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Sthapit Kandel J, Sandoya GV, Zhou W, Read QD, Mou B, Simko I. Identification of Quantitative Trait Loci Associated with Bacterial Leaf Spot Resistance in Baby Leaf Lettuce. PLANT DISEASE 2022; 106:2583-2590. [PMID: 35285269 DOI: 10.1094/pdis-09-21-2087-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: 06/14/2023]
Abstract
Spring mix is a popular packaged salad that contains lettuce (Lactuca sativa L.) as one of its main ingredients. Plants for baby leaf lettuce (BLL) production are grown at very high densities, which enhances the occurrence of bacterial leaf spot (BLS) caused by Xanthomonas hortorum pv. vitians (Xhv), a disease that can make the crop unmarketable. The market demands disease-free, high-quality BLL all year round. Growing highly BLS-resistant cultivars will reduce loss of yield and quality, thus minimizing economic detriment to lettuce and spring mix growers. The research objectives were to identify lettuce accessions resistant to BLS and associated quantitative trait loci (QTL). A total of 495 lettuce accessions were screened with six isolates (BS0347, BS2861, BS3127, L7, L44, and Sc8B) of Xhv. Accessions showing overall high-level resistance to all tested Xhv isolates were 'Bunte Forellen', PI 226514, 'La Brillante', ARM09-161-10-1-4, 'Grenadier', 'Bella', PI 491210, 'Delight', and 'Romana Verde del Mercado'. Genome-wide association studies of BLS resistance by mixed linear model analyses identified significant QTLs on four lettuce chromosomes (2, 4, 6, and 8). The most significant QTL was on Chromosome 8 (P = 1.42 × 10-7), which explained 6.7% of total phenotypic variation for the disease severity. Accessions with a high level of resistance detected in this study are valuable resources for lettuce germplasm improvement. Molecular markers closely linked to QTLs can be considered for marker-assisted selection to develop new BLL lettuce cultivars with resistance to multiple races of Xhv.
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Affiliation(s)
- Jinita Sthapit Kandel
- U.S. Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905
| | - Germán V Sandoya
- Horticultural Sciences Department, Everglades Research and Education Center, University of Florida, Belle Glade, FL 33430
| | - Wei Zhou
- U.S. Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905
| | - Quentin D Read
- U.S. Department of Agriculture, Agricultural Research Service, Southeast Area, North Carolina State University, Raleigh, NC 27607
| | - Beiquan Mou
- U.S. Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905
| | - Ivan Simko
- U.S. Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905
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Rosenthal E, Potnis N, Bull CT. Comparative Genomic Analysis of the Lettuce Bacterial Leaf Spot Pathogen, Xanthomonas hortorum pv. vitians, to Investigate Race Specificity. Front Microbiol 2022; 13:840311. [PMID: 35516433 PMCID: PMC9062649 DOI: 10.3389/fmicb.2022.840311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/09/2022] [Indexed: 01/01/2023] Open
Abstract
Bacterial leaf spot (BLS) of lettuce caused by Xanthomonas hortorum pv. vitians (Xhv) was first described over 100 years ago and remains a significant threat to lettuce cultivation today. This study investigated the genetic relatedness of the Xhv strains and the possible genetic sources of this race-specific pathogenicity. Whole genome sequences of eighteen Xhv strains representing the three races, along with eight related Xanthomonas strains, were included in the analysis. A maximum likelihood phylogeny based on concatenated whole genome SNPs confirmed previous results describing two major lineages of Xhv strains. Gene clusters encoding secretion systems, secondary metabolites, and bacteriocins were assessed to identify putative virulence factors that distinguish the Xhv races. Genome sequences were mined for effector genes, which have been shown to be involved in race specificity in other systems. Two effectors identified in this study, xopAQ and the novel variant xopAF2, were revealed as possible mediators of a gene-for-gene interaction between Xhv race 1 and 3 strains and wild lettuce Lactuca serriola ARM-09-161-10-1. Transposase sequence identified downstream of xopAF2 and prophage sequence found nearby within Xhv race 1 and 3 insertion sequences suggest that this gene may have been acquired through phage-mediated gene transfer. No other factors were identified from these analyses that distinguish the Xhv races.
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Affiliation(s)
- Emma Rosenthal
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
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Dia NC, Morinière L, Cottyn B, Bernal E, Jacobs J, Koebnik R, Osdaghi E, Potnis N, Pothier J. Xanthomonas hortorum - beyond gardens: Current taxonomy, genomics, and virulence repertoires. MOLECULAR PLANT PATHOLOGY 2022; 23:597-621. [PMID: 35068051 PMCID: PMC8995068 DOI: 10.1111/mpp.13185] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 05/02/2023]
Abstract
TAXONOMY Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Lysobacterales (earlier synonym of Xanthomonadales); Family Lysobacteraceae (earlier synonym of Xanthomonadaceae); Genus Xanthomonas; Species X. hortorum; Pathovars: pv. carotae, pv. vitians, pv. hederae, pv. pelargonii, pv. taraxaci, pv. cynarae, and pv. gardneri. HOST RANGE Xanthomonas hortorum affects agricultural crops, and horticultural and wild plants. Tomato, carrot, artichoke, lettuce, pelargonium, ivy, and dandelion were originally described as the main natural hosts of the seven separate pathovars. Artificial inoculation experiments also revealed other hosts. The natural and experimental host ranges are expected to be broader than initially assumed. Additionally, several strains, yet to be assigned to a pathovar within X. hortorum, cause diseases on several other plant species such as peony, sweet wormwood, lavender, and oak-leaf hydrangea. EPIDEMIOLOGY AND CONTROL X. hortorum pathovars are mainly disseminated by infected seeds (e.g., X. hortorum pvs carotae and vitians) or cuttings (e.g., X. hortorum pv. pelargonii) and can be further dispersed by wind and rain, or mechanically transferred during planting and cultivation. Global trade of plants, seeds, and other propagating material constitutes a major pathway for their introduction and spread into new geographical areas. The propagules of some pathovars (e.g., X. horturum pv. pelargonii) are spread by insect vectors, while those of others can survive in crop residues and soils, and overwinter until the following growing season (e.g., X. hortorum pvs vitians and carotae). Control measures against X. hortorum pathovars are varied and include exclusion strategies (i.e., by using certification programmes and quarantine regulations) to multiple agricultural practices such as the application of phytosanitary products. Copper-based compounds against X. hortorum are used, but the emergence of copper-tolerant strains represents a major threat for their effective management. With the current lack of efficient chemical or biological disease management strategies, host resistance appears promising, but is not without challenges. The intrastrain genetic variability within the same pathovar poses a challenge for breeding cultivars with durable resistance. USEFUL WEBSITES https://gd.eppo.int/taxon/XANTGA, https://gd.eppo.int/taxon/XANTCR, https://gd.eppo.int/taxon/XANTPE, https://www.euroxanth.eu, http://www.xanthomonas.org, http://www.xanthomonas.org/dokuwiki.
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Affiliation(s)
- Nay C. Dia
- Environmental Genomics and Systems Biology Research GroupInstitute for Natural Resource SciencesZurich University of Applied SciencesWädenswilSwitzerland
- Molecular Plant BreedingInstitute of Agricultural SciencesETH ZurichZurichSwitzerland
| | - Lucas Morinière
- University of LyonUniversité Claude Bernard Lyon 1CNRSINRAEUMR Ecologie MicrobienneVilleurbanneFrance
| | - Bart Cottyn
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and FoodMerelbekeBelgium
| | - Eduardo Bernal
- Department of Plant PathologyThe Ohio State UniversityColumbusOhioUSA
| | - Jonathan M. Jacobs
- Department of Plant PathologyThe Ohio State UniversityColumbusOhioUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOhioUSA
| | - Ralf Koebnik
- Plant Health Institute of MontpellierUniversity of Montpellier, CIRAD, INRAe, Institut Agro, IRDMontpellierFrance
| | - Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Neha Potnis
- Department of Entomology and Plant PathologyAuburn UniversityAlabamaUSA
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research GroupInstitute for Natural Resource SciencesZurich University of Applied SciencesWädenswilSwitzerland
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Morinière L, Burlet A, Rosenthal ER, Nesme X, Portier P, Bull CT, Lavire C, Fischer-Le Saux M, Bertolla F. Clarifying the taxonomy of the causal agent of bacterial leaf spot of lettuce through a polyphasic approach reveals that Xanthomonas cynarae Trébaol et al. 2000 emend. Timilsina et al. 2019 is a later heterotypic synonym of Xanthomonas hortorum Vauterin et al. 1995. Syst Appl Microbiol 2020; 43:126087. [PMID: 32690196 DOI: 10.1016/j.syapm.2020.126087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/21/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022]
Abstract
Assessment of the taxonomy and diversity of Xanthomonas strains causing bacterial leaf spot of lettuce (BLSL), commonly referred to as Xanthomonas campestris pv. vitians, has been a long-lasting issue which held back the global efforts made to understand this pathogen. In order to provide a sound basis essential to its study, we conducted a polyphasic approach on strains obtained through sampling campaigns or acquired from collections. Results of a multilocus sequence analysis crossed with phenotypic assays revealed that the pathotype strain does not match the description of the nomenspecies provided by Brown in 1918. However, strain LMG 938=CFBP 8686 does fit this description. Therefore, we propose that it replaces LMG 937=CFBP 2538 as pathotype strain of X. campestris pv. vitians. Then, whole-genome based phylogenies and overall genome relatedness indices calculated on taxonomically relevant strains exhibited the intermediate position of X. campestris pv. vitians between closely related species Xanthomonas hortorum and Xanthomonas cynarae. Phenotypic profiles characterized using Biolog microplates did not reveal stable diagnostic traits legitimizing their distinction. Therefore, we propose that X. cynarae Trébaol et al. 2000 emend. Timilsina et al. 2019 is a later heterotypic synonym of X. hortorum, to reclassify X. campestris pv. vitians as X. hortorum pv. vitians comb. nov. and to transfer X. cynarae pathovars in X. hortorum as X. hortorum pv. cynarae comb. nov. and X. hortorum pv. gardneri comb. nov. An emended description of X. hortorum is provided, making this extended species a promising model for the study of Xanthomonas quick adaptation to different hosts.
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Affiliation(s)
- Lucas Morinière
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
| | - Alexandre Burlet
- Station d'Expérimentation Rhône-Alpes Information Légumes, SERAIL, 69126 Brindas, France
| | - Emma R Rosenthal
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA
| | - Xavier Nesme
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
| | - Perrine Portier
- IRHS, INRAE, Agrocampus-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA
| | - Céline Lavire
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
| | - Marion Fischer-Le Saux
- IRHS, INRAE, Agrocampus-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France.
| | - Franck Bertolla
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
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Curland RD, Gao L, Hirsch CD, Ishimaru CA. Localized Genetic and Phenotypic Diversity of Xanthomonas translucens Associated With Bacterial Leaf Streak on Wheat and Barley in Minnesota. PHYTOPATHOLOGY 2020; 110:257-266. [PMID: 31448998 DOI: 10.1094/phyto-04-19-0134-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial leaf streak (BLS) of wheat and barley has been a disease of increasing concern in the Upper Midwest over the past decade. In this study, intra- and interfield genetic and pathogenic diversity of bacteria causing BLS in Minnesota was evaluated. In 2015, 89 strains were isolated from 100 leaf samples collected from two wheat and two barley fields naturally infected with BLS. Virulence assays and multilocus sequence alignments of four housekeeping genes supported pathovar identifications. All wheat strains were pathogenic on wheat and barley and belonged to the same lineage as the Xanthomonas translucens pv. undulosa-type strain. All barley strains were pathogenic on barley but not on wheat. Three lineages of barley strains were detected. The frequency and number of sequence types of each pathovar varied within and between fields. A significant population variance was detected between populations of X. translucens pv. undulosa collected from different wheat fields. Population stratification of X. translucens pv. translucens was not detected. Significant differences in virulence were detected among three dominant sequence types of X. translucens pv. undulosa but not those of X. translucens pv. translucens. Field trials with wheat and barley plants inoculated with strains of known sequence type and virulence did not detect significant race structures within either pathovar. Knowledge of virulence, sequence types, and population structures of X. translucens on wheat and barley can support studies on plant-bacterial interactions and breeding for BLS disease resistance.
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Affiliation(s)
- Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Liangliang Gao
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Carol A Ishimaru
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Curland RD, Gao L, Bull CT, Vinatzer BA, Dill-Macky R, Van Eck L, Ishimaru CA. Genetic Diversity and Virulence of Wheat and Barley Strains of Xanthomonas translucens from the Upper Midwestern United States. PHYTOPATHOLOGY 2018; 108:443-453. [PMID: 29165007 DOI: 10.1094/phyto-08-17-0271-r] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial leaf streak (BLS) of wheat and barley, caused by Xanthomonas translucens pv. undulosa and X. translucens pv. translucens, has been of growing concern in small grains production in the Upper Midwestern United States. To optimize disease resistance breeding, a greater awareness is needed of the pathovars and genetic diversity within the pathogens causing BLS in the region. Multilocus sequencing typing (MLST) and analysis (MLSA) of four common housekeeping genes (rpoD, dnaK, fyuA, and gyrB) was used to evaluate the genetic diversity of 82 strains of X. translucens isolated between 2006 and 2013 from wheat, barley, rye, and intermediate wheatgrass. In addition, in planta disease assays were conducted on 75 strains to measure relative virulence in wheat and barley. All strains were determined by MLSA to be related to X. translucens pv. undulosa and X. translucens pv. translucens. Clustering of strains based on Bayesian, network, and minimum spanning trees correlated with relative virulence levels in inoculated wheat and barley. Thus, phylogeny based on rpoD, dnaK, fyuA, and gyrB correlated with host of isolation and was an effective means for predicting virulence of strains belonging to X. translucens pv. translucens and X. translucens pv. undulosa.
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Affiliation(s)
- Rebecca D Curland
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Liangliang Gao
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Carolee T Bull
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Boris A Vinatzer
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Ruth Dill-Macky
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Leon Van Eck
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Carol A Ishimaru
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
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