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Salama EAA, Farid MA, El-Mahalawy YA, El-Akheder AAA, Aboshosha AA, Fayed AM, Yehia WMB, Lamlom SF. Exploring agro-morphological and fiber traits diversity in cotton (G. barbadense L.). BMC PLANT BIOLOGY 2024; 24:403. [PMID: 38750434 PMCID: PMC11095005 DOI: 10.1186/s12870-024-04912-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/15/2024] [Indexed: 05/19/2024]
Abstract
Cotton (Gossypium barbadense L.) is a leading fiber and oilseed crop globally, but genetic diversity among breeding materials is often limited. This study analyzed genetic variability in 14 cotton genotypes from Egypt and other countries, including both cultivated varieties and wild types, using agro-morphological traits and genomic SSR markers. Field experiments were conducted over two seasons to evaluate 12 key traits related to plant growth, yield components, and fiber quality. Molecular diversity analysis utilized 10 SSR primers to generate DNA profiles. The Molecular diversity analysis utilized 10 SSR primers to generate DNA profiles. Data showed wide variation for the morphological traits, with Egyptian genotypes generally exhibiting higher means for vegetative growth and yield parameters. The top-performing genotypes for yield were Giza 96, Giza 94, and Big Black Boll genotypes, while Giza 96, Giza 92, and Giza 70 ranked highest for fiber length, strength, and fineness. In contrast, molecular profiles were highly polymorphic across all genotypes, including 82.5% polymorphic bands out of 212. Polymorphism information content was high for the SSR markers, ranging from 0.76 to 0.86. Genetic similarity coefficients based on the SSR data varied extensively from 0.58 to 0.91, and cluster analysis separated genotypes into two major groups according to geographical origin. The cotton genotypes displayed high diversity in morphology and genetics, indicating sufficient variability in the germplasm. The combined use of physical traits and molecular markers gave a thorough understanding of the genetic diversity and relationships between Egyptian and global cotton varieties. The SSR markers effectively profiled the genotypes and can help select ideal parents for enhancing cotton through hybridization and marker-assisted breeding.
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Affiliation(s)
- Ehab A A Salama
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
| | - Mona A Farid
- Genetics Department, Faculty of Agriculture, Kafr El-Sheikh University, Kafr El-Sheikh, Egypt
| | - Youssef A El-Mahalawy
- Cotton Breeding Department, Agriculture Research Center, Cotton Research, Cotton Research Institute, Kafr El-Sheikh, Egypt
| | - A A A El-Akheder
- Cotton Breeding Department, Agriculture Research Center, Cotton Research, Cotton Research Institute, Kafr El-Sheikh, Egypt
| | - Ali A Aboshosha
- Genetics Department, Faculty of Agriculture, Kafr El-Sheikh University, Kafr El-Sheikh, Egypt
| | - Aysam M Fayed
- Molecular Biology Department, Genetic Engineering and Biotechnology Institute, University of Sadat City, Sadat, 32897, Egypt
| | - W M B Yehia
- Cotton Breeding Department, Agriculture Research Center, Cotton Research, Cotton Research Institute, Kafr El-Sheikh, Egypt
| | - Sobhi F Lamlom
- Plant Production Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt.
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Gunguniya DF, Kumar S, Patel MP, Sakure AA, Patel R, Kumar D, Khandelwal V. Morpho-biochemical characterization and molecular marker based genetic diversity of pearl millet ( Pennisetum glaucum (L.) R. Br.). PeerJ 2023; 11:e15403. [PMID: 37304873 PMCID: PMC10249620 DOI: 10.7717/peerj.15403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/20/2023] [Indexed: 06/13/2023] Open
Abstract
Pearl millet is a key food for millions living in semi-arid and arid regions and is a main diet for poorer populations. The genetic diversity existing in the pearl millet germplasm can be used to improve the micronutrient content and grain yield. Effective and organized exploitation of diversity at morphological and DNA levels is the strategy for any crop improvement program. In this study, the genetic diversity of 48 pearl millet genotypes was evaluated for eight morphological traits and eleven biochemical characters. All genotypes were also characterized using twelve SSR and six SRAP markers to evaluate genetic diversity. The significant mean difference between morphological and biochemical traits were detected. The productive tillers per plant varied from 2.65 to 7.60 with a mean of 4.80. The grain yield of genotypes varied more than 3× from 15.85 g (ICMR 07222) to 56.75 g (Nandi 75) with an average of 29.54 g per plant. Higher levels of protein, iron, and zinc contents were found to be present in ICMR 12555 (20.6%), ICMR 08666 (77.38 ppm), and IC 139900 (55.48 ppm), respectively, during the experiment. Substantial variability was observed for grain calcium as it ranged from 100.00 ppm (ICMR 10222) to 256.00 ppm (ICMR 12888). The top eight nutrient-dense genotypes flowered in 34-74 days and had 5.71-9.39 g 1,000 grain weight. Genotype ICMR 08666 was superior for Fe, Zn, K and P. The inter-genotype similarity coefficient at the genetic level, generated using DNA markers, ranged from 0.616 to 0.877 with a mean of 0.743. A combination of morpho-biochemical traits and DNA markers based diversity may help to differentiate the genotypes and diverse genotypes can be used in breeding programs to improve the mineral content in pearl millet.
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Affiliation(s)
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Mukesh P. Patel
- Agriculture and Horticulture Research Station, Anand Agricultural University, Khambholaj, Gujarat, India
| | - Amar A. Sakure
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Rumit Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Dileep Kumar
- Micronutrient Research Centre, Anand Agricultural University, Anand, Gujarat, India
| | - Vikas Khandelwal
- Plant Breeding, ICAR-All India Coordinated Research Project on Pearl Millet, Mandor, Rajasthan, India
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Yin J, Zhao H, Wu X, Ma Y, Zhang J, Li Y, Shao G, Chen H, Han R, Xu Z. SSR marker based analysis for identification and of genetic diversity of non-heading Chinese cabbage varieties. FRONTIERS IN PLANT SCIENCE 2023; 14:1112748. [PMID: 36814762 PMCID: PMC9939625 DOI: 10.3389/fpls.2023.1112748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
As a widely cultivated vegetable in China and Southeast Asia, the breeding of non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) is widespread; more than 400 varieties have been granted new plant variety rights (PVRs) in China. Distinctness is one of the key requirements for the granting of PVRs, and molecular markers are widely used as a robust supplementary method for similar variety selection in the distinctness test. Although many genome-wide molecular markers have been developed, they have not all been well used in variety identification and tests of distinctness of non-heading Chinese cabbage. In this study, by using 423 non-heading Chinese cabbage varieties collected from different regions of China, 287 simple sequence repeat (SSR) markers were screened for polymorphisms, and 23 core markers were finally selected. The polymorphic information content (PIC) values of the 23 SSR markers ranged from 0.555 to 0.911, with an average of 0.693, and the average number of alleles per marker was 13.65. Using these 23 SSR markers, 418 out of 423 varieties could be distinguished, with a discrimination rate of 99.994%. Field tests indicated that those undistinguished varieties were very similar and could be further distinguished by a few morphological characteristics. According to the clustering results, the 423 varieties could be divided into three groups: pak-choi, caitai, and tacai. The similarity coefficient between the SSR markers and morphological characteristics was moderate (0.53), and the efficiency of variety identification was significantly improved by using a combination of SSR markers and morphological characteristics.
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Affiliation(s)
- Jiwei Yin
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Hong Zhao
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xingting Wu
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yingxue Ma
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jingli Zhang
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Guirong Shao
- Research and development center, Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou, China
| | - Hairong Chen
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ruixi Han
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Zhenjiang Xu
- College of Agriculture, South China Agricultural University, Guangzhou, China
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Characterization and Application of EST-SSR Markers Developed from Transcriptome Sequences in Elymus breviaristatus (Poaceae: Triticeae). Genes (Basel) 2023; 14:genes14020302. [PMID: 36833229 PMCID: PMC9957396 DOI: 10.3390/genes14020302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Elymus L. is the largest genus in the Triticeae tribe. Most species in this genus are highly stress resistant, with excellent forage value. Elymus breviaristatus, a rare species endemic to the Qinghai-Tibet Plateau (QTP), is declining due to habitat fragmentation. However, genetic data for E. breviaristatus are limited, with expressed sequence tag (EST) markers being particularly rare, hampering genetic studies and protection measures. RESULTS We obtained 9.06 Gb clean sequences from the transcriptome of E. breviaristatus, generating 171,522 unigenes, which were assembled and functionally annotated against five public databases. We identified 30,668 SSRs in the E. breviaristatus transcriptome, from which 103 EST-SSR primer pairs were randomly selected. Of these, 58 pairs of amplified products of the expected size, and 18 of the amplified products were polymorphic. Model-based Bayesian clustering, the unweighted pair group method with arithmetic average (UPGMA), and principal coordinate analysis (PCoA) of 179 wild E. breviaristatus in 12 populations using these EST-SSRs were generally consistent, grouping the 12 populations into two major clades. Analysis of molecular variance (AMOVA) found 70% of the genetic variation among the 12 populations and 30% within the populations, indicating a high level of genetic differentiation (or low gene exchange) among the 12 populations. The transferability of the 58 successful EST-SSR primers to 22 related hexaploid species was 86.2-98.3%. UPGMA analysis generally grouped species with similar genome types together. CONCLUSIONS Here, we developed EST-SSR markers from the transcriptome of E. breviaristatus. The transferability of these markers was evaluated, and the genetic structure and diversity of E. breviaristatus were explored. Our results provide a basis for the conservation and management of this endangered species, and the obtained molecular markers represent valuable resources for the exploration of genetic relationships among species in the Elymus genus.
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Mavlyutov Y, Kostenko S, Shamustakimova A, Klimenko I. Genetic variability analysis of Russian cultivars of ryegrass (Lolium) based on SCoT markers. J Genet Eng Biotechnol 2022; 20:163. [PMID: 36512171 PMCID: PMC9748000 DOI: 10.1186/s43141-022-00446-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/04/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Ryegrass is a promising crop for the development of meadow farming in the world. More than 1000 cultivated varieties widely used in feed production have been developed, based on the main species - perennial ryegrass (Lolium perenne L.) and annual one (Lolium multiflorum Lam.). Development and implementation of the modern methods of plant varietal and species identification are of great importance. In recent years, molecular markers have been successfully used for these purposes, which increase the accuracy of the breeding material evaluation at a significant reduction of time and labor costs. The aim of this study was to assess the discriminatory potential of the new SCoT marking technique for the identification of Russian perennial (Lolium perenne L.) and annual (Lolium multiflorum Lam.) ryegrass varieties. RESULTS Out of the total number of the tested SCoT-primers, 8 polymorphic ones were selected, which demonstrates the high stability and reproducibly amplified DNA fragments. These primers generated 107 PCR products, where 37 were found to be polymorphic. The average number of amplicons per primer was 13. The size of the PCR products varied from 349 to 2718 bp (see Table 3). The polymorphic ratio of the tested markers was 30.8%. The marker SCoT-06 was characterized by the maximum number of PCR products and the highest level of polymorphism (50%). The effective number of alleles (ne) ranged from 1.35 to 1.58 with a mean of 1.48 per locus. The average value of the PIC and Shannon index (I) were 0.35 and 0.46, respectively. The unique PCR fragments were revealed for the identification of tested varieties. Analysis of molecular variance (AMOVA) showed that the level of genetic diversity between ryegrass species (59%) was more than between varieties within a species (41%). Based on binary matrix data, clustering and PCoA analysis (see Figs. 1 and 2) of the samples were carried out that divided them into two groups according to species. CONCLUSIONS We found a set of markers that can be useful tools for ryegrass varieties identification. The level of intravarietal polymorphism turned out to be higher than the differences between varieties because of the possible significant heterogeneity of the varietal material. The information obtained can be used in breeding programs to create improved ryegrass varieties adapted to Russian climatic conditions.
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Affiliation(s)
- Yulian Mavlyutov
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
| | - Sergey Kostenko
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
| | - Anastasia Shamustakimova
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
| | - Irina Klimenko
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
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Özkan G, Haliloğlu K, Türkoğlu A, Özturk HI, Elkoca E, Poczai P. Determining Genetic Diversity and Population Structure of Common Bean ( Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers. Genes (Basel) 2022; 13:1410. [PMID: 36011321 PMCID: PMC9407889 DOI: 10.3390/genes13081410] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Assessment of genetic diversity among different varieties helps to improve desired characteristics of crops, including disease resistance, early maturity, high yield, and resistance to drought. Molecular markers are one of the most effective tools for discovering genetic diversity that can increase reproductive efficiency. Simple sequence repeats (SSRs), which are codominant markers, are preferred for the determination of genetic diversity because they are highly polymorphic, multi-allelic, highly reproducible, and have good genome coverage. This study aimed to determine the genetic diversity of 40 common bean (Phaseolus vulgaris L.) landraces collected from the Ispir district located in the Northeast Anatolia region of Türkiye and five commercial varieties using SSR markers. The Twenty-seven SSR markers produced a total of 142 polymorphic bands, ranging from 2 (GATS91 and PVTT001) to 12 (BM153) alleles per marker, with an average number of 5.26 alleles. The gene diversity per marker varied between 0.37 and 0.87 for BM053 and BM153 markers, respectively. When heterozygous individuals are calculated proportional to the population, the heterozygosity ranged from 0.00 to 1.00, with an average of 0.30. The expected heterozygosity of the SSR locus ranged from 0.37 (BM053) to 0.88 (BM153), with an average of 0.69. Nei's gene diversity scored an average of 0.69. The polymorphic information content (PIC) values of SSR markers varied from 0.33 (BM053) to 0.86 (BM153), with an average of 0.63 per locus. The greatest genetic distance (0.83) was between lines 49, 50, 53, and cultivar Karacaşehir-90, while the shortest (0.08) was between lines 6 and 26. In cluster analysis using Nei's genetic distance, 45 common bean genotypes were divided into three groups and very little relationship was found between the genotypes and the geographical distances. In genetic structure analysis, three subgroups were formed, including local landraces and commercial varieties. The result confirmed that the rich diversity existing in Ispir bean landraces could be used as a genetic resource in designing breeding programs and may also contribute to Türkiye bean breeding programs.
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Affiliation(s)
- Güller Özkan
- Department of Biology, Faculty of Science, Ankara University, Ankara 06100, Türkiye
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye
- Department of Biology, Faculty of Science, Cankiri Karatekin University, Çankırı 18200, Türkiye
| | - Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya 42310, Türkiye
| | - Halil Ibrahim Özturk
- Health Services Vocational School, Binali Yıldırım University, Erzincan 24100, Türkiye
| | - Erdal Elkoca
- Vocational High School, Department of Plant and Animal Production, İbrahim Çeçen University, Ağrı 04100, Türkiye
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, FI-00014 Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), H-9731 Kőszeg, Hungary
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Xiong Y, Yang J, Xiong Y, Zhao J, Liu L, Liu W, Sha L, Zhou J, You M, Li D, Lei X, Bai S, Ma X. Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers in Kengyilia melanthera. FRONTIERS IN PLANT SCIENCE 2022; 13:959042. [PMID: 35958193 PMCID: PMC9358441 DOI: 10.3389/fpls.2022.959042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2023]
Abstract
As a typical psammophyte of the Triticeae, Kengyilia melanthera possesses high feeding potential and great utilization values in desertification control in the Qinghai-Tibet Plateau. However, few gene function and genetic studies have been performed in K. melanthera. In this study, single-molecule real-time sequencing technology was used to obtain the full-length transcriptome sequence of K. melanthera, following the functional annotation of transcripts and prediction of coding sequences (CDSs), transcription factors (TFs), and long noncoding RNA (lncRNA) sequences. Meanwhile, a total of 42,433 SSR loci were detected, with 5'-UTRs having the most SSR loci and trinucleotide being the most abundant type. In total, 108,399 SSR markers were designed, and 300 SSR markers were randomly selected for diversity verification of K. melanthera. A total of 49 polymorphic SSR markers were used to construct the genetic relationships of 56 K. melanthera accessions, among which 21 SSR markers showed good cross-species transferability among the related species. In conclusion, the full-length transcriptome sequence of the K. melanthera will assist gene prediction and promote molecular biology and genomics research, and the polymorphic SSR markers will promote molecular-assisted breeding and related research of K. melanthera and its relatives.
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Affiliation(s)
- Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jian Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lin Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lina Sha
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiqiong Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Minghong You
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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Roldán-Padrón O, Cruz-Pérez MS, Castro-Guillén JL, García-Arredondo JA, Mendiola-Olaya E, Saldaña-Gutiérrez C, Herrera-Paniagua P, Blanco-Labra A, García-Gasca T. Hybridization between Crotalus aquilus and Crotalus polystictus Species: A Comparison of Their Venom Toxicity and Enzymatic Activities. BIOLOGY 2022; 11:661. [PMID: 35625389 PMCID: PMC9138290 DOI: 10.3390/biology11050661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/15/2022] [Accepted: 04/17/2022] [Indexed: 06/15/2023]
Abstract
Hybridization is defined as the interbreeding of individuals from two populations distinguishable by one or more heritable characteristics. Snake hybridization represents an interesting opportunity to analyze variability and how genetics affect the venom components between parents and hybrids. Snake venoms exhibit a high degree of variability related to biological and biogeographical factors. The aim of this work is to analyze the protein patterns and enzymatic activity of some of the main hemotoxic enzymes in snake venoms, such as serine proteases (trypsin-like, chymotrypsin-like, and elastase-like), metalloproteases, hyaluronidases, and phospholipase A2. The lethal dose of 50 (LD50) of venom from the Crotalus aquilus (Cabf) and Crotalus polystictus (Cpbm) parents and their hybrids in captivity was determined, and phenetic analysis is also conducted, which showed a high similarity between the hybrids and C. polystictus. The protein banding patterns and enzymatic activity analyze by zymography resulted in a combination of proteins from the parental venoms in the hybrids, with variability among them. In some cases, the enzymatic activity is higher in the hybrids with a lower LD50 than in the parents, indicating higher toxicity. These data show the variability among snake venoms and suggest that hybridization is an important factor in changes in protein concentration, peptide variability, and enzymatic activity that affect toxicity and lethality.
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Affiliation(s)
- Octavio Roldán-Padrón
- Laboratorio de Biología Celular y Molecuar, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Queretaro 76230, Qro, Mexico; (O.R.-P.); (M.S.C.-P.); (C.S.-G.); (P.H.-P.)
| | - Martha Sandra Cruz-Pérez
- Laboratorio de Biología Celular y Molecuar, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Queretaro 76230, Qro, Mexico; (O.R.-P.); (M.S.C.-P.); (C.S.-G.); (P.H.-P.)
| | - José Luis Castro-Guillén
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Gto, Mexico; (J.L.C.-G.); (E.M.-O.)
| | - José Alejandro García-Arredondo
- Laboratorio de Química Medicinal, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Centro Universitario, Queretaro 76010, Qro, Mexico;
| | - Elizabeth Mendiola-Olaya
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Gto, Mexico; (J.L.C.-G.); (E.M.-O.)
| | - Carlos Saldaña-Gutiérrez
- Laboratorio de Biología Celular y Molecuar, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Queretaro 76230, Qro, Mexico; (O.R.-P.); (M.S.C.-P.); (C.S.-G.); (P.H.-P.)
| | - Patricia Herrera-Paniagua
- Laboratorio de Biología Celular y Molecuar, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Queretaro 76230, Qro, Mexico; (O.R.-P.); (M.S.C.-P.); (C.S.-G.); (P.H.-P.)
| | - Alejandro Blanco-Labra
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Gto, Mexico; (J.L.C.-G.); (E.M.-O.)
| | - Teresa García-Gasca
- Laboratorio de Biología Celular y Molecuar, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Queretaro 76230, Qro, Mexico; (O.R.-P.); (M.S.C.-P.); (C.S.-G.); (P.H.-P.)
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Jia Z, Fu K, Guo W, Jiang W, Ahmat T, Ding X, He J, Wang X. CAP Analysis of the Distribution of the Introduced Bemisia tabaci (Hemiptera: Aleyrodidae) Species Complex in Xinjiang, China and the Southerly Expansion of the Mediterranean Species. JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:14. [PMID: 33844016 PMCID: PMC8040787 DOI: 10.1093/jisesa/ieaa151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 06/12/2023]
Abstract
Bemisia tabaci (Gennadius) cryptic complex has invaded Xinjiang, China, since 1998. The distribution of Mediterranean (MED) and Middle East-Asia Minor 1 (MEAM1) B. tabaci substrains has been gradually identified due to the development of molecular technology. In this study, the distribution of MED and MEAM1 in Xinjiang was determined by cleaved amplified polymorphic sequence (CAPs). Results showed that MED dominated in northern Xinjiang (84%), whereas MEAM1 was dominant in southern Xinjiang (72%). Five pairs of simple sequence repeat (SSR) primers were used to analyze the genetic diversity of B. tabaci among 36 geographic populations. The genetic diversity of MED and MEAM1was low and varied little among populations in Xinjiang (0.09 ± 0.14 and 0.09 ± 0.13, respectively). Based on ∆K statistic, 13 populations of MEAM1 could be classified into two subgroups at K = 2, whereas the 23 populations of MED could be classified into four subgroups at K = 4. However, Mantel t-test demonstrated no correlation between geographical and genetic distances among B. tabaci complex (R = 0.42, P = 1.00). Neighbor-joining and principal coordinate analysis showed that geographical isolation and interspecific differences were the main causes of the genetic variation. Gene flow predicted that MEAM1 was most likely introduced from Urumqi to the southern Xinjiang. Meanwhile, a large proportion of MED in Kashi region came from Changji and Yining. To block ongoing dispersal, strict detection and flower quarantine regulations need to be enforced.
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Affiliation(s)
- Zunzun Jia
- College of Agriculture, Xinjiang Agricultural University, Xinjiang, China
| | - Kaiyun Fu
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture/Scientific Observing and Experimental Station of Korla, Ministry of Agriculture, Xinjiang, China
| | - Wenchao Guo
- Institute of Microbial Application, Xinjiang Academy of Agricultural Sciences, Xinjiang, China
| | - Weihua Jiang
- College of Plant pretection, Nanjing Agricultural University, Nanjing, China
| | - Tursun Ahmat
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture/Scientific Observing and Experimental Station of Korla, Ministry of Agriculture, Xinjiang, China
| | - Xinhua Ding
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture/Scientific Observing and Experimental Station of Korla, Ministry of Agriculture, Xinjiang, China
| | - Jiang He
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture/Scientific Observing and Experimental Station of Korla, Ministry of Agriculture, Xinjiang, China
| | - Xiaowu Wang
- Institute of Microbial Application, Xinjiang Academy of Agricultural Sciences, Xinjiang, China
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Khodaee L, Azizinezhad R, Etminan AR, Khosroshahi M. Assessment of genetic diversity among Iranian Aegilops triuncialis accessions using ISSR, SCoT, and CBDP markers. J Genet Eng Biotechnol 2021; 19:5. [PMID: 33428012 PMCID: PMC7801538 DOI: 10.1186/s43141-020-00107-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/21/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Crop wild relatives (CWRs) are commonly used as a suitable genetic reservoir for plant breeding. They can be used for enhancing the tolerance of plant varieties to biotic and abiotic stresses. Studying the genetic diversity of related wheat species in Iran could be useful to improve different traits of bread wheat, since the country is one of the major centers of genetic diversity and distribution of Aegilops species. Therefore, the aim of the present study was to determine the relationship among 48 Aegilops triuncialis accessions using three DNA marker systems, including start codon targeted (SCoT), CAAT box-derived polymorphism (CBDP), and inter-simple sequence repeat (ISSR) markers. RESULTS A total of 359 amplified DNA fragments were generated using 13 CBDP, 14 SCoT, and 16 ISSR primers that produced 96, 147, and 152 bands, respectively. The discriminating power of the three markers was assessed using polymorphism information content (PIC), marker index (MI), and resolving power (Rp). The mean values of PIC for ISSR, SCoT, and CBDP markers were 0.3, 0.26, and 0.34, respectively, indicating the efficiency of the three markers in detecting polymorphism among the studied accessions. ISSR markers had the highest values of MI, Rp, and polymorphism percentage as compared to SCoT and CBDP markers. Based on the Shannon index and heterozygosity values, genetic diversity in the Alborz population was more than in other populations. The accessions were classified into six, five, and five groups based on ISSR, SCoT, and CBDP using the UPGMA method. According to the results of cluster and PCoA analyses, the variation patterns corresponded with the geographical distribution of the Ae. triuncialis accessions. CONCLUSIONS The three markers provided a comprehensive pattern of the genetic diversity among the Iranian Ae. triuncialis accessions. This information could allow for a future insight into wheat breeding programs.
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Affiliation(s)
- Lavin Khodaee
- Department of Biotechnology and Plant Breeding, Islamic Azad University Science and Research Branch, Tehran, Iran
| | - Reza Azizinezhad
- Department of Biotechnology and Plant Breeding, Islamic Azad University Science and Research Branch, Tehran, Iran.
| | - Ali Reza Etminan
- Department of Plant Breeding and Biotechnology, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Mahmoud Khosroshahi
- Department of Biotechnology and Plant Breeding, Islamic Azad University Science and Research Branch, Tehran, Iran
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Xiong Y, Lei X, Bai S, Xiong Y, Liu W, Wu W, Yu Q, Dong Z, Yang J, Ma X. Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L. BMC PLANT BIOLOGY 2021; 21:3. [PMID: 33407133 PMCID: PMC7789342 DOI: 10.1186/s12870-020-02770-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/02/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Siberian wildrye (Elymus sibiricus L.) attracts considerable interest for grassland establishment and pasture recovery in the Qinghai-Tibet Plateau (QTP) due to its excellence in strong stress tolerance, high nutritional value and ease to cultivate. However, the lack of genomic information of E. sibiricus hampers its genetics study and breeding process. RESULTS In this study, we performed a genome survey and developed a set of SSR markers for E. sibiricus based on Next-generation sequencing (NGS). We generated 469.17 Gb clean sequence which is 58.64× of the 6.86 Gb estimated genome size. We assembled a draft genome of 4.34 Gb which has 73.23% repetitive elements, a heterozygosity ratio of 0.01% and GC content of 45.68%. Based on the gnomic sequences we identified 67,833 SSR loci and from which four hundred were randomly selected to develop markers. Finally, 30 markers exhibited polymorphism between accessions and ten were identified as single-locus SSR. These newly developed markers along with previously reported 30 ones were applied to analyze genetic polymorphism among 27 wild E. sibiricus accessions. We found that single-locus SSRs are superior to multi-loci SSRs in effectiveness. CONCLUSIONS This study provided insights into further whole genome sequencing of E. sibiricus in strategy selection. The novel developed SSR markers will facilitate genetics study and breeding for Elymus species.
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Affiliation(s)
- Yi Xiong
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiong Lei
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
- Sichuan Academy of Grassland Science, Chengdu, 611731, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, 611731, China
| | - Yanli Xiong
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, 81108, China
| | - Wendan Wu
- Sichuan Pratacultural Technology Research and Extension Center, Chengdu, 610041, China
| | - Qingqing Yu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhixiao Dong
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Yang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China.
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Hour AL, Hsieh WH, Chang SH, Wu YP, Chin HS, Lin YR. Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan. RICE (NEW YORK, N.Y.) 2020; 13:82. [PMID: 33315140 PMCID: PMC7736384 DOI: 10.1186/s12284-020-00445-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/06/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers', and breeders' selections is crucial for germplasm conservation and crop improvement. RESULTS A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. CONCLUSIONS The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.
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Affiliation(s)
- Ai-Ling Hour
- Department of Life Science, Fu-Jen Catholic University, New Taipei City, 242062, Taiwan
| | - Wei-Hsun Hsieh
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Su-Huang Chang
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Yong-Pei Wu
- Department of Agronomy, Chiayi Agricultural Experiment Branch, Taiwan Agricultural Research Institute, Chiayi, 600015, Taiwan
| | - Han-Shiuan Chin
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan.
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Zhang X, Li J, Kai W, Rui W, Ling L, Li D, Liu J, Guo H. Morphological characteristics and SRAP analysis of bermudagrass mutants generated by 60Co-γ radiation. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2020. [DOI: 10.1080/16878507.2020.1820269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Xiaoxiao Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
- The Jiangsu Provincial Engineering and Technology Research Center for Turf Germplasm Improvement and Breeding, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Jianjian Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
- The Jiangsu Provincial Engineering and Technology Research Center for Turf Germplasm Improvement and Breeding, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Wang Kai
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
- The Jiangsu Provincial Engineering and Technology Research Center for Turf Germplasm Improvement and Breeding, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Wang Rui
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
- The Jiangsu Provincial Engineering and Technology Research Center for Turf Germplasm Improvement and Breeding, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Li Ling
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
- The Jiangsu Provincial Engineering and Technology Research Center for Turf Germplasm Improvement and Breeding, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Dandan Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
- The Jiangsu Provincial Engineering and Technology Research Center for Turf Germplasm Improvement and Breeding, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Jianxiu Liu
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
- The Jiangsu Provincial Engineering and Technology Research Center for Turf Germplasm Improvement and Breeding, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
- The Jiangsu Provincial Engineering and Technology Research Center for Turf Germplasm Improvement and Breeding, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
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Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers. FORESTS 2019. [DOI: 10.3390/f10111019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.
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Shahabzadeh Z, Mohammadi R, Darvishzadeh R, Jaffari M. Genetic structure and diversity analysis of tall fescue populations by EST-SSR and ISSR markers. Mol Biol Rep 2019; 47:655-669. [PMID: 31707600 DOI: 10.1007/s11033-019-05173-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/30/2019] [Indexed: 12/14/2022]
Abstract
Tall fescue is a perennial cool-season grass with economic importance especially in temperate regions of the northern hemisphere. This study was done to assess the genetic diversity and population structure of 90 tall fescue populations and cultivars using ISSR and EST-SSR markers in order to categorize valuable populations for breeding programs and to construct the core collection of tall fescue collection in Iran. The 10 EST-SSR primer pairs amplified 92 alleles. The allele numbers varied from 4 to 13 alleles per locus with an average of 9.2 alleles, of which 84 (90.6%) were polymorphic with an average of 8.4 polymorphic bands per primer. The 39 ISSR primers totally produced 387 scorable bands, of which 335 (86.6%) were polymorphic with an average of 8.6 polymorphic bands per primer. The amplified markers by ISSR primers varied from 6 to 14 markers per primer with an average of 9.92 markers per primer. The 90 tall fescue populations using both EST-SSR and ISSR data were classified into two clusters by UPGMA method that was coincide with PCA and structure analysis results. The turf-type and forage-type populations were clearly separated. Based on the results, the Iranian populations provide a valuable and novel germplasm to employ in tall fescue varietal improvement programs for both forage and turf-type applications. This progression is an important step to introduce this collection for development of a core collection of tall fescue germplasm in Iran.
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Affiliation(s)
- Z Shahabzadeh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - R Mohammadi
- Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.
| | - R Darvishzadeh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - M Jaffari
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
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Genetic Diversity and Population Structure Analysis of Dalbergia Odorifera Germplasm and Development of a Core Collection Using Microsatellite Markers. Genes (Basel) 2019; 10:genes10040281. [PMID: 30959931 PMCID: PMC6523640 DOI: 10.3390/genes10040281] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022] Open
Abstract
Dalbergia odorifera T. Chen (Fabaceae) is a woody tree species indigenous to Hainan Island in China. Due to its high medicinal and commercial value, this tree species has been planted over 3500 ha2 in southern China. There is an urgent need for improvement of the D. odorifera germplasm, however, limited information on germplasm collection, conservation, and assessment of genetic resources is available. Therefore, we have built a database of 251 individuals collected across the whole of southern China, which included 42 wild trees and 210 cultivated trees, with the following objectives. (1) Evaluate genetic diversity and population structure of the database using 19 microsatellite markers and (2) develop a core collection for improvement and breeding programs. Totally, the 19 microsatellite markers harbored 77 alleles across the database with the polymorphic information content (PIC) ranging from 0.03 to 0.66. Medium genetic diversity level was inferred by Nei’s gene diversity (0.38), Shannon’s information index (0.65), and observed (0.33) and expected heterozygosity (0.38). Structure analysis showed that four was the optimum cluster size using the model-based Bayesian procedure, and the 251 D. odorifera individuals were grouped into five populations including four pure ones (RP1-4) and one mixed one (MIX) based on their maximum membership coefficients. Among these populations, the expected heterozygosity varied from 0.30 (RP3) to 0.38 (RP4). Analysis of molecular variance (AMOVA) showed 11% genetic variation existed among populations, and moderate population differentiation was inferred by the matrix of pairwise Fst (genetic differentiation among populations), which was in the range of 0.031 to 0.095. Moreover, a core collection of 31 D. odorifera individuals including six wild and 25 cultivated trees was developed, which was only 12.4% of the database but conserved the whole genetic diversity. The results of this study provided additional insight into the genetic structure of the large D. odorifera germplasm, and the core collection will be useful for the efficient and sustainable utilization of genetic resources, as well as efficient improvement in breeding programs.
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Genetic Diversity and Population Structure of Alnus cremastogyne as Revealed by Microsatellite Markers. FORESTS 2019. [DOI: 10.3390/f10030278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Alnus cremastogyne Burk. is a nonleguminous, nitrogen-fixing tree species. It is also the most important endemic species of Alnus Mill. in China, possessing important ecological functions. This study investigated population genetic variation in A. cremastogyne using 175 trees sampled from 14 populations native to Sichuan Province with 25 simple sequence repeat (SSR) markers. Our analysis showed that A. cremastogyne has an average of 5.83 alleles, 3.37 effective alleles, an expected heterozygosity of 0.63, and an observed heterozygosity of 0.739, indicating a relatively high level of genetic diversity. The A. cremastogyne populations in Liangshan Prefecture (Meigu, Mianning) showed the highest level of genetic diversity, whereas the Yanting population had the lowest. Our analysis also showed that the average genetic differentiation of 14 A. cremastogyne populations was 0.021. Analysis of molecular variance (AMOVA) revealed that 97% of the variation existed within populations; only 3% was among populations. Unweighted pair-group method with arithmetic means (UPGMA) clustering and genetic structure analysis showed that the 14 A. cremastogyne populations could be clearly divided into three clusters: Liangshan Prefecture population, Ganzi Prefecture population, the other population in the mountain area around the Sichuan Basin and central Sichuan hill area, indicating some geographical distribution. Further analysis using the Mantel test showed that this geographical distribution was significantly correlated with elevation.
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18
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De Novo Transcriptome Analysis of Dalbergia odorifera and Transferability of SSR Markers Developed from the Transcriptome. FORESTS 2019. [DOI: 10.3390/f10020098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Dalbergia odorifera T. Chen (Fabaceae), indigenous to Hainan Island, is a precious rosewood (Hainan hualimu) in China. However, only limited genomic information is available which has resulted in a lack of molecular markers, limiting the development and utilization of the germplasm resources. In this study, we aim to enrich genomic information of D. odorifera, and develop a series of transferable simple sequence repeat (SSR) markers for Dalbergia species. Therefore, we performed transcriptome sequencing for D. odorifera by pooling leaf tissues from three trees. A dataset of 138,516,418 reads was identified and assembled into 115,292 unigenes. Moreover, 35,774 simple sequence repeats (SSRs) were identified as potential SSR markers. A set of 19 SSR markers was successfully transferred across species of Dalbergia odorifera T. Chen, Dalbergia tonkinensis Prain, and Dalbergia cochinchinensis Pierre ex Laness. In total, 112 alleles (3–13 alleles/locus) were presented among 60 Dalbergia trees, and polymorphic information content ranged from 0.38 to 0.75. The mean observed and mean expected heterozygosity was 0.34 and 0.40 in D. odorifera, 0.27 and 0.32 in D. tonkinensis, and 0.29 and 0.33 in D. cochinchinensis, respectively. The cluster analysis classified these 60 trees into three major groups according to the three Dalbergia species based on the genetic similarity coefficients, indicating these newly developed transferable markers can be used to explore the relationships among Dalbergia species and assist genetic research. All these unigenes and SSR markers will be useful for breeding programs in the future.
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Tan J, Guo JJ, Yin MY, Wang H, Dong WP, Zeng J, Zhou SL. Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides. Molecules 2018; 23:E2963. [PMID: 30428601 PMCID: PMC6278481 DOI: 10.3390/molecules23112963] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/09/2018] [Accepted: 11/11/2018] [Indexed: 11/25/2022] Open
Abstract
Betula alnoides is a fast-growing valuable indigenous tree species with multiple uses in the tropical and warm subtropical regions in South-East Asia and southern China. It has been proved to be tetraploid in most parts of its distribution in China. In the present study, next generation sequencing (NGS) technology was applied to develop numerous SSR markers for B. alnoides, and 64,376 contig sequences of 106,452 clean reads containing 164,357 candidate SSR loci were obtained. Among the derived SSR repeats, mono-nucleotide was the main type (77.05%), followed by di- (10.18%), tetra- (6.12%), tri- (3.56%), penta- (2.14%) and hexa-nucleotide (0.95%). The short nucleotide sequence repeats accounted for 90.79%. Among the 291 repeat motifs, AG/CT (46.33%) and AT/AT (44.15%) were the most common di-nucleotide repeats, while AAT/ATT (48.98%) was the most common tri-nucleotide repeats. A total of 2549 primer sets were designed from the identified putative SSR regions of which 900 were randomly selected for evaluation of amplification successfulness and detection of polymorphism if amplified successfully. Three hundred and ten polymorphic markers were obtained through testing with 24 individuals from B. alnoides natural forest in Jingxi County, Guangxi, China. The number of alleles (NA) of each marker ranged from 2 to 19 with a mean of 5.14. The observed (HO) and expected (HE) heterozygosities varied from 0.04 to 1.00 and 0.04 to 0.92 with their means being 0.64 and 0.57, respectively. Shannon-Wiener diversity index (I) ranged from 0.10 to 2.68 with a mean of 1.12. Cross-species transferability was further examined for 96 pairs of SSR primers randomly selected, and it was found that 48.96⁻84.38% of the primer pairs could successfully amplify each of six related Betula species. The obtained SSR markers can be used to study population genetics and molecular marker assisted breeding, particularly genome-wide association study of these species in the future.
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Affiliation(s)
- Jing Tan
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Jun-Jie Guo
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Ming-Yu Yin
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Huan Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Wen-Pan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Jie Zeng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Shi-Liang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Genetic Diversity and Population Genetic Structure of Erythrophleum fordii Oliv., an Endangered Rosewood Species in South China. FORESTS 2018. [DOI: 10.3390/f9100636] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Erythrophleum fordii Oliv. is a valuable rosewood species indigenous to the tropical and warm sub-tropical zones of Vietnam, Laos, and South China. The natural forests have been heavily fragmented mostly due to over-exploitation and over-utilization, and alteration to croplands and fast-growing plantations. Therefore, it has been included in the IUCN Red List of Endangered Species as an endangered species. In the present study, genetic diversity and population genetic structure of 11 populations were estimated by SSR makers in South China. Five high polymorphic loci were studied with a total of 34 alleles, among which, seven were private alleles. The mean number of alleles per locus (A), the mean number of efficient alleles per locus (Ae), the observed (Ho) and expected (He) heterozygosity, and Shannon’s index (I) of the 11 populations were 3.40, 2.31, 0.52, 0.56, and 0.90, respectively. Correlation analysis between genetic parameters and geographical factors showed that He and I were in significant negative correlation with longitude, indicating that genetic diversity of E. fordii reduced gradually from West to East in south China. FIS of eight populations with above five samples was on average 0.01, most loci conformed to Hardy-Weinberg equilibrium in these populations; their genetic differentiation coefficient (FST) was 0.18, indicating that genetic differentiation among populations was relatively low and there existed 18% genetic variation among populations. Gene flow (Nm) between these populations was 1.28. The Mantel test showed that genetic distance was not significantly correlated with geographical distance (p > 0.05). It was concluded that populations with high genetic diversity or private alleles, especially Longmen, Wuming and Pingxiang populations should be a priority for in situ conservations, meanwhile more populations and as many families as possible in each population should be collected for ex situ conservations of germplasm resources of this species in the future.
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Hewitt S, Kilian B, Hari R, Koepke T, Sharpe R, Dhingra A. Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry ( Prunus avium L.). Comput Struct Biotechnol J 2017; 15:290-298. [PMID: 28392892 PMCID: PMC5376269 DOI: 10.1016/j.csbj.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 11/25/2022] Open
Abstract
Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus avium L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species. For the identification of polymorphisms in five closely related genotypes of sweet cherry, a gel-based approach (TRAP), reduced representation sequencing (TRAPseq), a 6k cherry SNParray, and whole genome sequencing (WGS) approaches were evaluated in the identification of genome-wide polymorphisms in sweet cherry cultivars. All platforms facilitated detection of polymorphisms among the genotypes with variable efficiency. In assessing multiple SNP detection platforms, this study has demonstrated that a combination of appropriate approaches is necessary for efficient polymorphism identification, especially between closely related cultivars of a species. The information generated in this study provides a valuable resource for future genetic and genomic studies in sweet cherry, and the insights gained from the evaluation of multiple approaches can be utilized for other closely related species with limited genetic diversity in the breeding germplasm.
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Affiliation(s)
- Seanna Hewitt
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Benjamin Kilian
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Ramyya Hari
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Tyson Koepke
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Richard Sharpe
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Amit Dhingra
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
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Giaj Merlera G, Muñoz S, Coelho I, Cavaglieri LR, Torres AM, Reynoso MM. Diversity of black Aspergilli isolated from raisins in Argentina: Polyphasic approach to species identification and development of SCAR markers for Aspergillus ibericus. Int J Food Microbiol 2015; 210:92-101. [PMID: 26114593 DOI: 10.1016/j.ijfoodmicro.2015.05.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/19/2015] [Accepted: 05/29/2015] [Indexed: 11/27/2022]
Abstract
Aspergillus section Nigri is a heterogeneous fungal group including some ochratoxin A producer species that usually contaminate raisins. The section contains the Series Carbonaria which includes the toxigenic species Aspergillus carbonarius and nontoxigenic Aspergillus ibericus that are phenotypically undistinguishable. The aim of this study was to examine the diversity of black aspergilli isolated from raisins and to develop a specific genetic marker to distinguish A. ibericus from A. carbonarius. The species most frequently found in raisins in this study were Aspergillus tubingensis (35.4%) and A. carbonarius (32.3%), followed by Aspergillus luchuensis (10.7%), Aspergillus japonicus (7.7%), Aspergillus niger (6.2%), Aspergillus welwitschiae (4.6%) and A. ibericus (3.1%). Based on inter-simple sequence repeat (ISSR) fingerprinting profiles of major Aspergillus section Nigri members, a sequence-characterized amplified region (SCAR) marker was identified. Primers were designed based on the conserved regions of the SCAR marker and were utilized in a PCR for simultaneous identification of A. carbonarius and A. ibericus. The detection level of the SCAR-PCR was found to be 0.01 ng of purified DNA. The present SCAR-PCR is rapid and less cumbersome than conventional identification techniques and could be a supplementary strategy and a reliable tool for high-throughput sample analysis.
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Affiliation(s)
- G Giaj Merlera
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina; CONICET, Argentina
| | - S Muñoz
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina
| | - I Coelho
- Laboratório de Bacteriologia Veterinária, IV-UFRRJ, Seropédica, RJ, Brazil
| | - L R Cavaglieri
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina; The Research Career of CONICET, Argentina
| | - A M Torres
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina; The Research Career of CONICET, Argentina.
| | - M M Reynoso
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina; The Research Career of CONICET, Argentina
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Genetic diversity and conservation evaluation of a critically endangered endemic maple, Acer yangbiense, analyzed using microsatellite markers. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.04.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Alcántara-Salinas G, Ellen RF, Valiñas-Coalla L, Caballero J, Argueta-Villamar A. Alternative ways of representing Zapotec and Cuicatec folk classification of birds: a multidimensional model and its implications for culturally-informed conservation in Oaxaca, México. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2013; 9:81. [PMID: 24321280 PMCID: PMC4120933 DOI: 10.1186/1746-4269-9-81] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/30/2013] [Indexed: 06/03/2023]
Abstract
BACKGROUND We report on a comparative ethno-ornithological study of Zapotec and Cuicatec communities in Northern Oaxaca, Mexico that provided a challenge to some existing descriptions of folk classification. Our default model was the taxonomic system of ranks developed by Brent Berlin. METHODS Fieldwork was conducted in the Zapotec village of San Miguel Tiltepec and in the Cuicatec village of San Juan Teponaxtla, using a combination of ethnographic interviews and pile-sorting tests. Post-fieldwork, Principal Component Analysis using NTSYSpc V. 2.11f was applied to obtain pattern variation for the answers from different participants. RESULTS AND CONCLUSION Using language and pile-sorting data analysed through Principal Component Analysis, we show how both Zapotec and Cuicatec subjects place a particular emphasis on an intermediate level of classification.These categories group birds with non-birds using ecological and behavioral criteria, and violate a strict distinction between symbolic and mundane (or ‘natural’), and between ‘general-purpose’ and ‘single-purpose’ schemes. We suggest that shared classificatory knowledge embodying everyday schemes for apprehending the world of birds might be better reflected in a multidimensional model that would also provide a more realistic basis for developing culturally-informed conservation strategies.
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Affiliation(s)
- Graciela Alcántara-Salinas
- Centro Regional de Investigaciones Multidisciplinarias, Universidad Nacional
Autónoma de México. UNAM, Av. Universidad s/n, circuito, Colonia
Chamilpa, Campus Morelos, Cuernavaca, Morelos C.P. 62210, Mexico
| | - Roy F Ellen
- Centre for Biocultural Diversity, School of Anthropology and Conservation,
University of Kent, Marlowe Building, Canterbury, UK
| | - Leopoldo Valiñas-Coalla
- Instituto de Investigaciones Antropológicas, Universidad Nacional
Autónoma de México. UNAM. Circuito Exterior, Ciudad Universitaria,
Coyoacán C.P. 04510, D.F, Mexico
| | - Javier Caballero
- Jardín Botánico Exterior, Instituto de Biología, Universidad
Nacional Autónoma de México. UNAM, Circuito Exterior s/n, Ciudad
Universitaria, Copilco, A.P. 70-614, Coyoacán Distrito Federal C.P. 04510,
Mexico
| | - Arturo Argueta-Villamar
- Centro Regional de Investigaciones Multidisciplinarias, Universidad Nacional
Autónoma de México. UNAM, Av. Universidad s/n, circuito, Colonia
Chamilpa, Campus Morelos, Cuernavaca, Morelos C.P. 62210, Mexico
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Li Y, van der Lee TAJ, Evenhuis A, van den Bosch GBM, van Bekkum PJ, Förch MG, van Gent-Pelzer MPE, van Raaij HMG, Jacobsen E, Huang SW, Govers F, Vleeshouwers VGAA, Kessel GJT. Population dynamics of Phytophthora infestans in the Netherlands reveals expansion and spread of dominant clonal lineages and virulence in sexual offspring. G3 (BETHESDA, MD.) 2012; 2:1529-40. [PMID: 23275876 PMCID: PMC3516475 DOI: 10.1534/g3.112.004150] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 09/22/2012] [Indexed: 11/18/2022]
Abstract
For a comprehensive survey of the structure and dynamics of the Dutch Phytophthora infestans population, 652 P. infestans isolates were collected from commercial potato fields in the Netherlands during the 10-year period 2000-2009. Genotyping was performed using 12 highly informative microsatellite markers and mitochondrial haplotypes. In addition, for each isolate, the mating type was determined. STRUCTURE analysis grouped the 322 identified genotypes in three clusters. Cluster 1 consists of a single clonal lineage NL-001, known as "Blue_13"; all isolates in this cluster have the A2 mating type and the Ia mitochondrial haplotype. Clusters 2 and 3 display a more elaborate substructure containing many unique genotypes. In Cluster 3, several distinct clonal lineages were also identified. This survey witnesses that the Dutch population underwent dramatic changes in the 10 years under study. The most notable change was the emergence and spread of A2 mating type strain NL-001 (or "Blue_13"). The results emphasize the importance of the sexual cycle in generating genetic diversity and the importance of the asexual cycle as the propagation and dispersal mechanism for successful genotypes. Isolates were also screened for absence of the Avrblb1/ipiO class I gene, which is indicative for virulence on Rpi-blb1. This is also the first report of Rpi-blb1 breakers in the Netherlands. Superimposing the virulence screening on the SSR genetic backbone indicates that lack the Avrblb1/ipiO class I gene only occurred in sexual progeny. So far, the asexual spread of the virulent isolates identified has been limited.
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Affiliation(s)
- Y. Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - T. A. J. van der Lee
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - A. Evenhuis
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - G. B. M. van den Bosch
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - P. J. van Bekkum
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - M. G. Förch
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - M. P. E van Gent-Pelzer
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - H. M. G. van Raaij
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - E. Jacobsen
- Laboratory of Plant Breeding, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - S. W. Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - F. Govers
- Laboratory of Phytopathology, Wageningen University, 6700 EE Wageningen, The Netherlands
- Centre for BioSystems Biology, 6700 AB Wageningen, The Netherlands
| | | | - G. J. T. Kessel
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
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Santoro PH, Neves PMOJ, Alexandre TM, Sartori D, Alves LFA, Fungaro MHP. Selection of Beauveria bassiana isolates to control Alphitobius diaperinus. J Invertebr Pathol 2008; 97:83-90. [PMID: 17869265 DOI: 10.1016/j.jip.2007.07.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Revised: 07/13/2007] [Accepted: 07/21/2007] [Indexed: 11/21/2022]
Abstract
This paper presents results on isolates of the entomopathogenic fungus Beauveria bassiana for Alphitobius diaperinus (Coleoptera: Tenebrionidae) control. Of the 30 isolates tested, four (CG 71, CG 152, UNIOESTE 4, and UNIOESTE 40) resulted in mortality rates >or= 40% within 10 days. These mortality rates could be considered high because of the resistance of these species to B. bassiana. Tests were conducted using these isolates to estimate LC(50), mortality rate over time, vegetative growth, and conidial production on artificial medium and on insects. Isolates CG 71, CG 152, and UNIOESTE 4 showed the best performance and great potential to be used in an integrated management program in poultry farms to control A. diaperinus. Also, the molecular profiles of 12 isolates were analyzed using the RAPD technique. The high-virulence isolates presented a more homogeneous RAPD pattern than the others. Genetic sequencing of the ITS region was performed for one of the virulent isolates (UNIOESTE 4) and compared with sequences deposited at the NCBI database, confirming its taxonomical position as belonging to B. bassiana Clade A.
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Affiliation(s)
- Patricia Helena Santoro
- Universidade Estadual de Londrina, Centro de Ciências Agrárias Rodovia Celso Garcia Cid, CEP 86051-990 Londrina, PR, Brazil.
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Azevedo ACR, Lainson R, Souza AA, Fé NF, Feliciangeli DM, Meneses CRV, Rangel EF. Comparative studies of populations of Lutzomyia umbratilis (Diptera: Psychodidae) in Brazil and Venezuela. JOURNAL OF MEDICAL ENTOMOLOGY 2002; 39:587-600. [PMID: 12144289 DOI: 10.1603/0022-2585-39.4.587] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We analyzed 64 quantitative and qualitative morphological characters in different populations of Lutzomyia (Nyssomyia) umbratilis Ward & Fraiha from Venezuela (Gran Sabana, Bolívar/BO) and Brazil (Serra do Navio, Amapá/AP Manaus, Amazonas/AM, Monte Dourado, Pará/ PA, and Peixoto de Azevedo, Mato Grosso/MT). Based on an analysis of qualitative characters, no differences were observed that could distinguish between the populations. Parametric tests were used to verify differences between sample means and variance homogeneity. The analysis-of-variance (ANOVA) test showed the existence of differences between character means in the five populations. In the graphic representation of the Student-Newman-Keuls test (Student-Newman-Keuls), we observed that 77% of the analyzed characters displayed disjunctions between the Venezuelan and Brazilian populations. Considering only the Brazilian population averages, we concluded that they are statistically different. When the Student-Newman-Keuls test was applied, no pattern was found that could separate them. However, in part, the phenetic analysis showed some evidences of heterogeneity in MT population.
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