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Lazaridi E, Kapazoglou A, Gerakari M, Kleftogianni K, Passa K, Sarri E, Papasotiropoulos V, Tani E, Bebeli PJ. Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:758. [PMID: 38592762 PMCID: PMC10975389 DOI: 10.3390/plants13060758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.
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Affiliation(s)
- Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Kondylia Passa
- Department of Agriculture, University of Patras, Nea Ktiria, 30200 Messolonghi, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Vasileios Papasotiropoulos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
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Chiangchin S, Thongyim S, Pandith H, Kaewkod T, Tragoolpua Y, Inta A, Watthana S, Pongamornkul W, Jangsutthivorawat S, Panya A. Clinacanthus nutans genetic diversity and its association with anti-apoptotic, antioxidant, and anti-bacterial activities. Sci Rep 2023; 13:19566. [PMID: 37949910 PMCID: PMC10638387 DOI: 10.1038/s41598-023-46105-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
Clinacanthus nutans (Burm. f.) Lindau has been extensively utilized in Thai folk medicine. However, there has been no prior exploration of its genetic diversity or its correlation with biological activity and phytochemical profiles. Herein, a total of 10 samples of C. nutans were collected from different geographic locations in different environments of Thailand, encompassing Northern, Northeastern, and Central regions. The genetic diversity study using sequence-related amplified polymorphism (SRAP) markers showed that all C. nutans samples were closely related, as indicated by UPGMA cluster analysis. When comparing the biological activities of C. nutans extracts, our findings demonstrated that those sourced from Northern Thailand exhibited the most potent activity in reducing lipopolysaccharide-inducing cell death, as accessed by cell viability assay. Furthermore, they showed remarkable antioxidant and antibacterial activities against Staphylococcus epidermidis, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. High-performance liquid chromatography (HPLC) analysis of phytochemical profiles revealed consistent chromatography peak patterns across all C. nutans extracts. However, they exhibited varying levels of phenolic contents, as judged by the Folin-Ciocalteu assay, which positively correlated with their observed activities. In conclusion, this study highlights the limited genetic variation within C. nutans population in Thailand. Furthermore, it underscores the association between the biological activity and the total phenolic contents which might be mainly impacted by environmental conditions.
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Affiliation(s)
- Salinee Chiangchin
- Department of Biology, Faculty of Science, Chiang Mai University, 239, Hauy Kaew Road, Muang District, Chiang Mai, 50200, Thailand
| | - Saruda Thongyim
- Department of Biology, Faculty of Science, Chiang Mai University, 239, Hauy Kaew Road, Muang District, Chiang Mai, 50200, Thailand
- National Extracts and Innovative Products for Alternative Healthcare Research Group, Chiang Mai University, Chiang Mai, 50200, Thailand
- Office of Research Administration, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Hataichanok Pandith
- Department of Biology, Faculty of Science, Chiang Mai University, 239, Hauy Kaew Road, Muang District, Chiang Mai, 50200, Thailand
| | - Thida Kaewkod
- Department of Biology, Faculty of Science, Chiang Mai University, 239, Hauy Kaew Road, Muang District, Chiang Mai, 50200, Thailand
- National Extracts and Innovative Products for Alternative Healthcare Research Group, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Yingmanee Tragoolpua
- Department of Biology, Faculty of Science, Chiang Mai University, 239, Hauy Kaew Road, Muang District, Chiang Mai, 50200, Thailand
- National Extracts and Innovative Products for Alternative Healthcare Research Group, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Angkhana Inta
- Department of Biology, Faculty of Science, Chiang Mai University, 239, Hauy Kaew Road, Muang District, Chiang Mai, 50200, Thailand
| | - Santi Watthana
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | | | - Siriphorn Jangsutthivorawat
- Department of Biology, Faculty of Science, Chiang Mai University, 239, Hauy Kaew Road, Muang District, Chiang Mai, 50200, Thailand
| | - Aussara Panya
- Department of Biology, Faculty of Science, Chiang Mai University, 239, Hauy Kaew Road, Muang District, Chiang Mai, 50200, Thailand.
- National Extracts and Innovative Products for Alternative Healthcare Research Group, Chiang Mai University, Chiang Mai, 50200, Thailand.
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Mosa KA, Ahmed AE, Hazem Y, Kanawati IS, Abdullah A, Hernandez-Sori L, Ali MA, Vendrame W. Insights into cryopreservation, recovery and genetic stability of medicinal plant tissues. Fitoterapia 2023; 169:105555. [PMID: 37295757 DOI: 10.1016/j.fitote.2023.105555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/24/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
Several plant secondary metabolites are used in the production of different pharmaceuticals based on their biological activities. The conservation and sustainable use of medicinal plants is important for the industrial production of plant-based medicines. Different cryopreservation methods are used for long-term culture preservation, which allows fast regeneration of the preserved plant material with the maintenance of its primary original traits. These methods could ensure the sustainable indefinite supply of plant tissues for theoretically unlimited periods of time, and have gained considerable attention in recent years. It is important to assess the recovery rate and the genetic stability of the recovered plant tissues after cryopreservation because cryopreservation efficiency differs among plant tissues and species. This review lays particular emphasis on the pharmaceutical applications of plant secondary metabolites that are produced through tissue culture approaches, highlighting the methods used for their cryopreservation, as well as their recovery and genetic stability.
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Affiliation(s)
- Kareem A Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates; Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt.
| | - Amro E Ahmed
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Yousef Hazem
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Israa S Kanawati
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Amenah Abdullah
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Lazaro Hernandez-Sori
- Laboratory for Plant Breeding and Conservation of Genetic Resources, Bioplant Center, University of Ciego de Ávila, 69450 Ciego de Ávila, Cuba
| | - Muna A Ali
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Wagner Vendrame
- Environmental Horticulture Department, University of Florida, Florida, USA
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Wang X, Gou W, Wang T, Xiong Y, Xiong Y, Yu Q, Dong Z, Ma X, Liu N, Zhao J. Genetic diversity analysis and molecular characteristics of wild centipedegrass using sequence-related amplified polymorphism (SRAP) markers. PeerJ 2023; 11:e15900. [PMID: 37641603 PMCID: PMC10460567 DOI: 10.7717/peerj.15900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023] Open
Abstract
Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is commonly used as a low-maintenance warm-season turfgrass owing to its excellent adaptation to various soil types. A better understanding of the genetic diversity pattern of centipedegrass is essential for the efficient development and utilization of accessions. This study used fifty-five pairs of primers to detect the genetic variation and genetic structure of twenty-three wild centipedegrass accessions by Sequence-related amplified polymorphism (SRAP) markers. A total of 919 reliable bands were amplified, among which 606 (65.80%) were polymorphic and 160 (2.91%) were the monomorphic loci. The average polymorphic information content (PIC) value was 0.228. The unweighted pair group method with arithmetic mean (UPGMA) clustering analysis grouped the twenty-three accessions into two clusters. Meanwhile, the structure analysis showed that the tested accessions possessed two main genetic memberships (K = 2). The Mantel test significantly correlated the genetic and geographic distance matrices (r = 0.3854, p = 0.000140). Furthermore, geographical groups showed moderate genetic differentiation, and the highest intragroup genetic diversity was found in the Sichuan group (He = 0.201). Overall, the present research findings could promote the protection and collection of centipedegrass and provide comprehensive information to develop novel breeding strategies.
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Affiliation(s)
- Xiaoyun Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Ting Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhixiao Dong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Nanqing Liu
- Jiangsu Vocational College Agriculture and Forestry, Gourong, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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Wang J, Dai W, Chen J, Ye K, Lai Q, Zhao D. Assessment of Genetic Diversity and Genetic Structure of Saussurea medusa (Asteraceae), a "Sky Island" Plant in the Qinghai-Tibet Plateau, Using SRAP Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:2463. [PMID: 37447024 DOI: 10.3390/plants12132463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/19/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
Saussurea medusa Maxim. is a typical "sky island" species and one with the highest altitude distributions among flowering plants. The present study aimed at analyzing the genetic diversity and population structure of 300 S. medusa accessions collected from 20 populations in the Qilian Mountains in the northeastern Qinghai-Tibet Plateau (QTP), using sequence-related amplified polymorphism (SRAP) markers. A total of 14 SRAP primer combinations were employed to analyze genetic diversity and population structure across all accessions. Out of 511 amplified bands, 496 (97.06%) were polymorphic. The populations in the eastern Qilian Mountains had significantly higher genetic diversity than those in the central and western groups. Population structure analysis revealed greater genetic differentiation among populations with a Gst of 0.4926. UPGMA-based clustering classified the 300 S. medusa accessions into 3 major clusters, while the Bayesian STRUCTURE analysis categorized them into 2 groups. Correlation analyses showed that the genetic affinity of the populations was based on differences in geographical distance, moisture conditions, and photothermal conditions between the habitats. This study represents the first comprehensive genetic assessment of S. medusa and provides important genetic baseline data for the conservation of the species.
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Affiliation(s)
- Jun Wang
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Academy of Agricultural Sciences, Mianyang 621022, China
| | - Wei Dai
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Academy of Agricultural Sciences, Mianyang 621022, China
| | - Jie Chen
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Academy of Agricultural Sciences, Mianyang 621022, China
| | - Kunhao Ye
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Academy of Agricultural Sciences, Mianyang 621022, China
| | - Qianglong Lai
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Academy of Agricultural Sciences, Mianyang 621022, China
| | - Dan Zhao
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Academy of Agricultural Sciences, Mianyang 621022, China
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Barh A, Kamal S, Sharma VP, Sharma K, Kumari B, Nath M. Identification and morpho-molecular characterization of low spore strain in oyster mushroom. Mol Biol Rep 2023; 50:5029-5038. [PMID: 37095362 DOI: 10.1007/s11033-023-08452-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND Sporocarps of oyster mushroom liberate enormous spores and cause allergic reactions to workers involved in its cultivation. These spore-related allergies include stiffness or pain in the forearms, limbs, itchy throat, grogginess, and respiratory problems and are major problems during oyster mushroom cultivation. METHODS AND RESULTS In this study, we have generated seven hybrids using single-spore isolates (SSIs) of Pleurotus ostreatus var. florida (DMRP-49) and P. ostreatus (DMRP-30). Chimera was observed during cultivation trial of these hybrids and led to the development of low spore-producing/sporeless strain (DMRP-395) as evident from spore print and microscopic analysis. Further, the cultivation trial of this sporeless strain revealed a bunchy fruiting pattern and required 20-24 °C temperature for fruiting. At par yield was observed in sporeless strain. Notably, a prominent infundibuliform-shaped pileus along with central attachment of stipe was observed in the sporeless strain. Moreover, genetic diversity and principal component biplot analysis revealed resemblance of sporeless strain with one of the parental strain, i.e., P. ostreatus var. florida (DMRP-49). CONCLUSIONS The developed sporeless strain (DMRP-395) contains high protein and at par yield as compared with the control (DMRP-136). This sporeless strain will be helpful to reduce spore-related allergic responses in mushroom growers.
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Affiliation(s)
- Anupam Barh
- ICAR-Directorate of Mushroom Research, Solan, 173213, India.
- ICAR-Indian Institute of Soil and Water Conservation, Dehradun, 248195, India.
| | - Shwet Kamal
- ICAR-Directorate of Mushroom Research, Solan, 173213, India
| | | | - Kanika Sharma
- ICAR-Directorate of Mushroom Research, Solan, 173213, India
| | - Babita Kumari
- ICAR-Directorate of Mushroom Research, Solan, 173213, India
| | - Manoj Nath
- ICAR-Directorate of Mushroom Research, Solan, 173213, India
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Cornea-Cipcigan M, Pamfil D, Sisea CR, Margaoan R. Characterization of Cyclamen genotypes using morphological descriptors and DNA molecular markers in a multivariate analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1100099. [PMID: 36778673 PMCID: PMC9909266 DOI: 10.3389/fpls.2023.1100099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Morphological and molecular characterization of germplasm is essential for the improvement of cultivated plants efforts. This study investigated the genetic diversity of 32 Cyclamen genotypes comprising 16 C. persicum varieties and 16 Cyclamen species using multivariate analysis for 36 morphological traits (19 quantitative and 17 qualitative) and molecular characterization (SRAP and SCoT markers). The color CIELab parameters were collected via PCE-CSM7 that separately measured the leaves dark and silvery patterns and the flower's slip (region of the petal top), eye (the region of the petal base) and sepal. Genetic diversity was also evaluated using Shannon Wiener (H') and Simpson's (λ) Indices, and Pilou evenness (J) using the library vegan from R software. According to the principal component analysis, the variables that contributed the most were leaf pattern color, leaf abaxial surface color, pedicel coiling, leaf and stem number. The color indicators of Cyclamen leaves showed decreased L* values in darker colored genotypes, whereas increased a* values were noticed in flower eye and lower in slip. Molecular characterization was based on 26 SRAP and 12 SCoT markers that produced clearly repeatable DNA bands and exhibited significant levels of polymorphism. Based on the morphological traits and molecular markers data, the UPGMA method for hierarchical clustering technique was used to generate the dendrograms, and their entanglement was obtained using the Tanglegram algorithm from the dendextend package with the R software. Entanglement analysis (0.30) between dendrograms obtained from the morphological and genetic analysis using SRAP markers showed a high association. Comparison between color measurements of flowers (entanglement=0.45) and leaves (entanglement=0.47) with SCoT analysis revealed differences at species level, discriminating between similar genotypes. Combined phenotypic and molecular analysis improved the comprehensive estimation of real diversity in the investigated Cyclamen genotypes. The findings of the present study are useful for quantifying diversity and genetic variability in Cyclamen breeding and genetic investigations.
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Affiliation(s)
- Mihaiela Cornea-Cipcigan
- Department of Horticulture and Business in Rural Development, Faculty of Horticulture, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Doru Pamfil
- Research Centre for Biotechnology in Agriculture Affiliated to Romanian Academy, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Cristian Radu Sisea
- Department of Horticulture and Business in Rural Development, Faculty of Horticulture, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Rodica Margaoan
- Laboratory of Cell Analysis and Spectrometry, Advanced Horticultural Research Institute of Transylvania, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
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Genetic and morphological comparisons of lesser celandine (Ficaria verna) invasions suggest regionally widespread sexual reproduction. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02921-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Assessment of genetic diversity and population structure of the endemic Hertia cheirifolia (L.) Kuntze based on ISSR and SRAP molecular markers. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01166-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Heikal YM, El-Esawi MA, Naidu R, Elshamy MM. Eco-biochemical responses, phytoremediation potential and molecular genetic analysis of Alhagi maurorum grown in metal-contaminated soils. BMC PLANT BIOLOGY 2022; 22:383. [PMID: 35909101 PMCID: PMC9341119 DOI: 10.1186/s12870-022-03768-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/20/2022] [Indexed: 05/09/2023]
Abstract
BACKGROUND Alhagi maurorum Medik. (camelthorn) is a dominant desert plant indigenous in various habitats, including the Western Desert of Egypt. The plant is especially prevalent in and around economic iron ore deposits. Nutrient and heavy metal levels in A. maurorum tissues and soil samples were assessed to identify associations between heavy metal levels in plants and soil. The objective was to evaluate this species as an indicator of heavy metal pollution. Photosynthetic pigments, protein, proline, alkaloids, flavonoids, 2,2-diphenyl-1-picrylhydrazylscavenging, reduced glutathione, malondialdehyde, antioxidant enzymes, and stress-related gene expression were assessed to determine their functional roles in metal stress adaptation in ultra- and molecular structure. Additionally, the molecular genetic variation in A. maurorum samples was assessed using co-dominant sequence-related amplified polymorphism (SRAP) and inter simple sequence repeats (ISSR). RESULTS A substantial difference in enzymatic and non-enzymatic antioxidants of A. maurorum was observed in samples collected from three sites. A. maurorum is suited to the climate in mineralized regions. Morphologically, the stem shows spines, narrow leaves, and a reduced shoot system. Anatomically, modifications included a cuticle coating on leaves and stems, sunken stomata, a compact epidermis, and a thick cortex. Significant anatomical-physiological differences were observed with varying heavy metal soil content, antioxidative enzyme activities increased as a tolerance strategy, and glutathione levels decreased in response to heavy metal toxicity. Heavy metal accumulation also affected the expression of stress-related genes. The highest levels of expression of GST, G6PDH, 6PGD, nitrate reductase 1, and sulfate transporter genes were found in plants collected from site A1. However, auxin-induced protein exhibited its highest expression in plants collected from A2. Six SRAP combinations yielded 25 scoreable markers with a polymorphism rate of 64%, and 5 ISSR markers produced 11 bands with a polymorphism rate of 36.36% for three A. maurorum genotypes. The ME1xEM7 primer combinations provided the most polymorphic information content and resolving power, making it the most useful primer for differentiating A. maurorum genotypes. SRAP markers exhibited a higher diversity index (0.24) than ISSR markers (0.16). CONCLUSIONS A. maurorum displayed adaptive characteristics for heavy metal sequestration from mining site soils and is proposed as a strong candidate for phytoremediation.
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Affiliation(s)
- Yasmin M Heikal
- Botany Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
| | - Mohamed A El-Esawi
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Maha M Elshamy
- Botany Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
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Molecular characterization of coconut (Cocos nucifera L.) varieties in Vietnam using sequence-related amplified polymorphism (SRAP) markers. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01136-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Assessment of Genetic Diversity and Population Structure of the Endangered Astragalus exscapus subsp. transsilvanicus through DNA-Based Molecular Markers. PLANTS 2021; 10:plants10122732. [PMID: 34961203 PMCID: PMC8707493 DOI: 10.3390/plants10122732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022]
Abstract
Astragalus exscapus L. subsp. transsilvanicus (Schur) Nyár. (Fabaceae) is a rare plant endemic to the Transylvanian Plateau, represented by 24 identified populations. Limited information on the genetic variation and population structure is available, which obstructs efficient measures for conservation strategy. The present study aimed to analyze the genetic diversity and population structure of eight populations of A. exscapus subsp. transsilvanicus revealed by sequence-related amplified polymorphism (SRAP) markers. A total of 164 bands were amplified, 96.7% of which (159) were polymorphic. Nei’s gene diversity index (He) was estimated to be 0.228 at the population level and 0.272 at the subspecies level. The genetic differentiation among populations (Gst) was 0.165, which indicated a low proportion of total genetic diversity. The analysis of molecular variance (AMOVA) indicated that 17% of the total variation of A. exscapus subsp. transsilvanicus is found among the populations, while 83% was found within the populations. A UPGMA dendrogram, principal coordinate analysis, and the STRUCTURE software grouped the populations into two clusters uncorrelated with the provenience of the 125 individuals, which might be attributed to fragmentation processes, insect pollination, population size, and specific environmental conditions of the habitats.
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Omar HS, Al Mutery A, Osman NH, Reyad NEHA, Abou-Zeid MA. Genetic diversity, antifungal evaluation and molecular docking studies of Cu-chitosan nanoparticles as prospective stem rust inhibitor candidates among some Egyptian wheat genotypes. PLoS One 2021; 16:e0257959. [PMID: 34767570 PMCID: PMC8589204 DOI: 10.1371/journal.pone.0257959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/14/2021] [Indexed: 11/21/2022] Open
Abstract
Wheat has a remarkable importance among cereals worldwide. Wheat stem and leaf rust constitute the main threats that destructively influence grain quality and yield production. Pursuing resistant cultivars and developing new genotypes including resistance genes is believed to be the most effective tool to overcome these challenges. This study is the first to use molecular markers to evaluate the genetic diversity of eighteen Egyptian wheat genotypes. Moreover, the molecular docking analysis was also used to assess the Cu-chitosan nanoparticle (CuChNp) treatment and its mode of action in disease control management. The tested genotypes were categorized into two main cluster groups depending on the similarity matrix, i.e the most resistant and susceptible genotypes to stem and leaf rust races. The results of SCoT primers revealed 140 polymorphic and 5 monomorphic bands with 97% polymorphism. While 121 polymorphic and 74 monomorphic bands were scored for SRAP primers (99% polymorphism). The genotypes Sakha 94, Sakha 95, Beni Sweif 4, Beni Sweif 7, Sohag 4 and Sohag 5 were resistant, while Giza 160 was highly susceptible to all stem rust races at the seedling stage. However, in the adult stage, the 18 genotypes were evaluated for stem and leaf rust-resistant in two different locations, i.e. Giza and Sids. In this investigation, for the first time, the activity of CuChNp was studied and shown to have the potential to inhibit stem and leaf rust in studied Egyptian wheat genotypes. The Spraying Cu-chitosan nanoparticles showed that the incubation and latent periods were increased in treated plants of the tested genotypes. Molecular modeling revealed their activity against the stem and leaf rust development. The SRAP and SCoT markers were highly useful tools for the classification of the tested wheat genotypes, although they displayed high similarities at the morphological stage. However, Cu-chitosan nanoparticles have a critical and effective role in stem and leaf rust disease control.
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Affiliation(s)
- Hanaa S. Omar
- Faculty of Agriculture, Genetics Department, Cairo University, Giza, Egypt
- GMO lab Faculty of Agriculture, Cairo University, Research Park, CURP, Giza, Egypt
| | - Abdullah Al Mutery
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Molecular Genetics and Stem Cell Research Laboratory, University of Sharjah, Sharjah, United Arab Emirates
| | - Neama H. Osman
- Faculty of Agriculture, Genetics Department, Cairo University, Giza, Egypt
| | | | - Mohamed A. Abou-Zeid
- Wheat Disease Research Department, Plant Pathology Research Institute, ARC, Giza, Egypt
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14
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Benke AP, Krishna R, Mahajan V, Ansari WA, Gupta AJ, Khar A, Shelke P, Thangasamy A, Shabeer TPA, Singh M, Bhagat KP, Manjunathagowda DC. Genetic diversity of Indian garlic core germplasm using agro-biochemical traits and SRAP markers. Saudi J Biol Sci 2021; 28:4833-4844. [PMID: 34354473 PMCID: PMC8324993 DOI: 10.1016/j.sjbs.2021.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 11/23/2022] Open
Abstract
The characterization of garlic germplasm improves its utility, despite the fact that garlic hasn't been used much in the past. Garlic has an untapped genetic pool of immense economic and medicinal value in India. Hence, using heuristic core collection approach, a core set of 46 accessions were selected from 625 Indian garlic accessions based on 13 quantitative and five qualitative traits. The statistical measures (CV per cent, CR per cent, VR per cent) were used to sort the core set using Shannon-Wiener diversity index and the Nei diversity index. In addition, the variation within the core set was tested for 18 agro-morphological and six biochemical characteristics (allicin, phenol content, pyruvic acid, protein, allyl methyl thiosulfinate (AMTHS), and methyl allyl thiosulfinate (MATHS)). Further study of the core set's molecular diversity was performed using sequence related amplified polymorphism (SRAP) markers, which revealed a wide range of diversity among the core set's accessions, with an average polymorphism efficiency (PE) of 80.59 percent, polymorphism information content (PIC) of 0.29, effective multiplex ratio (EMR) of 3.51, and marker index (MI) of 0.99. The findings of this study will be useful in identifying high-yielding, elite garlic germplasm lines with the trait of interest. Since this core set is indicative of total germplasm, these selected breeding lines will be used for genetic improvement of garlic in the future.
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Affiliation(s)
- Ashwini Prashant Benke
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - Ram Krishna
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - Vijay Mahajan
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - Waquar Akhter Ansari
- Department of Botany, Savitribai Phule Pune University, Pune 41100, Maharashtra, India
| | - Amar Jeet Gupta
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - Anil Khar
- Department of Vegetable Science, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Poonam Shelke
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - A. Thangasamy
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | | | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - Kiran P. Bhagat
- ICAR-Directorate of Floriculture, Pune 411005, Maharashtra, India
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Shamustakimova AO, Mavlyutov YM, Klimenko IA. Application of SRAP Markers for DNA Identification of Russian Alfalfa Cultivars. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421050112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Ma M, Wang T, Lu B. Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers. GENETIC RESOURCES AND CROP EVOLUTION 2021; 68:2655-2667. [PMID: 34031623 PMCID: PMC8134809 DOI: 10.1007/s10722-021-01204-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 05/05/2021] [Indexed: 05/27/2023]
Abstract
Amomum tsao-ko Crevost & Lemarié is an important crop that has been widely used in traditional Chinese medicine and daily diets for a long time. In this study, the genetic diversity and relationships of eight cultivated populations of A. tsao-ko grown in Southwest China were examined using sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers. The results showed that 139 (99.29%) of 140 and 185 (99.46%) of 186 bands were polymorphic by SRAP and ISSR primers amplification, respectively. The polymorphic information content of detected bands were 0.270 (SRAP) and 0.232 (ISSR), respectively. The average Nei's gene diversity (H = 0.217) and Shannon's information index (I = 0.348) at the species level generated by SRAP primer were higher than those by ISSR analysis (H = 0.158, I = 0.272). Genetic differentiation coefficients and molecular variance analysis (AMOVA) indicated that the genetic variance of A. tsao-ko mainly occurred within populations rather than among populations. The high genetic identity among populations was revealed by SRAP (0.937) and ISSR (0.963). Using UPGMA cluster analysis, principal coordinate analysis, and population structure analysis, the accessions were categorized into two major groups. Overall, results obtained here will be useful for A. tsao-ko germplasm characterization, conservation, and utilization.
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Affiliation(s)
- Mengli Ma
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan People’s Republic of China
| | - Tiantao Wang
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan People’s Republic of China
| | - Bingyue Lu
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan People’s Republic of China
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17
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Harfi T, Alireza MA, Farzad R, Fariborz ZN. Induced mutation in Agaricus bisporus by gamma ray to improve genetic variability, degradation enzyme activity, and yield. Int J Radiat Biol 2021; 97:1020-1031. [PMID: 33900888 DOI: 10.1080/09553002.2021.1913528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
PURPOSE Genetic variability in white button mushroom cultivars is very low due to the life cycle. Induction mutations using gamma irradiation is a useful way to generate diversity in white button mushrooms to obtain genotype(s) with desirable traits. METHODS Gamma irradiation Cobalt-60 was used for inducting genetic diversity in white button mushroom to obtain genotype(s) with desirable traits. Gamma irradiation with doses of 0-500 Gy was conducted on spores on Potato Dextrose Agar medium. RESULTS The results showed significant differences in days to pin production and harvest, fruit body number, fresh and dry weight, yield, laccase, and manganese peroxidase enzyme activity. After isolating variants, 15 variants were selected on the base of their high yield and enzyme degradation activity. Their genetic variation was confirmed by Sequence Related Amplified Polymorphism (SRAP) markers, and then incubated on three types of substrates (50:50, 75:25, and 100:0 % compost: raw straw). The results showed that all variants, except GR18, colonized in 75:25, and GR3, GR4, GR9, GR61, GR72, and GR74 variants colonized in 50:50. In 100:0 substrate, GR55 and GR63 were the earliest variants, and GR9 produced the highest fruit body number. In 75:25 substrate, GR9, GR3, GR61, GR4, GR74, GR4, GR61, and GR72 showed higher yields. The highest laccase and manganese peroxidase activity were recorded in GR3, GR4, GR9, GR72, and GR61. The isolated 15 variants were clustered into two main groups by cluster analysis and genetic variation was confirmed by SRAP markers. CONCLUSION The results showed that the diversity in the white button mushroom could be improved using gamma rays, and the variation would be useful for the development of future breeding programs.
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Affiliation(s)
- Tayebeh Harfi
- Department of Horticultural Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Motallebi-Azar Alireza
- Department of Horticultural Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Rasouli Farzad
- Department of Horticultural Science, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
| | - Zaare-Nahandi Fariborz
- Department of Horticultural Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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18
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Ağdamar S, Baysal Ö, Yıldız A, Tarkan AS. Genetic differentiation of non-native populations of Gibel Carp, Carassius gibelio in Western Turkey by ISSR and SRAP markers. ZOOLOGY IN THE MIDDLE EAST 2020. [DOI: 10.1080/09397140.2020.1835215] [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)
- Sevan Ağdamar
- Gökçeada School of Applied Sciences, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Ömür Baysal
- Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Ayşegül Yıldız
- Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Ali Serhan Tarkan
- Faculty of Fisheries, Muğla Sıtkı Koçman University, Muğla, Turkey
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
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19
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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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20
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Hassani SMR, Talebi R, Pourdad SS, Naji AM, Fayaz F. Morphological description, genetic diversity and population structure of safflower ( Carthamus tinctorius L.) mini core collection using SRAP and SSR markers. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1818620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
| | - Reza Talebi
- Department of Agronomy and Plant Breeding, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran
| | - Sayyed Saeid Pourdad
- Dryland Agricultural Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Kermanshah, Iran
| | - Amir Mohammad Naji
- Department of Plant Breeding, College of Agriculture, Shahed University, Tehran, Iran
| | - Farzad Fayaz
- Department of Agronomy and Plant Breeding, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran
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21
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Genetic Diversity among Selected Medicago sativa Cultivars Using Inter-Retrotransposon-Amplified Polymorphism, Chloroplast DNA Barcodes and Morpho-Agronomic Trait Analyses. PLANTS 2020; 9:plants9080995. [PMID: 32764359 PMCID: PMC7464242 DOI: 10.3390/plants9080995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/08/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022]
Abstract
Alfalfa (Medicago sativa L.) is a major forage crop of family Fabaceae and is frequently cultivated in Egypt. The present study is concerned with the genetic discrimination of fifteen alfalfa cultivars from three different countries (Egypt, Australia, and USA) using two molecular approaches: inter-retrotransposon-amplified polymorphism (IRAP) markers and two chloroplast DNA barcodes matK and the trnH in addition to the analysis of fifteen morpho-agronomic traits. The genetic relatedness, based on analysis of IRAP marker polymorphism and produced using eleven primers by clustering via principal component analysis (PCA) and multivariate heatmap biostatistical methods differentiated the two Egyptian cultivars EGY1-Ismailia1 and EGY2-Nubaria1 from the three Australian and seven American cultivars, with some distinction of the cv. USA6-SW9720 and cv. AUS4-SuperFast. The results were also supported by the sequence analysis of the matK and the trnH genes on the genetic relatedness between eight cultivars. Moreover, it might be suggested that breeding lines from M. sativa cultivars may provide novel insights and a better understanding of the domestication of M. sativa genetic diversity. The classification of the eight cultivars, as revealed by morpho-agronomic traits, confirmed the close genetic relationship between the two Egyptian cultivars and indicated some resemblance between them and the AUS2-Siri Nafa, whereas the two American cultivars, USA1-Super supreme and USA4-Cuf101, were clearly isolated from a cluster of other three cultivars USA7-SW9628, USA8-Magna901, and USA9-Perfect. The results are useful sources of genetic information for future breeding programs in crop development and open new possibilities of producing M. sativa lines harboring high forage quality, productivity, and resistance to biotic and abiotic stresses.
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Feng T, Jia Q, Meng X, Chen X, Wang F, Chai W, Liang Z. Evaluation of genetic diversity and construction of DNA fingerprinting in Polygonatum Mill. based on EST-SSR and SRAP molecular markers. 3 Biotech 2020; 10:322. [PMID: 32656055 DOI: 10.1007/s13205-020-02316-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
Polygonatum sibiricum is widely consumed as a traditional Chinese herb and edible plant in China. Despite its nutritional and medical values, research on Polygonatum Mill. has been scarce, particularly as far as its genetic diversity is concerned. In this study, fourteen expressed sequence tag-derived simple sequence repeat (EST-SSR) and seven sequence-related amplified polymorphism (SRAP) markers were used to evaluate the genetic diversity in fifty Polygonatum Mill. accessions. The EST-SSRs and SRAPs produced 173 (90.58%) and 113 (93.39%) polymorphic bands, respectively. Unweighted Pair-Group Method Analysis (UPGMA) based on the combined data matrices of EST-SSRs and SRAPs divided the fifty Polygonatum Mill. accessions into fourteen groups. In addition, accessions of P. cyrtonema Hua obtained from Anhui and Zhejiang provinces were clustered according to their geographic origin. Furthermore, some accessions were gathered together based on species, such as P. kingianum Coll. et Hemsl, P. punctatum Royle ex Kunth, P. odoratum (Mill.) Druce, and P. sibiricum Red., and bootstrap analysis for clustering fully supported the grouping of the accessions. The Analysis of Molecular Variance (AMOVA) results revealed higher variation within populations (95%) rather than among populations (5%), indicating that Polygonatum Mill. has a low genetic differentiation between populations, and Principal Coordinate Analysis (PCoA) greatly supported the results of cluster analysis and AMOVA analysis. Finally, five markers which could produce abundant and stable bands were used to construct DNA fingerprinting database of Polygonatum Mill.. Our results demonstrated the utility of both EST-SSR and SRAP markers to successfully evaluate and identify Polygonatum Mill..
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Affiliation(s)
- Tinghui Feng
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Qiaojun Jia
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Xin Meng
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Xiliang Chen
- Zhejiang WSKOO Biotechnology Co.,Ltd., Wuyi, 321200 Zhejiang China
| | - Feifeng Wang
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Weiguo Chai
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 Zhejiang China
| | - Zongsuo Liang
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
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Zhao X, Zou G, Zhao J, Hu L, Lan Y, He J. Genetic relationships and diversity among populations of Paris polyphylla assessed using SCoT and SRAP markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1281-1293. [PMID: 32549689 PMCID: PMC7266889 DOI: 10.1007/s12298-020-00808-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/07/2020] [Accepted: 03/27/2020] [Indexed: 05/22/2023]
Abstract
The genetic diversity of 33 Paris polyphylla samples collected from the Dabie Mountains was analyzed using SCoT and SRAP molecular markers, revealing the genetic relationships among Paris polyphylla resources in the Dabie Mountains at the molecular level and providing a theoretical basis for genetic improvement and conservation. As a result, a total of 134 bands were amplified with 9 SCoT primers, the percentage of polymorphic bands was 100%, the average number of primers amplified was 14.89, the PIC value was 94.83% and the genetic similarity coefficient ranged from 0.463 to 0.896. Ten pairs of SRAP primer combinations amplified 135 bands, including 129 polymorphic bands, and the percentage of polymorphic bands was 95.56%. The average number of polymorphic bands obtained with each pair of SRAP primer combinations was 12.9, the PIC value was 93.91%, and the genetic similarity coefficient ranged from 0.533 to 0.904. This study showed that both SCoT and SRAP markers were suitable for the genetic diversity analysis of P. polyphylla, which belongs to a genus in which SRAP marker technology has not previously been applied, despite its application in a variety of other plants.
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Affiliation(s)
- Xiaopei Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Gaofen Zou
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Jie Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Linyi Hu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Yuefeng Lan
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Jinling He
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
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Clapa D, Borsai O, Hârța M, Bonta V, Szabo K, Coman V, Bobiș O. Micropropagation, Genetic Fidelity and Phenolic Compound Production of Rheum rhabarbarum L. PLANTS 2020; 9:plants9050656. [PMID: 32456105 PMCID: PMC7284629 DOI: 10.3390/plants9050656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022]
Abstract
An efficient micropropagation protocol for Rheum rhabarbarum L. was developed in this study. The in vitro rhubarb plants obtained in the multiplication stage (proliferation rate: 5.0 ± 0.5) were rooted in vitro (96% rooting percentage) and acclimatized ex vitro in floating perlite, with 90% acclimatization percentage. To assess the genetic fidelity between the mother plant and in vitro propagated plants, sequence-related amplified polymorphism (SRAP) markers were used. All banding profiles from the micropropagated plants were monomorphic and similar to those of the mother plant indicating 100% similarity. Regarding the polyphenolic profile, gallic, protocatechuic, p-hydroxybenzoic, vanillic, chlorogenic, caffeic, syringic, p-coumaric and ferulic acid were present in different amounts (2.3-2690.3 μg g-1 dry plant), according to the extracted matrix. Aglicons and glycosides of different classes of flavonoids were also identified. The rhizome extracts (both from in vitro and field grown plants) contained resveratrol, a stilbene compound with high antioxidant properties, ranging between 229.4 to 371.7 μg g-1 plant. Our results suggest that in vitro propagation of Rheum rhabarbarum L. represents a reliable alternative to obtain a large number of true-to-type planting material with high bioactive compound content of this valuable nutritional and medicinal species.
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Affiliation(s)
- Doina Clapa
- Institute of Advanced Horticulture Research of Transylvania, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur st. 3-5, 400372 Cluj-Napoca, Romania;
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur st. 3-5, 400372 Cluj-Napoca, Romania; (M.H.); (V.B.); (K.S.); (V.C.)
| | - Orsolya Borsai
- AgroTransilvania Cluster, Dezmir, Crișeni FN, 407039 Cluj, Romania
- Correspondence: (O.B.); (O.B.); Tel.: +40264-596384 (O.B. & O.B.); Fax: +40264-593792 (O.B. & O.B.)
| | - Monica Hârța
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur st. 3-5, 400372 Cluj-Napoca, Romania; (M.H.); (V.B.); (K.S.); (V.C.)
| | - Victoriţa Bonta
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur st. 3-5, 400372 Cluj-Napoca, Romania; (M.H.); (V.B.); (K.S.); (V.C.)
| | - Katalin Szabo
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur st. 3-5, 400372 Cluj-Napoca, Romania; (M.H.); (V.B.); (K.S.); (V.C.)
| | - Vasile Coman
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur st. 3-5, 400372 Cluj-Napoca, Romania; (M.H.); (V.B.); (K.S.); (V.C.)
| | - Otilia Bobiș
- Life Science Institute, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur st. 3-5, 400372 Cluj-Napoca, Romania; (M.H.); (V.B.); (K.S.); (V.C.)
- Correspondence: (O.B.); (O.B.); Tel.: +40264-596384 (O.B. & O.B.); Fax: +40264-593792 (O.B. & O.B.)
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Zagorcheva T, Stanev S, Rusanov K, Atanassov I. SRAP markers for genetic diversity assessment of lavender (Lavandula angustifolia mill.) varieties and breeding lines. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1742788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Stanko Stanev
- Institute of Rose and Aromatic Plants, Agricultural Academy, Kazanlak, Bulgaria
| | - Krasimir Rusanov
- Molecular Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Ivan Atanassov
- Molecular Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
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Longya A, Talumphai S, Jantasuriyarat C. Morphological Characterization and Genetic Diversity of Rice Blast Fungus, Pyricularia oryzae, from Thailand Using ISSR and SRAP Markers. J Fungi (Basel) 2020; 6:jof6010038. [PMID: 32204416 PMCID: PMC7151035 DOI: 10.3390/jof6010038] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/11/2020] [Accepted: 03/18/2020] [Indexed: 01/31/2023] Open
Abstract
Rice blast disease is caused by the ascomycete fungus Pyricularia oryzae and is one of the most destructive rice diseases in the world. The objectives of this study were investigating various fungal morphological characteristics and performing a phylogenetic analysis. Inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers were used to examine the genetic variation of 59 rice blast fungus strains, including 57 strains collected from different fields in Thailand and two reference strains, 70-15 and Guy11. All isolates used in this study were determined to be P. oryzae by internal transcribed spacer (ITS) sequence confirmation. A total of 14 ISSR primers and 17 pairs of SRAP primers, which produced clear and polymorphic bands, were selected for assessing genetic diversity. A total of 123 polymorphic bands were generated. The similarity index value for the strains ranged from 0.25 to 0.95. The results showed that the blast fungus population in Thailand has both morphological and genetic variations. A high level of genetic variation, or genome adaptation, is one of the fungal mechanisms that could overcome host resistance to avoid host recognition. Results from this research study could bring substantial benefits and ultimately help to understand the blast fungal pathogen genome and the population structure in Thai blast fungus.
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Affiliation(s)
- Apinya Longya
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Sucheela Talumphai
- Major Biology, Department of Science and Technology, Faculty of Liberal Arts and Science Roi Et Rajabhat University, Roi Et 45120, Thailand;
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok 10900, Thailand
- Correspondence:
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Ahmadi B, Ebrahimzadeh H. In vitro androgenesis: spontaneous vs. artificial genome doubling and characterization of regenerants. PLANT CELL REPORTS 2020; 39:299-316. [PMID: 31974735 DOI: 10.1007/s00299-020-02509-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/13/2020] [Indexed: 05/11/2023]
Abstract
Androgenesis has become the most frequently chosen method of doubled haploid (DH) production in major crops. Theoretically, plantlets derived from in vitro cultured microspore encompass half of the normal chromosome number of donor plants and thus, considered to be haploid. However, depending on species/genotype and the method of haploid production, either via anther or isolated microspore culture, different ratios of spontaneous DHs and diploid (2n) or even polyploid plants originating from somatic tissues or unreduced gametes may also arise in the cultures. Adopting the method of haploid identification, anti-microtubular agent for restoring fertility, and discriminating spontaneous DHs from undesired heterozygote plants will substantially affect the success of androgenesis in breeding programs. The recent advances in the last 2 decades have made it possible to characterize the in vitro regenerants efficiently either prior to genome duplication or using in breeding programs. The herein described approaches and antimicotubular agents are, therefore, expected to improve the efficiency of DH-based breeding pipeline through the in vitro androgenesis.
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Affiliation(s)
- Behzad Ahmadi
- Department of Maize and Forage Crops Research, Agricultural Research, Education and Extension Organization (AREEO), Seed and Plant Improvement Institute (SPII), Karaj, Iran.
| | - Hamed Ebrahimzadeh
- Department of Tissue and Cell Culture, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
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Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy. PLANTS 2020; 9:plants9020160. [PMID: 32012949 PMCID: PMC7076643 DOI: 10.3390/plants9020160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/21/2020] [Accepted: 01/25/2020] [Indexed: 11/17/2022]
Abstract
The genetic relationship among three Streptocarpus parents and twelve F1 hybrids was assessed using sequence-related amplified polymorphism (SRAP) molecular markers and Fourier-transform infrared (FT-IR) spectroscopy. Both methods were able to discriminate F1 hybrids and parents as revealed by cluster analysis. For hybrid identification, the type III SRAP marker was the most effective due to the presence of male-specific bands in the hybrids. Different behaviors in the biochemical variability of DNA samples have been observed by FT-IR spectral analysis, which might be attributed to the inherent nature of the genomic DNA from parents and their F1 progenies. Mantel test was also carried out to compare morphological, SRAP, and FT-IR results based on genetic distances. The highest correlation coefficient was found between morphological and SRAP marker distances (R = 0.607; p ≤ 0.022). A lower correlation was observed between the morphological and FT-IR distance matrix (R = 0.231; p ≤0.008). Moreover, a positive correlation was found between the distances generated with SRAP and FT-IR analyses (R = 0.026) but was not statistically significant. These findings show that both SRAP and FT-IR techniques combined with morphological descriptions can be used effectively for nonconventional breeding programs for Streptocarpus to obtain new and valuable varieties.
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Braglia L, Gavazzi F, Morello L, Gianì S, Nick P, Breviario D. On the applicability of the Tubulin-Based Polymorphism (TBP) genotyping method: a comprehensive guide illustrated through the application on different genetic resources in the legume family. PLANT METHODS 2020; 16:86. [PMID: 32536963 PMCID: PMC7291473 DOI: 10.1186/s13007-020-00627-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/30/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plant discrimination is of relevance for taxonomic, evolutionary, breeding and nutritional studies. To this purpose, evidence is reported to demonstrate TBP (Tubulin-Based-Polymorphism) as a DNA-based method suitable for assessing plant diversity. RESULTS Exploiting one of the most valuable features of TBP, that is the convenient and immediate application of the assay to groups of individuals that may belong to different taxa, we show that the TBP method can successfully discriminate different agricultural species and their crop wild relatives within the Papilionoideae subfamily. Detection of intraspecific variability is demonstrated by the genotyping of 27 different accessions of Phaseolus vulgaris. CONCLUSIONS These data illustrate TBP as a useful and versatile tool for plant genotyping. Since its potential has not yet been fully appreciated by the scientific community, we carefully report all the experimental details of a successful TBP protocol, while describing different applications, so that the method can be replicated in other laboratories.
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Affiliation(s)
- Luca Braglia
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Floriana Gavazzi
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Laura Morello
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Silvia Gianì
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Peter Nick
- Department of Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 4, 76131 Karlsruhe, Baden-Württemberg Germany
| | - Diego Breviario
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
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Amiriyan M, Shojaeiyan A, Yadollahi A, Maleki M, Bahari Z. Genetic diversity analysis and population structure of some Iranian Fenugreek ( Trigonella foenum-graecum L.) landraces using SRAP Markers. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2019; 8:181-190. [PMID: 32042836 PMCID: PMC6995332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
Abstract
Fenugreek is one of the important edible and medicinal vegetables that have a long history of cultivation and consumption. Characterize the extent of the genetic diversity among landraces will provide a good context for future breeding programs and genetic resource preservation. Genetic diversity and population structure of 88 individuals of eight landraces of Iranian fenugreek evaluated based on SRAP markers. Seventy-two bands generated from 6 primers in which 56 (80.11%) band were polymorph. Hamadan landrace showed the lowest values of percentage of polymorphic loci (67.86), Nei's gene diversity index (0.24), number of effective alleles (1.40) and Shannon's Information index (0.36). Nei's genetic distance matrix revealed the highest genetic distance between Hamadan and Yazd (0.203) and the highest genetic similarity between Mahallat and Varamin (0.036) landraces. The most gene flow was between Mahallat and Varamin landraces (Nm=8.36) and the least was between Shiraz and Hamadan landraces (Nm=0.66). An extent admixture of alleles between the Iranian fenugreek landraces was observed by the population structure. Mantel test indicated that the genetic differentiation and gene flow is not associated with geographic distance in Iranian fenugreek landraces. Our observations indicated SRAP is an efficient technique to reveal genetic diversity and population structure of Iranian fenugreek landrace.
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Affiliation(s)
| | - Abdolali Shojaeiyan
- Corresponding Author: Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran. Tel: +98-21-48292111
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Production, physiology, and molecular characterization of sorghum (Sorghum bicolor (L.) Moench) genotypes under the interactions of abiotic stresses. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Genetic Diversity and Population Divergence of a Rare, Endemic Grass (Elymus breviaristatus) in the Southeastern Qinghai-Tibetan Plateau. SUSTAINABILITY 2019. [DOI: 10.3390/su11205863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Elymus breviaristatus is a grass species only distributed in the southeast of Qinghai-Tibetan Plateau (QTP), which has suffered from serious habitat fragmentation. Therefore, understanding patterns of genetic diversity within and among natural E. breviaristatus populations could provide insight for future conservation strategies. In this study, sequence-related amplified polymorphism markers were employed to investigate the genetic diversity and hierarchical structure of seven E. breviaristatus populations from QTP, China. Multiple measures of genetic diversity indicated that there is low to moderate genetic variation within E. breviaristatus populations, consistent with its presumed mating system. In spite of its rarity, E. breviaristatus presented high genetic diversity that was equivalent to or even higher than that of widespread species. Bayesian clustering approaches, along with clustering analysis and principal coordinate analysis partitioned the studied populations of E. breviaristatus into five genetic clusters. Differentiation coefficients (Fst, GST, etc.) and AMOVA analysis revealed considerable genetic divergence among different populations. BARRIER analyses indicated that there were two potential barriers to gene flow among the E. breviaristatus populations. Despite these patterns of differentiation, genetic distances between populations were independent of geographic distances (r = 0.2197, p = 0.2534), indicating little isolation by distance. Moreover, despite detecting a common outlier by two methods, bioclimatic factors (altitude, annual mean temperature, and annual mean precipitation) were not related to diversity parameters, indicating little evidence for isolation caused by the environment. These patterns of diversity within and between populations are used to propose a conservation strategy for E. breviaristatus.
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Cucho H, López Y, Caldeira C, Valverde A, Ordóñez C, Soler C. Comparison of three different staining methods for the morphometric characterization of Alpaca (Vicugna pacos) sperm, using ISAS® CASA-Morph system. NOVA BIOLOGICA REPERTA 2019. [DOI: 10.29252/nbr.6.3.284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Podyma W, Bolc P, Nocen J, Puchta M, Wlodarczyk S, Lapinski B, Boczkowska M. A multilevel exploration of Avena strigosa diversity as a prelude to promote alternative crop. BMC PLANT BIOLOGY 2019; 19:291. [PMID: 31269919 PMCID: PMC6610812 DOI: 10.1186/s12870-019-1819-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Sand oat (Avena strigosa Schreb.), one of the four cultivated species of the genus Avena, could be considered as another alternative crop. In gene banks 865 germplasm samples of this species have been preserved that have not been thoroughly investigated so far. The results of phenotyping (36 traits), isoenzymatic (12 systems) and genetic (8 pairs of Sequence-related amplified polymorphism markers) variation were used to obtain the complete description of 56 accessions diversity originated from different parts of world. RESULTS Breeded and weedy forms represented similar pool of morphological traits that indicated a short-term and extensive breeding process, albeit all accessions which we classified as cultivated were characterized by better grain and green mass parameters compared to the weedy ones. Isoenzymes showed relationships with geographical origin, which was not possible to detect by SRAP markers. There was no similarity between morphological and biochemical results. The polymorphism level of SRAP markers was lower than indicated by the available literature data for other species, however it may result from the analysis of pooled samples of accessions with a high internal variability. The extensive type of breeding and its relatively short duration was also reflected in the population structure results. Joint analysis revealed that a secondary centre of diversity is being created in South America and that it has its genealogy from the Iberian Peninsula. CONCLUSIONS Despite the relatively large representation of this species is in various gene banks, it is highly probable that the vast majority of stored worldwide accessions are duplicates, and the protected gene pool is relatively narrow. Sand oat meets all the requirements for an alternative crop species, but further studies are needed to identify the genotypes/populations with the most favourable distribution of utility and quality parameters.
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Affiliation(s)
- Wiesław Podyma
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
- Polish Academy of Sciences Botanical Garden - Center for Biological Diversity Conservation in Powsin, Warszawa, Poland
| | - Paulina Bolc
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Joanna Nocen
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Marta Puchta
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Sylwia Wlodarczyk
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Boguslaw Lapinski
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Maja Boczkowska
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland.
- Polish Academy of Sciences Botanical Garden - Center for Biological Diversity Conservation in Powsin, Warszawa, Poland.
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Saini P, Kamboj D, Yadav RC, Yadav NR. SRAPs and EST-SSRs provide useful molecular diversity for targeting drought and salinity tolerance in Indian mustard. Mol Biol Rep 2019; 46:1213-1225. [PMID: 30656491 DOI: 10.1007/s11033-019-04590-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/03/2019] [Indexed: 11/27/2022]
Abstract
Abiotic stress tolerance is one of the target trait in crop breeding under climate change scenario. Selection of suitable gene pools among available germplasm is first requisite for any crop improvement programme. Drought and salinity traits, being polygenic, are most difficult to target. The present investigation aimed at exploring and assessment of the genetic variability in Indian mustard at molecular level. A total of twenty-five genotypes and five related species were used. Sixty-three molecular markers including sequence related amplified polymorphism (SRAP) markers along with twenty-three expressed sequence tag-simple sequence repeats (EST-SSRs) were used for diversity analysis. Thirty-seven SRAPs and 18 EST-SSRs showed amplification producing a total of 423 alleles of which 422 were polymorphic. These markers gave an overall polymorphism of 99.78%, with 99.67% polymorphism in SRAPs and 100% polymorphism in EST-SSRs. The study revealed the genetic relationships among different genotypes of B. juncea and related species which could be used for Indian mustard improvement for targeting drought and salinity tolerance in future. Four SRAP and two EST-SSRs identified unique bands which may be related to abiotic stress tolerance. EST sequence BRMS-040 (IM7) was similar to Brassica and radish sequences related to PR-5 (pathogenesis-related) protein.
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Affiliation(s)
- Prince Saini
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
- Indian Institutes of Science Education and Research (IISER), Mohali, India
| | - Disha Kamboj
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - R C Yadav
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
- Centre for Plant Biotechnology, CCS HAU Campus, Hisar, India
| | - Neelam R Yadav
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India.
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Golkar P, Mokhtari N. Molecular diversity assessment of a world collection of safflower genotypes by SRAP and SCoT molecular markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:1261-1271. [PMID: 30425439 PMCID: PMC6214440 DOI: 10.1007/s12298-018-0545-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/06/2018] [Accepted: 05/02/2018] [Indexed: 05/05/2023]
Abstract
Safflower (Carthamus tinctorius L.) is considered as an oil crop that is rich in medicinal and industrial properties. In this study, the genetic diversity of safflower was assessed using 12 polymorphic sequence-related amplified polymorphism (SRAPs) and 11 polymorphic start codon targeted (SCoT) markers in 100 genotypes of safflower gathered from different geographical regions of the world. The 23 primers generated a total of 227 polymorphism fragments with a mean of 68.2% within the range of 3 (SCoT 31 and SCoT 35) to 13 (SCoT 35) bands per primer. Polymorphism per primer ranged between 100% (in Me4-Em1) and 18.1% (in SCoT19), with an average of 36.76%. The polymorphism information contents of the SRAP and SCoT markers were 0.35 and 0.30, respectively, indicating that SRAP markers were more effective than SCoT markers for assessing the degree of genetic diversity of the safflower. The results of the analysis of molecular variance showed a significant difference across cultivated safflower genotypes possessing a high intra-population variation. The examined accessions were categorized into five clusters based on similarity centers: the Middle East containing Iran, Iraq, Turkey, and Tajikistan; the Far East, including India, Pakistan, and Korea; Europe; the American continent; and Africa, including Egypt, Sudan and Libya. The present study shows the effectiveness of employing the mixture of SRAP and SCoT markers in the identification of safflower genetic diversity that would be useful for conservation and population genetics of safflower improvement in further studies.
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Affiliation(s)
- Pooran Golkar
- Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, 84156 83111 Iran
| | - Niloofar Mokhtari
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156 83111 Iran
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Ali Al-Somain BH, Migdadi HM, Al-Faifi SA, Alghamdi SS, Muharram AA, Mohammed NA, Refay YA. Assessment of genetic diversity of sesame accessions collected from different ecological regions using sequence-related amplified polymorphism markers. 3 Biotech 2017; 7:82. [PMID: 28500406 DOI: 10.1007/s13205-017-0680-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/27/2017] [Indexed: 11/30/2022] Open
Abstract
Sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity among a collection of 52 sesame accessions representing different geographical environments, including eight Saudi landraces. A combination of seventeen primers generated a high number of alleles (365) with 100% polymorphism. The polymorphic information content (PIC) and primer discrimination power (DP) recorded overall means of 0.88 and 5.88, respectively. Genetic similarity values based on Jaccard coefficients ranged from 0.12 to 0.49, with an average similarity value of 0.30, indicating both high genetic distance and a wide genetic basis of the investigated accessions. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram grouped 48 of 52 accessions into seven main clusters, and five accessions failed to form clusters and were separated individually. However, subclusters separated the accessions and, considering the relatedness of accessions and their geographical origin, formed distinct diversity among groups. Saudi landraces showed the widest genetic basis compared with other introduced accessions that were distributed throughout the dendrogram, indicating that agro-ecological zones were indistinguishable by cluster analysis. SRAP analysis revealed a high degree of genetic polymorphism in sesame accessions investigated and showed weak association between geographical origin and SRAP patterns. This wide genetic variability should be considered for sesame breeding programs.
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Affiliation(s)
- Bazel H Ali Al-Somain
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Hussein M Migdadi
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia.
| | - Sulieman A Al-Faifi
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Salem S Alghamdi
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Abdulmalek A Muharram
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Nabil A Mohammed
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Yahya A Refay
- Department of Plant Production, College of food and agricultural sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
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Toal TW, Burkart-Waco D, Howell T, Ron M, Kuppu S, Britt A, Chetelat R, Brady SM. Indel Group in Genomes (IGG) Molecular Genetic Markers. PLANT PHYSIOLOGY 2016; 172:38-61. [PMID: 27436831 PMCID: PMC5074621 DOI: 10.1104/pp.16.00354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
Genetic markers are essential when developing or working with genetically variable populations. Indel Group in Genomes (IGG) markers are primer pairs that amplify single-locus sequences that differ in size for two or more alleles. They are attractive for their ease of use for rapid genotyping and their codominant nature. Here, we describe a heuristic algorithm that uses a k-mer-based approach to search two or more genome sequences to locate polymorphic regions suitable for designing candidate IGG marker primers. As input to the IGG pipeline software, the user provides genome sequences and the desired amplicon sizes and size differences. Primer sequences flanking polymorphic insertions/deletions are produced as output. IGG marker files for three sets of genomes, Solanum lycopersicum/Solanum pennellii, Arabidopsis (Arabidopsis thaliana) Columbia-0/Landsberg erecta-0 accessions, and S. lycopersicum/S. pennellii/Solanum tuberosum (three-way polymorphic) are included.
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Affiliation(s)
- Ted W Toal
- Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616
| | - Diana Burkart-Waco
- Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616
| | - Tyson Howell
- Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616
| | - Mily Ron
- Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616
| | - Sundaram Kuppu
- Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616
| | - Anne Britt
- Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616
| | - Roger Chetelat
- Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616
| | - Siobhan M Brady
- Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616
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Analysis of Genetic Diversity and Development of SCAR Markers in a Mycogone perniciosa Population. Curr Microbiol 2016; 73:9-14. [PMID: 26960290 DOI: 10.1007/s00284-016-1020-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Abstract
The fungus Mycogone perniciosa is a major pathogen of the common button mushroom Agaricus bisporus. Analysis of genetic diversity in M. Perniciosa may assist in developing methods for prophylaxis and treatment of M. Perniciosa infections. For this, it is necessary to classify M. Perniciosa into relevant class groups quickly and efficiently. Random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), and sequence-related amplified polymorphism (SRAP) markers were used to obtain genetic fingerprints and assess the genetic variation among 49 strains of M. perniciosa collected from different areas of Fujian Province in China. Analysis of DNA sequence polymorphism revealed two major distinct groups (Group I and Group II). Specific DNA fragments that were identified through RAPD, ISSR, and SRAP markers were sequenced and used for the designing of stable sequence-characterized amplified region (SCAR) markers. The resulting SCAR markers were then validated against the classified groups of M. perniciosa.
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Idrissi O, Udupa SM, De Keyser E, McGee RJ, Coyne CJ, Saha GC, Muehlbauer FJ, Van Damme P, De Riek J. Identification of Quantitative Trait Loci Controlling Root and Shoot Traits Associated with Drought Tolerance in a Lentil (Lens culinaris Medik.) Recombinant Inbred Line Population. FRONTIERS IN PLANT SCIENCE 2016; 7:1174. [PMID: 27602034 PMCID: PMC4993778 DOI: 10.3389/fpls.2016.01174] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/21/2016] [Indexed: 05/20/2023]
Abstract
Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL) analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL (QRSratioIX-2.30) related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 and 28.9% for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL (QLRNIII-98.64) related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL (QSRLIV-61.63) associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labor-intensive conventional breeding methods.
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Affiliation(s)
- Omar Idrissi
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
- Institut National de la Recherche Agronomique du Maroc (INRA), Centre Régional de SettatSettat, Morocco
- *Correspondence: Omar Idrissi ;
| | - Sripada M. Udupa
- International Center for Agricultural Research in the Dry Areas, Institut National de la Recherche Agronomique Morocco Cooperative Research ProjectRabat, Morocco
| | - Ellen De Keyser
- Plant Sciences Unit, Applied Genetics and Breeding, The Institute for Agricultural and Fisheries Research (ILVO)Melle, Belgium
| | - Rebecca J. McGee
- United States Department of Agriculture, Agricultural Research Service Grain Legume Genetics and Physiology ResearchPullman, WA, USA
| | - Clarice J. Coyne
- United States Department of Agriculture, Agricultural Research Service Western Regional Plant Introduction, Washington State UniversityPullman, WA, USA
| | | | - Fred J. Muehlbauer
- United States Department of Agriculture, Agricultural Research Service Western Regional Plant Introduction, Washington State UniversityPullman, WA, USA
| | - Patrick Van Damme
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
- Faculty of Tropical AgriSciences, Czech University of Life SciencesPrague, Czech Republic
| | - Jan De Riek
- Plant Sciences Unit, Applied Genetics and Breeding, The Institute for Agricultural and Fisheries Research (ILVO)Melle, Belgium
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Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map. Int J Mol Sci 2015. [PMID: 26204838 PMCID: PMC4519972 DOI: 10.3390/ijms160716669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Molecular markers and genetic maps are useful tools in genetic studies. Novel molecular markers and their applications have been developed in recent years. With the recent advancements in sequencing technology, the genomic sequences of an increasingly great number of fungi have become available. A novel type of molecular marker was developed to construct the first reported linkage map of the edible and economically important basidiomycete Volvariella volvacea by using 104 structural variation (SV) markers that are based on the genomic sequences. Because of the special and simple life cycle in basidiomycete, SV markers can be effectively developed by genomic comparison and tested in single spore isolates (SSIs). This stable, convenient and rapidly developed marker may assist in the construction of genetic maps and facilitate genomic research for other species of fungi.
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