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Chongtham SK, Devi EL, Samantara K, Yasin JK, Wani SH, Mukherjee S, Razzaq A, Bhupenchandra I, Jat AL, Singh LK, Kumar A. Orphan legumes: harnessing their potential for food, nutritional and health security through genetic approaches. PLANTA 2022; 256:24. [PMID: 35767119 DOI: 10.1007/s00425-022-03923-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Legumes, being angiosperm's third-largest family as well as the second major crop family, contributes beyond 33% of human dietary proteins. The advent of the global food crisis owing to major climatic concerns leads to nutritional deprivation, hunger and hidden hunger especially in developing and underdeveloped nations. Hence, in the wake of promoting sustainable agriculture and nutritional security, apart from the popular legumes, the inclusion of lesser-known and understudied local crop legumes called orphan legumes in the farming systems of various tropical and sub-tropical parts of the world is indeed a need of the hour. Despite possessing tremendous potentialities, wide adaptability under diverse environmental conditions, and rich in nutritional and nutraceutical values, these species are still in a neglected and devalued state. Therefore, a major re-focusing of legume genetics, genomics, and biology is much crucial in pursuance of understanding the yield constraints, and endorsing underutilized legume breeding programs. Varying degrees of importance to these crops do exist among researchers of developing countries in establishing the role of orphan legumes as future crops. Under such circumstances, this article assembles a comprehensive note on the necessity of promoting these crops for further investigations and sustainable legume production, the exploitation of various orphan legume species and their potencies. In addition, an attempt has been made to highlight various novel genetic, molecular, and omics approaches for the improvement of such legumes for enhancing yield, minimizing the level of several anti-nutritional factors, and imparting biotic and abiotic stress tolerance. A significant genetic enhancement through extensive research in 'omics' areas is the absolute necessity to transform them into befitting candidates for large-scale popularization around the globe.
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Affiliation(s)
- Sunil Kumar Chongtham
- Multi Technology Testing Centre and Vocational Training Centre, CAEPHT, CAU, Ranipool, Gangtok, Sikkim, 737135, India
| | | | - Kajal Samantara
- Department of Genetics and Plant Breeding, Centurion University of Technology and Management, Odisha, 761211, India
| | - Jeshima Khan Yasin
- Division of Genomic Resources, ICAR-National Bureau Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, 192101, Jammu and Kashmir, India.
| | - Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, West Bengal, 742213, India
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Ingudam Bhupenchandra
- ICAR-KVK Tamenglong, ICAR RC for NEH Region, Manipur Centre, Lamphelpat, Imphal, Manipur, 795 004, India
| | - Aanandi Lal Jat
- Castor-Mustard Research Station, SDAU, S.K. Nagar, Banaskantha, Gujarat, 385 506, India
| | - Laishram Kanta Singh
- ICAR-KVK Imphal West, ICAR RC for NEH region, Manipur Centre, Lamphelpat, Imphal, Manipur, 795 004, India
| | - Amit Kumar
- ICAR Research Complex for NEH Region, Tadong, Sikkim Centre, 737102, India
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Osorio CE, Till BJ. A Bitter-Sweet Story: Unraveling the Genes Involved in Quinolizidine Alkaloid Synthesis in Lupinus albus. FRONTIERS IN PLANT SCIENCE 2022; 12:795091. [PMID: 35154186 PMCID: PMC8826574 DOI: 10.3389/fpls.2021.795091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/30/2021] [Indexed: 05/05/2023]
Abstract
Alkaloids are part of a structurally diverse group of over 21,000 cyclic nitrogen-containing secondary metabolites that are found in over 20% of plant species. Lupinus albus are naturally containing quinolizidine alkaloid (QA) legumes, with wild accessions containing up to 11% of QA in seeds. Notwithstanding their clear advantages as a natural protecting system, lupin-breeding programs have selected against QA content without proper understanding of quinolizidine alkaloid biosynthetic pathway. This review summarizes the current status in this field, with focus on the utilization of natural mutations such as the one contained in pauper locus, and more recently the development of molecular markers, which along with the advent of sequencing technology, have facilitated the identification of candidate genes located in the pauper region. New insights for future research are provided, including the utilization of differentially expressed genes located on the pauper locus, as candidates for genome editing. Identification of the main genes involved in the biosynthesis of QA will enable precision breeding of low-alkaloid, high nutrition white lupin. This is important as plant based high quality protein for food and feed is an essential for sustainable agricultural productivity.
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Affiliation(s)
- Claudia E. Osorio
- Instituto de Investigaciones Agropecuarias, INIA Carillanca, Temuco, Chile
| | - Bradley J. Till
- Veterinary Genetics Laboratory, University of California, Davis, Davis, CA, United States
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3
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Azizi MMF, Lau HY, Abu-Bakar N. Integration of advanced technologies for plant variety and cultivar identification. J Biosci 2021. [DOI: 10.1007/s12038-021-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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ITS barcoding using high resolution melting analysis of Cannabis sativa drug seizures in Chile: A forensic application. Forensic Sci Int 2020; 316:110550. [DOI: 10.1016/j.forsciint.2020.110550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022]
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5
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Rychel-Bielska S, Nazzicari N, Plewiński P, Bielski W, Annicchiarico P, Książkiewicz M. Development of PCR-based markers and whole-genome selection model for anthracnose resistance in white lupin (Lupinus albus L.). J Appl Genet 2020; 61:531-545. [PMID: 32968972 PMCID: PMC7652745 DOI: 10.1007/s13353-020-00585-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022]
Abstract
White lupin (Lupinus albus L.) is a high-protein grain legume crop, grown since ancient Greece and Rome. Despite long domestication history, its cultivation remains limited, partly because of susceptibility to anthracnose. Only some late-flowering, bitter, low-yielding landraces from Ethiopian mountains displayed resistance to this devastating disease. The resistance is controlled by various genes, thereby complicating the breeding efforts. The objective of this study was developing tools for molecular tracking of Ethiopian resistance genes based on genotyping-by-sequencing (GBS) data, envisaging linkage mapping and genomic selection approaches. Twenty GBS markers from two major quantitative trait loci (QTLs), antr04_1/antr05_1 and antr04_2/antr05_2, were converted to PCR-based markers using assigned transcriptome sequences. Newly developed markers improved mapping resolution around both anthracnose resistance loci, providing more precise QTL estimation. PCR-based screening of diversified domesticated and primitive germplasm revealed the high specificity of two markers for the antr04_1/antr05_1 locus (TP222136 and TP47110) and one for the antr04_2/antr05_2 locus (TP338761), highlighted by simple matching coefficients of 0.96 and 0.89, respectively. Moreover, a genomic selection approach based on GBS data of a recombinant inbred line mapping population was assessed, providing an average predictive ability of 0.56. These tools can be used for preselection of candidate white lupin germplasm for anthracnose resistance assays.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 24A, 50-363, Wrocław, Poland.,Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Nelson Nazzicari
- CREA-FLC, Council for Agricultural Research and Economics, Research Centre for Fodder Crops and Dairy Production, Viale Piacenza 29, 26900, Lodi, Italy
| | - Piotr Plewiński
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Wojciech Bielski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Paolo Annicchiarico
- CREA-FLC, Council for Agricultural Research and Economics, Research Centre for Fodder Crops and Dairy Production, Viale Piacenza 29, 26900, Lodi, Italy
| | - Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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Vishwakarma G, Sanyal RP, Saini A, Sahu PK, Singh Patel RR, Sharma D, Tiwari R, Das BK. GLADS: A gel-less approach for detection of STMS markers in wheat and rice. PLoS One 2019; 14:e0224572. [PMID: 31689318 PMCID: PMC6830750 DOI: 10.1371/journal.pone.0224572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/16/2019] [Indexed: 11/18/2022] Open
Abstract
Sequence tagged microsatellite site (STMS) are useful PCR based DNA markers. Wide genome coverage, high polymorphic index and co-dominant nature make STMS a preferred choice for marker assisted selection (MAS), genetic diversity analysis, linkage mapping, seed genetic purity analysis etc. Routine STMS analysis involving low-throughput, laborious and time-consuming polyacrylamide/agarose gels often limit their full utility in crop breeding experiments that involve large populations. Therefore, convenient, gel-less marker detection methods are highly desirable for STMS markers. The present study demonstrated the utility of SYBR Green dye based melt-profiling as a simple and convenient gel-less approach for detection of STMS markers (referred to as GLADS) in bread wheat and rice. The method involves use of SYBR Green dye during PCR amplification (or post-PCR) of STMS markers followed by generation of a melt-profile using controlled temperature ramp rate. The STMS amplicons yielded characteristic melt-profiles with differences in melting temperature (Tm) and profile shape. These characteristic features enabled melt-profile based detection and differentiation of STMS markers/alleles in a gel-less manner. The melt-profile approach allowed assessment of the specificity of the PCR assay unlike the end-point signal detection assays. The method also allowed multiplexing of two STMS markers with non-overlapping melt-profiles. In principle, the approach can be effectively used in any crop for STMS marker analysis. This SYBR Green melt-profiling based GLADS approach offers a convenient, low-cost (20–51%) and time-saving alternative for STMS marker detection that can reduce dependence on gel-based detection, and exposure to toxic chemicals.
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Affiliation(s)
- Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
| | - Ravi Prakash Sanyal
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
| | - Ajay Saini
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
| | - Parmeshwar Kumar Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ravi Raj Singh Patel
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ratan Tiwari
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Bikram Kishore Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- * E-mail:
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Iqbal MM, Huynh M, Udall JA, Kilian A, Adhikari KN, Berger JD, Erskine W, Nelson MN. The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop. BMC Genet 2019; 20:68. [PMID: 31412771 PMCID: PMC6694670 DOI: 10.1186/s12863-019-0767-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 07/17/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Yellow lupin (Lupinus luteus L.) is a promising grain legume for productive and sustainable crop rotations. It has the advantages of high tolerance to soil acidity and excellent seed quality, but its current yield potential is poor, especially in low rainfall environments. Key adaptation traits such as phenology and enhanced stress tolerance are often complex and controlled by several genes. Genomic-enabled technologies may help to improve our basic understanding of these traits and to provide selective markers in breeding. However, in yellow lupin there are very limited genomic resources to support research and no published information is available on the genetic control of adaptation traits. RESULTS We aimed to address these deficiencies by developing the first linkage map for yellow lupin and conducting quantitative trait locus (QTL) analysis of yield under well-watered (WW) and water-deficit (WT) conditions. Two next-generation sequencing marker approaches - genotyping-by-sequencing (GBS) and Diversity Array Technology (DArT) sequencing - were employed to genotype a recombinant inbred line (RIL) population developed from a bi-parental cross between wild and domesticated parents. A total of 2,458 filtered single nucleotide polymorphism (SNP) and presence / absence variation (PAV) markers were used to develop a genetic map comprising 40 linkage groups, the first reported for this species. A number of significant QTLs controlling total biomass and 100-seed weight under two water (WW and WD) regimes were found on linkage groups YL-03, YL-09 and YL-26 that together explained 9 and 28% of total phenotypic variability. QTLs associated with length of the reproductive phase and time to flower were found on YL-01, YL-21, YL-35 and YL-40 that together explained a total of 12 and 44% of total phenotypic variation. CONCLUSION These genomic resources and the QTL information offer significant potential for use in marker-assisted selection in yellow lupin.
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Affiliation(s)
- Muhammad Munir Iqbal
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia.
- Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
| | - Mark Huynh
- The College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Joshua A Udall
- USDA-ARS Southern Plains Agricultural Research Center, 2881 F&B Rd., College Station, TX, 77845, USA
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Canberra, Australia
| | - Kedar N Adhikari
- School of Life and Environmental Sciences, I A Watson Grains Research Centre, The University of Sydney, Narrabri, NSW, Australia
| | | | - William Erskine
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Matthew N Nelson
- Agriculture and Food, CSIRO, Floreat, WA, Australia
- The UWA Institute of Agriculture, Perth, WA, Australia
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8
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Rychel S, Książkiewicz M. Development of gene-based molecular markers tagging low alkaloid pauper locus in white lupin (Lupinus albus L.). J Appl Genet 2019; 60:269-281. [PMID: 31410824 PMCID: PMC6803572 DOI: 10.1007/s13353-019-00508-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
Abstract
White lupin (Lupinus albus L.) is a legume grain crop cultivated since ancient Greece and Egypt. Modern white lupin cultivars are appreciated as a source of protein with positive nutraceutical impact. However, white lupins produce anti-nutritional compounds, quinolizidine alkaloids, which provide bitter taste and have a negative influence on human health. During domestication of this species, several recessive alleles at unlinked loci controlling low alkaloid content were selected. One of these loci, pauper, was exploited worldwide providing numerous low-alkaloid cultivars. However, molecular tracking of pauper has been hampered due to the lack of diagnostic markers. In the present study, the synteny-based approach was harnessed to target pauper locus. Single-nucleotide polymorphisms flanking pauper locus on white lupin linkage map as well as candidate gene sequences elucidated from the narrow-leafed lupin (L. angustifolius L.) chromosome segment syntenic to the pauper linkage group region were transformed to PCR-based molecular markers. These markers were analyzed both in the mapping population and world germplasm collection. From fourteen markers screened, eleven were localized at a distance below 1.5 cM from this locus, including five co-segregating with pauper. The linkage of these markers was confirmed by high LOD values (up to 58.4). Validation performed in the set of 127 bitter and 23 sweet accessions evidenced high applicability of one marker, LAGI01_35805_F1_R1, for pauper locus selection, highlighted by the low ratio of false-positive scores (2.5%). LAGI01_35805 represents a homolog of L. angustifolius acyltransferase-like (LaAT) gene which might hypothetically participate in the alkaloid biosynthesis process in lupins.
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Affiliation(s)
- Sandra Rychel
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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Zhang Y, Cui Y, An R, Liang X, Li Q, Wang H, Wang H, Fan Y, Dong P, Li J, Cheng K, Wang W, Wang S, Wang G, Xue C, Komiyama M. Topologically Constrained Formation of Stable Z-DNA from Normal Sequence under Physiological Conditions. J Am Chem Soc 2019; 141:7758-7764. [PMID: 30844265 DOI: 10.1021/jacs.8b13855] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Z-DNA, a left-handed duplex, has been shown to form in vivo and regulate expression of the corresponding gene. However, its biological roles have not been satisfactorily understood, mainly because Z-DNA is easily converted to the thermodynamically favorable B-DNA. Here we present a new idea to form stable Z-DNA under normal physiological conditions and achieve detailed analysis on its fundamental features. Simply by mixing two complementary minicircles of single-stranded DNA with no chemical modification, the hybridization spontaneously induces topological constraint which twines one-half of the double-stranded DNA into stable Z-DNA. The formation of Z-conformation with high stability has been proved by using circular dichroism spectroscopy, Z-DNA-specific antibody binding assay, nuclease digestion, etc. Even at a concentration of MgCl2 as low as 0.5 mM, Z-DNA was successfully obtained, avoiding the use of high salt conditions, limited sequences, ancillary additives, or chemical modifications, criteria which have hampered Z-DNA research. The resultant Z-DNA has the potential to be used as a canonical standard sample in Z-DNA research. By using this approach, further developments of Z-DNA science and its applications become highly promising.
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Affiliation(s)
- Yaping Zhang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Yixiao Cui
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Ran An
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Xingguo Liang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Qi Li
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Haiting Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Hao Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Yiqiao Fan
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Ping Dong
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Jing Li
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Kai Cheng
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Weinan Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Sai Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Guoqing Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Changhu Xue
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Makoto Komiyama
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
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Abraham EM, Ganopoulos I, Madesis P, Mavromatis A, Mylona P, Nianiou-Obeidat I, Parissi Z, Polidoros A, Tani E, Vlachostergios D. The Use of Lupin as a Source of Protein in Animal Feeding: Genomic Tools and Breeding Approaches. Int J Mol Sci 2019; 20:ijms20040851. [PMID: 30781397 PMCID: PMC6413129 DOI: 10.3390/ijms20040851] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/08/2019] [Accepted: 02/10/2019] [Indexed: 12/05/2022] Open
Abstract
Livestock production in the European Union EU is highly dependent on imported soybean, exposing the livestock farming system to risks related to the global trade of soybean. Lupin species could be a realistic sustainable alternative source of protein for animal feeding. Lupinus is a very diverse genus with many species. However, only four of them—namely, L. albus, L. angustifolius, L. luteus and L. mutabilis—are cultivated. Their use in livestock farming systems has many advantages in relation to economic and environmental impact. Generally, lupin grains are characterized by high protein content, while their oil content is relatively low but of high quality. On the other hand, the presence of quinolizidine alkaloids and their specific carbohydrate composition are the main antinutritional factors that prevent their use in animal feeding. This research is mainly related to L. albus and to L. angustifolius, and to a lesser extent, to L. lauteus and L. mutabilis. The breeding efforts are mostly focused on yield stabilization, resistance to biotic and abiotic stresses, biochemical structure associated with seed quality and late maturing. Progress is made in improving lupin with respect to the seed quality, as well as the tolerance to biotic and abiotic stress. It has to be noted that modern cultivars, mostly of L. albus and L. angustifolius, contain low levels of alkaloids. However, for future breeding efforts, the implementation of marker-assisted selection and the available genomic tools is of great importance.
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Affiliation(s)
- Eleni M Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, Thermi, 57001 Thessaloniki, Greece.
| | | | - Athanasios Mavromatis
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Photini Mylona
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, Thermi, 57001 Thessaloniki, Greece.
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Zoi Parissi
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Alexios Polidoros
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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11
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di Rienzo V, Bubici G, Montemurro C, Cillo F. Rapid identification of tomato Sw-5 resistance-breaking isolates of Tomato spotted wilt virus using high resolution melting and TaqMan SNP Genotyping assays as allelic discrimination techniques. PLoS One 2018; 13:e0196738. [PMID: 29709020 PMCID: PMC5927427 DOI: 10.1371/journal.pone.0196738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/18/2018] [Indexed: 12/11/2022] Open
Abstract
In tomato, resistance to Tomato spotted wilt virus (TSWV) is conferred by the dominant gene, designated Sw-5. Virulent Sw-5 resistance breaking (SRB) mutants of TSWV have been reported on Sw-5 tomato cultivars. Two different PCR-based allelic discrimination techniques, namely Custom TaqMan™ SNP Genotyping and high-resolution melting (HRM) assays, were developed and compared for their ability to distinguish between avirulent (Sw-5 non-infecting, SNI) and SRB biotypes. TaqMan assays proved to be more sensitive (threshold of detection in a range of 50–70 TSWV RNA copies) and more reliable than HRM, assigning 25 TSWV isolates to their correct genotype with an accuracy of 100%. Moreover, the TaqMan SNP assays were further improved developing a rapid and simple protocol that included crude leaf extraction for RNA template preparations. On the other hand, HRM assays showed higher levels of sensitivity than TaqMan when used to co-detect both biotypes in different artificial mixtures. These diagnostic assays contributed to gain preliminary information on the epidemiology of TSWV isolates in open field conditions. In fact, the presented data suggest that SRB isolates are present as stable populations established year round, persisting on both winter (globe artichoke) and summer (tomato) crops, in the same cultivated areas of Southern Italy.
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Affiliation(s)
| | - Giovanni Bubici
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Cinzia Montemurro
- Spin off SINAGRI s.r.l., Bari, Italy
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Fabrizio Cillo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
- * E-mail:
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Lee CY, Lin HJ, Viswanath KK, Lin CP, Chang BCH, Chiu PH, Chiu CT, Wang RH, Chin SW, Chen FC. The development of functional mapping by three sex-related loci on the third whorl of different sex types of Carica papaya L. PLoS One 2018; 13:e0194605. [PMID: 29566053 PMCID: PMC5864051 DOI: 10.1371/journal.pone.0194605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/06/2018] [Indexed: 11/19/2022] Open
Abstract
Carica papaya L. is an important economic crop worldwide and is used as a model plant for sex-determination research. To study the different flower sex types, we screened sex-related genes using alternative splicing sequences (AS-seqs) from a transcriptome database of the three flower sex types, i.e., males, females, and hermaphrodites, established at 28 days before flowering using 15 bacterial artificial chromosomes (BACs) of C. papaya L. After screening, the cDNA regions of the three sex-related loci, including short vegetative phase-like (CpSVPL), the chromatin assembly factor 1 subunit A-like (CpCAF1AL), and the somatic embryogenesis receptor kinase (CpSERK), which contained eight sex-related single-nucleotide polymorphisms (SNPs) from the different sex types of C. papaya L., were genotyped using high-resolution melting (HRM). The three loci were examined regarding the profiles of the third whorl, as described below. CpSVPL, which had one SNP associated with the three sex genotypes, was highly expressed in the male and female sterile flowers (abnormal hermaphrodite flowers) that lacked the fourth whorl structure. CpCAF1AL, which had three SNPs associated with the male genotype, was highly expressed in male and normal hermaphrodite flowers, and had no AS-seqs, whereas it exhibited low expression and an AS-seqs in intron 11 in abnormal hermaphrodite flowers. Conversely, carpellate flowers (abnormal hermaphrodite flowers) showed low expression of CpSVPL and AS-seqs in introns 5, 6, and 7 of CpSERK, which contained four SNPs associated with the female genotype. Specifically, the CpSERK and CpCAF1AL loci exhibited no AS-seq expression in the third whorl of the male and normal hermaphrodite flowers, respectively, and variance in the AS-seq expression of all other types of flowers. Functional mapping of the third whorl of normal hermaphrodites indicated no AS-seq expression in CpSERK, low CpSVPL expression, and, for CpCAF1AL, high expression and no AS-seq expression on XYh-type chromosomes.
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Affiliation(s)
- Chen-Yu Lee
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
- * E-mail: (CYL); (FCC)
| | - Hui-Jun Lin
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Kotapati Kasi Viswanath
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chih-Peng Lin
- Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan
| | | | - Pei-Hsun Chiu
- Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan
| | - Chan-Tai Chiu
- Pingtung Seed & Seedling Research Center, Taiwan Seed Improvement and Propagation Station, Pingtung, Taiwan
| | - Ren-Huang Wang
- Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, Pingtung, Taiwan
| | - Shih-Wen Chin
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Fure-Chyi Chen
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
- * E-mail: (CYL); (FCC)
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A high-density consensus linkage map of white lupin highlights synteny with narrow-leafed lupin and provides markers tagging key agronomic traits. Sci Rep 2017; 7:15335. [PMID: 29127429 PMCID: PMC5681670 DOI: 10.1038/s41598-017-15625-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/30/2017] [Indexed: 11/15/2022] Open
Abstract
White lupin (Lupinus albus L.) is a valuable source of seed protein, carbohydrates and oil, but requires genetic improvement to attain its agronomic potential. This study aimed to (i) develop a new high-density consensus linkage map based on new, transcriptome-anchored markers; (ii) map four important agronomic traits, namely, vernalization requirement, seed alkaloid content, and resistance to anthracnose and Phomopsis stem blight; and, (iii) define regions of synteny between the L. albus and narrow-leafed lupin (L. angustifolius L.) genomes. Mapping of white lupin quantitative trait loci (QTLs) revealed polygenic control of vernalization responsiveness and anthracnose resistance, as well as a single locus regulating seed alkaloid content. We found high sequence collinearity between white and narrow-leafed lupin genomes. Interestingly, the white lupin QTLs did not correspond to previously mapped narrow-leafed lupin loci conferring vernalization independence, anthracnose resistance, low alkaloids and Phomopsis stem blight resistance, highlighting different genetic control of these traits. Our suite of allele-sequenced and PCR validated markers tagging these QTLs is immediately applicable for marker-assisted selection in white lupin breeding. The consensus map constitutes a platform for synteny-based gene cloning approaches and can support the forthcoming white lupin genome sequencing efforts.
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Borna T, Salami SA, Shokrpour M. High resolution melting curve analysis revealed SNPs in major cannabinoid genes associated with drug and non-drug types of cannabis. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1333456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Tahereh Borna
- Faculty of Agriculture and Natural Resources, University of Tehran, Tehran, Iran
| | - Seyed Alireza Salami
- Faculty of Agriculture and Natural Resources, University of Tehran, Tehran, Iran
| | - Majid Shokrpour
- Faculty of Agriculture and Natural Resources, University of Tehran, Tehran, Iran
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Hane JK, Ming Y, Kamphuis LG, Nelson MN, Garg G, Atkins CA, Bayer PE, Bravo A, Bringans S, Cannon S, Edwards D, Foley R, Gao L, Harrison MJ, Huang W, Hurgobin B, Li S, Liu C, McGrath A, Morahan G, Murray J, Weller J, Jian J, Singh KB. A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:318-330. [PMID: 27557478 PMCID: PMC5316927 DOI: 10.1111/pbi.12615] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/12/2016] [Accepted: 08/20/2016] [Indexed: 05/18/2023]
Abstract
Lupins are important grain legume crops that form a critical part of sustainable farming systems, reducing fertilizer use and providing disease breaks. It has a basal phylogenetic position relative to other crop and model legumes and a high speciation rate. Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is gaining popularity as a health food, which is high in protein and dietary fibre but low in starch and gluten-free. We report the draft genome assembly (609 Mb) of NLL cultivar Tanjil, which has captured >98% of the gene content, sequences of additional lines and a dense genetic map. Lupins are unique among legumes and differ from most other land plants in that they do not form mycorrhizal associations. Remarkably, we find that NLL has lost all mycorrhiza-specific genes, but has retained genes commonly required for mycorrhization and nodulation. In addition, the genome also provided candidate genes for key disease resistance and domestication traits. We also find evidence of a whole-genome triplication at around 25 million years ago in the genistoid lineage leading to Lupinus. Our results will support detailed studies of legume evolution and accelerate lupin breeding programmes.
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Affiliation(s)
- James K. Hane
- CSIRO AgricultureWembleyWAAustralia
- Department of Environment and AgricultureCCDM BioinformaticsCentre for Crop and Disease ManagementCurtin UniversityBentleyWAAustralia
- Curtin Institute for ComputationCurtin UniversityBentleyWAAustralia
| | - Yao Ming
- Department of Plant and Animal Genome ResearchBeijing Genome InstituteShenzhenChina
| | - Lars G. Kamphuis
- CSIRO AgricultureWembleyWAAustralia
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWAAustralia
| | - Matthew N. Nelson
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWAAustralia
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
- Present address: Royal Botanic Gardens KewNatural Capital and Plant HealthArdinglyRH17 6TNUK
| | | | - Craig A. Atkins
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWAAustralia
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
| | - Armando Bravo
- Boyce Thompson Institute for Plant ResearchIthacaNYUSA
| | | | - Steven Cannon
- USDA‐ARS Corn Insects and Crop Genetics Research UnitCrop Genome Informatics LabIowa State UniversityAmesIAUSA
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - David Edwards
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
- University of QueenslandBrisbaneQldAustralia
| | | | | | | | - Wei Huang
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Bhavna Hurgobin
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
- University of QueenslandBrisbaneQldAustralia
| | - Sean Li
- Data61CSIROCanberraACTAustralia
| | | | | | - Grant Morahan
- Centre for Diabetes ResearchUniversity of Western AustraliaCrawleyWAAustralia
| | | | - James Weller
- School of Biological SciencesUniversity of TasmaniaHobartTASAustralia
| | - Jianbo Jian
- Department of Plant and Animal Genome ResearchBeijing Genome InstituteShenzhenChina
| | - Karam B. Singh
- CSIRO AgricultureWembleyWAAustralia
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWAAustralia
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Frick KM, Kamphuis LG, Siddique KHM, Singh KB, Foley RC. Quinolizidine Alkaloid Biosynthesis in Lupins and Prospects for Grain Quality Improvement. FRONTIERS IN PLANT SCIENCE 2017; 8:87. [PMID: 28197163 PMCID: PMC5281559 DOI: 10.3389/fpls.2017.00087] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/16/2017] [Indexed: 05/21/2023]
Abstract
Quinolizidine alkaloids (QAs) are toxic secondary metabolites found within the genus Lupinus, some species of which are commercially important grain legume crops including Lupinus angustifolius (narrow-leafed lupin, NLL), L. luteus (yellow lupin), L. albus (white lupin), and L. mutabilis (pearl lupin), with NLL grain being the most largely produced of the four species in Australia and worldwide. While QAs offer the plants protection against insect pests, the accumulation of QAs in lupin grain complicates its use for food purposes as QA levels must remain below the industry threshold (0.02%), which is often exceeded. It is not well understood what factors cause grain QA levels to exceed this threshold. Much of the early work on QA biosynthesis began in the 1970-1980s, with many QA chemical structures well-characterized and lupin cell cultures and enzyme assays employed to identify some biosynthetic enzymes and pathway intermediates. More recently, two genes associated with these enzymes have been characterized, however, the QA biosynthetic pathway remains only partially elucidated. Here, we review the research accomplished thus far concerning QAs in lupin and consider some possibilities for further elucidation and manipulation of the QA pathway in lupin crops, drawing on examples from model alkaloid species. One breeding strategy for lupin is to produce plants with high QAs in vegetative tissues while low in the grain in order to confer insect resistance to plants while keeping grain QA levels within industry regulations. With the knowledge achieved on alkaloid biosynthesis in other plant species in recent years, and the recent development of genomic and transcriptomic resources for NLL, there is considerable scope to facilitate advances in our knowledge of QAs, leading to the production of improved lupin crops.
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Affiliation(s)
- Karen M. Frick
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
- School of Plant Biology, The University of Western AustraliaCrawley, WA, Australia
- The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Lars G. Kamphuis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
- The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | | | - Karam B. Singh
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
- The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Rhonda C. Foley
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
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Simko I. High-Resolution DNA Melting Analysis in Plant Research. TRENDS IN PLANT SCIENCE 2016; 21:528-537. [PMID: 26827247 DOI: 10.1016/j.tplants.2016.01.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/05/2015] [Accepted: 01/05/2016] [Indexed: 05/22/2023]
Abstract
Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually being developed to facilitate rapid and accurate mapping, sequencing, and analyzing of genes. Here, I review the recent progress in the application of high-resolution melting (HRM) analysis of DNA, a method that allows detecting polymorphism in double-stranded DNA by comparing profiles of melting curves. Use of HRM has expanded considerably in the past few years as the method was successfully applied for high-throughput genotyping, mapping genes, testing food products and seeds, and other areas of plant research.
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Affiliation(s)
- Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA 93905, USA.
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Zhou F, Sun R, Chen H, Fei J, Lu D. Myostatin Gene Mutated Mice Induced with TALE Nucleases. Anim Biotechnol 2015; 26:169-79. [DOI: 10.1080/10495398.2014.913598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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19
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Hong Y, Pandey MK, Liu Y, Chen X, Liu H, Varshney RK, Liang X, Huang S. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis. FRONTIERS IN PLANT SCIENCE 2015; 6:1068. [PMID: 26697032 PMCID: PMC4667090 DOI: 10.3389/fpls.2015.01068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 11/16/2015] [Indexed: 05/06/2023]
Abstract
The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.
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Affiliation(s)
- Yanbin Hong
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
| | - Manish K. Pandey
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Ying Liu
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoping Chen
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hong Liu
- College of Agriculture, South China Agricultural UniversityGuangzhou, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
| | - Xuanqiang Liang
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shangzhi Huang
- School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
- *Correspondence: Shangzhi Huang
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Zhang T, Yu LX, McCord P, Miller D, Bhamidimarri S, Johnson D, Monteros MJ, Ho J, Reisen P, Samac DA. Identification of molecular markers associated with Verticillium wilt resistance in alfalfa (Medicago sativa L.) using high-resolution melting. PLoS One 2014; 9:e115953. [PMID: 25536106 PMCID: PMC4275272 DOI: 10.1371/journal.pone.0115953] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/28/2014] [Indexed: 01/08/2023] Open
Abstract
Verticillium wilt, caused by the soilborne fungus, Verticillium alfalfae, is one of the most serious diseases of alfalfa (Medicago sativa L.) worldwide. To identify loci associated with resistance to Verticillium wilt, a bulk segregant analysis was conducted in susceptible or resistant pools constructed from 13 synthetic alfalfa populations, followed by association mapping in two F1 populations consisted of 352 individuals. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were used for genotyping. Phenotyping was done by manual inoculation of the pathogen to replicated cloned plants of each individual and disease severity was scored using a standard scale. Marker-trait association was analyzed by TASSEL. Seventeen SNP markers significantly associated with Verticillium wilt resistance were identified and they were located on chromosomes 1, 2, 4, 7 and 8. SNP markers identified on chromosomes 2, 4 and 7 co-locate with regions of Verticillium wilt resistance loci reported in M. truncatula. Additional markers identified on chromosomes 1 and 8 located the regions where no Verticillium resistance locus has been reported. This study highlights the value of SNP genotyping by high resolution melting to identify the disease resistance loci in tetraploid alfalfa. With further validation, the markers identified in this study could be used for improving resistance to Verticillium wilt in alfalfa breeding programs.
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Affiliation(s)
- Tiejun Zhang
- United States Department of Agriculture, Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, Washington, United States of America
| | - Long-Xi Yu
- United States Department of Agriculture, Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, Washington, United States of America
- * E-mail:
| | - Per McCord
- United States Department of Agriculture, Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, Washington, United States of America
| | - David Miller
- DuPont Pioneer, W8131 State HWY 60, Arlington, Wisconsin, United States of America
| | - Suresh Bhamidimarri
- DuPont Pioneer, W8131 State HWY 60, Arlington, Wisconsin, United States of America
| | - David Johnson
- Alforex Seeds, N4505 CTH M, West Salem, Wisconsin, United States of America
| | - Maria J. Monteros
- Forage Improvement Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma, United States of America
| | - Julie Ho
- Forage Genetics International, Inc. 7661 Becker Road, Davis, California, United States of America
| | - Peter Reisen
- Forage Genetics International, Inc. 7661 Becker Road, Davis, California, United States of America
| | - Deborah A. Samac
- United States Department of Agriculture, Agricultural Research Service, 495 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, Minnesota, United States of America
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Mondini L, Nachit MM, Pagnotta MA. Allelic variants in durum wheat (Triticum turgidum L. var. durum) DREB genes conferring tolerance to abiotic stresses. Mol Genet Genomics 2014; 290:531-44. [PMID: 25332074 DOI: 10.1007/s00438-014-0933-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 10/03/2014] [Indexed: 11/25/2022]
Abstract
To identify potential and useful markers able to discriminate promising lines of durum wheat (Triticum turgidum L. var durum) tolerant to salt and drought stresses, nucleotide sequences of Dehydration-Responsive-Element Binding Factor (DREB) genes were used to design primers probed with High Resolution Melting technology for the identification of allelic variants. DREB1, DREB2, DREB3, DREB4 and DREB5 conserved regions corresponding to EREBP/AP2 domain and containing the conserved core sequence (5'-TACCGACAT-3'), the protein site directly involved in DNA recognition, were analyzed. The validated primers were probed on four lines of durum wheat differentially tolerant to salt and drought stresses treated with solutions containing different salt concentrations. Some SNPs mutations were identified in the highly tolerant durum cultivar Jennah Khetifa treated with the maximum salt concentration (1.5 M). The SNPs mutations identified were non-synonymous (nsSNPs) causing changes in peptide sequences. These concerned amino acid residues directly involved in the maintenance of protein geometry, the recognition of the specific cis-element, and the contacts between the protein and DNA. A validation of the found SNPs was carried out by analyzing the regressions between DREBs SNPs allelic variants and some morpho-physiological characters in a RIL population, deriving from a cross between the two durum wheat genotypes utilized for SNPs detection, grown under contrasting environments. Several phenotypical characters have been assessed in the progeny across all the localities evaluating the different performances under different stress levels and related with SNPs occurrence. Significant relations between SNPs variants and morpho-physiological characteristics were found in the progeny growth in very severe drought environments, suggesting a role of the identified SNPs in conferring a superior capability to adverse stress conditions and, at the same time, the key role of these genes in empowering salt tolerance.
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Affiliation(s)
- Linda Mondini
- Department of Science and Technologies for Agriculture, Forestry, Nature and Energy (DAFNE), Tuscia University, via S. C. de Lellis, 01100, Viterbo, Italy
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Bohra A, Jha UC, Kishor PBK, Pandey S, Singh NP. Genomics and molecular breeding in lesser explored pulse crops: current trends and future opportunities. Biotechnol Adv 2014; 32:1410-28. [PMID: 25196916 DOI: 10.1016/j.biotechadv.2014.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 08/29/2014] [Accepted: 09/01/2014] [Indexed: 12/17/2022]
Abstract
Pulses are multipurpose crops for providing income, employment and food security in the underprivileged regions, notably the FAO-defined low-income food-deficit countries. Owing to their intrinsic ability to endure environmental adversities and the least input/management requirements, these crops remain central to subsistence farming. Given their pivotal role in rain-fed agriculture, substantial research has been invested to boost the productivity of these pulse crops. To this end, genomic tools and technologies have appeared as the compelling supplement to the conventional breeding. However, the progress in minor pulse crops including dry beans (Vigna spp.), lupins, lablab, lathyrus and vetches has remained unsatisfactory, hence these crops are often labeled as low profile or lesser researched. Nevertheless, recent scientific and technological breakthroughs particularly the next generation sequencing (NGS) are radically transforming the scenario of genomics and molecular breeding in these minor crops. NGS techniques have allowed de novo assembly of whole genomes in these orphan crops. Moreover, the availability of a reference genome sequence would promote re-sequencing of diverse genotypes to unlock allelic diversity at a genome-wide scale. In parallel, NGS has offered high-resolution genetic maps or more precisely, a robust genetic framework to implement whole-genome strategies for crop improvement. As has already been demonstrated in lupin, sequencing-based genotyping of the representative sample provided access to a number of functionally-relevant markers that could be deployed straight away in crop breeding programs. This article attempts to outline the recent progress made in genomics of these lesser explored pulse crops, and examines the prospects of genomics assisted integrated breeding to enhance and stabilize crop yields.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India.
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500007, India
| | | | - Narendra P Singh
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
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Rao PS, Kumar PS, Sonti RV. Excised radicle tips as a source of genomic DNA for PCR-based genotyping and melting curve analysis in cotton. J Biosci 2013; 38:167-72. [PMID: 23385824 DOI: 10.1007/s12038-012-9285-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genomic DNA isolation in cotton is complicated because of the presence of secondary metabolites that are inhibitory to PCR amplification. We report here that radicle tips, but not other parts of cotton seedlings, yield high-quality DNA that is readily amenable for PCR. The radicle-tip-excised seedlings retain viability because of the formation of adventitious roots. We demonstrate the utility of this method in distinguishing homozygotes from heterozygotes in a cotton breeding population and in hybrid seed purity testing.
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Affiliation(s)
- P Srinivasa Rao
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad 500 007, India
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Yan GX, Wu XM, Li D, Zeng CL, Lv PJ, Gao GZ, Chen BY, Xu K, Lv XD. Assessing high-resolution melt curve analysis for accurate detection of DNA polymorphisms in the chloroplast gene accD of Crucifer species. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Iqbal MJ, Mamidi S, Ahsan R, Kianian SF, Coyne CJ, Hamama AA, Narina SS, Bhardwaj HL. Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:517-30. [PMID: 22454146 DOI: 10.1007/s00122-012-1850-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 03/10/2012] [Indexed: 05/16/2023]
Abstract
White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.
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Affiliation(s)
- Muhammad Javed Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA.
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Mondini L, Nachit M, Porceddu E, Pagnotta MA. Identification of SNP mutations in DREB1, HKT1, and WRKY1 genes involved in drought and salt stress tolerance in durum wheat (Triticum turgidum L. var durum). OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:178-87. [PMID: 22433076 DOI: 10.1089/omi.2011.0081] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Tolerance mechanisms to salinity and drought stress are quite complex. Plants have developed a complex and elaborate signaling network that ensures their adaptation to this stress. For example, salinity tolerance is thought to be due to three main factors: Na(+) exclusion, tolerance to Na(+) in the tissues and osmotic tolerance. Recently, many transcription factors for tolerance to salt and drought stresses have been identified. In this study, multialignments of conserved domains in DREB1, WRKY1 transcription factors (TFs), and HKT-1 have been utilized to design specific primers in order to identify functional single nucleotide polymorphisms (SNPs). These primers have been used to probe on several genotypes of durum wheat that are differentially tolerant to salt and drought stress; they were grown in increasing concentrations of NaCl. The selected portions have been analyzed using high-resolution melting curve (HRM) technology that currently represents one of the most recent and powerful tools for detecting SNP and INDEL mutations. Analyzing the amplification profiles, observed in the resulting melting curves, samples corresponding to different treatment conditions were selected, sequenced, and aligned with the homolog sequences present in gene databases to identify and characterize potential SNP and INDEL mutations. The PCR amplicons, containing single and double SNPs, produced distinctive HRM profiles. By sequencing the polymerase chain reaction (PCR) products, several SNPs have been identified and validated. All the discovered mutations were able to generate changes in amino acid sequences of the corresponding proteins. Most of the identified SNPs were found in salt and drought tolerant durum wheat genotypes. These varieties are of great value for durum wheat breeding works.
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Affiliation(s)
- Linda Mondini
- Department of Science and Technologies for Agriculture, Forestry, Nature and Energy, Tuscia University, Viterbo, Italy
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Han Y, Khu DM, Monteros MJ. High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2012; 29:489-501. [PMID: 22363202 PMCID: PMC3275744 DOI: 10.1007/s11032-011-9566-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/12/2011] [Indexed: 05/22/2023]
Abstract
Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic polymorphism in plant genomes. SNP markers are valuable tools for genetic analysis of complex traits of agronomic importance, linkage and association mapping, genome-wide selection, map-based cloning, and marker-assisted selection. Current challenges for SNP genotyping in polyploid outcrossing species include multiple alleles per loci and lack of high-throughput methods suitable for variant detection. In this study, we report on a high-resolution melting (HRM) analysis system for SNP genotyping and mapping in outcrossing tetraploid genotypes. The sensitivity and utility of this technology is demonstrated by identification of the parental genotypes and segregating progeny in six alfalfa populations based on unique melting curve profiles due to differences in allelic composition at one or multiple loci. HRM using a 384-well format is a fast, consistent, and efficient approach for SNP discovery and genotyping, useful in polyploid species with uncharacterized genomes. Possible applications of this method include variation discovery, analysis of candidate genes, genotyping for comparative and association mapping, and integration of genome-wide selection in breeding programs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9566-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanhong Han
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Dong-Man Khu
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Maria J. Monteros
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
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Li YD, Chu ZZ, Liu XG, Jing HC, Liu YG, Hao DY. A cost-effective high-resolution melting approach using the EvaGreen dye for DNA polymorphism detection and genotyping in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:1036-1042. [PMID: 21106003 DOI: 10.1111/j.1744-7909.2010.01001.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
High-resolution melting (HRM) analysis relies on the use of fluorescent dyes, such as LCGreen, ResoLight, and SYTO9, which bind in a saturated manner to the double-stranded DNAs. These dyes are expensive in use and may not be affordable when dealing with a large quantity of samples. EvaGreen is a much cheaper DNA helix intercalating dye and has been used in quantitative real-time polymerase chain reaction (PCR) and post-PCR DNA melt curve analysis. Here we report on the development of an EvaGreen-based HRM analysis and its performance, in comparison with the popular LCGreen-based HRM analysis, in detection of DNA polymorphism in plants. We found that various polymorphisms ranged from single nucleotide polymorphisms (SNPs) to Indels were equally detected by using EvaGreen- or LCGreen-based HRM. EvaGreen dye was sensitive enough in discovery of SNPs in fivefold pooled samples. Using this economical dye we successfully identified multiple novel mutant alleles of Gln1-3 gene, which produces a cytosolic glutamine synthetase isoenzyme (GS1), in a maize ethyl methanesulfonate (EMS)-mutagenized library, and genotyped rice mapping populations with SNP markers. The current results suggest that EvaGreen is a promising dye for HRM analysis for its ease to use and cost effectiveness.
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Affiliation(s)
- Yi-Dan Li
- Biotechnology Research Centre, Jilin Academy of Agricultural Sciences, Changchun 130033, China
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29
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Rodríguez López CM, Guzmán Asenjo B, Lloyd AJ, Wilkinson MJ. Direct detection and quantification of methylation in nucleic acid sequences using high-resolution melting analysis. Anal Chem 2010; 82:9100-8. [PMID: 20945868 DOI: 10.1021/ac1024057] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
High-resolution melting (HRM) analysis exploits the reduced thermal stability of DNA fragments that contain base mismatches to detect single nucleotide polymorphisms (SNPs). However, the capacity of HRM to reveal other features of DNA chemistry remains unexplored. DNA methylation plays a key role in regulating gene expression and is essential for normal development in many higher organisms. The presence of methylated bases perturbs the double-stranded DNA structure, although its effect on DNA thermal stability is largely unknown. Here, we reveal that methylated DNA has enhanced thermal stability and is sufficiently divergent from nonmethylated DNA to allow detection and quantification by HRM analysis. This approach reliably distinguishes between sequence-identical DNA differing only in the methylation of one base. The method also provides accurate discrimination between mixes of methylated and nonmethylated DNAs, allowing discrimination between DNA that is 1% and 0% methylated and also between 97.5% and 100% methylated. Thus, the method provides a new means of adjusting thermal optima for DNA hybridization and PCR-based techniques and to empirically measure the impact of DNA methylation marks on the thermostability of regulatory regions. In the longer term, it could enable the development of new techniques to quantify methylated DNA.
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Affiliation(s)
- Carlos M Rodríguez López
- Aberystwyth University, IBERS-Institute of Biological, Environmental and Rural Sciences, Aberystwyth, Wales, SY23 3DA, UK
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Mader E, Ruzicka J, Schmiderer C, Novak J. Quantitative high-resolution melting analysis for detecting adulterations. Anal Biochem 2010; 409:153-5. [PMID: 20946863 DOI: 10.1016/j.ab.2010.10.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Revised: 10/01/2010] [Accepted: 10/01/2010] [Indexed: 11/17/2022]
Abstract
Admixtures of different plant species are a common problem in raw materials for medicinal use. Two exemplary assays were developed to admixtures in Helleborus niger with high-resolution melting analysis. HRM proved to be a very sensitive tool in detecting admixtures, able to detect a ratio of 1:1000 with unknown species, and of 1:200,000 with Veratrum nigrum. The example proves the ability of HRM for quantification in multiplex PCR. The method is not limited to detecting adulterations. It can also be used to quantify a specific target by integrating a second amplicon in the assay as internal standard.
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Affiliation(s)
- Eduard Mader
- Institute for Applied Botany, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Wien, Austria.
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Dunwell JM, Wilkinson MJ, Nelson S, Wening S, Sitorus AC, Mienanti D, Alfiko Y, Croxford AE, Ford CS, Forster BP, Caligari PDS. Production of haploids and doubled haploids in oil palm. BMC PLANT BIOLOGY 2010; 10:218. [PMID: 20929530 PMCID: PMC3017816 DOI: 10.1186/1471-2229-10-218] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 10/07/2010] [Indexed: 05/23/2023]
Abstract
BACKGROUND Oil palm is the world's most productive oil-food crop despite yielding well below its theoretical maximum. This maximum could be approached with the introduction of elite F1 varieties. The development of such elite lines has thus far been prevented by difficulties in generating homozygous parental types for F1 generation. RESULTS Here we present the first high-throughput screen to identify spontaneously-formed haploid (H) and doubled haploid (DH) palms. We secured over 1,000 Hs and one DH from genetically diverse material and derived further DH/mixoploid palms from Hs using colchicine. We demonstrated viability of pollen from H plants and expect to generate 100% homogeneous F1 seed from intercrosses between DH/mixoploids once they develop female inflorescences. CONCLUSIONS This study has generated genetically diverse H/DH palms from which parental clones can be selected in sufficient numbers to enable the commercial-scale breeding of F1 varieties. The anticipated step increase in productivity may help to relieve pressure to extend palm cultivation, and limit further expansion into biodiverse rainforest.
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Affiliation(s)
- Jim M Dunwell
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - Mike J Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Stephen Nelson
- Sumatra Bioscience Pte Ltd, 8 Eu Tong Sen Street, #16-94/95 The Central, 059818, Singapore
| | - Sri Wening
- PT Sumatra Bioscience, Bah Lias Research Station, North Sumatra, Indonesia
| | - Andrew C Sitorus
- PT Sumatra Bioscience, Bah Lias Research Station, North Sumatra, Indonesia
| | - Devi Mienanti
- PT Sumatra Bioscience, Bah Lias Research Station, North Sumatra, Indonesia
| | - Yuzer Alfiko
- PT Sumatra Bioscience, Bah Lias Research Station, North Sumatra, Indonesia
| | - Adam E Croxford
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Caroline S Ford
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | | | - Peter DS Caligari
- Sumatra Bioscience Pte Ltd, 8 Eu Tong Sen Street, #16-94/95 The Central, 059818, Singapore
- BioHybrids International Ltd, Earley, Reading, RG6 5FY, UK
- Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685, Talca, Chile
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Montgomery JL, Sanford LN, Wittwer CT. High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn 2010; 10:219-40. [PMID: 20214540 DOI: 10.1586/erm.09.84] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Among nucleic acid analytical methods, high-resolution melting analysis is gaining more and more attention. High-resolution melting provides simple, homogeneous solutions for variant scanning and genotyping, addressing the needs of today's overburdened laboratories with rapid turnaround times and minimal cost. The flexibility of the technique has allowed it to be adopted by a wide range of disciplines for a variety of applications. In this review we examine the broad use of high-resolution melting analysis, including gene scanning, genotyping (including small amplicon, unlabeled probe and snapback primers), sequence matching and methylation analysis. Four major application arenas are examined to demonstrate the methods and approaches commonly used in particular fields. The appropriate usage of high-resolution melting analysis is discussed in the context of known constraints, such as sample quality and quantity, with a particular focus placed on proper experimental design in order to produce successful results.
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Affiliation(s)
- Jesse L Montgomery
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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Population structures of genebank accessions of Salvia officinalis L. (Lamiaceae) revealed by high resolution melting analysis. BIOCHEM SYST ECOL 2010. [DOI: 10.1016/j.bse.2010.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ujino-Ihara T, Taguchi Y, Moriguchi Y, Tsumura Y. An efficient method for developing SNP markers based on EST data combined with high resolution melting (HRM) analysis. BMC Res Notes 2010; 3:51. [PMID: 20193087 PMCID: PMC2850910 DOI: 10.1186/1756-0500-3-51] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 03/02/2010] [Indexed: 11/24/2022] Open
Abstract
Background In order to identify single nucleotide polymorphisms (SNPs) efficiently from a species with a large genome, SNPs were identified from an expressed sequence tag (EST) database combined with High Resolution Melting (HRM) analysis. Findings A total of 574 sequence tagged sites (STSs) were generated from Cryptomeria japonica and HRM analysis was used to screen for polymorphisms in these STS markers. STSs were designed in two ways: 1) putative SNP sites were identified by comparing ESTs from specific contigs, then 226 primer pairs designed for the purpose to amplify these SNPs; 2) 348 primer pairs were randomly designed using reads from the 3' end of cDNA. HRM analysis revealed that 325 markers among eight individuals were polymorphic, and that STSs, including putative SNP sites, exhibited higher levels of polymorphism. Conclusion Our results indicate that the combination of SNP screening from an EST database combined with HRM analysis is a highly efficient way to develop SNP markers for expressed genes. This method will contribute to both genetic mapping and the identification of SNPs in non-model organisms.
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Affiliation(s)
- Tokuko Ujino-Ihara
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan.
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Hofinger BJ, Jing HC, Hammond-Kosack KE, Kanyuka K. High-resolution melting analysis of cDNA-derived PCR amplicons for rapid and cost-effective identification of novel alleles in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:851-65. [PMID: 19578831 DOI: 10.1007/s00122-009-1094-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 06/13/2009] [Indexed: 05/03/2023]
Abstract
An original method has been established for the identification of novel alleles of eukaryotic translation initiation factor 4E (eIF4E) gene, which is required for resistance to agronomically important bymoviruses, in barley germplasm. This method involves scanning for sequence variations in cDNA-derived PCR amplicons using High-resolution melting (HRM) followed by direct Sanger sequencing of only those amplicons which were predicted to carry nucleotide changes. HRM is a simple, cost-effective, rapid and high-throughput assay, which so far has only been widely used in clinical pathology for molecular diagnostic of diseases and patient genotyping. Application of HRM allowed significant reduction in the amount of expensive Sanger sequencing required for allele mining in plants. The method described here involved an investigation of total cDNA rather than genomic DNA, thus permitting the analyses of shorter (up to 300-bp) and fewer overlapping amplicons to cover the coding sequence. This strategy further reduced the allele mining costs. The sensitivity and accuracy of HRM for predicting genotypes carrying a wide range of nucleotide polymorphisms in eIF4E approached 100%. Results of the current study are promising and suggest that this method could also potentially be applied to the discovery of superior alleles controlling other important traits in barley as well in other model and crop plant species.
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Affiliation(s)
- Bernhard J Hofinger
- Department of Plant Pathology and Microbiology, Centre for Sustainable Pest and Disease Management, Rothamsted Research, Harpenden AL5 2JQ, UK
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Wu SB, Tavassolian I, Rabiei G, Hunt P, Wirthensohn M, Gibson JP, Ford CM, Sedgley M. Mapping SNP-anchored genes using high-resolution melting analysis in almond. Mol Genet Genomics 2009; 282:273-81. [PMID: 19526371 DOI: 10.1007/s00438-009-0464-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 05/29/2009] [Indexed: 10/20/2022]
Abstract
Peach and almond have been considered as model species for the family Rosaceae and other woody plants. Consequently, mapping and characterisation of genes in these species has important implications. High-resolution melting (HRM) analysis is a recent development in the detection of SNPs and other markers, and proved to be an efficient and cost-effective approach. In this study, we aimed to map genes corresponding to known proteins in other species using the HRM approach. Prunus unigenes were searched and compared with known proteins in the public databases. We developed single-nucleotide polymorphism (SNP) markers, polymorphic in a mapping population produced from a cross between the cloned cultivars Nonpareil and Lauranne. A total of 12 SNP-anchored putative genes were genotyped in the population using HRM, and mapped to an existing linkage map. These genes were mapped on six linkage groups, and the predicted proteins were compared to putative orthologs in other species. Amongst those genes, four were abiotic stress-responsive genes, which can provide a starting point for construction of an abiotic resistance map. Two allergy and detoxification related genes, respectively, were also mapped and analysed. Most of the investigated genes had high similarities to sequences from closely related species such as apricot, apple and other eudicots, and these are putatively orthologous. In addition, it was shown that HRM can be an effective means of genotyping populations for the purpose of constructing a linkage map. Our work provides basic genomic information for the 12 genes, which can be used for further genetic and functional studies.
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Affiliation(s)
- Shu-Biao Wu
- School of Environmental and Rural Science and The Institute of Genetics and Bioinformatics, The University of New England, NSW, Australia.
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