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Trinh MDL, Visintainer D, Günther J, Østerberg JT, da Fonseca RR, Fondevilla S, Moog MW, Luo G, Nørrevang AF, Crocoll C, Nielsen PV, Jacobsen S, Wendt T, Bak S, López‐Marqués RL, Palmgren M. Site-directed genotype screening for elimination of antinutritional saponins in quinoa seeds identifies TSARL1 as a master controller of saponin biosynthesis selectively in seeds. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2216-2234. [PMID: 38572508 PMCID: PMC11258981 DOI: 10.1111/pbi.14340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Climate change may result in a drier climate and increased salinization, threatening agricultural productivity worldwide. Quinoa (Chenopodium quinoa) produces highly nutritious seeds and tolerates abiotic stresses such as drought and high salinity, making it a promising future food source. However, the presence of antinutritional saponins in their seeds is an undesirable trait. We mapped genes controlling seed saponin content to a genomic region that includes TSARL1. We isolated desired genetic variation in this gene by producing a large mutant library of a commercial quinoa cultivar and screening the library for specific nucleotide substitutions using droplet digital PCR. We were able to rapidly isolate two independent tsarl1 mutants, which retained saponins in the leaves and roots for defence, but saponins were undetectable in the seed coat. We further could show that TSARL1 specifically controls seed saponin biosynthesis in the committed step after 2,3-oxidosqualene. Our work provides new important knowledge on the function of TSARL1 and represents a breakthrough for quinoa breeding.
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Affiliation(s)
- Mai Duy Luu Trinh
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Davide Visintainer
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Jan Günther
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | | | - Rute R. da Fonseca
- Section for BiodiversityGlobe Institute, University of CopenhagenKøbenhavn ØDenmark
| | | | - Max William Moog
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Guangbin Luo
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Anton F. Nørrevang
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Christoph Crocoll
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Philip V. Nielsen
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | | | | | - Søren Bak
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | | | - Michael Palmgren
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
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2
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Meiri M, Bar-Oz G. Unraveling the diversity and cultural heritage of fruit crops through paleogenomics. Trends Genet 2024; 40:398-409. [PMID: 38423916 PMCID: PMC11079635 DOI: 10.1016/j.tig.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.
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Affiliation(s)
- Meirav Meiri
- The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Guy Bar-Oz
- School of Archaeology and Maritime Cultures, University of Haifa, Haifa, 3498837 Mount Carmel, Israel
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3
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Zeibig F, Kilian B, Özkan H, Pantha S, Frei M. Grain quality traits within the wheat (Triticum spp.) genepool: prospects for improved nutrition through de novo domestication. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4400-4410. [PMID: 38318752 DOI: 10.1002/jsfa.13328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Wild relatives of wheat (Triticum spp.) harbor beneficial alleles for potential improvement and de novo domestication of selected genotypes with advantageous traits. We analyzed the nutrient composition in wild diploid and tetraploid wheats and their domesticated diploid, tetraploid and hexaploid relatives under field conditions in Germany and compared them with modern Triticum aestivum and Triticum durum cultivars. Grain iron (Fe) and zinc (Zn) concentrations, phytate:mineral molar ratios, grain protein content (GPC) and antioxidant activity were analyzed across 125 genotypes. RESULTS Grain Fe and Zn concentrations in wild wheats were 72 mg kg-1 and 59 mg kg-1, respectively, with improved bioavailability indicated by Phytate:Fe and Phytate:Zn molar ratios (11.7 and 16.9, respectively) and GPC (231 g kg-1). By comparison, grain Fe and Zn concentrations in landrace taxa were 54 mg kg-1 and 55 mg kg-1, respectively, with lower Phytate:Fe and Phytate:Zn molar ratios (15.1 and 17.5, respectively) and GPC (178 g kg-1). Average grain Fe accumulation in Triticum araraticum was 73 mg kg-1, reaching 116 mg kg-1, with high Fe bioavailability (Phyt:Fe: 11.7; minimum: 7.2). Wild wheats, landraces and modern cultivars showed no differences in antioxidant activity. Triticum zhukovskyi stood out with high grain micronutrient concentrations and favorable molar ratios. It was also the only taxon with elevated antioxidant activity. CONCLUSION Our results indicate alteration of grain quality during domestication. T. araraticum has promising genotypes with advantageous grain quality characteristics that could be selected for de novo domestication. Favorable nutritional traits in the GGAA wheat lineage (T. araraticum and T. zhukovskyi) hold promise for improving grain quality traits. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Frederike Zeibig
- Department of Agronomy and Crop Physiology, Institute of Agronomy and Plant Breeding I, Justus-Liebig-University, Giessen, Germany
| | | | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Sumitra Pantha
- Department of Agronomy and Crop Physiology, Institute of Agronomy and Plant Breeding I, Justus-Liebig-University, Giessen, Germany
| | - Michael Frei
- Department of Agronomy and Crop Physiology, Institute of Agronomy and Plant Breeding I, Justus-Liebig-University, Giessen, Germany
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4
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Correia PMP, Najafi J, Palmgren M. De novo domestication: what about the weeds? TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00057-8. [PMID: 38637173 DOI: 10.1016/j.tplants.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/06/2024] [Accepted: 03/01/2024] [Indexed: 04/20/2024]
Abstract
Most high-yielding crops are susceptible to abiotic and biotic stresses, making them particularly vulnerable to the potential effects of climate change. A possible alternative is to accelerate the domestication of wild plants that are already tolerant to harsh conditions and to increase their yields by methods such as gene editing. We foresee that crops' wild progenitors could potentially compete with the resulting de novo domesticated plants, reducing yields. To improve the recognition of weeds, we propose using gene editing techniques to introduce traits into de novo domesticated crops that will allow for visual recognition of the crops by weeding robots that have been trained by machine learning.
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Affiliation(s)
- Pedro M P Correia
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Javad Najafi
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Michael Palmgren
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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5
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Rogo U, Simoni S, Fambrini M, Giordani T, Pugliesi C, Mascagni F. Future-Proofing Agriculture: De Novo Domestication for Sustainable and Resilient Crops. Int J Mol Sci 2024; 25:2374. [PMID: 38397047 PMCID: PMC10888583 DOI: 10.3390/ijms25042374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
The worldwide agricultural system confronts a significant challenge represented by the increasing demand for food in the face of a growing global population. This challenge is exacerbated by a reduction in cultivable land and the adverse effects of climate change on crop yield quantity and quality. Breeders actively embrace cutting-edge omics technologies to pursue resilient genotypes in response to these pressing issues. In this global context, new breeding techniques (NBTs) are emerging as the future of agriculture, offering a solution to introduce resilient crops that can ensure food security, particularly against challenging climate events. Indeed, the search for domestication genes as well as the genetic modification of these loci in wild species using genome editing tools are crucial steps in carrying out de novo domestication of wild plants without compromising their genetic background. Current knowledge allows us to take different paths from those taken by early Neolithic farmers, where crop domestication has opposed natural selection. In this process traits and alleles negatively correlated with high resource environment performance are probably eradicated through artificial selection, while others may have been lost randomly due to domestication and genetic bottlenecks. Thus, domestication led to highly productive plants with little genetic diversity, owing to the loss of valuable alleles that had evolved to tolerate biotic and abiotic stresses. Recent technological advances have increased the feasibility of de novo domestication of wild plants as a promising approach for crafting optimal crops while ensuring food security and using a more sustainable, low-input agriculture. Here, we explore what crucial domestication genes are, coupled with the advancement of technologies enabling the precise manipulation of target sequences, pointing out de novo domestication as a promising application for future crop development.
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Affiliation(s)
| | | | | | | | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124 Pisa, Italy; (U.R.); (S.S.); (M.F.); (T.G.); (F.M.)
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6
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Gepts P. Biocultural diversity and crop improvement. Emerg Top Life Sci 2023; 7:ETLS20230067. [PMID: 38084755 PMCID: PMC10754339 DOI: 10.1042/etls20230067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earth's resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.
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Affiliation(s)
- Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95616-8780, U.S.A
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7
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Li T, Tang S, Li W, Zhang S, Wang J, Pan D, Lin Z, Ma X, Chang Y, Liu B, Sun J, Wang X, Zhao M, You C, Luo H, Wang M, Ye X, Zhai J, Shen Z, Du H, Song X, Huang G, Cao X. Genome evolution and initial breeding of the Triticeae grass Leymus chinensis dominating the Eurasian Steppe. Proc Natl Acad Sci U S A 2023; 120:e2308984120. [PMID: 37874858 PMCID: PMC10623014 DOI: 10.1073/pnas.2308984120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/19/2023] [Indexed: 10/26/2023] Open
Abstract
Leymus chinensis, a dominant perennial grass in the Eurasian Steppe, is well known for its remarkable adaptability and forage quality. Hardly any breeding has been done on the grass, limiting its potential in ecological restoration and forage productivity. To enable genetic improvement of the untapped, important species, we obtained a 7.85-Gb high-quality genome of L. chinensis with a particularly long contig N50 (318.49 Mb). Its allotetraploid genome is estimated to originate 5.29 million years ago (MYA) from a cross between the Ns-subgenome relating to Psathyrostachys and the unknown Xm-subgenome. Multiple bursts of transposons during 0.433-1.842 MYA after genome allopolyploidization, which involved predominantly the Tekay and Angela of LTR retrotransposons, contributed to its genome expansion and complexity. With the genome resource available, we successfully developed a genetic transformation system as well as the gene-editing pipeline in L. chinensis. We knocked out the monocot-specific miR528 using CRISPR/Cas9, resulting in the improvement of yield-related traits with increases in the tiller number and growth rate. Our research provides valuable genomic resources for Triticeae evolutionary studies and presents a conceptual framework illustrating the utilization of genomic information and genome editing to accelerate the improvement of wild L. chinensis with features such as polyploidization and self-incompatibility.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Shanjie Tang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding071000, China
| | - Shuaibin Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Jianli Wang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin150086, China
| | - Duofeng Pan
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin150086, China
| | - Zhelong Lin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Xuan Ma
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin300387, China
| | - Yanan Chang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Bo Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Xiaofei Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Mengjie Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Changqing You
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Haofei Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Meijia Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Zhongbao Shen
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin150086, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding071000, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
- Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Gai Huang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing100101, China
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8
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Nikalje GC, Rajput VD, Ntatsi G. Editorial: Putting wild vegetables to work for sustainable agriculture and food security. FRONTIERS IN PLANT SCIENCE 2023; 14:1268231. [PMID: 37841612 PMCID: PMC10569295 DOI: 10.3389/fpls.2023.1268231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Affiliation(s)
- Ganesh Chandrakant Nikalje
- Department of Botany, Seva Sadan’s R. K. Talreja College of Arts, Science and Commerce, University of Mumbai, Ulhasnagar, India
| | - Vishnu D. Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
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9
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Zhang J, Yu H, Li J. De novo domestication: retrace the history of agriculture to design future crops. Curr Opin Biotechnol 2023; 81:102946. [PMID: 37080109 DOI: 10.1016/j.copbio.2023.102946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Certain crops were domesticated from their wild progenitors and have served as the major staple food since then, but now suffered from the limited genetic diversity in breeding. Enormous wild species possess unique advantages such as stress tolerance, polyploidy, perennial habit, and natural nutrition. However, it remains a big challenge to utilize wild species in conventional breeding. With recent advances in biotechnologies, one new breeding strategy, de novo domestication, has emerged and been demonstrated by pioneer work. Here, we review the emergence and milestone progress of de novo domestication and discuss how wild relatives could be exploited into new types of crops. With the understanding of the genetic basis of crop domestication and the development of biotechnologies, various elite wild germplasms will be designed and practiced to fulfill particular breeding goals and create new types of crops. De novo domestication is paving a new way for breeding the future.
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Affiliation(s)
- Jingkun Zhang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, China; Hainan Yazhou Bay Seed Laboratory, China.
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10
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Tong S, Ashikari M, Nagai K, Pedersen O. Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication? RICE (NEW YORK, N.Y.) 2023; 16:13. [PMID: 36928797 PMCID: PMC10020418 DOI: 10.1186/s12284-023-00630-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
As climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.
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Affiliation(s)
- Shuai Tong
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan.
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark.
- School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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11
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Jackson D, Buell CR. Crop Domestication: Past, Present and Future. PLANT & CELL PHYSIOLOGY 2022; 63:1527-1528. [PMID: 36264208 DOI: 10.1093/pcp/pcac152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/08/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Affiliation(s)
- David Jackson
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - C Robin Buell
- Department of Crop and Soil Sciences, Institute for Plant Breeding, Genetics and Genomics, Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd, Athens, GA 30602, USA
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12
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Knudsen S, Wendt T, Dockter C, Thomsen HC, Rasmussen M, Egevang Jørgensen M, Lu Q, Voss C, Murozuka E, Østerberg JT, Harholt J, Braumann I, Cuesta-Seijo JA, Kale SM, Bodevin S, Tang Petersen L, Carciofi M, Pedas PR, Opstrup Husum J, Nielsen MTS, Nielsen K, Jensen MK, Møller LA, Gojkovic Z, Striebeck A, Lengeler K, Fennessy RT, Katz M, Garcia Sanchez R, Solodovnikova N, Förster J, Olsen O, Møller BL, Fincher GB, Skadhauge B. FIND-IT: Accelerated trait development for a green evolution. SCIENCE ADVANCES 2022; 8:eabq2266. [PMID: 36001660 PMCID: PMC9401622 DOI: 10.1126/sciadv.abq2266] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Improved agricultural and industrial production organisms are required to meet the future global food demands and minimize the effects of climate change. A new resource for crop and microbe improvement, designated FIND-IT (Fast Identification of Nucleotide variants by droplet DigITal PCR), provides ultrafast identification and isolation of predetermined, targeted genetic variants in a screening cycle of less than 10 days. Using large-scale sample pooling in combination with droplet digital PCR (ddPCR) greatly increases the size of low-mutation density and screenable variant libraries and the probability of identifying the variant of interest. The method is validated by screening variant libraries totaling 500,000 barley (Hordeum vulgare) individuals and isolating more than 125 targeted barley gene knockout lines and miRNA or promoter variants enabling functional gene analysis. FIND-IT variants are directly applicable to elite breeding pipelines and minimize time-consuming technical steps to accelerate the evolution of germplasm.
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Affiliation(s)
- Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Magnus Rasmussen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Qiongxian Lu
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Cynthia Voss
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Emiko Murozuka
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Jesper Harholt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ilka Braumann
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Jose A. Cuesta-Seijo
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sandip M. Kale
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sabrina Bodevin
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Lise Tang Petersen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Jeppe Opstrup Husum
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Kasper Nielsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Mikkel K. Jensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Lillian Ambus Møller
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Zoran Gojkovic
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Alexander Striebeck
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Klaus Lengeler
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ross T. Fennessy
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Michael Katz
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Rosa Garcia Sanchez
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Jochen Förster
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ole Olsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Centre for Synthetic Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Geoffrey B. Fincher
- Australian Research Council Centre of Excellence in Plant Cell Walls School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
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