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Bambara Groundnut (Vigna subterranea L. Verdc): A Crop for the New Millennium, Its Genetic Diversity, and Improvements to Mitigate Future Food and Nutritional Challenges. SUSTAINABILITY 2021. [DOI: 10.3390/su13105530] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The world’s food and agricultural schemes have gradually fallen into an alarming state due to challenges such as high population birth rates, diverse agro-climatic zones, a lack of measures to counter global warming, severe practices of sole-culture cultivation, and asset reduction. A very high dependency on limited staple food crops is associated with repetitious diets, deprivation of food, and shortages of trace minerals, which often causes dietary sicknesses. To ensure nutritious diets worldwide, a real-world and justifiable scheme is provided to garner extra attention towards variation in both agriculture/farming approaches and food habits. The EAT-Lancet statement emphasized an increase in agri-based diets as a way of attaining global generational health. Enlarging neglected crops with plenty of genomic stocks and potentially profitable attributes is a solution that could address food and nutritional security concerns. Bambara groundnut is one such imperative and neglected legume crop that contributes positively to improving global food and nutrient safety. As a “complete food”, this crop has recently been treated as a new millennium crop, and furthermore, it is more adjusted to poor soil and climatic conditions than other dominant crops. Bambara groundnut is a repository of vital nutrients that provides carbohydrates, crucial amino acids, proteins, and energy as well as minerals and vitamins to developed and low-income countries where animal proteins are not readily available. This review explores the potential of Bambara groundnut in ensuring food and nutrient security; its variables, production, processing, nutrient values, role in reducing the nutritional gap, and diverse uses; and attempts in improving its traits. To strengthen food production, an agricultural revolution is required for underutilized crop species to feed the ever-expanding population in the world. Henceforth, advanced plant-breeding procedures, such as next-generation breeding techniques, various molecular tools, TILLING, Eco-TILLING, proteomics, genomics, and transcriptomics (which has been used for major crops), also need to be practiced to intensify production. To boost productivity and to feed the most starved and malnourished populations of the world, it is assumed that the application of modern techniques will play a vital role in the advancement of the underutilized Bambara groundnut.
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Biswas MK, Bagchi M, Biswas D, Harikrishna JA, Liu Y, Li C, Sheng O, Mayer C, Yi G, Deng G. Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana. Genes (Basel) 2020; 11:genes11121479. [PMID: 33317074 PMCID: PMC7763637 DOI: 10.3390/genes11121479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.
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Affiliation(s)
- Manosh Kumar Biswas
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- Correspondence: (M.K.B.); (G.D.)
| | - Mita Bagchi
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- The College of Economics and Managements, South China Agricultural University, Guangzhou 510640, China
| | - Dhiman Biswas
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, West Bengal 700064, India;
| | - Jennifer Ann Harikrishna
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yuxuan Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Christoph Mayer
- Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113 Bonn, Germany;
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
- Correspondence: (M.K.B.); (G.D.)
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Tramontano A, Jarc L, Jankowicz-Cieslak J, Hofinger BJ, Gajek K, Szurman-Zubrzycka M, Szarejko I, Ingelbrecht I, Till BJ. Fragmentation of Pooled PCR Products for Highly Multiplexed TILLING. G3 (BETHESDA, MD.) 2019; 9:2657-2666. [PMID: 31213514 PMCID: PMC6686939 DOI: 10.1534/g3.119.400301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/12/2019] [Indexed: 01/16/2023]
Abstract
Improvements to massively parallel sequencing have allowed the routine recovery of natural and induced sequence variants. A broad range of biological disciplines have benefited from this, ranging from plant breeding to cancer research. The need for high sequence coverage to accurately recover single nucleotide variants and small insertions and deletions limits the applicability of whole genome approaches. This is especially true in organisms with a large genome size or for applications requiring the screening of thousands of individuals, such as the reverse-genetic technique known as TILLING. Using PCR to target and sequence chosen genomic regions provides an attractive alternative as the vast reduction in interrogated bases means that sample size can be dramatically increased through amplicon multiplexing and multi-dimensional sample pooling while maintaining suitable coverage for recovery of small mutations. Direct sequencing of PCR products is limited, however, due to limitations in read lengths of many next generation sequencers. In the present study we show the optimization and use of ultrasonication for the simultaneous fragmentation of multiplexed PCR amplicons for TILLING highly pooled samples. Sequencing performance was evaluated in a total of 32 pooled PCR products produced from 4096 chemically mutagenized Hordeum vulgare DNAs pooled in three dimensions. Evaluation of read coverage and base quality across amplicons suggests this approach is suitable for high-throughput TILLING and other applications employing highly pooled complex sampling schemes. Induced mutations previously identified in a traditional TILLING screen were recovered in this dataset further supporting the efficacy of the approach.
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Affiliation(s)
- Andrea Tramontano
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400 Vienna, Austria and
| | - Luka Jarc
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400 Vienna, Austria and
| | - Joanna Jankowicz-Cieslak
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400 Vienna, Austria and
| | - Bernhard J Hofinger
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400 Vienna, Austria and
| | - Katarzyna Gajek
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Miriam Szurman-Zubrzycka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Ivan Ingelbrecht
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400 Vienna, Austria and
| | - Bradley J Till
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400 Vienna, Austria and
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Gupta P, Reddaiah B, Salava H, Upadhyaya P, Tyagi K, Sarma S, Datta S, Malhotra B, Thomas S, Sunkum A, Devulapalli S, Till BJ, Sreelakshmi Y, Sharma R. Next-generation sequencing (NGS)-based identification of induced mutations in a doubly mutagenized tomato (Solanum lycopersicum) population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:495-508. [PMID: 28779536 DOI: 10.1111/tpj.13654] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 05/21/2023]
Abstract
The identification of mutations in targeted genes has been significantly simplified by the advent of TILLING (Targeting Induced Local Lesions In Genomes), speeding up the functional genomic analysis of animals and plants. Next-generation sequencing (NGS) is gradually replacing classical TILLING for mutation detection, as it allows the analysis of a large number of amplicons in short durations. The NGS approach was used to identify mutations in a population of Solanum lycopersicum (tomato) that was doubly mutagenized by ethylmethane sulphonate (EMS). Twenty-five genes belonging to carotenoids and folate metabolism were PCR-amplified and screened to identify potentially beneficial alleles. To augment efficiency, the 600-bp amplicons were directly sequenced in a non-overlapping manner in Illumina MiSeq, obviating the need for a fragmentation step before library preparation. A comparison of the different pooling depths revealed that heterozygous mutations could be identified up to 128-fold pooling. An evaluation of six different software programs (camba, crisp, gatk unified genotyper, lofreq, snver and vipr) revealed that no software program was robust enough to predict mutations with high fidelity. Among these, crisp and camba predicted mutations with lower false discovery rates. The false positives were largely eliminated by considering only mutations commonly predicted by two different software programs. The screening of 23.47 Mb of tomato genome yielded 75 predicted mutations, 64 of which were confirmed by Sanger sequencing with an average mutation density of 1/367 Kb. Our results indicate that NGS combined with multiple variant detection tools can reduce false positives and significantly speed up the mutation discovery rate.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Bodanapu Reddaiah
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Hymavathi Salava
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Pallawi Upadhyaya
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kamal Tyagi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Supriya Sarma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sneha Datta
- Plant Breeding and Genetics Laboratory, IAEA Seibersdorf Laboratories, Reaktorstrasse 1, Seibersdorf, Austria
| | - Bharti Malhotra
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sherinmol Thomas
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anusha Sunkum
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sameera Devulapalli
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Bradley John Till
- Plant Breeding and Genetics Laboratory, IAEA Seibersdorf Laboratories, Reaktorstrasse 1, Seibersdorf, Austria
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Raja RB, Agasimani S, Jaiswal S, Thiruvengadam V, Sabariappan R, Chibbar RN, Ram SG. EcoTILLING by sequencing reveals polymorphisms in genes encoding starch synthases that are associated with low glycemic response in rice. BMC PLANT BIOLOGY 2017; 17:13. [PMID: 28088172 PMCID: PMC5423428 DOI: 10.1186/s12870-016-0968-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/23/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Glycemic response, a trait that is tedious to be assayed in cereal staples, has been identified as a factor correlated with alarmingly increasing prevalence of Type II diabetes. Reverse genetics based discovery of allelic variants associated with this nutritional trait gains significance as they can provide scope for genetic improvement of this factor which is otherwise difficult to target through routine screening methods. RESULTS Through EcoTILLING by sequencing in 512 rice accessions, we report the discovery of six deleterious variants in the genes with potential to increase Resistant Starch (RS) and reduce Hydrolysis Index (HI) of starch. By deconvolution of the variant harbouring EcoTILLING DNA pools, we discovered accessions with a minimum of one to a maximum of three deleterious allelic variants in the candidate genes. CONCLUSIONS Through biochemical assays, we confirmed the potential role of the discovered alleles alone or in combinations in increasing RS the key factor for reduction in glycemic response.
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Affiliation(s)
- Ramadoss Bharathi Raja
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Somanath Agasimani
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Sarita Jaiswal
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Venkatesan Thiruvengadam
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Robin Sabariappan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Ravindra N Chibbar
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Sundaram Ganesh Ram
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India.
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Bajaj D, Srivastava R, Nath M, Tripathi S, Bharadwaj C, Upadhyaya HD, Tyagi AK, Parida SK. EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea. FRONTIERS IN PLANT SCIENCE 2016; 7:450. [PMID: 27148286 PMCID: PMC4835497 DOI: 10.3389/fpls.2016.00450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/22/2016] [Indexed: 05/22/2023]
Abstract
The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10-15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.
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Affiliation(s)
- Deepak Bajaj
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Rishi Srivastava
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Manoj Nath
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | | | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Akhilesh K. Tyagi
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Swarup K. Parida
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
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Kitavi M, Downing T, Lorenzen J, Karamura D, Onyango M, Nyine M, Ferguson M, Spillane C. The triploid East African Highland Banana (EAHB) genepool is genetically uniform arising from a single ancestral clone that underwent population expansion by vegetative propagation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:547-61. [PMID: 26743524 DOI: 10.1007/s00122-015-2647-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/30/2015] [Indexed: 05/04/2023]
Abstract
All East African Highland Banana varieties are genetically uniform having arisen from a single clone introduced to Africa. East African Highland bananas (EAHBs) are a subgroup of triploid (AAA genome) bananas of importance to food security in the Great Lakes region of Africa. Little is known about their genetic variation, population structure and evolutionary history. Ninety phenotypically diverse EAHB cultivars were genotyped at 100 SSR microsatellite markers to investigate population genetic diversity, the correlation of genetic variability with morphological classes, and evolutionary origins since introduction to Africa. Population-level statistics were compared to those for plantain (AAB) and dessert (AAA) cultivars representing other M. acuminata subgroups. EAHBs displayed minimal genetic variation and are largely genetically uniform, irrespective of whether they were derived from the distinct Ugandan or Kenyan germplasm collections. No association was observed between EAHB genetic diversity and currently employed morphological taxonomic systems for EAHB germplasm. Population size dynamics indicated that triploid EAHBs arose as a single hybridization event, which generated a genetic bottleneck during foundation of the EAHB genepool. As EAHB triploids are sterile, subsequent asexual vegetative propagation of EAHBs allowed a recent rapid expansion in population size. This provided a basis for emergence of genetically near-isogenic somatic mutants selected across farmers and environments in East Africa over the past 2000 years since EAHBs were first introduced to the African continent.
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Affiliation(s)
- Mercy Kitavi
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, C306 Aras de Brun, National University of Ireland Galway, University Road, Galway, Ireland
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Tim Downing
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, University Road, Galway, Ireland
| | - Jim Lorenzen
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
- Bill and Melinda Gates Foundation, 500 5th Ave N, Seattle, WA, 98102, USA
| | - Deborah Karamura
- Bioversity International, PLOT 106, Katalima Road, P.O. Box 24384, Kampala, Uganda
| | - Margaret Onyango
- Kenya Agricultural Research Institute (KARI), KARI, Kisii Centre, P.O. Box 523-40200, Kisii, Kenya
| | - Moses Nyine
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Morag Ferguson
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Charles Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, C306 Aras de Brun, National University of Ireland Galway, University Road, Galway, Ireland.
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Maghuly F, Jankowicz-Cieslak J, Pabinger S, Till BJ, Laimer M. Geographic origin is not supported by the genetic variability found in a large living collection of Jatropha curcas with accessions from three continents. Biotechnol J 2015; 10:536-51. [PMID: 25511658 PMCID: PMC4413048 DOI: 10.1002/biot.201400196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 11/19/2014] [Accepted: 12/12/2014] [Indexed: 01/15/2023]
Abstract
Increasing economic interest in Jatropha curcas requires a major research focus on the genetic background and geographic origin of this non-edible biofuel crop. To determine the worldwide genetic structure of this species, amplified fragment length polymorphisms, inter simple sequence repeats, and novel single nucleotide polymorphisms (SNPs) were employed for a large collection of 907 J. curcas accessions and related species (RS) from three continents, 15 countries and 53 regions. PCoA, phenogram, and cophenetic analyses separated RS from two J. curcas groups. Accessions from Mexico, Bolivia, Paraguay, Kenya, and Ethiopia with unknown origins were found in both groups. In general, there was a considerable overlap between individuals from different regions and countries. The Bayesian approach using structure demonstrated two groups with a low genetic variation. Analysis of molecular varience revealed significant variation among individuals within populations. SNPs found by in silico analyses of Δ12 fatty acid desaturase indicated possible changes in gene expression and thus in fatty acid profiles. SNP variation was higher in the curcin gene compared to genes involved in oil production. Novel SNPs allowed separating toxic, non-toxic, and Mexican accessions. The present study confirms that human activities had a major influence on the genetic diversity of J. curcas, not only because of domestication, but also because of biased selection.
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Affiliation(s)
- Fatemeh Maghuly
- Plant Biotechnology Unit (PBU), Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Vienna, Austria
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Mahendhiran M, Ramirez-Prado JH, Escobedo-Gracia Medrano RM, Canto-Canché B, Tzec-Simá M, Grijalva-Arango R, James-Kay A. Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes. ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2014.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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10
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Ortiz R, Swennen R. From crossbreeding to biotechnology-facilitated improvement of banana and plantain. Biotechnol Adv 2014; 32:158-69. [DOI: 10.1016/j.biotechadv.2013.09.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/16/2013] [Accepted: 09/24/2013] [Indexed: 12/30/2022]
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Lee LS, Till BJ, Hill H, Huynh OA, Jankowicz-Cieslak J. Mutation and mutation screening. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 1099:77-95. [PMID: 24243197 DOI: 10.1007/978-1-62703-715-0_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Molecular techniques have created the opportunity for great advances in plant mutation genetics and the science of mutation breeding. The powerful targeted induced local lesions in genomes (TILLING) technique has introduced the possibility of reverse genetics-the ability to screen for mutations at the DNA level prior to assessing phenotype. Fundamental to TILLING is the induction of mutant populations (or alternatively, the identification of mutants in the environment); and mutation induction requires an understanding and assessment of the appropriate mutagen dose required. The techniques of mutation induction, dose optimization, and TILLING are explained.
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Affiliation(s)
- L Slade Lee
- Cooperative Research Centre for Remote Economic Participation, Division of Research, Southern Cross University, Lismore, NSW, Australia
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12
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Hofinger BJ, Huynh OA, Jankowicz-Cieslak J, Müller A, Otto I, Kumlehn J, Till BJ. Validation of doubled haploid plants by enzymatic mismatch cleavage. PLANT METHODS 2013; 9:43. [PMID: 24220637 PMCID: PMC3831592 DOI: 10.1186/1746-4811-9-43] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/01/2013] [Indexed: 05/25/2023]
Abstract
BACKGROUND Doubled haploidy is a fundamental tool in plant breeding as it provides the fastest way to generate populations of meiotic recombinants in a genetically fixed state. A wide range of methods has been developed to produce doubled haploid (DH) plants and recent advances promise efficient DH production in otherwise recalcitrant species. Since the cellular origin of the plants produced is not always certain, rapid screening techniques are needed to validate that the produced individuals are indeed homozygous and genetically distinct from each other. Ideal methods are easily implemented across species and in crops where whole genome sequence and marker resources are limited. RESULTS We have adapted enzymatic mismatch cleavage techniques commonly used for TILLING (Targeting Induced Local Lesions IN Genomes) for the evaluation of heterozygosity in parental, F1 and putative DH plants. We used barley as a model crop and tested 26 amplicons previously developed for TILLING. Experiments were performed using self-extracted single-strand-specific nuclease and standard native agarose gels. Eleven of the twenty-six tested primers allowed unambiguous assignment of heterozygosity in material from F1 crosses and loss of heterozygosity in the DH plants. Through parallel testing of previously developed Simple Sequence Repeat (SSR) markers, we show that 3/32 SSR markers were suitable for screening. This suggests that enzymatic mismatch cleavage approaches can be more efficient than SSR based screening, even in species with well-developed markers. CONCLUSIONS Enzymatic mismatch cleavage has been applied for mutation discovery in many plant species, including those with little or no available genomic DNA sequence information. Here, we show that the same methods provide an efficient system to screen for the production of DH material without the need of specialized equipment. This gene target based approach further allows discovery of novel nucleotide polymorphisms in candidate genes in the parental lines.
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Affiliation(s)
- Bernhard J Hofinger
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
| | - Owen A Huynh
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
| | - Joanna Jankowicz-Cieslak
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
| | - Andrea Müller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Plant Reproductive Biology, Corrensstrasse 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Ingrid Otto
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Plant Reproductive Biology, Corrensstrasse 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Plant Reproductive Biology, Corrensstrasse 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Bradley J Till
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
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13
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Sabetta W, Blanco A, Zelasco S, Lombardo L, Perri E, Mangini G, Montemurro C. Fad7 gene identification and fatty acids phenotypic variation in an olive collection by EcoTILLING and sequencing approaches. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 69:1-8. [PMID: 23685785 DOI: 10.1016/j.plaphy.2013.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/11/2013] [Indexed: 05/01/2023]
Abstract
The ω-3 fatty acid desaturases (FADs) are enzymes responsible for catalyzing the conversion of linoleic acid to α-linolenic acid localized in the plastid or in the endoplasmic reticulum. In this research we report the genotypic and phenotypic variation of Italian Olea europaea L. germoplasm for the fatty acid composition. The phenotypic oil characterization was followed by the molecular analysis of the plastidial-type ω-3 FAD gene (fad7) (EC 1.14.19), whose full-length sequence has been here identified in cultivar Leccino. The gene consisted of 2635 bp with 8 exons and 5'- and 3'-UTRs of 336 and 282 bp respectively, and showed a high level of heterozygousity (1/110 bp). The natural allelic variation was investigated both by a LiCOR EcoTILLING assay and the PCR product direct sequencing. Only three haplotypes were identified among the 96 analysed cultivars, highlighting the strong degree of conservation of this gene.
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Affiliation(s)
- Wilma Sabetta
- Department of Soil, Plant and Food Sciences, Section of Genetics and Breeding, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy.
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14
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Frerichmann SLM, Kirchhoff M, Müller AE, Scheidig AJ, Jung C, Kopisch-Obuch FJ. EcoTILLING in Beta vulgaris reveals polymorphisms in the FLC-like gene BvFL1 that are associated with annuality and winter hardiness. BMC PLANT BIOLOGY 2013; 13:52. [PMID: 23531083 PMCID: PMC3636108 DOI: 10.1186/1471-2229-13-52] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 02/21/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND Sugar beet (Beta vulgaris ssp. vulgaris L.) is an important crop for sugar and biomass production in temperate climate regions. Currently sugar beets are sown in spring and harvested in autumn. Autumn-sown sugar beets that are grown for a full year have been regarded as a cropping system to increase the productivity of sugar beet cultivation. However, for the development of these "winter beets" sufficient winter hardiness and a system for bolting control is needed. Both require a thorough understanding of the underlying genetics and its natural variation. RESULTS We screened a diversity panel of 268 B. vulgaris accessions for three flowering time genes via EcoTILLING. This panel had been tested in the field for bolting behaviour and winter hardiness. EcoTILLING identified 20 silent SNPs and one non-synonymous SNP within the genes BTC1, BvFL1 and BvFT1, resulting in 55 haplotypes. Further, we detected associations of nucleotide polymorphisms in BvFL1 with bolting before winter as well as winter hardiness. CONCLUSIONS These data provide the first genetic indication for the function of the FLC homolog BvFL1 in beet. Further, it demonstrates for the first time that EcoTILLING is a powerful method for exploring genetic diversity and allele mining in B. vulgaris.
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Affiliation(s)
- Sebastian LM Frerichmann
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, Kiel, 24098, Germany
| | - Martin Kirchhoff
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, Kiel, 24098, Germany
- Nordsaat Saatzucht GmbH, Böhnshauser Straße, Langenstein, 38895, Germany
| | - Andreas E Müller
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, Kiel, 24098, Germany
- Strube Research GmbH & Co. KG, Hauptstr. 1, Söllingen, 38387, Germany
| | - Axel J Scheidig
- Zoological Institute, Department of Structural Biology, Christian-Albrechts-University of Kiel, Am Botanischen Garten 1-9, Kiel, 24118, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, Kiel, 24098, Germany
| | - Friedrich J Kopisch-Obuch
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, Kiel, 24098, Germany
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15
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Induced Mutations Unleash the Potentials of Plant Genetic Resources for Food and Agriculture. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3010200] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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16
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Negrão S, Almadanim MC, Pires IS, Abreu IA, Maroco J, Courtois B, Gregorio GB, McNally KL, Oliveira MM. New allelic variants found in key rice salt-tolerance genes: an association study. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:87-100. [PMID: 23116435 DOI: 10.1111/pbi.12010] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Revised: 09/17/2012] [Accepted: 09/19/2012] [Indexed: 05/18/2023]
Abstract
Salt stress is a complex physiological trait affecting plants by limiting growth and productivity. Rice, one of the most important food crops, is rated as salt-sensitive. High-throughput screening methods are required to exploit novel sources of genetic variation in rice and further improve salinity tolerance in breeding programmes. To search for genotypic differences related to salt stress, we genotyped 392 rice accessions by EcoTILLING. We targeted five key salt-related genes involved in mechanisms such as Na(+) /K(+) ratio equilibrium, signalling cascade and stress protection, and we found 40 new allelic variants in coding sequences. By performing association analyses using both general and mixed linear models, we identified 11 significant SNPs related to salinity. We further evaluated the putative consequences of these SNPs at the protein level using bioinformatic tools. Amongst the five nonsynonymous SNPs significantly associated with salt-stress traits, we found a T67K mutation that may cause the destabilization of one transmembrane domain in OsHKT1;5, and a P140A alteration that significantly increases the probability of OsHKT1;5 phosphorylation. The K24E mutation can putatively affect SalT interaction with other proteins thus impacting its function. Our results have uncovered allelic variants affecting salinity tolerance that may be important in breeding.
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Affiliation(s)
- Sónia Negrão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal; iBET, Oeiras, Portugal
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17
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Jankowicz-Cieslak J, Huynh OA, Brozynska M, Nakitandwe J, Till BJ. Induction, rapid fixation and retention of mutations in vegetatively propagated banana. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:1056-66. [PMID: 22928630 PMCID: PMC3533788 DOI: 10.1111/j.1467-7652.2012.00733.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/12/2012] [Accepted: 07/16/2012] [Indexed: 05/25/2023]
Abstract
Mutation discovery technologies have enabled the development of reverse genetics for many plant species and allowed sophisticated evaluation of the consequences of mutagenesis. Such methods are relatively straightforward for seed-propagated plants. To develop a platform suitable for vegetatively propagated species, we treated isolated banana shoot apical meristems with the chemical mutagen ethyl methanesulphonate, recovered plantlets and screened for induced mutations. A high density of GC-AT transition mutations were recovered, similar to that reported in seed-propagated polyploids. Through analysis of the inheritance of mutations, we observed that genotypically heterogeneous stem cells resulting from mutagenic treatment are rapidly sorted to fix a single genotype in the meristem. Further, mutant genotypes are stably inherited in subsequent generations. Evaluation of natural nucleotide variation showed the accumulation of potentially deleterious heterozygous alleles, suggesting that mutation induction may uncover recessive traits. This work therefore provides genotypic insights into the fate of totipotent cells after mutagenesis and suggests rapid approaches for mutation-based functional genomics and improvement of vegetatively propagated crops.
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Affiliation(s)
| | | | | | | | - Bradley J Till
- *Correspondence (Tel +43(1) 2600-28260; fax +43(1) 2600-28222; email )
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18
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High-throughput discovery of chloroplast and mitochondrial DNA polymorphisms in Brassicaceae species by ORG-EcoTILLING. PLoS One 2012. [PMID: 23185237 PMCID: PMC3504036 DOI: 10.1371/journal.pone.0047284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Information on polymorphic DNA in organelle genomes is essential for evolutionary and ecological studies. However, it is challenging to perform high-throughput investigations of chloroplast and mitochondrial DNA polymorphisms. In recent years, EcoTILLING stands out as one of the most universal, low-cost, and high-throughput reverse genetic methods, and the identification of natural genetic variants can provide much information about gene function, association mapping and linkage disequilibrium analysis and species evolution. Until now, no report exists on whether this method is applicable to organelle genomes and to what extent it can be used. Methodology/Principal Findings To address this problem, we adapted the CEL I-based heteroduplex cleavage strategy used in Targeting Induced Local Lesions in Genomes (TILLING) for the discovery of nucleotide polymorphisms in organelle genomes. To assess the applicability and accuracy of this technology, designated ORG-EcoTILLING, at different taxonomic levels, we sampled two sets of taxa representing accessions from the Brassicaceae with three chloroplast genes (accD, matK and rbcL) and one mitochondrial gene (atp6). The method successfully detected nine, six and one mutation sites in the accD, matK and rbcL genes, respectively, in 96 Brassica accessions. These mutations were confirmed by DNA sequencing, with 100% accuracy at both inter- and intraspecific levels. We also detected 44 putative mutations in accD in 91 accessions from 45 species and 29 genera of seven tribes. Compared with DNA sequencing results, the false negative rate was 36%. However, 17 SNPs detected in atp6 were completely identical to the sequencing results. Conclusions/Significance These results suggest that ORG-EcoTILLING is a powerful and cost-effective alternative method for high-throughput genome-wide assessment of inter- and intraspecific chloroplast and mitochondrial DNA polymorphisms. It will play an important role in evolutionary and ecological biology studies, in identification of related genes associated with agronomic importance such as high yield and improved cytoplasmic quality, and for identifying mitochondrial point mutations responsible for diseases in humans and other animals.
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19
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Abstract
Targeting induced local lesions in genomes (TILLING), initially a functional genomics tool in model plants, has been extended to many plant species and become of paramount importance to reverse genetics in crops species. Because it is readily applicable to most plants, it remains a dominant non-transgenic method for obtaining mutations in known genes. The process has seen many technological changes over the last 10 years; a major recent change has been the application of next-generation sequencing (NGS) to the process, which permits multiplexing of gene targets and genomes. NGS will ultimately lead to TILLING becoming an in silico procedure. We review here the history and technology in brief, but focus more importantly on recent developments in polyploids, vegetatively propagated crops and the future of TILLING for plant breeding.
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Affiliation(s)
- Trevor L Wang
- John Innes Centre, Norwich Research Park, Norwich, UK.
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20
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Xia Y, Ning Z, Bai G, Li R, Yan G, Siddique KHM, Baum M, Guo P. Allelic variations of a light harvesting chlorophyll a/b-binding protein gene (Lhcb1) associated with agronomic traits in barley. PLoS One 2012; 7:e37573. [PMID: 22662173 PMCID: PMC3360778 DOI: 10.1371/journal.pone.0037573] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 04/21/2012] [Indexed: 11/19/2022] Open
Abstract
Light-harvesting chlorophyll a/b-binding protein (LHCP) is one of the most abundant chloroplast proteins in plants. Its main function is to collect and transfer light energy to photosynthetic reaction centers. However, the roles of different LHCPs in light-harvesting antenna systems remain obscure. Exploration of nucleotide variation in the genes encoding LHCP can facilitate a better understanding of the functions of LHCP. In this study, nucleotide variations in Lhcb1, a LHCP gene in barley, were investigated across 292 barley accessions collected from 35 different countries using EcoTILLING technology, a variation of the Targeting Induced Local Lesions In Genomes (TILLING). A total of 23 nucleotide variations were detected including three insert/deletions (indels) and 20 single nucleotide polymorphisms (SNPs). Among them, 17 SNPs were in the coding region with nine missense changes. Two SNPs with missense changes are predicted to be deleterious to protein function. Seventeen SNP formed 31 distinguishable haplotypes in the barley collection. The levels of nucleotide diversity in the Lhcb1 locus differed markedly with geographic origins and species of accessions. The accessions from Middle East Asia exhibited the highest nucleotide and haplotype diversity. H. spontaneum showed greater nucleotide diversity than H. vulgare. Five SNPs in Lhcb1 were significantly associated with at least one of the six agronomic traits evaluated, namely plant height, spike length, number of grains per spike, thousand grain weight, flag leaf area and leaf color, and these SNPs may be used as potential markers for improvement of these barley traits.
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Affiliation(s)
- Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, China
| | - Zhengxiang Ning
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, China
| | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service, Manhattan, Kansas, United States of America
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Guijun Yan
- The Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Kadambot H. M. Siddique
- The Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas, Aleppo, Syria
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
- * E-mail:
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21
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Kurowska M, Daszkowska-Golec A, Gruszka D, Marzec M, Szurman M, Szarejko I, Maluszynski M. TILLING: a shortcut in functional genomics. J Appl Genet 2011; 52:371-90. [PMID: 21912935 PMCID: PMC3189332 DOI: 10.1007/s13353-011-0061-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 08/16/2011] [Accepted: 08/17/2011] [Indexed: 11/01/2022]
Abstract
Recent advances in large-scale genome sequencing projects have opened up new possibilities for the application of conventional mutation techniques in not only forward but also reverse genetics strategies. TILLING (Targeting Induced Local Lesions IN Genomes) was developed a decade ago as an alternative to insertional mutagenesis. It takes advantage of classical mutagenesis, sequence availability and high-throughput screening for nucleotide polymorphisms in a targeted sequence. The main advantage of TILLING as a reverse genetics strategy is that it can be applied to any species, regardless of its genome size and ploidy level. The TILLING protocol provides a high frequency of point mutations distributed randomly in the genome. The great mutagenic potential of chemical agents to generate a high rate of nucleotide substitutions has been proven by the high density of mutations reported for TILLING populations in various plant species. For most of them, the analysis of several genes revealed 1 mutation/200-500 kb screened and much higher densities were observed for polyploid species, such as wheat. High-throughput TILLING permits the rapid and low-cost discovery of new alleles that are induced in plants. Several research centres have established a TILLING public service for various plant species. The recent trends in TILLING procedures rely on the diversification of bioinformatic tools, new methods of mutation detection, including mismatch-specific and sensitive endonucleases, but also various alternatives for LI-COR screening and single nucleotide polymorphism (SNP) discovery using next-generation sequencing technologies. The TILLING strategy has found numerous applications in functional genomics. Additionally, wide applications of this throughput method in basic and applied research have already been implemented through modifications of the original TILLING strategy, such as Ecotilling or Deletion TILLING.
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Affiliation(s)
- Marzena Kurowska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Agata Daszkowska-Golec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Marek Marzec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Miriam Szurman
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Miroslaw Maluszynski
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
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Carpentier SC, Panis B, Renaut J, Samyn B, Vertommen A, Vanhove AC, Swennen R, Sergeant K. The use of 2D-electrophoresis and de novo sequencing to characterize inter- and intra-cultivar protein polymorphisms in an allopolyploid crop. PHYTOCHEMISTRY 2011; 72:1243-1250. [PMID: 21109271 DOI: 10.1016/j.phytochem.2010.10.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 09/27/2010] [Accepted: 10/26/2010] [Indexed: 05/30/2023]
Abstract
Polyploidy and allopolyploidy have played an important role in the evolution of many plants and crops. Several techniques exist to characterize allopolyploid varieties. Analyzing the consequences of genomic reorganization at the gDNA level is a prerequisite but a better insight into the consequences for the phenotype is also primordial. As such, protein polymorphism analysis is important in understanding plant and crop biodiversity and is a driving force behind crop improvement. Our strategy to analyze protein isoforms and to detect possible gene silencing or deletion in bananas was based on protein analysis. Bananas are a good representative of a complex allopolyploid and important crop. We combined two-dimensional electrophoresis (2DE) and 2D DIGE with de novo MS/MS sequence determination to characterize a range of triploid varieties. Via Principal Component Analysis (PCA) and hierarchical clustering we were able to blindly classify the different varieties according to their presumed genome constitution. We report for the first time the application of an automated approach for the derivatization of peptides for facilitated MS/MS de novo sequence determination. We conclude that the proteome does not always correspond to the presumed genome formulae and that proteomics is a powerful tool to characterize varieties. The observations at the protein level provide good indications for a more complex genome structure and genomic rearrangement in some banana varieties.
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