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Chen C, Keunecke H, Bemm F, Gyetvai G, Neu E, Kopisch‐Obuch FJ, McDonald BA, Stapley J. GWAS reveals a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogen. MOLECULAR PLANT PATHOLOGY 2024; 25:e13407. [PMID: 38009399 PMCID: PMC10799204 DOI: 10.1111/mpp.13407] [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: 07/31/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
The major resistance gene BvCR4 recently bred into sugar beet hybrids provides a high level of resistance to Cercospora leaf spot caused by the fungal pathogen Cercospora beticola. The occurrence of pathogen strains that overcome BvCR4 was studied using field trials in Switzerland conducted under natural disease pressure. Virulence of a subset of these strains was evaluated in a field trial conducted under elevated artificial disease pressure. We created a new C. beticola reference genome and mapped whole genome sequences of 256 isolates collected in Switzerland and Germany. These were combined with virulence phenotypes to conduct three separate genome-wide association studies (GWAS) to identify candidate avirulence genes. We identified a locus associated with avirulence containing a putative avirulence effector gene named AvrCR4. All virulent isolates either lacked AvrCR4 or had nonsynonymous mutations within the gene. AvrCR4 was present in all 74 isolates from non-BvCR4 hybrids, whereas 33 of 89 isolates from BvCR4 hybrids carried a deletion. We also mapped genomic data from 190 publicly available US isolates to our new reference genome. The AvrCR4 deletion was found in only one of 95 unique isolates from non-BvCR4 hybrids in the United States. AvrCR4 presents a unique example of an avirulence effector in which virulent alleles have only recently emerged. Most likely these were selected out of standing genetic variation after deployment of BvCR4. Identification of AvrCR4 will enable real-time screening of C. beticola populations for the emergence and spread of virulent isolates.
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Affiliation(s)
- Chen Chen
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZürichSwitzerland
| | | | | | | | - Enzo Neu
- KWS SAAT SE & Co. KGaAEinbeckGermany
| | | | - Bruce A. McDonald
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZürichSwitzerland
| | - Jessica Stapley
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZürichSwitzerland
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2
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Wolff K, Friedhoff R, Schwarzer F, Pucker B. Data literacy in genome research. J Integr Bioinform 2023; 20:jib-2023-0033. [PMID: 38047760 PMCID: PMC10777367 DOI: 10.1515/jib-2023-0033] [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: 09/02/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023] Open
Abstract
With an ever increasing amount of research data available, it becomes constantly more important to possess data literacy skills to benefit from this valuable resource. An integrative course was developed to teach students the fundamentals of data literacy through an engaging genome sequencing project. Each cohort of students performed planning of the experiment, DNA extraction, nanopore sequencing, genome sequence assembly, prediction of genes in the assembled sequence, and assignment of functional annotation terms to predicted genes. Students learned how to communicate science through writing a protocol in the form of a scientific paper, providing comments during a peer-review process, and presenting their findings as part of an international symposium. Many students enjoyed the opportunity to own a project and to work towards a meaningful objective.
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Affiliation(s)
- Katharina Wolff
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Ronja Friedhoff
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Friderieke Schwarzer
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
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3
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Khoshnami M, Zare B, Mardani-Mehrabad H, Rakhshandehroo F, Baghery MA, Malboobi MA. Assessment of co-infection with BNYVV and BSCTV on resistance against Rhizomania disease in transgenic sugar beet plants. Transgenic Res 2023; 32:475-485. [PMID: 37656262 DOI: 10.1007/s11248-023-00364-8] [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: 09/13/2022] [Accepted: 08/17/2023] [Indexed: 09/02/2023]
Abstract
Sugar beet is an economically important crop and one of the major sources of sucrose around the world. Beet necrotic yellow vein virus (BNYVV) and Beet severe curly top virus (BSCTV) are two widespread viruses in sugar beet that cause severe damage to its performance. Previously, we have successfully produced resistance to BNYVV based on RNA silencing in sugar beet by introducing constructs carrying the viral coat-protein-encoding DNA sequence, CP21, in sense and anti-sense orientations. Yet, the RNA silencing-mediated resistance to a specific virus could be affected by other ones as a part of synergistic interactions. In this study, we assayed the specificity of the induced resistance against BNYVV in two sets of transgenic events, S3 and S6 carrying 5'-UTR with or without CP21-coding sequences, respectively. These events were subjected to viral challenges with either BNYVV, an Iranian isolate of BSCTV (BSCTV-Ir) or both. All the plants inoculated with just BSCTV-Ir displayed curly-leaf symptoms. However, partial resistance was evident in S3 events as shown by mild symptoms and reduced PCR amplification of the BSCTV-Ir coat protein encoding sequence. Based on the presented data, resistance to BNYVV was stable in almost all the transgenic plants co-infected with BSCTV-Ir, except for one event, S3-229. In general, it seems that the co-infection does not affect the resistance to BNYVV in transgenic plants. These findings demonstrated that the introduced RNA silencing-mediated resistance against BNYVV in transgenic sugar beets is specific and is not suppressed after co-infection with a heterologous virus.
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Affiliation(s)
- Maryam Khoshnami
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Pazhouhesh Boulevard, Karaj Highway, Tehran, Iran
- Department of Plant Pathology, College of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, Shohadaye Hesarak Boulevard, Daneshgah Square, Satary Highway, Tehran, Iran
| | - Bahar Zare
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Pazhouhesh Boulevard, Karaj Highway, Tehran, Iran
| | - Hamideh Mardani-Mehrabad
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Pazhouhesh Boulevard, Karaj Highway, Tehran, Iran
- Department of Plant Pathology, College of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, Shohadaye Hesarak Boulevard, Daneshgah Square, Satary Highway, Tehran, Iran
| | - Farshad Rakhshandehroo
- Department of Plant Pathology, College of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, Shohadaye Hesarak Boulevard, Daneshgah Square, Satary Highway, Tehran, Iran
| | - Mohammad Amin Baghery
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Pazhouhesh Boulevard, Karaj Highway, Tehran, Iran
| | - Mohammad Ali Malboobi
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Pazhouhesh Boulevard, Karaj Highway, Tehran, Iran.
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4
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Piau M, Schmitt-Keichinger C. The Hypersensitive Response to Plant Viruses. Viruses 2023; 15:2000. [PMID: 37896777 PMCID: PMC10612061 DOI: 10.3390/v15102000] [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: 09/11/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Plant proteins with domains rich in leucine repeats play important roles in detecting pathogens and triggering defense reactions, both at the cellular surface for pattern-triggered immunity and in the cell to ensure effector-triggered immunity. As intracellular parasites, viruses are mostly detected intracellularly by proteins with a nucleotide binding site and leucine-rich repeats but receptor-like kinases with leucine-rich repeats, known to localize at the cell surface, have also been involved in response to viruses. In the present review we report on the progress that has been achieved in the last decade on the role of these leucine-rich proteins in antiviral immunity, with a special focus on our current understanding of the hypersensitive response.
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Wang L, Zhang Z, Han P, Liang Y, Zhang H, Fu Z, Zhao S, E Y, Zhang H, Wu X, Zhang B, Chang Y, Tang K, Zheng W, Chen L, Wang R, Gao W, Hasi A, Li X, Bai C. Association analysis of agronomic traits and construction of genetic networks by resequencing of 306 sugar beet (Beta vulgaris L.) lines. Sci Rep 2023; 13:15422. [PMID: 37723186 PMCID: PMC10507079 DOI: 10.1038/s41598-023-42182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023] Open
Abstract
Due to the relatively brief domestication history of sugar beet (Beta vulgaris ssp. vulgaris), our understanding of the genomic diversity and functional genes in its cultivars is limited, resulting in slow breeding progress. To address this issue, a total of 306 germplasm materials of major cultivars and breeding lines from China, the USA, and Europe were selected for genome resequencing. We investigated population structure and genetic diversity and performed selective scanning of genomic regions, identifying six novel genes associated with important agronomic traits: the candidate genes DFAX2 and P5CS for skin roughness; the candidate genes FRO5, GL24, and PPR91 for root yield and sugar yield, and the pleiotropic candidate gene POLX for flourishing growth vigour, plant height, crown size, flesh coarseness, and sugar yield. In addition, we constructed a protein-protein interaction network map and a phenotype-gene network map, which provide valuable information for identifying and characterizing functional genes affecting agronomic traits in sugar beet. Overall, our study sheds light on the future improvement of sugar beet agronomic traits at the molecular level.
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Affiliation(s)
- Liang Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Ziqiang Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Pingan Han
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yahui Liang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Huizhong Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Zengjuan Fu
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Shangmin Zhao
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yuanyuan E
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hui Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Xinrong Wu
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Bizhou Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yue Chang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Kuangang Tang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Wenzhe Zheng
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Li Chen
- College of Modern Agriculture and Ecological Environment, Heilongjiang University, Heilongjiang, China
| | - Ronghua Wang
- Beet Breeding and Seed Processing Laboratory, Institute for Sugar Beet Research, Shihezi Academy of Agricultural Sciences, Shihezi, China
| | - Weishi Gao
- Research Industrial of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumuqi, China
| | - Agula Hasi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Xiaodong Li
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.
| | - Chen Bai
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.
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Liu D, Tan W, Wang H, Li W, Fu J, Li J, Zhou Y, Lin M, Xing W. Genetic diversity and genome-wide association study of 13 agronomic traits in 977 Beta vulgaris L. germplasms. BMC Genomics 2023; 24:413. [PMID: 37488485 PMCID: PMC10364417 DOI: 10.1186/s12864-023-09522-y] [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: 03/09/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Sugar beet (Beta vulgaris L.) is an economically essential sugar crop worldwide. Its agronomic traits are highly diverse and phenotypically plastic, influencing taproot yield and quality. The National Beet Medium-term Gene Bank in China maintains more than 1700 beet germplasms with diverse countries of origin. However, it lacks detailed genetic background associated with morphological variability and diversity. RESULTS Here, a comprehensive genome-wide association study (GWAS) of 13 agronomic traits was conducted in a panel of 977 sugar beet accessions. Almost all phenotypic traits exhibited wide genetic diversity and high coefficient of variation (CV). A total of 170,750 high-quality single-nucleotide polymorphisms (SNPs) were obtained using the genotyping-by-sequencing (GBS). Neighbour-joining phylogenetic analysis, principal component analysis, population structure and kinship showed no obvious relationships among these genotypes based on subgroups or regional sources. GWAS was carried out using a mixed linear model, and 159 significant associations were detected for these traits. Within the 25 kb linkage disequilibrium decay of the associated markers, NRT1/PTR FAMILY 6.3 (BVRB_5g097760); nudix hydrolase 15 (BVRB_8g182070) and TRANSPORT INHIBITOR RESPONSE 1 (BVRB_8g181550); transcription factor MYB77 (BVRB_2g023500); and ethylene-responsive transcription factor ERF014 (BVRB_1g000090) were predicted to be strongly associated with the taproot traits of root groove depth (RGD); root shape (RS); crown size (CS); and flesh colour (FC), respectively. For the aboveground traits, UDP-glycosyltransferase 79B6 (BVRB_9g223780) and NAC domain-containing protein 7 (BVRB_5g097990); F-box protein At1g10780 (BVRB_6g140760); phosphate transporter PHO1 (BVRB_3g048660); F-box protein CPR1 (BVRB_8g181140); and transcription factor MYB77 (BVRB_2g023500) and alcohol acyltransferase 9 (BVRB_2g023460) might be associated with the hypocotyl colour (HC); plant type (PT); petiole length (PL); cotyledon size (C); and fascicled leaf type (FLT) of sugar beet, respectively. AP-2 complex subunit mu (BVRB_5g106130), trihelix transcription factor ASIL2 (BVRB_2g041790) and late embryogenesis abundant protein 18 (BVRB_5g106150) might be involved in pollen quantity (PQ) variation. The candidate genes extensively participated in hormone response, nitrogen and phosphorus transportation, secondary metabolism, fertilization and embryo maturation. CONCLUSIONS The genetic basis of agronomical traits is complicated in heterozygous diploid sugar beet. The putative valuable genes found in this study will help further elucidate the molecular mechanism of each phenotypic trait for beet breeding.
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Affiliation(s)
- Dali Liu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Wenbo Tan
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Hao Wang
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Wangsheng Li
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Jingjing Fu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Jiajia Li
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Yuanhang Zhou
- Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Ming Lin
- Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Wang Xing
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China.
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China.
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Felkel S, Dohm JC, Himmelbauer H. Genomic variation in the genus Beta based on 656 sequenced beet genomes. Sci Rep 2023; 13:8654. [PMID: 37244945 DOI: 10.1038/s41598-023-35691-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/22/2023] [Indexed: 05/29/2023] Open
Abstract
Cultivated beets (Beta vulgaris ssp. vulgaris) constitute important crop plants, in particular sugar beet as an indispensable source of sucrose. Several species of wild beets of the genus Beta with distribution along the European Atlantic coast, Macaronesia, and throughout the Mediterranean area exist. Thorough characterization of beet genomes is required for straightforward access to genes promoting genetic resistance against biotic and abiotic stress. Analysing short-read data of 656 sequenced beet genomes, we identified 10 million variant positions in comparison to the sugar beet reference genome RefBeet-1.2. The main groups of species and subspecies were distinguishable based on shared variation, and the separation of sea beets (Beta vulgaris ssp. maritima) into a Mediterranean and an Atlantic subgroup as suggested by previous studies could be confirmed. Complementary approaches of variant-based clustering were employed based on PCA, genotype likelihoods, tree calculations, and admixture analysis. Outliers suggested the occurrence of inter(sub)specific hybridisation, independently confirmed by different analyses. Screens for regions under artificial selection in the sugar beet genome identified 15 Mbp of the genome as variation-poor, enriched for genes involved in shoot system development, stress response, and carbohydrate metabolism. The resources presented herein will be valuable for crop improvement and wild species monitoring and conservation efforts, and for studies on beet genealogy, population structure and population dynamics. Our study provides a wealth of data for in-depth analyses of further aspects of the beet genome towards a thorough understanding of the biology of this important complex of a crop species and its wild relatives.
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Affiliation(s)
- Sabine Felkel
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
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Song S, Wang J, Yang X, Zhang X, Xin X, Liu C, Zou J, Cheng X, Zhang N, Hu Y, Wang J, Chen Q, Xin D. GsRSS3L, a Candidate Gene Underlying Soybean Resistance to Seedcoat Mottling Derived from Wild Soybean (Glycine soja Sieb. and Zucc). Int J Mol Sci 2022; 23:ijms23147577. [PMID: 35886929 PMCID: PMC9318458 DOI: 10.3390/ijms23147577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022] Open
Abstract
Soybeans are a major crop that produce the best vegetable oil and protein for use in food and beverage products worldwide. However, one of the most well-known viral infections affecting soybeans is the Soybean Mosaic Virus (SMV), a member of the Potyviridae family. A crucial method for preventing SMV damage is the breeding of resistant soybean cultivars. Adult resistance and resistance of seedcoat mottling are two types of resistance to SMV. Most studies have focused on adult-plant resistance but not on the resistance to seedcoat mottling. In this study, chromosome segment-substituted lines derived from a cross between Suinong14 (cultivated soybean) and ZYD00006 (wild soybean) were used to identify the chromosome region and candidate genes underlying soybean resistance to seed coat mottling. Herein, two quantitative trait loci (QTLs) were found on chromosome 17, and eighteen genes were found in the QTL region. RNA-seq was used to evaluate the differentially expressed genes (DEGs) among the eighteen genes located in the QTLs. According to the obtained data, variations were observed in the expression of five genes following SMV infection. Furthermore, Nicotiana benthamiana was subjected to an Agrobacterium-mediated transient expression assay to investigate the role of the five candidate genes in SMV resistance. It has also been revealed that Glyma.17g238900 encoding a RICE SALT SENSITIVE 3-like protein (RSS3L) can inhibit the multiplication of SMV in N.benthamiana. Moreover, two nonsynonymous single-nucleotide polymorphisms (SNPs) were found in the coding sequence of Glyma.17g238900 derived from the wild soybean ZYD00006 (GsRSS3L), and the two amino acid mutants may be associated with SMV resistance. Hence, it has been suggested that GsRSS3L confers seedcoat mottling resistance, shedding light on the mechanism of soybean resistance to SMV.
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9
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Andolfo G, Dohm JC, Himmelbauer H. Prediction of NB-LRR resistance genes based on full-length sequence homology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1592-1602. [PMID: 35365907 PMCID: PMC9322396 DOI: 10.1111/tpj.15756] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/10/2022] [Accepted: 03/29/2022] [Indexed: 05/11/2023]
Abstract
The activation of plant immunity is mediated by resistance (R)-gene receptors, also known as nucleotide-binding leucine-rich repeat (NB-LRR) genes, which in turn trigger the authentic defense response. R-gene identification is a crucial goal for both classic and modern plant breeding strategies for disease resistance. The conventional method identifies NB-LRR genes using a protein motif/domain-based search (PDS) within an automatically predicted gene set of the respective genome assembly. PDS proved to be imprecise since repeat masking prior to automatic genome annotation unwittingly prevented comprehensive NB-LRR gene detection. Furthermore, R-genes have diversified in a species-specific manner, so that NB-LRR gene identification cannot be universally standardized. Here, we present the full-length Homology-based R-gene Prediction (HRP) method for the comprehensive identification and annotation of a genome's R-gene repertoire. Our method has substantially addressed the complex genomic organization of tomato (Solanum lycopersicum) NB-LRR gene loci, proving to be more performant than the well-established RenSeq approach. HRP efficiency was also tested on three differently assembled and annotated Beta sp. genomes. Indeed, HRP identified up to 45% more full-length NB-LRR genes compared to previous approaches. HRP also turned out to be a more refined strategy for R-gene allele mining, testified by the identification of hitherto undiscovered Fom-2 homologs in five Cucurbita sp. genomes. In summary, our high-performance method for full-length NB-LRR gene discovery will propel the identification of novel R-genes towards development of improved cultivars.
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Affiliation(s)
- Giuseppe Andolfo
- Department of Agricultural SciencesUniversity of Naples ‘Federico II’Via Università 10080055Portici (Naples)Italy
| | - Juliane C. Dohm
- Institute of Computational Biology, Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaMuthgasse 181190ViennaAustria
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaMuthgasse 181190ViennaAustria
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Lange TM, Rotärmel M, Müller D, Mahone GS, Kopisch-Obuch F, Keunecke H, Schmitt AO. Non-linear transformation of enzyme-linked immunosorbent assay (ELISA) measurements allows usage of linear models for data analysis. Virol J 2022; 19:85. [PMID: 35585588 PMCID: PMC9118653 DOI: 10.1186/s12985-022-01804-3] [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: 01/31/2022] [Accepted: 04/22/2022] [Indexed: 11/12/2022] Open
Abstract
Background In research questions such as in resistance breeding against the Beet necrotic yellow vein virus it is of interest to compare the virus concentrations of samples from different groups. The enzyme-linked immunosorbent assay (ELISA) counts as the standard tool to measure virus concentrations. Simple methods for data analysis such as analysis of variance (ANOVA), however, are impaired due to non-normality of the resulting optical density (OD) values as well as unequal variances in different groups. Methods To understand the relationship between the OD values from an ELISA test and the virus concentration per sample, we used a large serial dilution and modelled its non-linear form using a five parameter logistic regression model. Furthermore, we examined if the quality of the model can be increased if one or several of the model parameters are defined beforehand. Subsequently, we used the inverse of the best model to estimate the virus concentration for every measured OD value. Results We show that the transformed data are essentially normally distributed but provide unequal variances per group. Thus, we propose a generalised least squares model which allows for unequal variances of the groups to analyse the transformed data. Conclusions ANOVA requires normally distributed data as well as equal variances. Both requirements are not met with raw OD values from an ELISA test. A transformation with an inverse logistic function, however, gives the possibility to use linear models for data analysis of virus concentrations. We conclude that this method can be applied in every trial where virus concentrations of samples from different groups are to be compared via OD values from an ELISA test. To encourage researchers to use this method in their studies, we provide an R script for data transformation as well as the data from our trial. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01804-3.
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Affiliation(s)
- Thomas M Lange
- Breeding Informatics Group, University of Göttingen, Margarethe von Wrangell-Weg 7, 37075, Göttingen, Germany
| | - Maria Rotärmel
- Breeding Informatics Group, University of Göttingen, Margarethe von Wrangell-Weg 7, 37075, Göttingen, Germany
| | | | | | | | | | - Armin O Schmitt
- Breeding Informatics Group, University of Göttingen, Margarethe von Wrangell-Weg 7, 37075, Göttingen, Germany. .,Center of Integrated Breeding Research (CiBreed), University of Göttingen, Carl Sprengel-Weg 1, 37075, Göttingen, Germany.
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11
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Sandell FL, Stralis-Pavese N, McGrath JM, Schulz B, Himmelbauer H, Dohm JC. Genomic distances reveal relationships of wild and cultivated beets. Nat Commun 2022; 13:2021. [PMID: 35440134 PMCID: PMC9019029 DOI: 10.1038/s41467-022-29676-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/28/2022] [Indexed: 12/01/2022] Open
Abstract
Cultivated beets (Beta vulgaris ssp. vulgaris), including sugar beet, rank among the most important crops. The wild ancestor of beet crops is the sea beet Beta vulgaris ssp. maritima. Species and subspecies of wild beets are readily crossable with cultivated beets and are thus available for crop improvement. To study genomic relationships in the genus Beta, we sequence and analyse 606 beet genomes, encompassing sugar beet, sea beet, B. v. adanensis, B. macrocarpa, and B. patula. We observe two genetically distinct groups of sea beets, one from the Atlantic coast and the other from the Mediterranean area. Genomic comparisons based on k-mers identify sea beets from Greece as the closest wild relatives of sugar beet, suggesting that domestication of the ancestors of sugar beet may be traced to this area. Our work provides comprehensive insight into the phylogeny of wild and cultivated beets and establishes a framework for classification of further accessions of unknown (sub-)species assignment.
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Affiliation(s)
- Felix L Sandell
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria
| | - Nancy Stralis-Pavese
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria
| | | | | | - Heinz Himmelbauer
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria.
| | - Juliane C Dohm
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Vienna, Austria.
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12
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Trifonova AA, Paradnya ER, Boris KV, Kudryavtsev AM. NBS-LRR Resistance Genes Polymorphism of Sugar Beet Hybrids according to NBS-Profiling Data. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Sielemann K, Pucker B, Schmidt N, Viehöver P, Weisshaar B, Heitkam T, Holtgräwe D. Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. BMC Genomics 2022; 23:113. [PMID: 35139817 PMCID: PMC8830136 DOI: 10.1186/s12864-022-08336-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. Results We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. Conclusion In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08336-8.
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Affiliation(s)
- Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.,Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.,Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,Institute of Plant Biology, TU Braunschweig, Braunschweig, Germany
| | - Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.
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14
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Salgotra RK, Thompson M, Chauhan BS. Unravelling the genetic potential of untapped crop wild genetic resources for crop improvement. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01242-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Wetzel V, Willlems G, Darracq A, Galein Y, Liebe S, Varrelmann M. The Beta vulgaris-derived resistance gene Rz2 confers broad-spectrum resistance against soilborne sugar beet-infecting viruses from different families by recognizing triple gene block protein 1. MOLECULAR PLANT PATHOLOGY 2021; 22:829-842. [PMID: 33951264 PMCID: PMC8232027 DOI: 10.1111/mpp.13066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 05/03/2023]
Abstract
Sugar beet cultivation is dependent on an effective control of beet necrotic yellow vein virus (BNYVV, family Benyviridae), which causes tremendous economic losses in sugar production. As the virus is transmitted by a soilborne protist, the use of resistant cultivars is currently the only way to control the disease. The Rz2 gene product belongs to a family of proteins conferring resistance towards diverse pathogens in plants. These proteins contain coiled-coil and leucine-rich repeat domains. After artificial inoculation of homozygous Rz2 resistant sugar beet lines, BNYVV and beet soilborne mosaic virus (BSBMV, family Benyviridae) were not detected. Analysis of the expression of Rz2 in naturally infected plants indicated constitutive expression in the root system. In a transient assay, coexpression of Rz2 and the individual BNYVV-encoded proteins revealed that only the combination of Rz2 and triple gene block protein 1 (TGB1) resulted in a hypersensitive reaction (HR)-like response. Furthermore, HR was also triggered by the TGB1 homologues from BSBMV as well as from the more distantly related beet soilborne virus (family Virgaviridae). This is the first report of an R gene providing resistance across different plant virus families.
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16
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Dubiella U, Serrano I. The Ubiquitin Proteasome System as a Double Agent in Plant-Virus Interactions. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10050928. [PMID: 34066628 PMCID: PMC8148538 DOI: 10.3390/plants10050928] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 05/03/2023]
Abstract
The ubiquitin proteasome is a rapid, adaptive mechanism for selective protein degradation, crucial for proper plant growth and development. The ubiquitin proteasome system (UPS) has also been shown to be an integral part of plant responses to stresses, including plant defence against pathogens. Recently, significant progress has been made in the understanding of the involvement of the UPS in the signalling and regulation of the interaction between plants and viruses. This review aims to discuss the current knowledge about the response of plant viral infection by the UPS and how the viruses counteract this system, or even use it for their own benefit.
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Affiliation(s)
- Ullrich Dubiella
- KWS SAAT SE & Co. KGaA, Grimsehlstraße 31, 37574 Einbeck, Germany;
| | - Irene Serrano
- Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, 37077 Göttingen, Germany
- Correspondence:
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17
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Lehner R, Blazek L, Minoche AE, Dohm JC, Himmelbauer H. Assembly and characterization of the genome of chard (Beta vulgaris ssp. vulgaris var. cicla). J Biotechnol 2021; 333:67-76. [PMID: 33932500 DOI: 10.1016/j.jbiotec.2021.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/09/2021] [Accepted: 04/25/2021] [Indexed: 10/21/2022]
Abstract
Chard (Beta vulgaris ssp. vulgaris var. cicla) is a member of one of four different cultigroups of beets. While the genome of sugar beet, the most prominent beet crop, has been studied extensively, molecular data on other beet cultivars is scant. Here, we present a genome assembly of chard, a vegetable crop grown for its fleshy leaves. We report a de novo genome assembly of 604 Mbp, slightly larger than sugar beet assemblies presented so far. About 57 % of the assembly was annotated as repetitive sequence, of which LTR retrotransposons were the most abundant. Based on the presence of conserved genes, the chard assembly was estimated to be at least 96 % complete regarding its gene space. We predicted 34,521 genes of which 27,582 genes were supported by evidence from transcriptomic sequencing reads, and 5503 of the evidence-supported genes had multiple isoforms. We compared the chard gene set with gene sets from sugar beet and two wild beets (i.e. Beta vulgaris ssp. maritima and Beta patula) to find orthology relationships and identified genome-wide syntenic regions between chard and sugar beet. Lastly, we determined genomic variants that distinguish sugar beet and chard. Assessing the variation distribution along the chard chromosomes, we found extensive haplotype sharing between the two cultivars. In summary, our work provides a foundation for the molecular analysis of Beta vulgaris cultigroups as a basis for chard genomics and to unravel the domestication history of beet crops.
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Affiliation(s)
- Reinhard Lehner
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Lisa Blazek
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - André E Minoche
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.
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18
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Nóbrega H, Freitas G, Zavattieri MA, Ragonezi C, Pinheiro de Carvalho MÂA. Structure and floristic composition associated with an endangered species Beta patula Aiton (Amaranthaceae) in the Islands of Madeira Archipelago. Biodivers Data J 2021; 9:e61091. [PMID: 33654451 PMCID: PMC7907053 DOI: 10.3897/bdj.9.e61091] [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: 11/24/2020] [Accepted: 01/07/2021] [Indexed: 11/12/2022] Open
Abstract
Background Twenty-two native Crop Wild Relatives (CWR) occur in specific dry environments of Madeira Archipelago, like Desembarcadouro islet in Ponta de São Lourenço and Chão islet in Desertas Islands. Nine of them share the same gene pool with crop species included in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Amongst them, Beta patula Aiton, an IUCN Critically Endangered species, has been studied in detail for in situ and ex situ conservation. The present paper summarises the information recorded during the Beta patula population assessment. Valuable information on plant communities associated with this species was obtained. New information The data provides information of a vegetation census spanning 7 years, from 2014 to 2020, in two uninhabited islets where Beta patula occurs, Desembarcadouro and Chão islets. The collected dataset consists of 1,786 vegetation descriptions, where 31 species were recorded. All generated data have been published and will be used towards the implementation of conservation actions and to establish a middle term management protocol for Beta patula and other CWR in situ conservation in the framework of a genetic reserve. This work is part of a EU LIFE Project, LIFE RECOVER NATURA and was conducted by members of the ISOPlexis Center, University of Madeira.
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Affiliation(s)
- Humberto Nóbrega
- ISOPlexis, Centre of Sustainable Agriculture and Food Technology. University of Madeira. Campus da Penteada. 9020-105, Funchal, Portugal ISOPlexis, Centre of Sustainable Agriculture and Food Technology. University of Madeira. Campus da Penteada. 9020-105 Funchal Portugal
| | - Gregório Freitas
- ISOPlexis, Centre of Sustainable Agriculture and Food Technology. University of Madeira. Campus da Penteada. 9020-105, Funchal, Portugal ISOPlexis, Centre of Sustainable Agriculture and Food Technology. University of Madeira. Campus da Penteada. 9020-105 Funchal Portugal
| | - M A Zavattieri
- ISOPlexis, Centre of Sustainable Agriculture and Food Technology. University of Madeira. Campus da Penteada. 9020-105, Funchal, Portugal ISOPlexis, Centre of Sustainable Agriculture and Food Technology. University of Madeira. Campus da Penteada. 9020-105 Funchal Portugal.,Biology Department, Colégio da Mitra, University of Évora, Ap. 94. 7002-554, Évora, Portugal Biology Department, Colégio da Mitra, University of Évora, Ap. 94. 7002-554 Évora Portugal.,Institute of Earth Sciences (ICT), Colégio Luís António Verney, University of Évora. Rua Romão Ramalho, 59. 7002-554, Évora, Portugal Institute of Earth Sciences (ICT), Colégio Luís António Verney, University of Évora. Rua Romão Ramalho, 59. 7002-554 Évora Portugal
| | - Carla Ragonezi
- ISOPlexis, Centre of Sustainable Agriculture and Food Technology. University of Madeira. Campus da Penteada. 9020-105, Funchal, Portugal ISOPlexis, Centre of Sustainable Agriculture and Food Technology. University of Madeira. Campus da Penteada. 9020-105 Funchal Portugal.,CITAB Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Vila Real, Portugal CITAB Centre for the Research and Technology of Agro-Environmental and Biological Sciences Vila Real Portugal
| | - Miguel  A Pinheiro de Carvalho
- ISOPlexis, Centre of Sustainable Agriculture and Food Technology. University of Madeira. Campus da Penteada. 9020-105, Funchal, Portugal ISOPlexis, Centre of Sustainable Agriculture and Food Technology. University of Madeira. Campus da Penteada. 9020-105 Funchal Portugal.,Life Sciences Faculty, University of Madeira. Campus da Penteada. 9020-105, Funchal, Portugal Life Sciences Faculty, University of Madeira. Campus da Penteada. 9020-105 Funchal Portugal.,CITAB Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Vila Real, Portugal CITAB Centre for the Research and Technology of Agro-Environmental and Biological Sciences Vila Real Portugal
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19
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An extreme-phenotype genome-wide association study identifies candidate cannabinoid pathway genes in Cannabis. Sci Rep 2020; 10:18643. [PMID: 33122674 PMCID: PMC7596533 DOI: 10.1038/s41598-020-75271-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
Cannabis produces a class of isoprenylated resorcinyl polyketides known as cannabinoids, a subset of which are medically important and exclusive to this plant. The cannabinoid alkyl group is a critical structural feature that governs therapeutic activity. Genetic enhancement of the alkyl side-chain could lead to the development of novel chemical phenotypes (chemotypes) for pharmaceutical end-use. However, the genetic determinants underlying in planta variation of cannabinoid alkyl side-chain length remain uncharacterised. Using a diversity panel derived from the Ecofibre Cannabis germplasm collection, an extreme-phenotype genome-wide association study (XP-GWAS) was used to enrich for alkyl cannabinoid polymorphic regions. Resequencing of chemotypically extreme pools revealed a known cannabinoid synthesis pathway locus as well as a series of chemotype-associated genomic regions. One of these regions contained a candidate gene encoding a β-keto acyl carrier protein (ACP) reductase (BKR) putatively associated with polyketide fatty acid starter unit synthesis and alkyl side-chain length. Association analysis revealed twenty-two polymorphic variants spanning the length of this gene, including two nonsynonymous substitutions. The success of this first reported application of XP-GWAS for an obligate outcrossing and highly heterozygote plant genus suggests that this approach may have generic application for other plant species.
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20
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Holtgräwe D, Rosleff Soerensen T, Hausmann L, Pucker B, Viehöver P, Töpfer R, Weisshaar B. A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' ( Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping. FRONTIERS IN PLANT SCIENCE 2020; 11:156. [PMID: 32194587 PMCID: PMC7064618 DOI: 10.3389/fpls.2020.00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar 'Börner,' carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of 'Börner' to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 'Börner' genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.
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Affiliation(s)
- Daniela Holtgräwe
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Ludger Hausmann
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Siebeldingen, Germany
| | - Boas Pucker
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Prisca Viehöver
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Reinhard Töpfer
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Siebeldingen, Germany
| | - Bernd Weisshaar
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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21
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Wiśniewska A, Andryka-Dudek P, Czerwiński M, Chołuj D. Fodder beet is a reservoir of drought tolerance alleles for sugar beet breeding. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:120-131. [PMID: 31677543 DOI: 10.1016/j.plaphy.2019.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/12/2019] [Accepted: 10/23/2019] [Indexed: 05/20/2023]
Abstract
Drought leads to serious yield losses and followed by increasing food prices. Thereby, drought tolerance is one of most important, pivotal issues for plant breeding and is determined by the very complex genetic architecture, which involves a lot of genes engaged in many cell processes. Within genomes of currently cultivated sugar beet forms, the number of favourable allelic variants is limited. However, there is a potential to identify genes related to drought tolerance deposited in genomes of wild or fodder relatives. Therefore, the goal of our study, was to identify the source of allelic variants involved in drought tolerance using a large spectrum of sugar or fodder beets and their wild relatives for analyses. Based on the drought tolerance index, calculated for morphophysiological traits, it was demonstrated that some of selected fodder beets showed the highest level of drought tolerance. The most drought tolerant fodder beet genotype did not show differences in the level of expression of genes engaged in osmoprotection and the antioxidative system, between control and drought condition, compared to sugar and wild beets. The genetic distance between selected beet forms was broad and ranged from 18 to 87%, however the most drought tolerant sugar, fodder and wild beets showed high genetic similarity and formed the common clade. Based on obtained results we propose that an adequate broad source of genes related to drought tolerance occurs in fodder beets, the crossing with which is easier, less time-consuming and more cost-effective than with wild forms of beets.
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Affiliation(s)
- Anita Wiśniewska
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland.
| | - Paulina Andryka-Dudek
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Mateusz Czerwiński
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Danuta Chołuj
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
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22
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Rodríguez del Río Á, Minoche AE, Zwickl NF, Friedrich A, Liedtke S, Schmidt T, Himmelbauer H, Dohm JC. Genomes of the wild beets Beta patula and Beta vulgaris ssp. maritima. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1242-1253. [PMID: 31104348 PMCID: PMC9546096 DOI: 10.1111/tpj.14413] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/23/2019] [Accepted: 05/02/2019] [Indexed: 05/04/2023]
Abstract
We present draft genome assemblies of Beta patula, a critically endangered wild beet endemic to the Madeira archipelago, and of the closely related Beta vulgaris ssp. maritima (sea beet). Evidence-based reference gene sets for B. patula and sea beet were generated, consisting of 25 127 and 27 662 genes, respectively. The genomes and gene sets of the two wild beets were compared with their cultivated sister taxon B. vulgaris ssp. vulgaris (sugar beet). Large syntenic regions were identified, and a display tool for automatic genome-wide synteny image generation was developed. Phylogenetic analysis based on 9861 genes showing 1:1:1 orthology supported the close relationship of B. patula to sea beet and sugar beet. A comparative analysis of the Rz2 locus, responsible for rhizomania resistance, suggested that the sequenced B. patula accession was rhizomania susceptible. Reference karyotypes for the two wild beets were established, and genomic rearrangements were detected. We consider our data as highly valuable and comprehensive resources for wild beet studies, B. patula conservation management, and sugar beet breeding research.
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Affiliation(s)
- Álvaro Rodríguez del Río
- University of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
- Present address:
Centro de Biotecnología y Genómica de PlantasUPM – INIA28223MadridSpain
| | - André E. Minoche
- Garvan Institute of Medical ResearchDarlinghurst2010NSWAustralia
| | - Nikolaus F. Zwickl
- University of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
| | - Anja Friedrich
- University of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
- Present address:
FH Campus WienUniversity of Applied Sciences1030ViennaAustria
| | | | | | - Heinz Himmelbauer
- University of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
| | - Juliane C. Dohm
- University of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
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23
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Aubry S. The Future of Digital Sequence Information for Plant Genetic Resources for Food and Agriculture. FRONTIERS IN PLANT SCIENCE 2019; 10:1046. [PMID: 31543884 PMCID: PMC6728410 DOI: 10.3389/fpls.2019.01046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/29/2019] [Indexed: 05/27/2023]
Abstract
The recent debates on the legal status of "digital sequence information" (DSI) at the international level could have extensive consequences for the future of agriculture and food security. A large majority of recent advances in biology, medicine, or agriculture were achieved by sharing and mining of freely accessible sequencing data. It is most probably because of the tremendous success of modern genomics and advances of synthetic biology that concerns were raised about possible fair and equitable ways of sharing data. The DSI concept is relatively new, and all concerned parties agreed upon the need for a clear definition. For example, the extent to which DSI understanding is limited only to genetic sequence data has to be clarified. In this paper, I focus on a subset of DSI essential to humankind: the DSI originating from plant genetic resources for food and agriculture (PGRFA). Two international agreements shape the conservation and use of plant genetic resources: the Convention on Biodiversity and the International Treaty for Plant Genetic Resources for Food and Agriculture. In an attempt to mobilize DSI users and producers involved in research, breeding, and conservation, I describe here how the increasing amount of genomic data, information, and studies interact with the existing legal framework at the global level. Using possible scenarios, I will emphasize the complexity of the issues surrounding DSI for PGRFA and propose potential ways forward for developing an inclusive governance and fair use of these genetic resources.
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Affiliation(s)
- Sylvain Aubry
- Department of Plant and Microbial Science, University of Zurich, Zurich, Switzerland
- Section Genetic Resources and Technology, Swiss Federal Office for Agriculture, Bern, Switzerland
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24
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Weiland JJ, Bornemann K, Neubauer JD, Khan MFR, Bolton MD. Prevalence and Distribution of Beet Necrotic Yellow Vein Virus Strains in North Dakota and Minnesota. PLANT DISEASE 2019; 103:2083-2089. [PMID: 31210599 DOI: 10.1094/pdis-02-19-0360-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Beet necrotic yellow vein virus (BNYVV) is the causal agent of rhizomania, a disease of global importance to the sugar beet industry. The most widely implemented resistance gene to rhizomania to date is Rz1, but resistance has been circumvented by resistance-breaking (RB) isolates worldwide. In an effort to gain greater understanding of the distribution of BNYVV and the nature of RB isolates in Minnesota and eastern North Dakota, sugar beet plants were grown in 594 soil samples obtained from production fields and subsequently were analyzed for the presence of BNYVV as well as coding variability in the viral P25 gene, the gene previously implicated in the RB pathotype. Baiting of virus from the soil with sugar beet varieties possessing no known resistance to rhizomania resulted in a disease incidence level of 10.6% in the region examined. Parallel baiting analysis of sugar beet genotypes possessing Rz1, the more recently introgressed Rz2, and with the combination of Rz1 + Rz2 resulted in a disease incidence level of 4.2, 1.0, and 0.8%, respectively. Virus sequences recovered from sugar beet bait plants possessing resistance genes Rz1 and/or Rz2 exhibited reduced genetic diversity in the P25 gene relative to those recovered from the susceptible genotype while confirming the hypervariable nature of the coding for amino acids (AAs) at position 67 and 68 in the P25 protein. In contrast to previous reports, we did not find an association between any one specific AA signature at these positions and the ability to circumvent Rz1-mediated resistance. The data document ongoing virulence development in BNYVV populations to previously resistant varieties and provide a baseline for the analysis of genetic change in the virus population that may accompany the implementation of new resistance genes to manage rhizomania.
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Affiliation(s)
- John J Weiland
- 1United States Department of Agriculture - Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
| | - Kathrin Bornemann
- 1United States Department of Agriculture - Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
- 2Department of Plant Pathology, North Dakota State University, Fargo, ND
| | - Jonathan D Neubauer
- 1United States Department of Agriculture - Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
| | - Mohamed F R Khan
- 2Department of Plant Pathology, North Dakota State University, Fargo, ND
- 3Department of Plant Pathology, University of Minnesota, St. Paul, MN
| | - Melvin D Bolton
- 1United States Department of Agriculture - Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND
- 2Department of Plant Pathology, North Dakota State University, Fargo, ND
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25
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Vong M, Manny AR, Smith KL, Gao W, Nibert ML. Beta vulgaris mitovirus 1 in diverse cultivars of beet and chard. Virus Res 2019; 265:80-87. [PMID: 30853586 DOI: 10.1016/j.virusres.2019.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/15/2019] [Accepted: 02/17/2019] [Indexed: 01/04/2023]
Abstract
Recent results indicate that mitoviruses, which replicate persistently in host mitochondria, are not restricted to fungi, but instead are found also in plants. Beta vulgaris mitovirus 1 (BevuMV1) is an example first discovered in sugar beet cultivars. For the current study, complete coding sequences of 42 BevuMV1 strains were newly determined, derived from not only sugar beet but also fodder beet, table beet, and Swiss chard cultivars of Beta vulgaris, as well as wild sea beet. BevuMV1 is thus a common phytobiome component of this valuable crop species. Most of the new BevuMV1 sequences originated from RNA extracted from B. vulgaris seed clusters, consistent with vertical transmission of this virus. Results suggest that BevuMV1 entered the B. vulgaris lineage prior to human cultivation and also provides a marker for tracing the maternal ancestry of B. vulgaris cultivars. Especially notable is the monophyletic relationship and limited sequence divergence among BevuMV1 strains from cultivars that are thought or shown to share the "Owen" trait for cytoplasmic male sterility, which is transmitted by maternal mitochondria and has been broadly established in commercial breeding lines of B. vulgaris since the mid-20th century.
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Affiliation(s)
- Minh Vong
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Austin R Manny
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Kathryn L Smith
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - William Gao
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Max L Nibert
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
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26
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Lorang J. Necrotrophic Exploitation and Subversion of Plant Defense: A Lifestyle or Just a Phase, and Implications in Breeding Resistance. PHYTOPATHOLOGY 2019; 109:332-346. [PMID: 30451636 DOI: 10.1094/phyto-09-18-0334-ia] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Breeding disease-resistant plants is a critical, environmentally friendly component of any strategy to sustainably feed and clothe the 9.8 billion people expected to live on Earth by 2050. Here, I review current literature detailing plant defense responses as they relate to diverse biological outcomes; disease resistance, susceptibility, and establishment of mutualistic plant-microbial relationships. Of particular interest is the degree to which these outcomes are a function of plant-associated microorganisms' lifestyles; biotrophic, hemibiotrophic, necrotrophic, or mutualistic. For the sake of brevity, necrotrophic pathogens and the necrotrophic phase of pathogenicity are emphasized in this review, with special attention given to the host-specific pathogens that exploit defense. Defense responses related to generalist necrotrophs and mutualists are discussed in the context of excellent reviews by others. In addition, host evolutionary trade-offs of disease resistance with other desirable traits are considered in the context of breeding for durable disease resistance.
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Affiliation(s)
- Jennifer Lorang
- Department of Botany, 2082 Cordley Hall, Oregon State University, Corvallis 97331
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27
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Fernando Gil J, Liebe S, Thiel H, Lennefors B, Kraft T, Gilmer D, Maiss E, Varrelmann M, Savenkov EI. Massive up-regulation of LBD transcription factors and EXPANSINs highlights the regulatory programs of rhizomania disease. MOLECULAR PLANT PATHOLOGY 2018; 19:2333-2348. [PMID: 30011123 PMCID: PMC6638176 DOI: 10.1111/mpp.12702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Rhizomania of sugar beet, caused by Beet necrotic yellow vein virus (BNYVV), is characterized by excessive lateral root (LR) formation leading to dramatic reduction of taproot weight and massive yield losses. LR formation represents a developmental process tightly controlled by auxin signaling through AUX/IAA-ARF responsive module and LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcriptional network. Several LBD transcription factors play central roles in auxin-regulated LR development and act upstream of EXPANSINS (EXPs), cell wall (CW)-loosening proteins involved in plant development via disruption of the extracellular matrix for CW relaxation and expansion. Here, we present evidence that BNYVV hijacks these auxin-regulated pathways resulting in formation LR and root hairs (RH). We identified an AUX/IAA protein (BvAUX28) as interacting with P25, a viral virulence factor. Mutational analysis indicated that P25 interacts with domains I and II of BvAUX28. Subcellular localization of co-expressed P25 and BvAUX28 showed that P25 inhibits BvAUX28 nuclear localization. Moreover, root-specific LBDs and EXPs were greatly upregulated during rhizomania development. Based on these data, we present a model in which BNYVV P25 protein mimics action of auxin by removing BvAUX28 transcriptional repressor, leading to activation of LBDs and EXPs. Thus, the evidence highlights two pathways operating in parallel and leading to uncontrolled formation of LRs and RHs, the main manifestation of the rhizomania syndrome.
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Affiliation(s)
- Jose Fernando Gil
- Department of Plant BiologyUppsala BioCenter SLU, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology75007UppsalaSweden
| | - Sebastian Liebe
- Institute of Sugar Beet Research, Department of Phytopathology37079GöttingenGermany
| | - Heike Thiel
- Institute of Sugar Beet Research, Department of Phytopathology37079GöttingenGermany
- Present address:
K+S KALI GmbHBertha‐von‐Suttner‐Straße 7,34131KasselGermany
| | | | - Thomas Kraft
- MariboHilleshög Research AB26123LandskronaSweden
| | - David Gilmer
- Institut de biologie moléculaire des plantesCNRS, Université de Strasbourg67084StrasbourgFrance
| | - Edgar Maiss
- Institute of Horticultural Production Systems, Department of PhytomedicineLeibniz University Hannover30419HannoverGermany
| | - Mark Varrelmann
- Institute of Sugar Beet Research, Department of Phytopathology37079GöttingenGermany
| | - Eugene I. Savenkov
- Department of Plant BiologyUppsala BioCenter SLU, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology75007UppsalaSweden
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Monteiro F, Nishimura MT. Structural, Functional, and Genomic Diversity of Plant NLR Proteins: An Evolved Resource for Rational Engineering of Plant Immunity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:243-267. [PMID: 29949721 DOI: 10.1146/annurev-phyto-080417-045817] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants employ a diverse intracellular system of NLR (nucleotide binding-leucine-rich repeat) innate immune receptors to detect pathogens of all types. These receptors represent valuable agronomic traits that plant breeders rely on to maximize yield in the face of devastating pathogens. Despite their importance, the mechanistic underpinnings of NLR-based disease resistance remain obscure. The rapidly increasing numbers of plant genomes are revealing a diverse array of NLR-type immune receptors. In parallel, mechanistic studies are describing diverse functions for NLR immune receptors. In this review, we intend to broadly describe how the structural, functional, and genomic diversity of plant immune receptors can provide a valuable resource for rational engineering of plant immunity.
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Affiliation(s)
- Freddy Monteiro
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280, USA
| | - Marc T Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870;
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29
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Berni R, Cantini C, Romi M, Hausman JF, Guerriero G, Cai G. Agrobiotechnology Goes Wild: Ancient Local Varieties as Sources of Bioactives. Int J Mol Sci 2018; 19:E2248. [PMID: 30071603 PMCID: PMC6121869 DOI: 10.3390/ijms19082248] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 11/23/2022] Open
Abstract
The identification and use of species that have best adapted to their growth territory is of paramount importance to preserve biodiversity while promoting sustainable agricultural practices. Parameters including resistance to natural conditions (biotic and abiotic risk factors), biomass and fruit productivity, and phytochemical content with nutraceutical potential, could be used as quantitative markers of the adaptability of plants to wild environments characterized by minimal human impact. Ancient varieties, which are plant varieties growing in regional territories and not destined for market distribution, are a source of unique genetic characters derived from many years of adaptation to the original territory. These plants are often more resistant to biotic and abiotic stresses. In addition, these varieties have a high phytochemical (also known as bioactives) content considered health-beneficial. Notably, the content of these compounds is often lower in commercial cultivars. The use of selected territorial varieties according to the cultivation area represents an opportunity in the agricultural sector in terms of biodiversity preservation, environmental sustainability, and valorization of the final products. Our survey highlights the nutraceutical potential of ancient local varieties and stresses the importance of holistic studies (-omics) to investigate their physiology and secondary metabolism.
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Affiliation(s)
- Roberto Berni
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, 53100 Siena, Italy.
- Trees and Timber Institute-National Research Council of Italy (CNR-IVALSA), via Aurelia 49, 58022 Follonica (GR), Italy.
| | - Claudio Cantini
- Trees and Timber Institute-National Research Council of Italy (CNR-IVALSA), via Aurelia 49, 58022 Follonica (GR), Italy.
| | - Marco Romi
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, 53100 Siena, Italy.
| | - Jean-Francois Hausman
- Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Gea Guerriero
- Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, 53100 Siena, Italy.
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30
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Funk A, Galewski P, McGrath JM. Nucleotide-binding resistance gene signatures in sugar beet, insights from a new reference genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:659-671. [PMID: 29797366 DOI: 10.1111/tpj.13977] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/19/2018] [Accepted: 05/04/2018] [Indexed: 05/28/2023]
Abstract
Nucleotide-binding (NB-ARC), leucine-rich-repeat genes (NLRs) account for 60.8% of resistance (R) genes molecularly characterized from plants. NLRs exist as large gene families prone to tandem duplication and transposition, with high sequence diversity among crops and their wild relatives. This diversity can be a source of new disease resistance, but difficulty in distinguishing specific sequences from homologous gene family members hinders characterization of resistance for improving crop varieties. Current genome sequencing and assembly technologies, especially those using long-read sequencing, are improving resolution of repeat-rich genomic regions and clarifying locations of duplicated genes, such as NLRs. Using the conserved NB-ARC domain as a model, 231 tentative NB-ARC loci were identified in a highly contiguous genome assembly of sugar beet, revealing diverged and truncated NB-ARC signatures as well as full-length sequences. The NB-ARC-associated proteins contained NLR resistance gene domains, including TIR, CC and LRR, as well as other integrated domains. Phylogenetic relationships of partial and complete domains were determined, and patterns of physical clustering in the genome were evaluated. Comparison of sugar beet NB-ARC domains to validated R-genes from monocots and eudicots suggested extensive Beta vulgaris-specific subfamily expansions. The NLR landscape in the rhizomania resistance conferring Rz region of Chromosome 3 was characterized, identifying 26 NLR-like sequences spanning 20 MB. This work presents the first detailed view of NLR family composition in a member of the Caryophyllales, builds a foundation for additional disease resistance work in B. vulgaris, and demonstrates an additional nucleic-acid-based method for NLR prediction in non-model plant species.
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Affiliation(s)
- Andrew Funk
- Department of Plant, Soil, and Microbial Science, Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Paul Galewski
- Department of Plant, Soil, and Microbial Science, Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI, 48824, USA
| | - J Mitchell McGrath
- USDA-ARS, Sugarbeet and Bean Research Unit, 1066 Bogue Street, 494 PSSB, East Lansing, MI, 48824, USA
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31
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Monteiro F, Frese L, Castro S, Duarte MC, Paulo OS, Loureiro J, Romeiras MM. Genetic and Genomic Tools to Asssist Sugar Beet Improvement: The Value of the Crop Wild Relatives. FRONTIERS IN PLANT SCIENCE 2018; 9:74. [PMID: 29467772 PMCID: PMC5808244 DOI: 10.3389/fpls.2018.00074] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 01/15/2018] [Indexed: 05/21/2023]
Abstract
Sugar beet (Beta vulgaris L. ssp. vulgaris) is one of the most important European crops for both food and sugar production. Crop improvement has been developed to enhance productivity, sugar content or other breeder's desirable traits. The introgression of traits from Crop Wild Relatives (CWR) has been done essentially for lessening biotic stresses constraints, namely using Beta and Patellifolia species which exhibit disease resistance characteristics. Several studies have addressed crop-to-wild gene flow, yet, for breeding programs genetic variability associated with agronomically important traits remains unexplored regarding abiotic factors. To accomplish such association from phenotype-to-genotype, screening for wild relatives occurring in habitats where selective pressures are in play (i.e., populations in salt marshes for salinity tolerance; populations subjected to pathogen attacks and likely evolved resistance to pathogens) are the most appropriate streamline to identify causal genetic information. By selecting sugar beet CWR species based on genomic tools, rather than random variations, is a promising but still seldom explored route toward the development of improved crops. In this perspective, a viable streamline for sugar beet improvement is proposed through the use of different genomic tools by recurring to sugar beet CWRs and focusing on agronomic traits associated with abiotic stress tolerance. Overall, identification of genomic and epigenomic landscapes associated to adaptive ecotypes, along with the cytogenetic and habitat characterization of sugar beet CWR, will enable to identify potential hotspots for agrobiodiversity of sugar beet crop improvement toward abiotic stress tolerance.
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Affiliation(s)
- Filipa Monteiro
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Lothar Frese
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Quedlinburg, Germany
| | - Sílvia Castro
- Department of Life Sciences, Centre for Functional Ecology, Universidade de Coimbra, Coimbra, Portugal
| | - Maria C. Duarte
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, Universidade de Coimbra, Coimbra, Portugal
| | - Maria M. Romeiras
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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32
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Stevanato P, Broccanello C, Pajola L, Biscarini F, Richards C, Panella L, Hassani M, Formentin E, Chiodi C, Concheri G, Heidari B. Targeted Next-Generation Sequencing Identification of Mutations in Disease Resistance Gene Analogs (RGAs) in Wild and Cultivated Beets. Genes (Basel) 2017; 8:genes8100264. [PMID: 29019931 PMCID: PMC5664114 DOI: 10.3390/genes8100264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 11/16/2022] Open
Abstract
Resistance gene analogs (RGAs) were searched bioinformatically in the sugar beet (Beta vulgaris L.) genome as potential candidates for improving resistance against different diseases. In the present study, Ion Torrent sequencing technology was used to identify mutations in 21 RGAs. The DNA samples of ninety-six individuals from six sea beets (Beta vulgaris L. subsp. maritima) and six sugar beet pollinators (eight individuals each) were used for the discovery of single-nucleotide polymorphisms (SNPs). Target amplicons of about 200 bp in length were designed with the Ion AmpliSeq Designer system in order to cover the DNA sequences of the RGAs. The number of SNPs ranged from 0 in four individuals to 278 in the pollinator R740 (which is resistant to rhizomania infection). Among different groups of beets, cytoplasmic male sterile lines had the highest number of SNPs (132) whereas the lowest number of SNPs belonged to O-types (95). The principal coordinates analysis (PCoA) showed that the polymorphisms inside the gene Bv8_184910_pkon (including the CCCTCC sequence) can effectively differentiate wild from cultivated beets, pointing at a possible mutation associated to rhizomania resistance that originated directly from cultivated beets. This is unlike other resistance sources that are introgressed from wild beets. This gene belongs to the receptor-like kinase (RLK) class of RGAs, and is associated to a hypothetical protein. In conclusion, this first report of using Ion Torrent sequencing technology in beet germplasm suggests that the identified sequence CCCTCC can be used in marker-assisted programs to differentiate wild from domestic beets and to identify other unknown disease resistance genes in beet.
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Affiliation(s)
- Piergiorgio Stevanato
- Department of Agronomy, Animals, Natural Resources and Environment-DAFNAE, University of Padova, 35020 Legnaro (Padova), Italy; (P.S.); (C.B.); (L.P.); (C.C.); (G.C.)
| | - Chiara Broccanello
- Department of Agronomy, Animals, Natural Resources and Environment-DAFNAE, University of Padova, 35020 Legnaro (Padova), Italy; (P.S.); (C.B.); (L.P.); (C.C.); (G.C.)
| | - Luca Pajola
- Department of Agronomy, Animals, Natural Resources and Environment-DAFNAE, University of Padova, 35020 Legnaro (Padova), Italy; (P.S.); (C.B.); (L.P.); (C.C.); (G.C.)
| | - Filippo Biscarini
- Cardiff University, School of Medicine, Heath Park, CF14 4XN Cardiff, UK
- Consiglio Nazionale delle Ricerche (CNR), 20133 Milan, Italy;
| | - Chris Richards
- USDA-ARS, National Laboratory for Genetic Resources Preservation, Fort Collins, 80521 CO, USA;
| | - Lee Panella
- Colorado State University, Department of Soil and Crop Sciences, Fort Collins, 80521 CO, USA;
| | - Mahdi Hassani
- Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, 7144165186 Shiraz, Iran; (B.H.); (M.H.)
- Sugar Beet Seed Institute (SBSI), 315854114 Karaj, Iran
| | - Elide Formentin
- Department of Biology, University of Padova, 35131 Padova, Italy
- Correspondence:
| | - Claudia Chiodi
- Department of Agronomy, Animals, Natural Resources and Environment-DAFNAE, University of Padova, 35020 Legnaro (Padova), Italy; (P.S.); (C.B.); (L.P.); (C.C.); (G.C.)
| | - Giuseppe Concheri
- Department of Agronomy, Animals, Natural Resources and Environment-DAFNAE, University of Padova, 35020 Legnaro (Padova), Italy; (P.S.); (C.B.); (L.P.); (C.C.); (G.C.)
| | - Bahram Heidari
- Colorado State University, Department of Soil and Crop Sciences, Fort Collins, 80521 CO, USA;
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