) marker mapping approaches. The phenotypic effect of qRFS12.01 on RFS resistance reached 28.74%, suggesting that SSR markers linked to qRFS12.01 are valuable for marker-assisted breeding of RFS resistance in rice. The prediction of putative candidate genes within qRFS12.01 revealed five disease resistance proteins containing NB-ARC domains. In conclusion, our findings provide a new rice chromosome region carrying genes/QTLs for resistance to RFS.
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Affiliation(s)
- Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Liyu Zhao
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
| | - Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
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11
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He L, Sui Y, Che Y, Wang H, Rashid KY, Cloutier S, You FM. Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax. FRONTIERS IN PLANT SCIENCE 2023; 14:1229457. [PMID: 37954993 PMCID: PMC10634603 DOI: 10.3389/fpls.2023.1229457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 11/14/2023]
Abstract
Introduction Flax (Linum usitatissimum L.) is an economically important crop due to its oil and fiber. However, it is prone to various diseases, including pasmo caused by the fungus Septoria linicola. Methods In this study, we conducted field evaluations of 445 flax accessions over a five-year period (2012-2016) to assess their resistance to pasmo A total of 246,035 single nucleotide polymorphisms (SNPs) were used for genetic analysis. Four statistical models, including the single-locus model GEMMA and the multi-locus models FarmCPU, mrMLM, and 3VmrMLM, were assessed to identify quantitative trait nucleotides (QTNs) associated with pasmo resistance. Results We identified 372 significant QTNs or 132 tag QTNs associated with pasmo resistance from five pasmo resistance datasets (PAS2012-PAS2016 and the 5-year average, namely PASmean) and three genotypic datasets (the all SNPs/ALL, the gene-based SNPs/GB and the RGA-based SNPs/RGAB). The tag QTNs had R2 values of 0.66-16.98% from the ALL SNP dataset, 0.68-20.54%from the GB SNP dataset, and 0.52-22.42% from the RGAB SNP dataset. Of these tag QTNs, 93 were novel. Additionally, 37 resistance gene analogs (RGAs)co-localizing with 39 tag QTNs were considered as potential candidates for controlling pasmo resistance in flax and 50 QTN-by-environment interactions(QEIs) were identified to account for genes by environmental interactions. Nine RGAs were predicted as candidate genes for ten QEIs. Discussion Our results suggest that pasmo resistance in flax is polygenic and potentially influenced by environmental factors. The identified QTNs provide potential targets for improving pasmo resistance in flax breeding programs. This study sheds light on the genetic basis of pasmo resistance and highlights the importance of considering both genetic and environmental factors in breeding programs for flax.
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Affiliation(s)
- Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Yao Sui
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Yanru Che
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Huixian Wang
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Khalid Y. Rashid
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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12
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Escolà G, González-Miguel VM, Campo S, Catala-Forner M, Domingo C, Marqués L, San Segundo B. Development and Genome-Wide Analysis of a Blast-Resistant japonica Rice Variety. PLANTS (BASEL, SWITZERLAND) 2023; 12:3536. [PMID: 37896000 PMCID: PMC10667994 DOI: 10.3390/plants12203536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/06/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023]
Abstract
Rice is one of the most important crops in the world, and its production is severely affected by the rice blast disease caused by the fungus Magnaporthe oryzae. Several major blast resistance genes and QTLs associated with blast resistance have been described and mostly identified in indica rice varieties. In this work, we report the obtention of a blast-resistant rice breeding line derived from crosses between the resistant indica variety CT13432 and the japonica elite cultivar JSendra (highly susceptible to blast). The breeding line, named COPSEMAR9, was found to exhibit resistance to leaf blast and panicle blast, as demonstrated by disease assays under controlled and field conditions. Furthermore, a high-quality genome sequence of the blast-resistant breeding line was obtained using a strategy that combines short-read sequencing (Illumina sequencing) and long-read sequencing (Pacbio sequencing). The use of a whole-genome approach allowed the fine mapping of DNA regions of indica and japonica origin present in the COPSEMAR9 genome and the identification of parental gene regions potentially contributing to blast resistance in the breeding line. Rice blast resistance genes (including Pi33 derived from the resistant parent) and defense-related genes in the genome of COPSEMAR9 were identified. Whole-genome analyses also revealed the presence of microRNAs (miRNAs) with a known function in the rice response to M. oryzae infection in COPSEMAR9, which might also contribute to its phenotype of blast resistance. From this study, the genomic information and analysis methods provide valuable knowledge that will be useful in breeding programs for blast resistance in japonica rice cultivars.
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Affiliation(s)
- Glòria Escolà
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Víctor M. González-Miguel
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Mar Catala-Forner
- Institute of Agrifood Research and Technology (IRTA), Field Crops, Ctra. Balada km. 1, 43870 Tarragona, Spain;
| | - Concha Domingo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Departamento del Arroz and Centro de Genómica. Ctra Moncada-Náquera km 10.7, 46113 Moncada, Spain;
| | - Luis Marqués
- Cooperativa de Productores de Semillas de Arroz, S.C.L. (COPSEMAR) Avda del Mar 1, 46410 Sueca, Spain;
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
- Consejo Superior de Investigaciones Científicas (CSIC), 08193 Barcelona, Spain
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13
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Favre F, Jourda C, Grisoni M, Chiroleu F, Dijoux JB, Jade K, Rivallan R, Besse P, Charron C. First Vanilla planifolia High-Density Genetic Linkage Map Provides Quantitative Trait Loci for Resistance to Fusarium oxysporum. PLANT DISEASE 2023; 107:2997-3006. [PMID: 36856646 DOI: 10.1094/pdis-10-22-2386-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fusarium oxysporum f. sp. radicis-vanillae (Forv), the causal agent of root and stem rot disease, is the main pathogen affecting vanilla production. Sources of resistance have been reported in Vanilla planifolia G. Jackson ex Andrews, the main cultivated vanilla species. In this study, we developed the first high-density genetic map in this species with 1,804 genotyping-by-sequencing (GBS)-generated single nucleotide polymorphism (SNP) markers using 125 selfed progenies of the CR0040 traditional vanilla cultivar. Sixteen linkage groups (LG) were successfully constructed, with a mean of 113 SNPs and an average length of 207 cM per LG. The map had a high density with an average of 5.45 SNP every 10 cM and an average distance of 1.85 cM between adjacent markers. The first three LG were aligned against the first assembled chromosome of CR0040, and the other 13 LG were correctly associated with the other 13 assembled chromosomes. The population was challenged with the highly pathogenic Forv strain Fo072 using the root-dip inoculation method. Five traits were mapped, and 20 QTLs were associated with resistance to Fo072. Among the genes retrieved in the CR0040 physical regions associated with QTLs, genes potentially involved in biotic resistance mechanisms, coding for kinases, E3 ubiquitin ligases, pentatricopeptide repeat-containing proteins, and one leucine-rich repeat receptor underlying the qFo72_08.1 QTL have been highlighted. This study should provide useful resources for marker-assisted selection in V. planifolia.
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Affiliation(s)
- Félicien Favre
- University of Reunion Island, UMR PVBMT, F-97410 St. Pierre, Reunion Island, France
| | - Cyril Jourda
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
| | | | | | | | - Katia Jade
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pascale Besse
- University of Reunion Island, UMR PVBMT, F-97410 St. Pierre, Reunion Island, France
| | - Carine Charron
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
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14
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Amas JC, Bayer PE, Hong Tan W, Tirnaz S, Thomas WJW, Edwards D, Batley J. Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2100-2112. [PMID: 37431308 PMCID: PMC10502758 DOI: 10.1111/pbi.14116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/11/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023]
Abstract
Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield-limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa, these were mainly based on a single genome reference and do not represent the full range of RGA diversity in B. rapa. In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa. We show that 309 RGAs were affected by presence-absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine-rich repeat (TM-LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide-binding site leucine-rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa. This further clarifies the genetic relationship of these loci, which may be useful in narrowing-down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives.
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Affiliation(s)
- Junrey C. Amas
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Wei Hong Tan
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - William J. W. Thomas
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Centre for Applied BioinformaticsThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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15
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Şahin ES, Talapov T, Ateş D, Can C, Tanyolaç MB. Genome wide association study of genes controlling resistance to Didymella rabiei Pathotype IV through genotyping by sequencing in chickpeas (Cicer arietinum). Genomics 2023; 115:110699. [PMID: 37597791 DOI: 10.1016/j.ygeno.2023.110699] [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: 02/28/2023] [Revised: 08/08/2023] [Accepted: 08/15/2023] [Indexed: 08/21/2023]
Abstract
Ascochyta blight (AB) is a major disease in chickpeas (Cicer arietinum L.) that can cause a yield loss of up to 100%. Chickpea germplasm collections at the center of origin offer great potential to discover novel sources of resistance to pests and diseases. Herein, 189 Cicer arietinum samples were genotyped via genotyping by sequencing. This chickpea collection was phenotyped for resistance to an aggressive Turkish Didymella rabiei Pathotype IV isolate. Genome-wide association studies based on different models revealed 19 single nucleotide polymorphism (SNP) associations on chromosomes 1, 2, 3, 4, 7, and 8. Although eight of these SNPs have been previously reported, to the best of our knowledge, the remaining ten were associated with AB resistance for the first time. The regions identified in this study can be addressed in future studies to reveal the genetic mechanism underlying AB resistance and can also be utilized in chickpea breeding programs to improve AB resistance in new chickpea varieties.
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Affiliation(s)
- Erdem Sefa Şahin
- Republic of Turkey, Ministry of Agriculture and Forestry, Aegean Agricultural Research Institute, Izmir, Turkey; Department of Bioengineering, Molecular Genetic Laboratory, Ege University, Izmir, Turkey
| | - Talap Talapov
- Department of Biology, Gaziantep University, Gaziantep, Turkey
| | - Duygu Ateş
- Department of Bioengineering, Molecular Genetic Laboratory, Ege University, Izmir, Turkey
| | - Canan Can
- Department of Biology, Gaziantep University, Gaziantep, Turkey
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16
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Oladzad A, Roy J, Mamidi S, Miklas PN, Lee R, Clevenger J, Myers Z, Korani W, McClean PE. Linked candidate genes of different functions for white mold resistance in common bean ( Phaseolus vulgaris L) are identified by multiple QTL mapping approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1233285. [PMID: 37583595 PMCID: PMC10425182 DOI: 10.3389/fpls.2023.1233285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023]
Abstract
White mold (WM) is a major disease in common bean (Phaseolus vulgaris L.), and its complex quantitative genetic control limits the development of WM resistant cultivars. WM2.2, one of the nine meta-QTL with a major effect on WM tolerance, explains up to 35% of the phenotypic variation and was previously mapped to a large genomic interval on Pv02. Our objective was to narrow the interval of this QTL using combined approach of classic QTL mapping and QTL-based bulk segregant analysis (BSA), and confirming those results with Khufu de novo QTL-seq. The phenotypic and genotypic data from two RIL populations, 'Raven'/I9365-31 (R31) and 'AN-37'/PS02-029C-20 (Z0726-9), were used to select resistant and susceptible lines to generate subpopulations for bulk DNA sequencing. The QTL physical interval was determined by considering overlapping interval of the identified QTL or peak region in both populations by three independent QTL mapping analyses. Our findings revealed that meta-QTL WM2.2 consists of three regions, WM2.2a (4.27-5.76 Mb; euchromatic), WM 2.2b (12.19 to 17.61 Mb; heterochromatic), and WM2.2c (23.01-25.74 Mb; heterochromatic) found in both populations. Gene models encoding for gibberellin 2-oxidase 8, pentatricopeptide repeat, and heat-shock proteins are the likely candidate genes associated with WM2.2a resistance. A TIR-NBS-LRR class of disease resistance protein (Phvul.002G09200) and LRR domain containing family proteins are potential candidate genes associated with WM2.2b resistance. Nine gene models encoding disease resistance protein [pathogenesis-related thaumatin superfamily protein and disease resistance-responsive (dirigent-like protein) family protein etc] found within the WM2.2c QTL interval are putative candidate genes. WM2.2a region is most likely associated with avoidance mechanisms while WM2.2b and WM2.2c regions trigger physiological resistance based on putative candidate genes.
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Affiliation(s)
- Atena Oladzad
- Genomics Data Scientist II, Sound Agriculture, Emeryville, CA, United States
| | - Jayanta Roy
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Sujan Mamidi
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Phillip N. Miklas
- Grain Legume Genetics and Physiology Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Prosser, WA, United States
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Josh Clevenger
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Zachary Myers
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Walid Korani
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- Genomics, Phenomics, and Bioinformatics Program, North Dakota State University, Fargo, ND, United States
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17
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Nazareno ES, Fiedler JD, Ardayfio NK, Miller ME, Figueroa M, Kianian SF. Genetic Analysis and Physical Mapping of Oat Adult Plant Resistance Loci Against Puccinia coronata f. sp. avenae. PHYTOPATHOLOGY 2023; 113:1307-1316. [PMID: 36721375 DOI: 10.1094/phyto-10-22-0395-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Six quantitative trait loci (QTLs) for adult plant resistance against oat crown rust (Puccinia coronata f. sp. avenae) were identified from mapping three recombinant inbred populations. Using genotyping-by-sequencing with markers called against the OT3098 v1 reference genome, the QTLs were mapped on six different chromosomes: Chr1D, Chr4D, Chr5A, Chr5D, Chr7A, and Chr7C. Composite interval mapping with marker cofactor selection showed that the phenotypic variance explained by all identified QTLs for coefficient of infection range from 12.2 to 46.9%, whereas heritability estimates ranged from 0.11 to 0.38. The significant regions were narrowed down to intervals of 3.9 to 25 cM, equivalent to physical distances of 11 to 133 Mb. At least two flanking single-nucleotide polymorphism markers were identified within 10 cM of each QTL that could be used in marker-assisted introgression, pyramiding, and selection. The additive effects of the QTLs in each population were determined using single-nucleotide polymorphism haplotype data, which showed a significantly lower coefficient of infection in lines homozygous for the resistant alleles. Analysis of pairwise linkage disequilibrium also revealed high correlation of markers and presence of linkage blocks in the significant regions. To further facilitate marker-assisted breeding, polymerase chain reaction allelic competitive extension (PACE) markers for the adult plant resistance loci were developed. Putative candidate genes were also identified in each of the significant regions, which include resistance gene analogs that encode for kinases, ligases, and predicted receptors of avirulence proteins from pathogens.
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Affiliation(s)
- Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Jason D Fiedler
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, U.S.A
| | - Naa Korkoi Ardayfio
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, U.S.A
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
- Pairwise Plants, LLC, 807 East Main Street, Suite 4-100, Durham, NC, U.S.A
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Shahryar F Kianian
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, U.S.A
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18
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Sun Y, Kou DR, Li Y, Ni JP, Wang J, Zhang YM, Wang QN, Jiang B, Wang X, Sun YX, Xu XT, Tan XJ, Zhang YJ, Kong XD. Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection. BMC Genomics 2023; 24:332. [PMID: 37322453 DOI: 10.1186/s12864-023-09443-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023] Open
Abstract
The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.
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Affiliation(s)
- Yang Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.
| | - Dou-Rong Kou
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yan Li
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | | | - Jing Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yong-Mei Zhang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Qing-Nan Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Bin Jiang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xu Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yue-Xin Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xin-Tong Xu
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xiao-Juan Tan
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yong-Jun Zhang
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Fan W, Liu S, Feng Y, Xu Y, Liu C, Zhu P, Zhang S, Xia Z, Zhao A. Stigma type and transcriptome analyses of mulberry revealed the key factors associated with Ciboria shiraiana resistance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 200:107743. [PMID: 37186979 DOI: 10.1016/j.plaphy.2023.107743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/09/2023] [Accepted: 05/03/2023] [Indexed: 05/17/2023]
Abstract
Ciboria shiraiana is a fungal pathogen and the causal agent of hypertrophy sorosis scleroteniosis (HSS) in mulberry, leading to substantial economic losses in the mulberry fruit-related industry. To obtain HSS resistant resources and investigate the resistance mechanism, the resistances of 14 mulberry varieties were assessed. Morus laevigata Wall. (MLW) varieties showed strong resistance to C. shiraiana, and the pathogen's infection was associated with mulberry fluorescence. Stigmas were identified as the infection site through cutting experiments. Susceptible varieties (S-varieties) displayed secretory droplets on their stigma papillar cell surfaces, while MLWs lacked these secretions. Correlation analysis between the secretion rate and the diseased fruit rate indicated that the differences between resistant varieties (R-varieties) and S-varieties were related to the stigma type. Furthermore, comparative transcriptome analysis was performed on stigma and ovary samples from R- and S-varieties. Compared with the stigma of R-varieties, the key differentially expressed genes (DEGs) with significantly higher expression in S-variety stigmas mainly participated in the fatty acid biosynthetic process. In R-variety stigmas and ovaries, the transcript levels of DEGs involved in defense response, including resistance (R) genes, were significantly higher than that of S-varieties. Overexpression of MlwRPM1-2 and MlwRGA3 enhances resistance to C. shiraiana and Sclerotinia sclerotiorum, but not Botrytis cinerea in tobacco. These findings help us explain the different resistance mechanisms of mulberry to C. shiraiana, and the critical defense genes in R-varieties can be applied to breeding antifungal plant varieties.
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Affiliation(s)
- Wei Fan
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China
| | - Shuman Liu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China
| | - Yang Feng
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China
| | - Yazhen Xu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, 610106, China
| | - Panpan Zhu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China
| | - Shuai Zhang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China
| | - Zhongqiang Xia
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China
| | - Aichun Zhao
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China.
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Toporek SM, Branham SE, Keinath AP, Wechter WP. QTL mapping of resistance to Pseudoperonospora cubensis clade 2, mating type A1, in Cucumis melo and dual-clade marker development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:91. [PMID: 37009963 DOI: 10.1007/s00122-023-04333-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
This is the first identification of QTLs underlying resistance in Cucumis melo to an isolate of Pseudoperonospora cubensis identified as Clade 2/mating type A1. Pseudoperonospora cubensis, causal organism of cucurbit downy mildew (CDM), causes severe necrosis and defoliation on Cucumis melo (melon). A recombinant inbred line population (N = 169) was screened against an isolate of P. cubensis (Clade 2/mating type A1) in replicated greenhouse and growth chamber experiments. SNPs (n = 5633 bins) identified in the RIL population were used for quantitative trait loci (QTL) mapping. A single major QTL on chromosome 10 (qPcub-10.3-10.4) was consistently associated with resistance across all experiments, while a second major QTL on chromosome 8 (qPcub-8.3) was identified only in greenhouse experiments. These two major QTLs were identified on the same chromosomes (8 and 10) but in different locations as two major QTLs (qPcub-8.2 and qPcub-10.1) previously identified for resistance to P. cubensis Clade 1/mating type A2. Kompetitive allele-specific PCR (KASP) markers were developed for these four major QTLs and validated in the RIL population through QTL mapping. These markers will provide melon breeders a high-throughput genotyping toolkit for development of melon cultivars with broad tolerance to CDM.
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Affiliation(s)
- Sean M Toporek
- Department of Plant and Environmental Sciences, Clemson University, Coastal Research and Education Center, Charleston, SC, 29414, USA.
| | - Sandra E Branham
- Department of Plant and Environmental Sciences, Clemson University, Coastal Research and Education Center, Charleston, SC, 29414, USA
| | - Anthony P Keinath
- Department of Plant and Environmental Sciences, Clemson University, Coastal Research and Education Center, Charleston, SC, 29414, USA
| | - W Patrick Wechter
- US Vegetable Laboratory, USDA, ARS, 2700 Savannah Highway, Charleston, SC, 29414, USA
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21
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Amas JC, Thomas WJW, Zhang Y, Edwards D, Batley J. Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species. PHYTOPATHOLOGY 2023:PHYTO08220289FI. [PMID: 36324059 DOI: 10.1094/phyto-08-22-0289-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.
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Affiliation(s)
- Junrey C Amas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - William J W Thomas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Yueqi Zhang
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - David Edwards
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Jacqueline Batley
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
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22
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Banerjee N, Khan MS, Swapna M, Yadav S, Tiwari GJ, Jena SN, Patel JD, Manimekalai R, Kumar S, Dattamajuder SK, Kapur R, Koebernick JC, Singh RK. QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane. 3 Biotech 2023; 13:82. [PMID: 36778768 PMCID: PMC9911584 DOI: 10.1007/s13205-023-03481-7] [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: 08/03/2022] [Accepted: 01/13/2023] [Indexed: 02/12/2023] Open
Abstract
Sugarcane (Saccharum species hybrid) is one of the most important commercial crops cultivated worldwide for products like white sugar, bagasse, ethanol, etc. Red rot is a major sugarcane disease caused by a hemi-biotrophic fungus, Colletotrichum falcatum Went., which can potentially cause a reduction in yield up to 100%. Breeding for red rot-resistant sugarcane varieties has become cumbersome due to its complex genome and frequent generation of new pathotypes of red rot fungus. In the present study, a genetic linkage map was developed using a selfed population of a popular sugarcane variety CoS 96268. A QTL linked to red rot resistance (qREDROT) was identified, which explained 26% of the total phenotypic variation for the trait. A genotype-phenotype network analysis performed to account for epistatic interactions, identified the key markers involved in red rot resistance. The differential expression of the genes located in the genomic region between the two flanking markers of the qREDROT as well as in the vicinity of the markers identified through the genotype-phenotype network analysis in a set of contrasting genotypes for red rot infection further confirmed the mapping results. Further, the expression analysis revealed that the plant defense-related gene coding 26S protease regulatory subunit is strongly associated with the red rot resistance. The findings can help in the screening of disease resistant genotypes for developing red rot-resistant varieties of sugarcane. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03481-7.
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Affiliation(s)
- Nandita Banerjee
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Mohammad Suhail Khan
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - M. Swapna
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Sonia Yadav
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Gopal Ji Tiwari
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Satya N. Jena
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Jinesh D. Patel
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - R. Manimekalai
- Biotechnology Lab, Sugarcane Breeding Institute, Coimbatore, 641007 India
| | - Sanjeev Kumar
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - S. K. Dattamajuder
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Raman Kapur
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
| | - Jenny C. Koebernick
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849 USA
| | - Ram K. Singh
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, 226002 India
- Present Address: Crop Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001 India
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23
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Padgitt-Cobb LK, Pitra NJ, Matthews PD, Henning JA, Hendrix DA. An improved assembly of the "Cascade" hop ( Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. HORTICULTURE RESEARCH 2023; 10:uhac281. [PMID: 36818366 PMCID: PMC9930403 DOI: 10.1093/hr/uhac281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/22/2022] [Indexed: 06/16/2023]
Abstract
We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly were fragmented. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously reported Cascade assembly generated with PacBio long-read sequencing and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assessed molecular evolution in gene sequences, gene family expansion and contraction, and time of divergence from Cannabis sativa and other closely related plant species using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the estimate for the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
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Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Nicholi J Pitra
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
| | - Paul D Matthews
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
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Isolation and characterization of glycoprotein (CNP) isolated from Cocos nucifera L. nutshell and its immunomodulatory role on macrophage activation. J Funct Foods 2023. [DOI: 10.1016/j.jff.2022.105380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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25
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Nishmitha K, Singh R, Dubey SC, Akthar J, Tripathi K, Kamil D. Resistance screening and in silico characterization of cloned novel RGA from multi-race resistant lentil germplasm against Fusarium wilt ( Fusarium oxysporum f. sp. lentis). FRONTIERS IN PLANT SCIENCE 2023; 14:1147220. [PMID: 37152180 PMCID: PMC10160667 DOI: 10.3389/fpls.2023.1147220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/03/2023] [Indexed: 05/09/2023]
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. lentis (Fol) is the most devastating disease of lentil present worldwide. Identification of multi-race fusarium wilt resistance genes and their incorporation into existing cultivars will help to reduce yield losses. In the present study, 100 lentil germplasms belonging to seven lentil species were screened against seven prevalent races of Fol, and accessions IC201561 (Lens culinaris subsp. culinaris), EC714243 (L. c. subsp. odemensis), and EC718238 (L. nigricans) were identified as resistant. The typical R gene codes for the nucleotide-binding site and leucine-rich repeats (NBS-LRR) at the C terminal are linked to either the Toll/interleukin 1-like receptor (TIR) or coiled coil (CC) at the N terminal. In the present study, degenerate primers, designed from the NBS region amplifying the P-loop to the GLPLA motif, isolated forty-five resistance gene analogues (RGAs) from identified resistant accessions. The sequence alignment identified both classes of RGAs, TIR and non-TIR, based on the presence of aspartate (D) and tryptophan (W) at the end of the kinase motif, respectively. The phylogenetic analysis grouped the RGAs into six classes, from LRGA1 to LRGA6, which determined the diversity of the RGAs present in the host. Grouping of the RGAs identified from Lens nigricans, LnRGA 2, 9, 13 with I2 revealed the structural similarity with the fusarium resistance gene. The similarity index ranged from 27.85% to 86.98% among the RGAs and from 26.83% to 49.41% among the known R genes, I2, Gpa2, M, and L6. The active binding sites present along the conserved motifs grouped the RGAs into 13 groups. ADP/ATP, being the potential ligand, determines the ATP binding and ATP hydrolysis activity of the RGAs. The isolated RGAs can be used to develop markers linked to the functional R gene. Furthermore, expression analysis and full-length gene isolation pave the path to identifying the molecular mechanism involved in resistance.
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Affiliation(s)
- K. Nishmitha
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
- *Correspondence: Deeba Kamil, ; Rakesh Singh,
| | - Sunil C. Dubey
- Indian Council of Agricultural Research, New Delhi, India
| | - Jameel Akthar
- Division of Plant Quarantine, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kuldeep Tripathi
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Deeba Kamil
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Deeba Kamil, ; Rakesh Singh,
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26
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Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses. BIOTECHNOLOGIA 2022; 103:355-384. [PMID: 36685700 PMCID: PMC9837557 DOI: 10.5114/bta.2022.120706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 07/25/2022] [Accepted: 09/16/2022] [Indexed: 01/06/2023] Open
Abstract
Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.
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Genome-Wide Association Study (GWAS) of White Mold Resistance in Snap Bean. Genes (Basel) 2022; 13:genes13122297. [PMID: 36553566 PMCID: PMC9777983 DOI: 10.3390/genes13122297] [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: 10/01/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
White mold can result in snap bean yield losses of 90 to 100% when field conditions favor the pathogen. A genome-wide association study (GWAS) was conducted to detect loci significantly associated with white mold resistance in a panel of snap bean (Phaseolus vulgaris L.) cultivars. Two populations of snap bean were used in this study. The first population was the BeanCAP (Coordinated Agriculture Project) Snap Bean Diversity Panel (SBDP) (n = 136), and the second population was the Snap Bean Association Panel (SnAP) (n = 378). SBDP was evaluated for white mold reaction in the field in 2012 and 2013, and SnAP was screened in a greenhouse only using the seedling straw test in 2016. Two reference genomes representing the Andean and Middle American centers of domestication were utilized to align the genotyping-by-sequencing (GBS) data. A GWAS was performed using FarmCPU with one principal component after comparing five models. Thirty-four single-nucleotide polymorphisms (SNPs) significantly associated with white mold resistance were detected. Eleven significant SNPs were identified by the seedling straw test, and 23 significant SNPs were identified by field data. Fifteen SNPs were identified within a 100 kb window containing pentatricopeptide repeat (PPR)-encoding genes, and eleven were close to leucine-rich repeat (LRR)-encoding genes, suggesting that these two classes are of outsized importance for snap bean resistance to white mold.
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Cantila AY, Thomas WJW, Bayer PE, Edwards D, Batley J. Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:3010. [PMID: 36432742 PMCID: PMC9693284 DOI: 10.3390/plants11223010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars.
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29
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Nazareno ES, Fiedler J, Miller ME, Figueroa M, Kianian SF. A reference-anchored oat linkage map reveals quantitative trait loci conferring adult plant resistance to crown rust (Puccinia coronata f. sp. avenae). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3307-3321. [PMID: 36029319 DOI: 10.1007/s00122-022-04128-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
We mapped three adult plant resistance (APR) loci on oat chromosomes 4D and 6C and developed flanking KASP/PACE markers for marker-assisted selection and gene pyramiding. Using sequence orthology search and the available oat genomic and transcriptomic data, we surveyed these genomic regions for genes that may control disease resistance. Sources of durable disease resistance are needed to minimize yield losses in cultivated oat caused by crown rust (Puccinia coronata f. sp. avenae). In this study, we developed five oat recombinant inbred line mapping populations to identify sources of adult plant resistance from crosses between five APR donors and Otana, a susceptible variety. The preliminary bulk segregant mapping based on allele frequencies showed two regions in linkage group Mrg21 (Chr4D) that are associated with the APR phenotype in all five populations. Six markers from these regions in Chr4D were converted to high-throughput allele specific PCR assays and were used to genotype all individuals in each population. Simple interval mapping showed two peaks in Chr4D, named QPc.APR-4D.1 and QPc.APR-4D.2, which were detected in the OtanaA/CI4706-2 and OtanaA/CI9416-2 and in the Otana/PI189733, OtanaD/PI260616, and OtanaA/CI8000-4 populations, respectively. These results were validated by mapping two entire populations, Otana/PI189733 and OtanaA/CI9416, genotyped using Illumina HiSeq, in which polymorphisms were called against the OT3098 oat reference genome. Composite interval mapping results confirmed the presence of the two quantitative trait loci (QTL) located on oat chromosome 4D and an additional QTL with a smaller effect located on chromosome 6C. This mapping approach also narrowed down the physical intervals to between 5 and 19 Mb, and indicated that QPc.APR-4D.1, QPc.APR-4D.2, and QPc.APR-6C explained 43.4%, 38.5%, and 21.5% of the phenotypic variation, respectively. In a survey of the gene content of each QTL, several clusters of disease resistance genes that may contribute to APR were found. The allele specific PCR markers developed for these QTL regions would be beneficial for marker-assisted breeding, gene pyramiding, and future cloning of resistance genes from oat.
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Affiliation(s)
- Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Jason Fiedler
- US Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, USA
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Pairwise Plants, LLC. 807 East Main Street, Suite 4-100, Durham, NC, USA
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Shahryar F Kianian
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, USA.
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30
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Yu T, Ma X, Liu Z, Feng X, Wang Z, Ren J, Cao R, Zhang Y, Nie F, Song X. TVIR: a comprehensive vegetable information resource database for comparative and functional genomic studies. HORTICULTURE RESEARCH 2022; 9:uhac213. [PMID: 36483087 PMCID: PMC9719039 DOI: 10.1093/hr/uhac213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/14/2022] [Indexed: 06/17/2023]
Abstract
Vegetables are an indispensable part of the daily diet of humans. Therefore, it is vital to systematically study the genomic data of vegetables and build a platform for data sharing and analysis. In this study, a comprehensive platform for vegetables with a user-friendly Web interface-The Vegetable Information Resource (TVIR, http://tvir.bio2db.com)-was built based on the genomes of 59 vegetables. TVIR database contains numerous important functional genes, including 5215 auxin genes, 2437 anthocyanin genes, 15 002 flowering genes, 79 830 resistance genes, and 2639 glucosinolate genes of 59 vegetables. In addition, 2597 N6-methyladenosine (m6A) genes were identified, including 513 writers, 1058 erasers, and 1026 readers. A total of 2 101 501 specific clustered regularly interspaced short palindromic repeat (CRISPR) guide sequences and 17 377 miRNAs were detected and deposited in TVIR database. Information on gene synteny, duplication, and orthologs is also provided for 59 vegetable species. TVIR database contains 2 346 850 gene annotations by the Swiss-Prot, TrEMBL, Gene Ontology (GO), Pfam, and Non-redundant (Nr) databases. Synteny, Primer Design, Blast, and JBrowse tools are provided to facilitate users in conducting comparative genomic analyses. This is the first large-scale collection of vegetable genomic data and bioinformatic analysis. All genome and gene sequences, annotations, and bioinformatic results can be easily downloaded from TVIR. Furthermore, transcriptome data of 98 vegetables have been collected and collated, and can be searched by species, tissues, or different growth stages. TVIR is expected to become a key hub for vegetable research globally. The database will be updated with newly assembled vegetable genomes and comparative genomic studies in the future.
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Affiliation(s)
| | | | | | | | - Zhiyuan Wang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Jun Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yingchao Zhang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fulei Nie
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
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Moncada MM, Elvir MA, Lopez JR, Ortiz AS. Predicción bioinformática de proteínas NBS-LRR en el genoma de Coffea arabica. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.03.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Gracias al acceso al genoma completo de Coffea arabica y el Desarrollo de multiples herramientas de bioinformartica que permite la búsqueda de genes de resistencia de plantas (R-genes), ha sido posible implementar estas estrategias en programas de mejora genética. En las plantas, los R-genes codifican proteínas involucradas en mecanismos de defensa contra patógenos. Los genes con dominios tipo Nucleotide-Binding-Site Leucine-Rich-Repeat (NBS-LRR) forman la familia de R-genes de plantas más grande. El objetivo de este estudio fue identificar genes de proteínas NBS-LRR en el genoma de C. arabica utilizando un enfoque bioinformático. Identificamos motivos conservados de R-genes de C. arabica relacionados con genes similares encontrados en Coffea canephora y Coffea eugenoides, dos especies evolutivas relacionadas con C. arabica. Los resultados de estos análisis revelaron proteínas con origen evolutivo provenientes de dicotiledóneo ancestrales, así como proteínas de resistencia específicas del género Coffea. Además, todas las secuencias de los R-genes de C. arabica mostraron una gran similitud con proteína CNL de Arabidopsis thaliana. Finalmente, la presencia de motivos altamente conservados, la distribución cromosómica y las relaciones filogenéticas de los R-genes de C. arabica muestran procesos de coevolución con patógenos adaptados, demostrando de esta manera la importancia del estudio de estos genes en la inmunidad del café.
Palabras clave: Café, NBS-LRR, Proteínas de Resistencia, Bioinformática.
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Affiliation(s)
| | | | | | - Andrés S. Ortiz
- Universidad Nacional Autónoma de Honduras Instituto de Investigaciones en Microbiología
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Zhang L, Liu Y, Wang Q, Wang C, Lv S, Wang Y, Wang J, Wang Y, Yuan J, Zhang H, Kang Z, Ji W. An alternative splicing isoform of wheat TaYRG1 resistance protein activates immunity by interacting with dynamin-related proteins. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5474-5489. [PMID: 35652375 DOI: 10.1093/jxb/erac245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Wheat (Triticum aestivum) is a commercially important crop and its production is seriously threatened by the fungal pathogen Puccinia striiformis f. sp. tritici West (Pst). Resistance (R) genes are critical factors that facilitate plant immune responses. Here, we report a wheat R gene NB-ARC-LRR ortholog, TaYRG1, that is associated with distinct alternative splicing events in wheat infected by Pst. The native splice variant, TaYRG1.6, encodes internal-motif-deleted polypeptides with the same N- and C-termini as TaYRG1.1, resulting in gain of function. Transient expression of protein variants in Nicotiana benthamiana showed that the NB and ARC domains, and TaYRG1.6 (half LRR domain), stimulate robust elicitor-independent cell death based on a signal peptide, although the activity was negatively modulated by the CC and complete LRR domains. Furthermore, molecular genetic analyses indicated that TaYRG1.6 enhanced resistance to Pst in wheat. Moreover, we provide multiple lines of evidence that TaYRG1.6 interacts with a dynamin-related protein, TaDrp1. Proteome profiling suggested that the TaYRG1.6-TaDrp1-DNM complex in the membrane trafficking systems may trigger cell death by mobilizing lipid and kinase signaling in the endocytosis pathway. Our findings reveal a unique mechanism by which TaYRG1 activates cell death and enhances disease resistance by reconfiguring protein structure through alternative splicing.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuanming Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiaohui Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Chao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Shikai Lv
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
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Sharma A, Abrahamian P, Carvalho R, Choudhary M, Paret ML, Vallad GE, Jones JB. Future of Bacterial Disease Management in Crop Production. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:259-282. [PMID: 35790244 DOI: 10.1146/annurev-phyto-021621-121806] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial diseases are a constant threat to crop production globally. Current management strategies rely on an array of tactics, including improved cultural practices; application of bactericides, plant activators, and biocontrol agents; and use of resistant varieties when available. However, effective management remains a challenge, as the longevity of deployed tactics is threatened by constantly changing bacterial populations. Increased scrutiny of the impact of pesticides on human and environmental health underscores the need for alternative solutions that are durable, sustainable, accessible to farmers, and environmentally friendly. In this review, we discuss the strengths and shortcomings of existing practices and dissect recent advances that may shape the future of bacterial disease management. We conclude that disease resistance through genome modification may be the most effective arsenal against bacterial diseases. Nonetheless, more research is necessary for developing novel bacterial disease management tactics to meet the food demand of a growing global population.
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Affiliation(s)
- Anuj Sharma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
| | - Peter Abrahamian
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
- Plant Pathogen Confirmatory Diagnostic Laboratory, USDA-APHIS, Beltsville, Maryland, USA
| | - Renato Carvalho
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
| | - Manoj Choudhary
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
| | - Mathews L Paret
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
- North Florida Research and Education Center, University of Florida, Quincy, Florida, USA
| | - Gary E Vallad
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
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Vining KJ, Pandelova I, Lange I, Parrish AN, Lefors A, Kronmiller B, Liachko I, Kronenberg Z, Srividya N, Lange BM. Chromosome-level genome assembly of Mentha longifolia L. reveals gene organization underlying disease resistance and essential oil traits. G3 GENES|GENOMES|GENETICS 2022; 12:6584825. [PMID: 35551385 PMCID: PMC9339296 DOI: 10.1093/g3journal/jkac112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Mentha longifolia (L.) Huds., a wild, diploid mint species, has been developed as a model for mint genetic and genomic research to aid breeding efforts that target Verticillium wilt disease resistance and essential oil monoterpene composition. Here, we present a near-complete, chromosome-scale mint genome assembly for M. longifolia USDA accession CMEN 585. This new assembly is an update of a previously published genome draft, with dramatic improvements. A total of 42,107 protein-coding genes were annotated and placed on 12 chromosomal scaffolds. One hundred fifty-three genes contained conserved sequence domains consistent with nucleotide binding site-leucine-rich-repeat plant disease resistance genes. Homologs of genes implicated in Verticillium wilt resistance in other plant species were also identified. Multiple paralogs of genes putatively involved in p-menthane monoterpenoid biosynthesis were identified and several cases of gene clustering documented. Heterologous expression of candidate genes, purification of recombinant target proteins, and subsequent enzyme assays allowed us to identify the genes underlying the pathway that leads to the most abundant monoterpenoid volatiles. The bioinformatic and functional analyses presented here are laying the groundwork for using marker-assisted selection in improving disease resistance and essential oil traits in mints.
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Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University , Corvallis, OR 97331, USA
| | - Iovanna Pandelova
- Department of Horticulture, Oregon State University , Corvallis, OR 97331, USA
| | - Iris Lange
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - Amber N Parrish
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - Andrew Lefors
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - Brent Kronmiller
- Center for Quantitative Life Sciences, Oregon State University , Corvallis, OR 97331, USA
| | | | | | - Narayanan Srividya
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - B Markus Lange
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
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Inturrisi F, Bayer PE, Cantila AY, Tirnaz S, Edwards D, Batley J. In silico integration of disease resistance QTL, genes and markers with the Brassica juncea physical map. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:37. [PMID: 37309382 PMCID: PMC10248627 DOI: 10.1007/s11032-022-01309-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/09/2022] [Indexed: 06/14/2023]
Abstract
Brassica juncea (AABB), Indian mustard, is a source of disease resistance genes for a wide range of pathogens. The availability of reference genome sequences for B. juncea has made it possible to characterise the genomic structure and distribution of these disease resistance genes. Potentially functional disease resistance genes can be identified by co-localization with genetically mapped disease resistance quantitative trait loci (QTL). Here we identify and characterise disease resistance gene analogs (RGAs), including nucleotide-binding site-leucine-rich repeat (NLR), receptor-like kinase (RLK) and receptor-like protein (RLP) classes, and investigate their association with disease resistance QTL intervals. The molecular genetic marker sequences for four white rust (Albugo candida) disease resistance QTL, six blackleg (Leptosphaeria maculans) disease resistance QTL and BjCHI1, a gene cloned from B. juncea for hypocotyl rot disease, were extracted from previously published studies and used to compare with candidate RGAs. Our results highlight the complications for the identification of functional resistance genes, including the duplicated appearance of genetic markers for several resistance loci, including Ac2(t), AcB1-A4.1, AcB1-A5.1, Rlm6 and PhR2 in both the A and B genomes, due to the presence of homoeologous regions. Furthermore, the white rust loci, Ac2(t) and AcB1-A4.1, mapped to the same position on chromosome A04 and may be different alleles of the same gene. Despite these challenges, a total of nine candidate genomic regions hosting 14 RLPs, 28 NLRs and 115 RLKs were identified. This study facilitates the mapping and cloning of functional resistance genes for applications in crop improvement programs. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01309-5.
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Affiliation(s)
- Fabian Inturrisi
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Aldrin Y. Cantila
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
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Mondal KK, Kulshreshtha A, Handique PJ, Borbora D, Rajrana Y, Verma G, Bhattacharya A, Qamar A, Lakshmi A, Reddy K, Soni M, Ghoshal T, Rashmi ER, Mrutyunjaya S, Kalaivanan NS, Mani C. Rice transcriptome upon infection with Xanthomonas oryzae pv. oryzae relative to its avirulent T3SS-defective strain exposed modulation of many stress responsive genes. 3 Biotech 2022; 12:130. [PMID: 35607392 DOI: 10.1007/s13205-022-03193-4] [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: 01/07/2022] [Accepted: 04/28/2022] [Indexed: 11/01/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a destructive pathogen that causes bacterial blight disease of rice worldwide. Xoo uses T3SS (type III secretion system) effectors to subvert rice innate immunity. However, the comprehensive knowledge of rice genes involved in T3SS effectors-mediated interaction remains unclear. In this study, the transcriptome profiles of rice infected with a virulent Xoo strain from North-eastern region of India relatives to its avirulent strain (that lacks functional T3SS) were analyzed at early (2-6 hpi) and late (16-24 hpi) hours of infection. Out of total 255 differentially expressed genes (DEGs), during early infection, 62 and 70 genes were upregulated and downregulated, respectively. At late infection, 70 and 53 genes were upregulated and downregulated, respectively. The transcriptomic data identified many differentially expressed resistant genes, transposons, transcription factors, serine/threonine protein kinase, cytochrome P450 and peroxidase genes that are involved in plant defense. Pathway analysis revealed that these DEGs are involved in hormone signaling, plant defense, cellular metabolism, growth and development processes. DEGs associated with plant defense were also validated through quantitative real-time PCR. Our study brings a comprehensive picture of the rice genes that are being differentially expressed during bacterial blight infection. Nevertheless, the DEG-associated pathways would provide sensible targets for developing resistance to bacterial blight. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03193-4.
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Affiliation(s)
- Kalyan K Mondal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Aditya Kulshreshtha
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | | | - Yuvika Rajrana
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Geeta Verma
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Aarzoo Qamar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Amrutha Lakshmi
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - KishoreKumar Reddy
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Madhvi Soni
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Thungri Ghoshal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - E R Rashmi
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India.,Department of Biotechnology, Gauhati University, Assam, India
| | - S Mrutyunjaya
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - N S Kalaivanan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Chander Mani
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana. BIOLOGY 2022; 11:biology11060821. [PMID: 35741342 PMCID: PMC9220128 DOI: 10.3390/biology11060821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary Developing cultivars with resistance genes (R genes) is an effective strategy to support high yield and quality in Brassica crops. The availability of clone R gene and genomic sequences in Brassica species and Arabidopsis thaliana provide the opportunity to compare genomic regions and survey R genes across genomic databases. In this paper, we aim to identify genes related to cloned genes through sequence identity, providing a repertoire of species-wide related R genes in Brassica crops. The comprehensive list of candidate R genes can be used as a reference for functional analysis. Abstract Various diseases severely affect Brassica crops, leading to significant global yield losses and a reduction in crop quality. In this study, we used the complete protein sequences of 49 cloned resistance genes (R genes) that confer resistance to fungal and bacterial diseases known to impact species in the Brassicaceae family. Homology searches were carried out across Brassica napus, B. rapa, B. oleracea, B. nigra, B. juncea, B. carinata and Arabidopsis thaliana genomes. In total, 660 cloned disease R gene homologs (CDRHs) were identified across the seven species, including 431 resistance gene analogs (RGAs) (248 nucleotide binding site-leucine rich repeats (NLRs), 150 receptor-like protein kinases (RLKs) and 33 receptor-like proteins (RLPs)) and 229 non-RGAs. Based on the position and distribution of specific homologs in each of the species, we observed a total of 87 CDRH clusters composed of 36 NLR, 16 RLK and 3 RLP homogeneous clusters and 32 heterogeneous clusters. The CDRHs detected consistently across the seven species are candidates that can be investigated for broad-spectrum resistance, potentially providing resistance to multiple pathogens. The R genes identified in this study provide a novel resource for the future functional analysis and gene cloning of Brassicaceae R genes towards crop improvement.
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Paluchowska P, Śliwka J, Yin Z. Late blight resistance genes in potato breeding. PLANTA 2022; 255:127. [PMID: 35576021 PMCID: PMC9110483 DOI: 10.1007/s00425-022-03910-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
Using late blight resistance genes targeting conservative effectors of Phytophthora infestans and the constructing gene pyramids may lead to durable, broad-spectrum resistance, which could be accelerated through genetic engineering. Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. In 2020, potato production was estimated to be more than 359 million tons according to the Food and Agriculture Organization (FAO). Potato is affected by many pathogens, among which Phytophthora infestans, causing late blight, is of the most economic importance. Crop protection against late blight requires intensive use of fungicides, which has an impact on the environment and humans. Therefore, new potato cultivars have been bred using resistance genes against P. infestans (Rpi genes) that originate from wild relatives of potato. Such programmes were initiated 100 years ago, but the process is complex and long. The development of genetic engineering techniques has enabled the direct transfer of resistance genes from potato wild species to cultivars and easier pyramiding of multiple Rpi genes, which potentially increases the durability and spectrum of potato resistance to rapidly evolving P. infestans strains. In this review, we summarize the current knowledge concerning Rpi genes. We also discuss the use of Rpi genes in breeding as well as their detection in existing potato cultivars. Last, we review new sources of Rpi genes and new methods used to identify them and discuss interactions between P. infestans and host.
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Affiliation(s)
- Paulina Paluchowska
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
| | - Jadwiga Śliwka
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - Zhimin Yin
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
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Bhadmus OA, Badu-Apraku B, Adeyemo OA, Agre PA, Queen ON, Ogunkanmi AL. Genome-Wide Association Analysis Reveals Genetic Architecture and Candidate Genes Associated with Grain Yield and Other Traits under Low Soil Nitrogen in Early-Maturing White Quality Protein Maize Inbred Lines. Genes (Basel) 2022; 13:genes13050826. [PMID: 35627211 PMCID: PMC9141126 DOI: 10.3390/genes13050826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 02/01/2023] Open
Abstract
Maize production in the savannas of sub-Saharan Africa (SSA) is constrained by the low nitrogen in the soils. The identification of quantitative trait loci (QTL) conferring tolerance to low soil nitrogen (low-N) is crucial for the successful breeding of high-yielding QPM maize genotypes under low-N conditions. The objective of this study was to identify QTLs significantly associated with grain yield and other low-N tolerance-related traits under low-N. The phenotypic data of 140 early-maturing white quality protein maize (QPM) inbred lines were evaluated under low-N. The inbred lines were genotyped using 49,185 DArTseq markers, from which 7599 markers were filtered for population structure analysis and genome-wide association study (GWAS). The inbred lines were grouped into two major clusters based on the population structure analysis. The GWAS identified 24, 3, 10, and 3 significant SNPs respectively associated with grain yield, stay-green characteristic, and plant and ear aspects, under low-N. Sixteen SNP markers were physically located in proximity to 32 putative genes associated with grain yield, stay-green characteristic, and plant and ear aspects. The putative genes GRMZM2G127139, GRMZM5G848945, GRMZM2G031331, GRMZM2G003493, GRMZM2G067964, GRMZM2G180254, on chromosomes 1, 2, 8, and 10 were involved in cellular nitrogen assimilation and biosynthesis, normal plant growth and development, nitrogen assimilation, and disease resistance. Following the validation of the markers, the putative candidate genes and SNPs could be used as genomic markers for marker-assisted selection, to facilitate genetic gains for low-N tolerance in maize production.
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Affiliation(s)
- Olatunde A. Bhadmus
- Department of Cell Biology and Genetics, University of Lagos, Lagos 101017, Nigeria; (O.A.B.); (O.A.A.); (A.L.O.)
- International Institute of Tropical Agriculture, IITA, PMB 5320 Oyo Road, Ibadan 200285, Nigeria; (P.A.A.); (O.N.Q.)
| | - Baffour Badu-Apraku
- International Institute of Tropical Agriculture, IITA, PMB 5320 Oyo Road, Ibadan 200285, Nigeria; (P.A.A.); (O.N.Q.)
- Correspondence:
| | - Oyenike A. Adeyemo
- Department of Cell Biology and Genetics, University of Lagos, Lagos 101017, Nigeria; (O.A.B.); (O.A.A.); (A.L.O.)
| | - Paterne A. Agre
- International Institute of Tropical Agriculture, IITA, PMB 5320 Oyo Road, Ibadan 200285, Nigeria; (P.A.A.); (O.N.Q.)
| | - Offornedo N. Queen
- International Institute of Tropical Agriculture, IITA, PMB 5320 Oyo Road, Ibadan 200285, Nigeria; (P.A.A.); (O.N.Q.)
| | - Adebayo L. Ogunkanmi
- Department of Cell Biology and Genetics, University of Lagos, Lagos 101017, Nigeria; (O.A.B.); (O.A.A.); (A.L.O.)
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Jyothsna S, Alagu M. Role of phasiRNAs in plant-pathogen interactions: molecular perspectives and bioinformatics tools. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:947-961. [PMID: 35722509 PMCID: PMC9203634 DOI: 10.1007/s12298-022-01189-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/01/2022] [Accepted: 05/18/2022] [Indexed: 05/03/2023]
Abstract
The genome of an organism is regulated in concert with the organized action of various genetic regulators at different hierarchical levels. Small non-coding RNAs are one of these regulators, among which microRNAs (miRNAs), a distinguished sRNA group with decisive functions in the development, growth and stress-responsive activities of both plants as well as animals, are keenly explored over a good number of years. Recent studies in plants revealed that apart from the silencing activity exhibited by miRNAs on their targets, miRNAs of specific size and structural features can direct the phasing pattern of their target loci to form phased secondary small interfering RNAs (phasiRNAs). These trigger-miRNAs were identified to target both coding and long non-coding RNAs that act as potent phasiRNA precursors or PHAS loci. The phasiRNAs produced thereby exhibit a role in enhancing further downstream regulation either on their own precursors or on those transcripts that are distinct from their genetic source of origin. Hence, these tiny regulators can stimulate an elaborative cascade of interacting RNA networks via cis and trans-regulatory mechanisms. Our review focuses on the comprehensive understanding of phasiRNAs and their trigger miRNAs, by giving much emphasis on their role in the regulation of plant defense responses, together with a summary of the computational tools available for the prediction of the same.
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Affiliation(s)
- S. Jyothsna
- Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala 671316 India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala 671316 India
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Sun Y, Wang J, Li Y, Jiang B, Wang X, Xu WH, Wang YQ, Zhang PT, Zhang YJ, Kong XD. Pan-Genome Analysis Reveals the Abundant Gene Presence/Absence Variations Among Different Varieties of Melon and Their Influence on Traits. FRONTIERS IN PLANT SCIENCE 2022; 13:835496. [PMID: 35401600 PMCID: PMC8990847 DOI: 10.3389/fpls.2022.835496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Melon (Cucumismelo L.) is an important vegetable crop that has been subjected to domestication and improvement. Several varieties of melons with diverse phenotypes have been produced. In this study, we constructed a melon pan-genome based on 297 accessions comprising 168 Mb novel sequences and 4,325 novel genes. Based on the results, there were abundant genetic variations among different melon groups, including 364 unfavorable genes in the IMP_A vs. LDR_A group, 46 favorable genes, and 295 unfavorable genes in the IMP_M vs. LDR_M group. The distribution of 709 resistance gene analogs (RGAs) was also characterized across 297 melon lines, of which 603 were core genes. Further, 106 genes were found to be variable, 55 of which were absent in the reference melon genome. Using gene presence/absence variation (PAV)-based genome-wide association analysis (GWAS), 13 gene PAVs associated with fruit length, fruit shape, and fruit width were identified, four of which were located in pan-genome additional contigs.
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Affiliation(s)
- Yang Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Jing Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yan Li
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Jiang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Xu Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Wen-Hui Xu
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yu-Qing Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Pei-Tao Zhang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yong-Jun Zhang
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Giordani W, Gama HC, Chiorato AF, Marques JPR, Huo H, Benchimol-Reis LL, Camargo LEA, Garcia AAF, Vieira MLC. Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection. THE PLANT GENOME 2022; 15:e20161. [PMID: 34806826 DOI: 10.1002/tpg2.20161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Root-knot nematodes (RKNs), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crops. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging because little has been done to discover resistance genes or markers to assist selection. We performed genome-wide association studies and quantitative trait loci mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and the root-galling index were evaluated. Complex genetic architecture and independent genomic regions were associated with each trait. Single nucleotide polymorphisms on chromosomes Pv06, Pv07, Pv08, and Pv11 were associated with the number of egg masses, and SNPs on Pv01, Pv02, Pv05, and Pv10 were associated with root-galling. A total of 216 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA sequencing analysis. Histochemical analysis indicated that reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance, and the candidate genes are valuable targets for functional investigation and gene editing approaches.
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Affiliation(s)
- Willian Giordani
- "Luiz de Queiroz" College of Agriculture, Univ. of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - Henrique Castro Gama
- "Luiz de Queiroz" College of Agriculture, Univ. of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | | | | | - Heqiang Huo
- Mid-Florida Research and Education Center, Univ. of Florida, Apopka, FL, 32703, USA
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Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int J Mol Sci 2022; 23:2671. [PMID: 35269811 PMCID: PMC8910360 DOI: 10.3390/ijms23052671] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (C.G.T.F.); (B.J.N.); (M.F.D.); (M.G.); (J.P.); (P.E.B.); (P.M.F.); (J.B.)
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Zhang X, Wang G, Qu X, Wang M, Guo H, Zhang L, Li T, Wang Y, Zhang H, Ji W. A truncated CC-NB-ARC gene TaRPP13L1-3D positively regulates powdery mildew resistance in wheat via the RanGAP-WPP complex-mediated nucleocytoplasmic shuttle. PLANTA 2022; 255:60. [PMID: 35133503 DOI: 10.1007/s00425-022-03843-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
A wheat RPP13-like isoform interacting with WPP1 contributes to quantitative and/or basal resistance to powdery mildew (Blumeria graminis f. sp. tritici) by restricting the development of Bgt conidia. Plant disease resistance (R) genes confer an ability to resist infection by pathogens expressing specific avirulence genes. Recognition of Peronospora parasitica 13-like (RPP13-like) genes belong to the nucleotide-binding site and leucine-rich repeat (NBS-LRR) superfamily and play important roles in resistance to various plant diseases. Previously, we detected a TaRPP13-like gene located on chromosome 3D (TaRPP13L1-3D) in the TaSpl1 resided region, which is strongly induced by the cell death phenotype (Zhang et al. 2021). Here, we investigated the expression and functional role of TaRPP13L1-3D in wheat responding to fungal stress. TaRPP13L1-3D encoded a typical NB-ARC structure characterized by Rx-N and P-loop NTPase domains. TaRPP13L1-3D transcripts were strongly upregulated in wheat by powdery mildew (Blumeria graminis f. sp. tritici; Bgt) and stripe rust (Puccinia striiformis f. sp. tritici; Pst) infection although opposing expression patterns were observed in response to wheat-Bgt in incompatible and compatible backgrounds. Overexpression of TaRPP13L1-3D enhanced disease resistance to Bgt, accompanied by upregulation of the defense-related marker genes encoding phytoalexin-deficient4 (PAD4), thaumatin-like protein (TLP) and chitinase 8-like protein (Chi8L), while silencing of TaRPP13L1-3D disrupted the resistance to Bgt infection. Subcellular localization studies showed that TaRPP13L1-3D is located in both the plasma membrane and nucleus, while yeast-two-hybrid (Y2H) assays indicated that TaRPP13L1-3D interacts with WPP domain-containing protein 1 (TaWPP1). This indicates that TaRPP13L1-3D shuttles between the nucleus and cytoplasm membrane via a mechanism that is mediated by the RanGAP-WPP complex in nuclear pores. This insight into TaRPP13L1-3D will be useful in dissecting the mechanism of fungal resistance in wheat, and understanding the interaction between R gene expression and pathogen defense.
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Affiliation(s)
- Xiangyu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guanghao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaojian Qu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Mengmeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Huan Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, Shaanxi, 712100, People's Republic of China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Shaanxi, 712100, People's Republic of China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A and F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Shaanxi, 712100, People's Republic of China.
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Yin J, Yan J, Hou L, Jiang L, Xian W, Guo Q. Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici. BMC Genomics 2021; 22:868. [PMID: 34856924 PMCID: PMC8638555 DOI: 10.1186/s12864-021-08183-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. RESULTS In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. CONCLUSIONS This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.
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Affiliation(s)
- Junliang Yin
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Agriculture, Yangtze University, 434000 Jingzhou, Hubei China
| | - Jiahui Yan
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Lu Hou
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Liling Jiang
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Wenrong Xian
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Qingyun Guo
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
- Qinghai Academy of Agriculture and Forestry Science, Qinghai University, 810016 Xining, China
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Ray T, Pandey A, Pandey SS, Singh S, Shanker K, Kalra A. Molecular insights into enhanced resistance of Papaver somniferum against downy mildew by application of endophyte bacteria Microbacterium sp. SMR1. PHYSIOLOGIA PLANTARUM 2021; 173:1862-1881. [PMID: 34407205 DOI: 10.1111/ppl.13528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/30/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Downy mildew is one of the most serious diseases of Papaver somniferum. Endophytes isolated from different parts of P. somniferum were screened for their ability to enhance resistance against downy mildew caused by the obligate biotrophic oomycete Peronospora meconopsidis. Two endophytes (SMR1 and SMR2) reduced the downy mildew on three P. somniferum genotypes (Sampada, J-16, and I-14). SMR1 (Microbacterium sp.) also enhanced the resistance of P. somniferum against downy mildew under field conditions. The biochemical markers of plant susceptibility under biotic stresses (proline and malondialdehyde) were found to be reduced in P. somniferum upon SMR1 treatment. To understand the mechanisms underlying the enhanced resistance to downy mildew in SMR1 endophyte-treated P. somniferum genotype J-16, we compared the expression profiles using the next-generation RNA sequencing approach between P. somniferum pretreated with SMR1 and untreated endophyte-free control plants following exposure to downy mildew pathogen. Comparative transcriptome analysis revealed differential expression of transcripts belonging to broad classes of signal transduction, protein modification, disease/defense proteins, transcription factors, and phytohormones in SMR1-primed P. somniferum after infection with downy mildew pathogen. Furthermore, enhanced salicylic acid content was observed in SMR1-primed P. somniferum after exposure to downy mildew pathogen. This study sheds light on molecular mechanisms underlying enhanced resistance to downy mildew in SMR1-primed P. somniferum. Finally, we propose that the SA-dependent defense pathway, the hallmark of systemic acquired resistance, is activated in SMR1-primed P. somniferum, triggering the endophyte-induced resistance.
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Affiliation(s)
- Tania Ray
- Microbial Technology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Alok Pandey
- Microbial Technology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Shiv S Pandey
- Microbial Technology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Sucheta Singh
- Microbial Technology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Karuna Shanker
- Analytical Chemistry Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Alok Kalra
- Microbial Technology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
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Branham SE, Kousik C, Mandal MK, Wechter WP. Quantitative Trait Loci Mapping of Resistance to Powdery Mildew Race 1 in a Recombinant Inbred Line Population of Melon. PLANT DISEASE 2021; 105:3809-3815. [PMID: 34253041 DOI: 10.1094/pdis-12-20-2643-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Powdery mildew, caused by the fungus Podosphaera xanthii, is one of the most important diseases of melon. Although there are several pathogenic races of P. xanthii, race 1 is the predominant race in South Carolina and in other parts of the United States. We used a densely genotyped recombinant inbred line melon population for traditional quantitative trait loci (QTL) mapping, to identify two major (qPx1-5 and qPx1-12) and two minor (qPx1-4 and qPx1-10) QTLs (named according to race - chromosome number) associated with resistance to P. xanthii race 1. QTL mapping of disease severity in multiple tissues (hypocotyl, cotyledons, true leaves, and stems) identified the same genetic basis of resistance in all tissue types. Whole-genome resequencing of the parents was used for marker development across the major QTLs and functional annotation of single nucleotide polymorphisms (SNPs) for candidate gene analysis. Kompetitive allele-specific PCR (KASP) markers were tightly linked to the QTL peaks of qPx1-5 (pm1-5_25329892, pm1-5_25461503 and pm1-5_25625375) and qPx1-12 (pm1-12_22848920 and pm1-12_22904659) in the population and will enable efficient marker-assisted introgression of powdery mildew resistance into improved germplasm. Candidate genes were identified in both major QTL intervals that encode putative R genes with missense mutations between the parents. The candidate genes provide targets for future breeding efforts and a fundamental examination of resistance to powdery mildew in melon.
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Affiliation(s)
- Sandra E Branham
- Coastal Research and Education Center, Clemson University, Charleston, SC
| | - Chandrasekar Kousik
- USDA, ARS, US Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414
| | - Mihir K Mandal
- Department of Biology, Claflin University, Orangeburg, SC 29115
| | - W Patrick Wechter
- USDA, ARS, US Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414
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Calle García J, Guadagno A, Paytuvi-Gallart A, Saera-Vila A, Amoroso CG, D'Esposito D, Andolfo G, Aiese Cigliano R, Sanseverino W, Ercolano MR. PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process. Nucleic Acids Res 2021; 50:D1483-D1490. [PMID: 34850118 PMCID: PMC8729912 DOI: 10.1093/nar/gkab1087] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/11/2021] [Accepted: 11/19/2021] [Indexed: 12/03/2022] Open
Abstract
The Plant Resistance Genes database (PRGdb; http://prgdb.org/prgdb4/) has been greatly expanded, keeping pace with the increasing amount of available knowledge and data (sequenced proteomes, cloned genes, public analysis data, etc.). The easy-to-use style of the database website has been maintained, while an updated prediction tool, more data and a new section have been added. This new section will contain plant resistance transcriptomic experiments, providing additional easy-to-access experimental information. DRAGO3, the tool for automatic annotation and prediction of plant resistance genes behind PRGdb, has been improved in both accuracy and sensitivity, leading to more reliable predictions. PRGdb offers 199 reference resistance genes and 586.652 putative resistance genes from 182 sequenced proteomes. Compared to the previous release, PRGdb 4.0 has increased the number of reference resistance genes from 153 to 199, the number of putative resistance genes from 177K from 76 proteomes to 586K from 182 sequenced proteomes. A new section has been created that collects plant-pathogen transcriptomic data for five species of agricultural interest. Thereby, with these improvements and data expansions, PRGdb 4.0 aims to serve as a reference to the plant scientific community and breeders worldwide, helping to further study plant resistance mechanisms that contribute to fighting pathogens.
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Affiliation(s)
- Joan Calle García
- Sequentia Biotech SL, Calle Comte D'Urgell 240, 08036 Barcelona, Spain
| | - Anna Guadagno
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | | | | | - Ciro Gianmaria Amoroso
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | - Daniela D'Esposito
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | - Giuseppe Andolfo
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | | | | | - Maria Raffaella Ercolano
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
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Petry VS, Stefenon VM, Machado LO, Costa NCFDA, Klabunde GHF, Nodari RO. Patterns of genetic diversity, spatial genetic structure and gene flow in Campomanesia xanthocarpa: insights from SSR markers of different genomic origins. AN ACAD BRAS CIENC 2021; 93:e20210134. [PMID: 34787172 DOI: 10.1590/0001-3765202120210134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/17/2021] [Indexed: 11/21/2022] Open
Abstract
Campomanesia xanthocarpa (Mart.) O. Berg is a South American fruit tree species with important ecological and medicinal properties, which remnants are currently found mainly in isolated forest fragments. In this study, SSR markers from three different genomic origins (gene-linked, nuclear neutral, and organellar) were used to evaluate the patterns of genetic diversity, fine-scale spatial genetic structure and historical gene flow in fragmented forest formations of C. xanthocarpa from the Atlantic Forest in southern Brazil. Our results show that the forest fragments present moderate to high levels of genetic diversity in comparison to species presenting similar life traits, although a trend opposite to expected was observed concerning gene-linked and neutral SSR markers. The fine-scale spatial genetic structure revealed different patterns in short and large distance classes, with a distinct influence of gene-linked and neutral markers in driving the genetic structure in each distance class. The presence of an isolation-by-adaptation pattern implies the need for maintenance of the current remnants to assure the conservation of the private alleles. Finally, as the genetic diversity is found predominantly within forest fragments, programs of seed collection and/or genetic rescue should prioritize a larger number of individuals within each fragment, to increase the sampled diversity.
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Affiliation(s)
- Vanessa S Petry
- Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, SC, Brazil
| | - Valdir M Stefenon
- Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, SC, Brazil.,Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal do Pampa, Rodovia Osvaldo Aranha, BR 290, Km 423, 97307-020 São Gabriel, RS, Brazil
| | - Lilian O Machado
- Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, SC, Brazil
| | - Newton C F DA Costa
- Universidade do Estado de Santa Catarina, Centro de Ciências Agrárias, Av. Luiz de Camões, 2090, 88520-000 Lages, SC, Brazil
| | - Gustavo H F Klabunde
- Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina (EPAGRI), Rod. Antônio Heil, 6800, 88318-112 Itajaí, SC, Brazil
| | - Rubens O Nodari
- Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, SC, Brazil
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Gela T, Ramsay L, Haile TA, Vandenberg A, Bett K. Identification of anthracnose race 1 resistance loci in lentil by integrating linkage mapping and genome-wide association study. THE PLANT GENOME 2021; 14:e20131. [PMID: 34482633 DOI: 10.1002/tpg2.20131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/08/2021] [Indexed: 05/24/2023]
Abstract
Anthracnose, caused byColletotrichum lentis, is a devastating disease of lentil (Lens culinaris Medik.) in western Canada. Growing resistant lentil cultivars is the most cost-effective and environmentally friendly approach to prevent seed yield losses that can exceed 70%. To identify loci conferring resistance to anthracnose race 1 in lentil, biparental quantitative trait loci (QTL) mapping of two recombinant inbred line (RIL) populations was integrated with a genome-wide association study (GWAS) using 200 diverse lentil accessions from a lentil diversity panel. A major-effect QTL (qAnt1.Lc-3) conferring resistance to race 1 was mapped to lentil chromosome 3 and colocated on the lentil physical map for both RIL populations. Clusters of candidate nucleotide-binding leucine-rich repeat (NB-LRR) and other defense-related genes were uncovered within the QTL region. A GWAS detected 14 significant single nucleotide polymorphism (SNP) markers associated with race 1 resistance on chromosomes 3, 4, 5, and 6. The most significant GWAS SNPs on chromosome 3 supported qAnt1.Lc-3 and delineated a region of 1.6 Mb containing candidate resistance genes. The identified SNP markers can be directly applied in marker-assisted selection (MAS) to accelerate the introgression of race 1 resistance in lentil breeding.
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Affiliation(s)
- Tadesse Gela
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Larissa Ramsay
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Teketel A Haile
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Albert Vandenberg
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Kirstin Bett
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan, S7N 5A8, Canada
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