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Wang C, Feng X, Yuan Q, Lin K, Zhang X, Yan L, Nan J, Zhang W, Wang R, Wang L, Xue Q, Yang X, Liu Z, Lin S. Upgrading the genome of an elite japonica rice variety Kongyu 131 for lodging resistance improvement. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:419-432. [PMID: 36382925 PMCID: PMC9884016 DOI: 10.1111/pbi.13963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/08/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Developing a new rice variety requires tremendous efforts and years of input. To improve the defect traits of the excellent varieties becomes more cost and time efficient than breeding a completely new variety. Kongyu 131 is a high-performing japonica variety with early maturity, high yield, wide adaptability and cold resistance, but the poor-lodging resistance hinders the industrial production of Kongyu 131 in the Northeastern China. In this study, we attempted to improve the lodging resistance of Kongyu 131 from perspectives of both gene and trait. On the one hand, by QTL analysis and fine mapping we discovered the candidate gene loci. The following CRISPR/Cas9 and transgenic complementation study confirmed that Sd1 dominated the lodging resistance and favourable allele was mined for precise introduction and improvement. On the other hand, the Sd1 allelic variant was identified in Kongyu 131 by sequence alignment, then introduced another excellent allelic variation by backcrossing. Then, the two new resulting Kongyu 131 went through the field evaluation under different environments, planting densities and nitrogen fertilizer conditions. The results showed that the plant height of upgraded Kongyu 131 was 17%-26% lower than Kongyu 131 without penalty in yield. This study demonstrated a precise and targeted way to update the rice genome and upgrade the elite rice varieties by improving only a few gene defects from the perspective of breeding.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Xiaomin Feng
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhouChina
| | - Qingbo Yuan
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Kangxue Lin
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Xiaohui Zhang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Li Yan
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Jianzong Nan
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Wenqi Zhang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Rongsheng Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Lihong Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Qian Xue
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Xiaowen Yang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Zhixia Liu
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhouChina
| | - Shaoyang Lin
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
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Genotyping and multivariate regression trees reveal ecological diversification within the Microcystis aeruginosa complex along a wide environmental gradient. Appl Environ Microbiol 2021; 88:e0147521. [PMID: 34818109 DOI: 10.1128/aem.01475-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Addressing the ecological and evolutionary processes underlying biodiversity patterns is essential to identify the mechanisms shaping community structure and function. In bacteria, the formation of new ecologically distinct populations (ecotypes) is proposed as one of the main drivers of diversification. New ecotypes arise when mutations in key functional genes or acquisition of new metabolic pathways by horizontal gene transfer allow the population to exploit new resources, permitting their coexistence with the parental population. We previously reported the presence of microcystin-producing organisms of the Microcystis aeruginosa complex (toxic MAC) through an 800 km environmental gradient ranging from freshwater to estuarine-marine waters in South America. We hypothesize that the success of toxic MAC in such a gradient is due to the existence of very closely related populations that are ecologically distinct (ecotypes), each specialized to a specific arrangement of environmental variables. Here, we analyzed toxic MAC genetic diversity through qPCR and high-resolution melting analysis (HRMA) of a functional gene (mcyJ, microcystin synthetase cluster). We explored the variability of the mcyJ gene along the environmental gradient by multivariate classification and regression trees (mCART). Six groups of mcyJ genotypes were distinguished and associated with different combinations of water temperature, conductivity and turbidity. We propose that each mcyJ variant associated to a defined environmental condition is an ecotype (or species) whose relative abundances vary according to their fitness in the local environment. This mechanism would explain the success of toxic MAC in such a wide array of environmental conditions. Importance Organisms of the Microcystis aeruginosa Complex form harmful algal blooms (HABs) in nutrient-rich water bodies worldwide. MAC HABs are difficult to manage owing to the production of potent toxins (microcystins) that resist water treatment. Besides, the role of microcystins in the ecology of MAC organisms is still elusive, meaning that the environmental conditions driving the toxicity of the bloom are not clear. Furthermore, the lack of coherence between morphology-based and genomic-based species classification makes it difficult to draw sound conclusions about when and where each member species of the MAC will dominate the bloom. Here, we propose that the diversification process and success of toxic MAC in a wide range of waterbodies involves the generation of ecotypes, each specialized in a particular niche, whose relative abundance varies according to its fitness in the local environment. This knowledge can improve the generation of accurate prediction models of MAC growth and toxicity, helping to prevent human and animal intoxication.
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Kruk C, Martínez A, Martínez de la Escalera G, Trinchin R, Manta G, Segura AM, Piccini C, Brena B, Yannicelli B, Fabiano G, Calliari D. Rapid freshwater discharge on the coastal ocean as a mean of long distance spreading of an unprecedented toxic cyanobacteria bloom. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142362. [PMID: 33254935 DOI: 10.1016/j.scitotenv.2020.142362] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/21/2020] [Accepted: 09/12/2020] [Indexed: 06/12/2023]
Abstract
Cyanobacterial toxic blooms are a worldwide problem. The Río de la Plata (RdlP) basin makes up about one fourth of South America areal surface, second only to the Amazonian. Intensive agro-industrial land use and the construction of dams have led to generalized eutrophication of main tributaries and increased the intensity and duration of cyanobacteria blooms. Here we analyse the evolution of an exceptional bloom at the low RdlP basin and Atlantic coast during the summer of 2019. A large array of biological, genetic, meteorological, oceanographic and satellite data is combined to discuss the driving mechanisms. The bloom covered the whole stripe of the RdlP estuary and the Uruguayan Atlantic coasts (around 500 km) for approximately 4 months. It was caused by the Microcystis aeruginosa complex (MAC), which produces hepatotoxins (microcystin). Extreme precipitation in the upstream regions of Uruguay and Negro rivers' basins caused high water flows and discharges. The evolution of meteorological and oceanographic conditions as well as the similarity of organisms' traits in the affected area suggest that the bloom originated in eutrophic reservoirs at the lower RdlP basin, Salto Grande in the Uruguay river, and Negro river reservoirs. High temperatures and weak Eastern winds prompted the rapid dispersion of the bloom over the freshwater plume along the RdlP northern and Atlantic coasts. The long-distance rapid drift allowed active MAC organisms to inoculate freshwater bodies from the Atlantic basin, impacting environments relevant for biodiversity conservation. Climate projections for the RdlP basin suggest an increase in precipitation and river water flux, which, in conjunction with agriculture intensification and dams' construction, might turn this extraordinary event into an ordinary situation.
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Affiliation(s)
- Carla Kruk
- Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, UDELAR, Iguá 4225, 11400 Montevideo, Uruguay; Ecología Funcional de Sistemas Acuáticos, Centro Universitario Regional del Este (CURE), UdelaR, Ruta nacional 9 intersección con ruta 15, 27000 Rocha, Uruguay.
| | - Ana Martínez
- Dirección Nacional de Recursos Acuáticos, La Paloma, MGAP, Avenida del Puerto s/n, Puerto la Paloma, La Paloma, CP 27001, Rocha, Uruguay
| | - Gabriela Martínez de la Escalera
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av Italia 3318, 11600 Montevideo, Uruguay
| | - Romina Trinchin
- Departamento de Ciencias de la Atmósfera, Facultad de Ciencias, UDELAR, Iguá 4225, 11400 Montevideo, Uruguay; Instituto Uruguayo de meteorología, Dr Javier Barrios Amorín 1488, 11200 Montevideo, Uruguay
| | - Gastón Manta
- Departamento de Ciencias de la Atmósfera, Facultad de Ciencias, UDELAR, Iguá 4225, 11400 Montevideo, Uruguay
| | - Angel M Segura
- Modelación y Análisis de Recursos Naturales, CURE, UDELAR, Ruta nacional 9 intersección con ruta 15, 27000 Rocha, Uruguay
| | - Claudia Piccini
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av Italia 3318, 11600 Montevideo, Uruguay
| | - Beatriz Brena
- Bioquímica-DEPBIO, Facultad de Química, UDELAR, Av. Gral. Flores 2124, 11800 Montevideo, Uruguay
| | - Beatriz Yannicelli
- Ecología Funcional de Sistemas Acuáticos, Centro Universitario Regional del Este (CURE), UdelaR, Ruta nacional 9 intersección con ruta 15, 27000 Rocha, Uruguay
| | - Graciela Fabiano
- Instituto de Investigaciones Pesqueras, Facultad de Veterinaria, UDELAR, Tomás Basáñez 1160, Montevideo 11400, Uruguay
| | - Danilo Calliari
- Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, UDELAR, Iguá 4225, 11400 Montevideo, Uruguay; Ecología Funcional de Sistemas Acuáticos, Centro Universitario Regional del Este (CURE), UdelaR, Ruta nacional 9 intersección con ruta 15, 27000 Rocha, Uruguay
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Geng L, Li M, Xie S, Wu D, Ye L, Zhang G. Identification of genetic loci and candidate genes related to β-glucan content in barley grain by genome-wide association study in International Barley Core Selected Collection. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:6. [PMID: 37309529 PMCID: PMC10236047 DOI: 10.1007/s11032-020-01199-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/28/2020] [Indexed: 06/13/2023]
Abstract
β-glucan is an important trait to be improved in barley breeding programs, as it greatly affects the quality of the end products when barley grains are used as raw material of feed or malt production or consumed as food for human. Although the genes associated with β-glucan synthesis have been identified, genetic regulation of β-glucan accumulation in barley grains is still completely unclear. In this study, 100 accessions from International Barley Core Selected Collection (BCS) were planted in two environments for two consecutive years to determine the genotypic variation of grain β-glucan content. A genome-wide association study (GWAS) identified 14 stable marker-trait associations (MTAs) (-Log10(P)> 4) for grain β-glucan content. Significantly positive correlation was found between grain β-glucan content and the number of favorable alleles of 14 stable MTAs. Seven putative candidate genes encoding some enzymes in glucose metabolism were found to be associated with β-glucan content. One of the putative genes, HORVU6Hr1G088380, could be an important gene controlling barely β-glucan content, with the SNPs being closely linked in all tested accessions and divided into two haplotypes. High resolution melting (HRM) analysis of the first SNP suggested that the HRM-SNP marker is valid for marker-assisted selection in barley breeding. This study provides useful information for the genes and markers related to grain β-glucan content in barley. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-020-01199-5.
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Affiliation(s)
- La Geng
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
| | - Mengdi Li
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
| | - Shanggeng Xie
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
| | - Dezhi Wu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
| | - Lingzhen Ye
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000 China
| | - Guoping Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000 China
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Camerlengo F, Frittelli A, Sparks C, Doherty A, Martignago D, Larré C, Lupi R, Sestili F, Masci S. CRISPR-Cas9 Multiplex Editing of the α-Amylase/Trypsin Inhibitor Genes to Reduce Allergen Proteins in Durum Wheat. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00104] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Rapid and sensitive screening and identification of CRISPR/Cas9 edited rice plants using quantitative real-time PCR coupled with high resolution melting analysis. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107088] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Li S, Liu SM, Fu HW, Huang JZ, Shu QY. High-resolution melting-based TILLING of γ ray-induced mutations in rice. J Zhejiang Univ Sci B 2018; 19:620-629. [PMID: 30070085 DOI: 10.1631/jzus.b1700414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics strategy for the high-throughput screening of induced mutations. γ radiation, which often induces both insertion/deletion (Indel) and point mutations, has been widely used in mutation induction and crop breeding. The present study aimed to develop a simple, high-throughput TILLING system for screening γ ray-induced mutations using high-resolution melting (HRM) analysis. Pooled rice (Oryza sativa) samples mixed at a 1:7 ratio of Indel mutant to wild-type DNA could be distinguished from the wild-type controls by HRM analysis. Thus, an HRM-TILLING system that analyzes pooled samples of four M2 plants is recommended for screening γ ray-induced mutants in rice. For demonstration, a γ ray-mutagenized M2 rice population (n=4560) was screened for mutations in two genes, OsLCT1 and SPDT, using this HRM-TILLING system. Mutations including one single nucleotide substitution (G→A) and one single nucleotide insertion (A) were identified in OsLCT1, and one trinucleotide (TTC) deletion was identified in SPDT. These mutants can be used in rice breeding and genetic studies, and the findings are of importance for the application of γ ray mutagenesis to the breeding of rice and other seed crops.
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Affiliation(s)
- Shan Li
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.,Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Song-Mei Liu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hao-Wei Fu
- Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, China
| | - Jian-Zhong Huang
- Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Qing-Yao Shu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.,Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
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Feng X, Wang C, Nan J, Zhang X, Wang R, Jiang G, Yuan Q, Lin S. Updating the elite rice variety Kongyu 131 by improving the Gn1a locus. RICE (NEW YORK, N.Y.) 2017; 10:35. [PMID: 28730413 PMCID: PMC5519510 DOI: 10.1186/s12284-017-0174-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/12/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Kongyu 131 is an elite japonica rice variety of Heilongjiang Province, China. It has the characteristics of early maturity, superior quality, high yield, cold tolerance and wide adaptability. However, there is potential to improve the yield of Kongyu 131 because of the relatively few grains per panicle compared with other varieties. Hence, we rebuilt the genome of Kongyu 131 by replacing the GRAIN NUMBER1a (Gn1a) locus with a high-yielding allele from a big panicle indica rice variety, GKBR. High-resolution melting (HRM) analysis was used for single nucleotide polymorphism (SNP) genotyping. RESULTS Quantitative trait locus (QTL) analysis of the BC3F2 population showed that the introgressed segment carrying the Gn1a allele of GKBR significantly increased the branch number and grain number per panicle. Using 5 SNP markers designed against the sequence within and around Gn1a, the introgressed chromosome segment was shortened to approximately 430 Kb to minimize the linkage drag by screening recombinants in the target region. Genomic components of the new Kongyu 131 were detected using 220 SNP markers evenly distributed across 12 chromosomes, suggesting that the recovery ratio of the recurrent parent genome (RRPG) was 99.89%. Compared with Kongyu 131, the yield per plant of the new Kongyu 131 increased by 8.3% and 11.9% at Changchun and Jiamusi, respectively. CONCLUSIONS To achieve the high yield potential of Kongyu 131, a minute chromosome fragment carrying the favorable Gn1a allele from the donor parent was introgressed into the genome of Kongyu 131, which resulted in a larger panicle and subsequent yield increase in the new Kongyu 131. These results indicate the feasibility of improving an undesirable trait of an elite variety by replacing only a small chromosome segment carrying a favorable allele.
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Affiliation(s)
- Xiaomin Feng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, No.3 South Zhongguancun Road, Haidian District, Beijing, 100190, People's Republic of China
| | - Chen Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, No.3 South Zhongguancun Road, Haidian District, Beijing, 100190, People's Republic of China
| | - Jianzong Nan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, No.3 South Zhongguancun Road, Haidian District, Beijing, 100190, People's Republic of China
| | - Xiaohui Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, No.3 South Zhongguancun Road, Haidian District, Beijing, 100190, People's Republic of China
| | - Rongsheng Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, No.3 South Zhongguancun Road, Haidian District, Beijing, 100190, People's Republic of China
| | - Guoqiang Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, No.3 South Zhongguancun Road, Haidian District, Beijing, 100190, People's Republic of China
| | - Qingbo Yuan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, No.3 South Zhongguancun Road, Haidian District, Beijing, 100190, People's Republic of China
| | - Shaoyang Lin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, No.3 South Zhongguancun Road, Haidian District, Beijing, 100190, People's Republic of China.
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Borna T, Salami SA, Shokrpour M. High resolution melting curve analysis revealed SNPs in major cannabinoid genes associated with drug and non-drug types of cannabis. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1333456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Tahereh Borna
- Faculty of Agriculture and Natural Resources, University of Tehran, Tehran, Iran
| | - Seyed Alireza Salami
- Faculty of Agriculture and Natural Resources, University of Tehran, Tehran, Iran
| | - Majid Shokrpour
- Faculty of Agriculture and Natural Resources, University of Tehran, Tehran, Iran
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Li S, Zheng YC, Cui HR, Fu HW, Shu QY, Huang JZ. Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing. J Zhejiang Univ Sci B 2017; 17:905-915. [PMID: 27921396 DOI: 10.1631/jzus.b1600125] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ ray irradiation has been widely used since the 1960s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ-irradiated M2 rice plants were sequenced; a total of 144-188 million high-quality (Q>20) reads were generated for each M2 plant, resulting in genome coverage of >45 times for each plant. Single base substitution (SBS) and short insertion/deletion (Indel) mutations were detected at the average frequency of 7.5×10-6-9.8×10-6 in the six M2 rice plants (SBS being about 4 times more frequent than Indels). Structural and copy number variations, though less frequent than SBS and Indel, were also identified and validated. The mutations were scattered in all genomic regions across 12 rice chromosomes without apparent hotspots. The present study is the first genome-wide single-nucleotide resolution study on the feature and frequency of γ irradiation-induced mutations in a seed propagated crop; the findings are of practical importance for mutation breeding of rice and other crop species.
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Affiliation(s)
- Shan Li
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.,Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Yun-Chao Zheng
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.,Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
| | - Hai-Rui Cui
- Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Hao-Wei Fu
- Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, China
| | - Qing-Yao Shu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.,Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
| | - Jian-Zhong Huang
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.,Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
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Yang P, Habekuß A, Hofinger BJ, Kanyuka K, Kilian B, Graner A, Ordon F, Stein N. Sequence diversification in recessive alleles of two host factor genes suggests adaptive selection for bymovirus resistance in cultivated barley from East Asia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:331-344. [PMID: 27830284 PMCID: PMC5263206 DOI: 10.1007/s00122-016-2814-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 10/14/2016] [Indexed: 05/04/2023]
Abstract
Two distinct patterns of sequence diversity for the recessive alleles of two host factors HvPDIL5 - 1 and HvEIF4E indicated the adaptive selection for bymovirus resistance in cultivated barley from East Asia. Plant pathogens are constantly challenging plant fitness and driving resistance gene evolution in host species. Little is known about the evolution of sequence diversity in host recessive resistance genes that interact with plant viruses. Here, by combining previously published and newly generated targeted re-sequencing information, we systematically analyzed natural variation in a broad collection of wild (Hordeum spontaneum; Hs) and domesticated barleys (Hordeum vulgare; Hv) using the full-length coding sequence of the two host factor genes, HvPDIL5-1 and HvEIF4E, conferring recessive resistance to the agriculturally important Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV). Interestingly, two types of gene evolution conferred by sequence variation in domesticated barley, but not in wild barley were observed. Whereas resistance-conferring alleles of HvEIF4E exclusively contained non-synonymous amino acid substitutions (including in-frame sequence deletions and insertions), loss-of-function alleles were predominantly responsible for the HvPDIL5-1 conferred bymovirus resistance. A strong correlation between the geographic origin and the frequency of barley accessions carrying resistance-conferring alleles was evident for each of the two host factor genes, indicating adaptive selection for bymovirus resistance in cultivated barley from East Asia.
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Affiliation(s)
- Ping Yang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, 06484, Quedlinburg, Germany
| | - Bernhard J Hofinger
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Kostya Kanyuka
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, 06484, Quedlinburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany.
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Perovic D, Krämer I, Habekuss A, Perner K, Pickering R, Proeseler G, Kanyuka K, Ordon F. Genetic analyses of BaMMV/BaYMV resistance in barley accession HOR4224 result in the identification of an allele of the translation initiation factor 4e (Hv-eIF4E) exclusively effective against Barley mild mosaic virus (BaMMV). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1061-71. [PMID: 24522725 DOI: 10.1007/s00122-014-2279-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/27/2014] [Indexed: 05/20/2023]
Abstract
Based on a strategy combining extensive segregation analyses and tests for allelism with allele-specific re-sequencing an Hv-eIF4E allele exclusively effective against BaMMV was identified and closely linked markers for BaYMV resistance were developed. Soil-borne barley yellow mosaic disease is one of the most important diseases of winter barley. In extensive screenings for resistance, accession 'HOR4224' being resistant to three strains of Barley mild mosaic virus (BaMMV-ASL1, BaMMV-Sil, and BaMMV-Teik) and two strains of Barley yellow mosaic virus (BaYMV-1 and BaYMV-2) was identified. Analyses using Bmac29, being to some extent diagnostic for the rym4/5 locus, gave hint to the presence of the susceptibility-encoding allele at this locus. Therefore, 107 DH lines derived from the cross 'HOR4224' × 'HOR10714' (susceptible) were screened for resistance. Genetic analyses revealed an independent inheritance of resistance to BaMMV and BaYMV ([Formula: see text] = 5.58) both encoded by a single gene (BaMMV [Formula: see text] = 0.477; BaYMV [Formula: see text] = 0.770). Although Bmac29 indicated the susceptibility-encoding allele, BaMMV resistance of 'HOR4224' co-localized with rym4/rym5. The BaYMV resistance was mapped to chromosome 5H in the region of rym3. Sequencing of full length cDNA of the Hv-eIF4E gene displayed an already sequenced allele described to be efficient against BaMMV and BaYMV. However, the F1 progenies of crosses involving 'HOR4224' and rym4/rym5 donors were all resistant to BaMMV but susceptible to BaYMV. Therefore, this is the first report of an allele at the rym4/rym5 locus exclusively efficient against BaMMV. Changes in the specificity are due to one non-synonymous amino acid substitution (I118K). Results obtained elucidate that combining extensive segregation analyses and tests for allelism involving different strains of BaMMV/BaYMV in combination with allele-specific re-sequencing is an efficient strategy for gene and allele detection in complex pathosystems.
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Affiliation(s)
- Dragan Perovic
- Julius Kuehn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany,
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13
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Hart JP, Griffiths PD. A series of eIF4E alleles at the Bc-3 locus are associated with recessive resistance to Clover yellow vein virus in common bean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2849-2863. [PMID: 23933781 DOI: 10.1007/s00122-013-2176-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 07/27/2013] [Indexed: 05/29/2023]
Abstract
Clover yellow vein virus (ClYVV) is capable of causing severe damage to common bean (Phaseolus vulgaris L.) production worldwide. The snap bean market class is particularly vulnerable because infection may lead to distortion and necrosis of the fresh green pods and rejection of the harvest. Three putatively independent recessive genes (cyv, desc, bc-3) have been reported to condition resistance to ClYVV; however, their allelic relationships have not been resolved. We identified, evaluated, and characterized the phenotypic and molecular genetic variation present in 21 informative common bean genotypes for resistance to ClYVV. Allelism testing phenotypes from multiple populations provided clear evidence that the three genes were a series of recessive alleles at the Bc-3 locus that condition unique potyvirus strain- and species-specific resistance spectra. Candidate gene analysis revealed complete association between the recessive resistance alleles and unique patterns of predicted amino acid substitutions in P. vulgaris eukaryotic translation initiation factor 4E (PveIF4E). This led to the discovery and characterization of two novel PveIF4E alleles associated with resistance to ClYVV, PveIF4E (3) , and PveIF4E (4) . We developed KASPar allele-specific SNP genotyping assays and demonstrated their ability to accurately detect and differentiate all of the PveIF4E haplotypes present in the germplasm, allelism testing, and in three separate segregating populations. The results contribute to an enhanced understanding and accessibility of the important potyvirus resistance conditioned by recessive alleles at Bc-3. The KASPar assays should be useful to further enable germplasm exploration, allelic discrimination, and marker-assisted introgression of bc-3 alleles in common bean.
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Affiliation(s)
- John P Hart
- Department of Plant Breeding and Genetics, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
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Hipper C, Brault V, Ziegler-Graff V, Revers F. Viral and cellular factors involved in Phloem transport of plant viruses. FRONTIERS IN PLANT SCIENCE 2013; 4:154. [PMID: 23745125 PMCID: PMC3662875 DOI: 10.3389/fpls.2013.00154] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 05/05/2013] [Indexed: 05/03/2023]
Abstract
Phloem transport of plant viruses is an essential step in the setting-up of a complete infection of a host plant. After an initial replication step in the first cells, viruses spread from cell-to-cell through mesophyll cells, until they reach the vasculature where they rapidly move to distant sites in order to establish the infection of the whole plant. This last step is referred to as systemic transport, or long-distance movement, and involves virus crossings through several cellular barriers: bundle sheath, vascular parenchyma, and companion cells for virus loading into sieve elements (SE). Viruses are then passively transported within the source-to-sink flow of photoassimilates and are unloaded from SE into sink tissues. However, the molecular mechanisms governing virus long-distance movement are far from being understood. While most viruses seem to move systemically as virus particles, some viruses are transported in SE as viral ribonucleoprotein complexes (RNP). The nature of the cellular and viral factors constituting these RNPs is still poorly known. The topic of this review will mainly focus on the host and viral factors that facilitate or restrict virus long-distance movement.
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Affiliation(s)
| | | | - Véronique Ziegler-Graff
- Laboratoire Propre du CNRS (UPR 2357), Virologie Végétale, Institut de Biologie Moléculaire des Plantes, Université de StrasbourgStrasbourg, France
| | - Frédéric Revers
- UMR 1332 de Biologie du Fruit et Pathologie, INRA, Université de BordeauxVillenave d’Ornon, France
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Wang A, Krishnaswamy S. Eukaryotic translation initiation factor 4E-mediated recessive resistance to plant viruses and its utility in crop improvement. MOLECULAR PLANT PATHOLOGY 2012; 13:795-803. [PMID: 22379950 PMCID: PMC6638641 DOI: 10.1111/j.1364-3703.2012.00791.x] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The use of genetic resistance is considered to be the most effective and sustainable approach to the control of plant pathogens. Although most of the known natural resistance genes are monogenic dominant R genes that are predominant against fungi and bacteria, more and more recessive resistance genes against viruses have been cloned in the last decade. Interestingly, of the 14 natural recessive resistance genes against plant viruses that have been cloned from diverse plant species thus far, 12 encode the eukaryotic translation initiation factor 4E (eIF4E) or its isoform eIF(iso)4E. This review is intended to summarize the current state of knowledge about eIF4E and the possible mechanisms underlying its essential role in virus infection, and to discuss recent progress and the potential of eIF4E as a target gene in the development of genetic resistance to viruses for crop improvement.
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Affiliation(s)
- Aiming Wang
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada, N5V 4T3.
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16
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Developing tools for investigating the multiple roles of ethylene: identification and mapping genes for ethylene biosynthesis and reception in barley. Mol Genet Genomics 2012; 287:793-802. [PMID: 22915301 DOI: 10.1007/s00438-012-0716-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 08/02/2012] [Indexed: 10/28/2022]
Abstract
The plant hormone ethylene is important to many plant processes from germination through senescence, including responses to in vitro growth and plant regeneration. Knowledge of the number and function of genes that are involved in ethylene biosynthesis and reception is necessary to determine the role of specific genes within gene families known to influence ethylene biosynthesis and other aspects of ethylene function in plants. Our objective was built on previous studies that have established the critical role of ethylene in the in vitro response of barley (Hordeum vulgare L.), and that have identified ethylene-related QTL in the barley genome. In this study, we have identified the locations of genes in the barley 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), ACC oxidase (ACO), and ethylene receptor (ETR) gene families. Specific primers for PCR amplification of each gene were developed and used to map these genes in the Oregon Wolf Barley mapping population. Five ACS, 8 ACO, and 7 ETR genes were identified and mapped to six of the barley chromosomes. Gene locations were syntenous to the orthologs in rice except for two that mapped to chromosome 6H. Gene duplication was evident for ACO genes on chromosomes 5H and 6H. Gene-specific primers will be useful for determining expression of each gene under various environmental conditions, including in vitro environments, to better understand the role of ethylene. Of the six known QTL for green plant regeneration in barley, three were located near the genes mapped in this study.
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Gori A, Cerboneschi M, Tegli S. High-resolution melting analysis as a powerful tool to discriminate and genotype Pseudomonas savastanoi pathovars and strains. PLoS One 2012; 7:e30199. [PMID: 22295075 PMCID: PMC3266268 DOI: 10.1371/journal.pone.0030199] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 12/12/2011] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas savastanoi is a serious pathogen of Olive, Oleander, Ash, and several other Oleaceae. Its epiphytic or endophytic presence in asymptomatic plants is crucial for the spread of Olive and Oleander knot disease, as already ascertained for P. savastanoi pv. savastanoi (Psv) on Olive and for pv. nerii (Psn) on Oleander, while no information is available for pv. fraxini (Psf) on Ash. Nothing is known yet about the distribution on the different host plants and the real host range of these pathovars in nature, although cross-infections were observed following artificial inoculations. A multiplex Real-Time PCR assay was recently developed to simultaneously and quantitatively discriminate in vitro and in planta these P. savastanoi pathovars, for routine culture confirmation and for epidemiological and diagnostical studies. Here an innovative High-Resolution Melting Analysis (HRMA)-based assay was set up to unequivocally discriminate Psv, Psn and Psf, according to several single nucleotide polymorphisms found in their Type Three Secretion System clusters. The genetic distances among 56 P. savastanoi strains belonging to these pathovars were also evaluated, confirming and refining data previously obtained by fAFLP. To our knowledge, this is the first time that HRMA is applied to a bacterial plant pathogen, and one of the few multiplex HRMA-based assays developed so far. This protocol provides a rapid, sensitive, specific tool to differentiate and detect Psv, Psn and Psf strains, also in vivo and against other related bacteria, with lower costs than conventional multiplex Real-Time PCR. Its application is particularly suitable for sanitary certification programs for P. savastanoi, aimed at avoiding the spreading of this phytopathogen through asymptomatic plants.
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Affiliation(s)
- Andrea Gori
- Laboratorio di Patologia Vegetale e Molecolare, Dipartimento di Biotecnologie Agrarie, Università degli Studi di Firenze, Sesto Fiorentino, Firenze, Italy
| | - Matteo Cerboneschi
- Laboratorio di Patologia Vegetale e Molecolare, Dipartimento di Biotecnologie Agrarie, Università degli Studi di Firenze, Sesto Fiorentino, Firenze, Italy
| | - Stefania Tegli
- Laboratorio di Patologia Vegetale e Molecolare, Dipartimento di Biotecnologie Agrarie, Università degli Studi di Firenze, Sesto Fiorentino, Firenze, Italy
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Botticella E, Sestili F, Hernandez-Lopez A, Phillips A, Lafiandra D. High resolution melting analysis for the detection of EMS induced mutations in wheat SBEIIa genes. BMC PLANT BIOLOGY 2011; 11:156. [PMID: 22074448 PMCID: PMC3228712 DOI: 10.1186/1471-2229-11-156] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 11/10/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Manipulation of the amylose-amylopectin ratio in cereal starch has been identified as a major target for the production of starches with novel functional properties. In wheat, silencing of starch branching enzyme genes by a transgenic approach reportedly caused an increase of amylose content up to 70% of total starch, exhibiting novel and interesting nutritional characteristics. In this work, the functionality of starch branching enzyme IIa (SBEIIa) has been targeted in bread wheat by TILLING. An EMS-mutagenised wheat population has been screened using High Resolution Melting of PCR products to identify functional SNPs in the three homoeologous genes encoding the target enzyme in the hexaploid genome. RESULTS This analysis resulted in the identification of 56, 14 and 53 new allelic variants respectively for SBEIIa-A, SBEIIa-B and SBEIIa-D. The effects of the mutations on protein structure and functionality were evaluated by a bioinformatic approach. Two putative null alleles containing non-sense or splice site mutations were identified for each of the three homoeologous SBEIIa genes; qRT-PCR analysis showed a significant decrease of their gene expression and resulted in increased amylose content. Pyramiding of different single null homoeologous allowed to isolate double null mutants showing an increase of amylose content up to 21% compared to the control. CONCLUSION TILLING has successfully been used to generate novel alleles for SBEIIa genes known to control amylose content in wheat. Single and double null SBEIIa genotypes have been found to show a significant increase in amylose content.
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Affiliation(s)
- Ermelinda Botticella
- Department of Agriculture, Forests, Nature and Energy, University of Tuscia, 01100 Viterbo, Italy
| | - Francesco Sestili
- Department of Agriculture, Forests, Nature and Energy, University of Tuscia, 01100 Viterbo, Italy
| | | | - Andrew Phillips
- Plant Science Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Domenico Lafiandra
- Department of Agriculture, Forests, Nature and Energy, University of Tuscia, 01100 Viterbo, Italy
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HENRI H, MOUTON L. High‐Resolution Melting technology: a new tool for studying the
Wolbachia
endosymbiont diversity in the field. Mol Ecol Resour 2011; 12:75-81. [DOI: 10.1111/j.1755-0998.2011.03064.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- H. HENRI
- Université de Lyon, Université Lyon1, Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - L. MOUTON
- Université de Lyon, Université Lyon1, Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
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Hofinger BJ, Russell JR, Bass CG, Baldwin T, dos Reis M, Hedley PE, Li Y, Macaulay M, Waugh R, Hammond-Kosack KE, Kanyuka K. An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations. Mol Ecol 2011; 20:3653-68. [PMID: 21806691 DOI: 10.1111/j.1365-294x.2011.05201.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognized as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars, two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study, the sequence of eIF4E was analysed in 1090 barley landraces and noncurrent cultivars originating from 84 countries. An exceptionally high nucleotide diversity was evident in the coding sequence of eIF4E but not in either the adjacent MCT-1 gene or the sequence-related eIF(iso)4E gene situated on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in the coding sequence of eIF4E resulted in amino acid changes. A total of 47 eIF4E haplotypes were identified, and phylogenetic analysis using maximum likelihood provided evidence of strong positive selection acting on this barley gene. The majority of eIF4E haplotypes were found to be specific to distinct geographic regions. Furthermore, the eI4FE haplotype diversity (uh) was found to be considerably higher in East Asia, whereas SNP genotyping identified a comparatively low degree of genome-wide genetic diversity in 16 of 17 tested accessions (each carrying a different eIF4E haplotype) from this same region. In addition, selection statistic calculations using coalescent simulations showed evidence of non-neutral variation for eIF4E in several geographic regions, including East Asia, the region with a long history of the bymovirus-induced yellow mosaic disease. Together these findings suggest that eIF4E may play a role in barley adaptation to local habitats.
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Affiliation(s)
- Bernhard J Hofinger
- Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden AL5 2JQ, UK
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Luchi N, Pratesi N, Simi L, Pazzagli M, Capretti P, Scala A, Slippers B, Pinzani P. High-resolution melting analysis: a new molecular approach for the early detection of Diplodia pinea in Austrian pine. Fungal Biol 2011; 115:715-23. [PMID: 21802051 DOI: 10.1016/j.funbio.2011.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 05/06/2011] [Accepted: 05/13/2011] [Indexed: 01/31/2023]
Abstract
The differentiation of Diplodia pinea from closely related species, such as Diplodia scrobiculata and Diplodia seriata, and its detection in plant tissue, represented a critical issue for a long time. Molecular screening tools have recently been developed to address this topic. In this study we applied one of the most sensitive and rapid diagnostic screening method so far developed, called High-Resolution Melting Analysis (HRMA), to detect D. pinea in Austrian pine (Pinus nigra). HRMA exploits differences in the melting behaviour of PCR products to rapidly identify DNA sequence variants without the need for cumbersome post-PCR methods. We developed a HRMA method to detect specific fungal sequences in the mitochondrial small subunit ribosome gene (mt SSU rDNA). The reliability of this technique was firstly assessed on DNA extracted from pure cultures of D. pinea and closely related species. Amplicon differences were screened by HRMA and the results confirmed by direct DNA sequencing. Subsequently, HRMA was tested on DNA from symptomatic and symptomless pine shoots, and the presence of the fungus was also confirmed by both conventional and molecular quantitative approaches. The HRMA allowed the distinction of D. pinea from closely related species, showing specific melting profiles for the each pathogen. This new molecular technique, here tested in a plant-fungus pathosystem for the first time, was very reliable in both symptomatic and symptomless shoots. HRMA is therefore a highly effective and accurate technique that permits the rapid screening of pathogens in the host.
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Affiliation(s)
- Nicola Luchi
- Department of Agricultural Biotechnology, Section of Plant Protection, University of Florence, Piazzale delle Cascine 28, I-50144 Florence, Italy.
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Li YD, Chu ZZ, Liu XG, Jing HC, Liu YG, Hao DY. A cost-effective high-resolution melting approach using the EvaGreen dye for DNA polymorphism detection and genotyping in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:1036-1042. [PMID: 21106003 DOI: 10.1111/j.1744-7909.2010.01001.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
High-resolution melting (HRM) analysis relies on the use of fluorescent dyes, such as LCGreen, ResoLight, and SYTO9, which bind in a saturated manner to the double-stranded DNAs. These dyes are expensive in use and may not be affordable when dealing with a large quantity of samples. EvaGreen is a much cheaper DNA helix intercalating dye and has been used in quantitative real-time polymerase chain reaction (PCR) and post-PCR DNA melt curve analysis. Here we report on the development of an EvaGreen-based HRM analysis and its performance, in comparison with the popular LCGreen-based HRM analysis, in detection of DNA polymorphism in plants. We found that various polymorphisms ranged from single nucleotide polymorphisms (SNPs) to Indels were equally detected by using EvaGreen- or LCGreen-based HRM. EvaGreen dye was sensitive enough in discovery of SNPs in fivefold pooled samples. Using this economical dye we successfully identified multiple novel mutant alleles of Gln1-3 gene, which produces a cytosolic glutamine synthetase isoenzyme (GS1), in a maize ethyl methanesulfonate (EMS)-mutagenized library, and genotyped rice mapping populations with SNP markers. The current results suggest that EvaGreen is a promising dye for HRM analysis for its ease to use and cost effectiveness.
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Affiliation(s)
- Yi-Dan Li
- Biotechnology Research Centre, Jilin Academy of Agricultural Sciences, Changchun 130033, China
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Ibiza VP, Cañizares J, Nuez F. EcoTILLING in Capsicum species: searching for new virus resistances. BMC Genomics 2010; 11:631. [PMID: 21073716 PMCID: PMC3091766 DOI: 10.1186/1471-2164-11-631] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 11/12/2010] [Indexed: 12/05/2022] Open
Abstract
Background The EcoTILLING technique allows polymorphisms in target genes of natural populations to be quickly analysed or identified and facilitates the screening of genebank collections for desired traits. We have developed an EcoTILLING platform to exploit Capsicum genetic resources. A perfect example of the utility of this EcoTILLING platform is its application in searching for new virus-resistant alleles in Capsicum genus. Mutations in translation initiation factors (eIF4E, eIF(iso)4E, eIF4G and eIF(iso)4G) break the cycle of several RNA viruses without affecting the plant life cycle, which makes these genes potential targets to screen for resistant germplasm. Results We developed and assayed a cDNA-based EcoTILLING platform with 233 cultivated accessions of the genus Capsicum. High variability in the coding sequences of the eIF4E and eIF(iso)4E genes was detected using the cDNA platform. After sequencing, 36 nucleotide changes were detected in the CDS of eIF4E and 26 in eIF(iso)4E. A total of 21 eIF4E haplotypes and 15 eIF(iso)4E haplotypes were identified. To evaluate the functional relevance of this variability, 31 possible eIF4E/eIF(iso)4E combinations were tested against Potato virus Y. The results showed that five new eIF4E variants (pvr210, pvr211, pvr212, pvr213 and pvr214) were related to PVY-resistance responses. Conclusions EcoTILLING was optimised in different Capsicum species to detect allelic variants of target genes. This work is the first to use cDNA instead of genomic DNA in EcoTILLING. This approach avoids intronic sequence problems and reduces the number of reactions. A high level of polymorphism has been identified for initiation factors, showing the high genetic variability present in our collection and its potential use for other traits, such as genes related to biotic or abiotic stresses, quality or production. Moreover, the new eIF4E and eIF(iso)4E alleles are an excellent collection for searching for new resistance against other RNA viruses.
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Affiliation(s)
- Vicente P Ibiza
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, 8E CPI, Camino de Vera s/n, 46022 Valencia, Spain
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Population structures of genebank accessions of Salvia officinalis L. (Lamiaceae) revealed by high resolution melting analysis. BIOCHEM SYST ECOL 2010. [DOI: 10.1016/j.bse.2010.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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