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Song J, Tang L, Fan H, Xu X, Peng X, Cui Y, Wang J. Enhancing Yield and Improving Grain Quality in Japonica Rice: Targeted EHD1 Editing via CRISPR-Cas9 in Low-Latitude Adaptation. Curr Issues Mol Biol 2024; 46:3741-3751. [PMID: 38666963 PMCID: PMC11049033 DOI: 10.3390/cimb46040233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
The "Indica to Japonica" initiative in China focuses on adapting Japonica rice varieties from the northeast to the unique photoperiod and temperature conditions of lower latitudes. While breeders can select varieties for their adaptability, the sensitivity to light and temperature often complicates and prolongs the process. Addressing the challenge of cultivating high-yield, superior-quality Japonica rice over expanded latitudinal ranges swiftly, in the face of these sensitivities, is critical. Our approach harnesses the CRISPR-Cas9 technology to edit the EHD1 gene in the premium northeastern Japonica cultivars Jiyuanxiang 1 and Yinongxiang 12, which are distinguished by their exceptional grain quality-increased head rice rates, gel consistency, and reduced chalkiness and amylose content. Field trials showed that these new ehd1 mutants not only surpass the wild types in yield when grown at low latitudes but also retain the desirable traits of their progenitors. Additionally, we found that disabling Ehd1 boosts the activity of Hd3a and RFT1, postponing flowering by approximately one month in the ehd1 mutants. This research presents a viable strategy for the accelerated breeding of elite northeastern Japonica rice by integrating genomic insights with gene-editing techniques suitable for low-latitude cultivation.
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Affiliation(s)
- Jian Song
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.S.); (L.T.); (H.F.); (Y.C.)
| | - Liqun Tang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.S.); (L.T.); (H.F.); (Y.C.)
| | - Honghuan Fan
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.S.); (L.T.); (H.F.); (Y.C.)
| | - Xiaozheng Xu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou 311300, China; (X.X.); (X.P.)
| | - Xinlu Peng
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou 311300, China; (X.X.); (X.P.)
| | - Yongtao Cui
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.S.); (L.T.); (H.F.); (Y.C.)
| | - Jianjun Wang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.S.); (L.T.); (H.F.); (Y.C.)
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Guha PK, Magar ND, Kommana M, Barbadikar KM, Suneel B, Gokulan C, Lakshmi DV, Patel HK, Sonti RV, Sundaram RM, Madhav MS. Strong culm: a crucial trait for developing next-generation climate-resilient rice lines. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:665-686. [PMID: 38737321 PMCID: PMC11087419 DOI: 10.1007/s12298-024-01445-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024]
Abstract
Lodging, a phenomenon characterized by the bending or breaking of rice plants, poses substantial constraints on productivity, particularly during the harvesting phase in regions susceptible to strong winds. The rice strong culm trait is influenced by the intricate interplay of genetic, physiological, epigenetic, and environmental factors. Stem architecture, encompassing morphological and anatomical attributes, alongside the composition of both structural and non-structural carbohydrates, emerges as a critical determinant of lodging resistance. The adaptive response of the rice culm to various biotic and abiotic environmental factors further modulates the propensity for lodging. Advancements in next-generation sequencing technologies have expedited the genetic dissection of lodging resistance, enabling the identification of pertinent genes, quantitative trait loci, and novel alleles. Concurrently, contemporary breeding strategies, ranging from biparental approaches to more sophisticated methods such as multi-parent-based breeding, gene pyramiding, genomic selection, genome-wide association studies, and haplotype-based breeding, offer perspectives on the genetic underpinnings of culm strength. This review comprehensively delves into physiological attributes, culm histology, epigenetic determinants, and gene expression profiles associated with lodging resistance, with a specialized focus on leveraging next-generation sequencing for candidate gene discovery.
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Affiliation(s)
- Pritam Kanti Guha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Microbiology, Yogi Vemana University., Y.S.R Kadapa, India
| | - Nakul D. Magar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Madhavilatha Kommana
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Kalyani M. Barbadikar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - B. Suneel
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C. Gokulan
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - D. Vijay Lakshmi
- Department of Microbiology, Yogi Vemana University., Y.S.R Kadapa, India
| | - Hitendra Kumar Patel
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - Ramesh V. Sonti
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - R. M. Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Maganti Sheshu Madhav
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- ICAR-Central Tobacco Research Institute, Rajahmundry, India
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Ahmar S, Hensel G, Gruszka D. CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives. Biotechnol Adv 2023; 69:108248. [PMID: 37666372 DOI: 10.1016/j.biotechadv.2023.108248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany; Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland.
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Chen YH, Lu J, Yang X, Huang LC, Zhang CQ, Liu QQ, Li QF. Gene editing of non-coding regulatory DNA and its application in crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6158-6175. [PMID: 37549968 DOI: 10.1093/jxb/erad313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
The development of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has provided precise and efficient strategies to edit target genes and generate transgene-free crops. Significant progress has been made in the editing of protein-coding genes; however, studies on the editing of non-coding DNA with regulatory roles lags far behind. Non-coding regulatory DNAs, including those which can be transcribed into long non-coding RNAs (lncRNAs), and miRNAs, together with cis-regulatory elements (CREs), play crucial roles in regulating plant growth and development. Therefore, the combination of CRISPR/Cas technology and non-coding regulatory DNA has great potential to generate novel alleles that affect various agronomic traits of crops, thus providing valuable genetic resources for crop breeding. Herein, we review recent advances in the roles of non-coding regulatory DNA, attempts to edit non-coding regulatory DNA for crop improvement, and potential application of novel editing tools in modulating non-coding regulatory DNA. Finally, the existing problems, possible solutions, and future applications of gene editing of non-coding regulatory DNA in modern crop breeding practice are also discussed.
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Affiliation(s)
- Yu-Hao Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Jun Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Xia Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Li-Chun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qian-Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, Jiangsu, China
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Yoon DK, Choi I, Won YJ, Shin Y, Cheon KS, Oh H, Lee C, Lee S, Cho MH, Jun S, Kim Y, Kim SL, Baek J, Jeong H, Lyu JI, Lee GS, Kim KH, Ji H. QTL Mapping of Tiller Number in Korean Japonica Rice Varieties. Genes (Basel) 2023; 14:1593. [PMID: 37628644 PMCID: PMC10454613 DOI: 10.3390/genes14081593] [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: 07/04/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Tiller number is an important trait associated with yield in rice. Tiller number in Korean japonica rice was analyzed under greenhouse conditions in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae and Unbong40 to identify quantitative trait loci (QTLs). A genetic map comprising 239 kompetitive allele-specific PCR (KASP) and 57 cleaved amplified polymorphic sequence markers was constructed. qTN3, a major QTL for tiller number, was identified at 132.4 cm on chromosome 3. This QTL was also detected under field conditions in a backcross population; thus, qTN3 was stable across generations and environments. qTN3 co-located with QTLs associated with panicle number per plant and culm diameter, indicating it had pleiotropic effects. The qTN3 regions of Odae and Unbong40 differed in a known functional variant (4 bp TGTG insertion/deletion) in the 5' UTR of OsTB1, a gene underlying variation in tiller number and culm strength. Investigation of variation in genotype and tiller number revealed that varieties with the insertion genotype had lower tiller numbers than those with the reference genotype. A high-resolution melting marker was developed to enable efficient marker-assisted selection. The QTL qTN3 will therefore be useful in breeding programs developing japonica varieties with optimal tiller numbers for increased yield.
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Affiliation(s)
- Dong-Kyung Yoon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Inchan Choi
- Department of Agricultural Engineering, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54875, Republic of Korea;
| | - Yong Jae Won
- Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Republic of Korea;
| | - Yunji Shin
- Genecell Biotech Inc., Wanju 55322, Republic of Korea;
| | - Kyeong-Seong Cheon
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea;
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Chaewon Lee
- Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration (RDA), Suwon 16429, Republic of Korea;
| | - Seoyeon Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Mi Hyun Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Soojin Jun
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Yeongtae Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Song Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - HwangWeon Jeong
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Jae Il Lyu
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
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Ishizaki T, Ueda Y, Takai T, Maruyama K, Tsujimoto Y. In-frame mutation in rice TEOSINTE BRANCHED1 (OsTB1) improves productivity under phosphorus deficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111627. [PMID: 36737003 DOI: 10.1016/j.plantsci.2023.111627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/04/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Tillering is an important trait in rice productivity. We introduced mutations into the coding region of rice TEOSINTE BRANCHED1 (OsTB1), which is a negative regulator of tillering, using CRISPR/Cas9. The frameshift mutants exhibited substantially enhanced tillering and produced 3.5 times more panicles than the non-mutated plants at maturity. This enhanced tillering resulted in increased spikelet number; however, grain yields did not increase due to substantially reduced filled grain rate and 1,000-grain weight. In contrast, in-frame mutations in OsTB1 had the effect of slightly increasing tiller numbers, and the in-frame mutants had 40% more panicles than non-mutated plants. The grain yield of in-frame mutants also did not increase on nutrient-rich soil; however, under phosphorus-deficient conditions, where tillering is constrained, the in-frame mutants gave a significantly higher grain yield than non-mutated plants due to higher spikelet number and maintained filled grain rate. Rice grassy tiller1 (OsGT1)/OsHox12, which is directly regulated by OsTB1 to suppress tillering, was moderately down-regulated in in-frame mutants, suggesting that OsTB1 with the in-frame mutation shows partial function of intact OsTB1 in regulating OsGT1/OsHox12. We propose that mildly enhanced tillering by in-frame mutation of OsTB1 can improve grain yield under low phosphorus conditions.
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Affiliation(s)
- Takuma Ishizaki
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences (JIRCAS), Ishigaki, Okinawa 907-0002, Japan.
| | - Yoshiaki Ueda
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
| | - Toshiyuki Takai
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
| | - Kyonoshin Maruyama
- Biological Resources and Post-harvest Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
| | - Yasuhiro Tsujimoto
- Crop, Livestock and Environment Division, JIRCAS, Tsukuba, Ibaraki 305-8686, Japan.
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Ferreira SS, Reis RS. Using CRISPR/Cas to enhance gene expression for crop trait improvement by editing miRNA targets. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2208-2212. [PMID: 36626564 PMCID: PMC10082926 DOI: 10.1093/jxb/erad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/04/2023] [Indexed: 06/06/2023]
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Beretta VM, Franchini E, Ud Din I, Lacchini E, Van den Broeck L, Sozzani R, Orozco-Arroyo G, Caporali E, Adam H, Jouannic S, Gregis V, Kater MM. The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37009647 DOI: 10.1111/tpj.16229] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
The architecture of the rice inflorescence is an important determinant of crop yield. The length of the inflorescence and the number of branches are among the key factors determining the number of spikelets, and thus grains, that a plant will develop. In particular, the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem governs the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in Oryza sativa (rice). Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq, we observed that two ALOG genes, OsG1-like 1 (OsG1L1) and OsG1L2, have expression profiles similar to that of TAW1. Here, we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes to the phenotype of the previously published taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the data sets were used for the construction of a gene regulatory network (GRN), proposing interactions among genes potentially involved in controlling inflorescence development in rice. In this GRN, we selected the homeodomain-leucine zipper transcription factor encoding the gene OsHOX14 for further characterization. The spatiotemporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new proteins involved in rice inflorescence development.
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Affiliation(s)
- Veronica M Beretta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Emanuela Franchini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Israr Ud Din
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Elia Lacchini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Lisa Van den Broeck
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gregorio Orozco-Arroyo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Elisabetta Caporali
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Martin M Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
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Zhou J, Liu G, Zhao Y, Zhang R, Tang X, Li L, Jia X, Guo Y, Wu Y, Han Y, Bao Y, He Y, Han Q, Yang H, Zheng X, Qi Y, Zhang T, Zhang Y. An efficient CRISPR-Cas12a promoter editing system for crop improvement. NATURE PLANTS 2023; 9:588-604. [PMID: 37024659 DOI: 10.1038/s41477-023-01384-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Promoter editing represents an innovative approach to introduce quantitative trait variation (QTV) in crops. However, an efficient promoter editing system for QTV needs to be established. Here we develop a CRISPR-Cas12a promoter editing (CAPE) system that combines a promoter key-region estimating model and an efficient CRISPR-Cas12a-based multiplexed or singular editing system. CAPE is benchmarked in rice to produce QTV continuums for grain starch content and size by targeting OsGBSS1 and OsGS3, respectively. We then apply CAPE for promoter editing of OsD18, a gene encoding GA3ox in the gibberellin biosynthesis pathway. The resulting lines carry a QTV continuum of semidwarfism without significantly compromising grain measures. Field trials demonstrated that the OsD18 promoter editing lines have the same yield performance and antilodging phenotype as the Green Revolution OsSD1 mutants in different genetic backgrounds. Hence, promoter editing of OsD18 generates a quantitative Green Revolution trait. Together, we demonstrate a CAPE-based promoter editing and tuning pipeline for efficient production of useful QTV continuum in crops.
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Affiliation(s)
- Jianping Zhou
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yuxin Zhao
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Rui Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xu Tang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ling Li
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xinyu Jia
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yachong Guo
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yao He
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qinqin Han
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Han Yang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Rockville, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China.
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China.
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10
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Hashimoto S, Okada S, Araki-Nakamura S, Ohmae-Shinohara K, Miura K, Kawaguchi H, Ogino C, Kasuga S, Sazuka T. An analysis of sugary endosperm in sorghum: Characterization of mutant phenotypes depending on alleles of the corresponding starch debranching enzyme. FRONTIERS IN PLANT SCIENCE 2023; 14:1114935. [PMID: 36860899 PMCID: PMC9969085 DOI: 10.3389/fpls.2023.1114935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Sorghum is the fifth most important cereal crop. Here we performed molecular genetic analyses of the 'SUGARY FETERITA' (SUF) variety, which shows typical sugary endosperm traits (e.g., wrinkled seeds, accumulation of soluble sugars, and distorted starch). Positional mapping indicated that the corresponding gene was located on the long arm of chromosome 7. Within the candidate region of 3.4 Mb, a sorghum ortholog for maize Su1 (SbSu) encoding a starch debranching enzyme ISA1 was found. Sequencing analysis of SbSu in SUF uncovered nonsynonymous single nucleotide polymorphisms (SNPs) in the coding region, containing substitutions of highly conserved amino acids. Complementation of the rice sugary-1 (osisa1) mutant line with the SbSu gene recovered the sugary endosperm phenotype. Additionally, analyzing mutants obtained from an EMS-induced mutant panel revealed novel alleles with phenotypes showing less severe wrinkles and higher Brix scores. These results suggested that SbSu was the corresponding gene for the sugary endosperm. Expression profiles of starch synthesis genes during the grain-filling stage demonstrated that a loss-of-function of SbSu affects the expression of most starch synthesis genes and revealed the fine-tuned gene regulation in the starch synthetic pathway in sorghum. Haplotype analysis using 187 diverse accessions from a sorghum panel revealed the haplotype of SUF showing severe phenotype had not been used among the landraces and modern varieties. Thus, weak alleles (showing sweet and less severe wrinkles), such as in the abovementioned EMS-induced mutants, are more valuable for grain sorghum breeding. Our study suggests that more moderate alleles (e.g. produced by genome editing) should be beneficial for improving grain sorghum.
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Affiliation(s)
- Shumpei Hashimoto
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Satoshi Okada
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | | | | | - Kotaro Miura
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, Fukui, Japan
| | - Hideo Kawaguchi
- Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Shigemitsu Kasuga
- Faculty of Agriculture, Education and Research Center of Alpine Field Science, Shinshu University, Minamiminowa, Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
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11
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Ma B, Zhang L, He Z. Understanding the regulation of cereal grain filling: The way forward. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:526-547. [PMID: 36648157 DOI: 10.1111/jipb.13456] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
During grain filling, starch and other nutrients accumulate in the endosperm; this directly determines grain yield and grain quality in crops such as rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum). Grain filling is a complex trait affected by both intrinsic and environmental factors, making it difficult to explore the underlying genetics, molecular regulation, and the application of these genes for breeding. With the development of powerful genetic and molecular techniques, much has been learned about the genes and molecular networks related to grain filling over the past decades. In this review, we highlight the key factors affecting grain filling, including both biological and abiotic factors. We then summarize the key genes controlling grain filling and their roles in this event, including regulators of sugar translocation and starch biosynthesis, phytohormone-related regulators, and other factors. Finally, we discuss how the current knowledge of valuable grain filling genes could be integrated with strategies for breeding cereal varieties with improved grain yield and quality.
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Affiliation(s)
- Bin Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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12
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Yang X, Lai Y, Wang L, Zhao M, Wang J, Li M, Chi L, Lv G, Liu Y, Cui Z, Li R, Wu L, Sun B, Zhang X, Jiang S. Isolation of a Novel QTL, qSCM4, Associated with Strong Culm Affects Lodging Resistance and Panicle Branch Number in Rice. Int J Mol Sci 2023; 24:ijms24010812. [PMID: 36614255 PMCID: PMC9821088 DOI: 10.3390/ijms24010812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Rice breeders are now developing new varieties with semi-high or even high plant height to further increase the grain yield, and the problem of lodging has re-appeared. We identified a major quantitative trait locus (QTL), qSCM4, for resistance to lodging by using an F2 segregant population and a recombinant self-incompatible line population from the cross between Shennong265 (SN265) and Lijiangxintuanheigu (LTH) after multiple years and multiple environments. Then, the residual heterozygous derived segregant population which consisted of 1781 individual plants, and the BC3F2 segregant population which consisted of 3216 individual plants, were used to shorten the physical interval of qSCM4 to 58.5 kb including 11 genes. DNA sequencing revealed the most likely candidate gene for qSCM4 was Os04g0615000, which encoded a functional protein with structural domains of serine and cysteine. There were 13 DNA sequence changes in LTH compared to SN265 in this gene, including a fragment deletion, two base changes in the 3' UTR region, six base changes in the exons, and four base changes in the introns. A near-isogenic line carrying qSCM4 showed that it improved the lodging resistance through increasing stem thickness by 25.3% and increasing stem folding resistance by 20.3%. Furthermore, it was also discovered that qSCM4 enhanced the primary branch per panicle by 16.7%, secondary branch by per panicle 9.9%, and grain number per panicle by 14.7%. All the above results will give us a valuable genetic resource for concurrently boosting culm strength and lodging resistance, and they will also provide a basis for further research on the lodging resistance mechanism of rice.
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Affiliation(s)
- Xianli Yang
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
| | - Yongcai Lai
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
| | - Lizhi Wang
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
| | - Minghui Zhao
- Rice Research Institute, Shenyang Agricultural University, Collaborative Innovation Center Co-Sponsored by Liaoning Provincial Government and Ministry of Education for Northeast Japonica Rice Genetic Improvement and High Efficiency Production, Shenyang 110161, China; (M.Z.); (J.W.); (Z.C.)
| | - Jiayu Wang
- Rice Research Institute, Shenyang Agricultural University, Collaborative Innovation Center Co-Sponsored by Liaoning Provincial Government and Ministry of Education for Northeast Japonica Rice Genetic Improvement and High Efficiency Production, Shenyang 110161, China; (M.Z.); (J.W.); (Z.C.)
| | - Mingxian Li
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
| | - Liyong Chi
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
| | - Guoyi Lv
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
| | - Youhong Liu
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
| | - Zhibo Cui
- Rice Research Institute, Shenyang Agricultural University, Collaborative Innovation Center Co-Sponsored by Liaoning Provincial Government and Ministry of Education for Northeast Japonica Rice Genetic Improvement and High Efficiency Production, Shenyang 110161, China; (M.Z.); (J.W.); (Z.C.)
| | - Rui Li
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
| | - Liren Wu
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
| | - Bing Sun
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
| | - Xijuan Zhang
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
- Correspondence: (X.Z.); (S.J.)
| | - Shukun Jiang
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
- Qiqihar Branch, Heilongjiang Academy of Agricultural Sciences, Qiqihar 161006, China
- Correspondence: (X.Z.); (S.J.)
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13
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Bretani G, Shaaf S, Tondelli A, Cattivelli L, Delbono S, Waugh R, Thomas W, Russell J, Bull H, Igartua E, Casas AM, Gracia P, Rossi R, Schulman AH, Rossini L. Multi-environment genome -wide association mapping of culm morphology traits in barley. FRONTIERS IN PLANT SCIENCE 2022; 13:926277. [PMID: 36212331 PMCID: PMC9539552 DOI: 10.3389/fpls.2022.926277] [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: 04/22/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
In cereals with hollow internodes, lodging resistance is influenced by morphological characteristics such as internode diameter and culm wall thickness. Despite their relevance, knowledge of the genetic control of these traits and their relationship with lodging is lacking in temperate cereals such as barley. To fill this gap, we developed an image analysis-based protocol to accurately phenotype culm diameters and culm wall thickness across 261 barley accessions. Analysis of culm trait data collected from field trials in seven different environments revealed high heritability values (>50%) for most traits except thickness and stiffness, as well as genotype-by-environment interactions. The collection was structured mainly according to row-type, which had a confounding effect on culm traits as evidenced by phenotypic correlations. Within both row-type subsets, outer diameter and section modulus showed significant negative correlations with lodging (<-0.52 and <-0.45, respectively), but no correlation with plant height, indicating the possibility of improving lodging resistance independent of plant height. Using 50k iSelect SNP genotyping data, we conducted multi-environment genome-wide association studies using mixed model approach across the whole panel and row-type subsets: we identified a total of 192 quantitative trait loci (QTLs) for the studied traits, including subpopulation-specific QTLs and 21 main effect loci for culm diameter and/or section modulus showing effects on lodging without impacting plant height. Providing insights into the genetic architecture of culm morphology in barley and the possible role of candidate genes involved in hormone and cell wall-related pathways, this work supports the potential of loci underpinning culm features to improve lodging resistance and increase barley yield stability under changing environments.
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Affiliation(s)
- Gianluca Bretani
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Salar Shaaf
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Stefano Delbono
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - William Thomas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Hazel Bull
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ernesto Igartua
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Ana M. Casas
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Pilar Gracia
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Roberta Rossi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Alan H. Schulman
- Viikki Plant Sciences Centre, Natural Resources Institue (LUKE), HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
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14
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Ookawa T, Nomura T, Kamahora E, Jiang M, Ochiai Y, Samadi AF, Yamaguchi T, Adachi S, Katsura K, Motobayashi T. Pyramiding of multiple strong-culm genes originating from indica and tropical japonica to the temperate japonica rice. Sci Rep 2022; 12:15400. [PMID: 36100633 PMCID: PMC9470567 DOI: 10.1038/s41598-022-19768-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Severe lodging has recurrently occurred at strong typhoon’s hitting in recent climate change. The identification of quantitative trait loci and their responsible genes associated with a strong culm and their pyramiding are important for developing high-yielding varieties with a superior lodging resistance. To evaluate the effects of four strong-culm genes on lodging resistance, the temperate japonica near isogenic line (NIL) with the introgressed SCM1 or SCM2 locus of the indica variety, Habataki and the other NIL with the introgeressed SCM3 or SCM4 locus of the tropical japonica variety, Chugoku 117 were developed. Then, we developed the pyramiding lines with double,triple and quadruple combinations derived from step-by-step crosses among NIL-SCM1–NIL-SCM4. Quadruple pyramiding line (NIL-SCM1 + 2 + 3 + 4) showed the largest culm diameter and the highest culm strength among the combinations and increased spikelet number due to the pleiotropic effects of these genes. Pyramiding of strong culm genes resulted in much increased culm thickness, culm strength and spikelet number due to their additive effect. SCM1 mainly contributed to enhance their pyramiding effect. These results in this study suggest the importance of identifying the combinations of superior alleles of strong culm genes among natural variation and pyramiding these genes for improving high-yielding varieties with a superior lodging resistance.
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Affiliation(s)
- Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
| | - Tomohiro Nomura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Eri Kamahora
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Mingjin Jiang
- Rice Research Institute of Guizhou Academy of Agricultural Science, Guiyang, 550006, Guizhou, China
| | - Yusuke Ochiai
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Ahmad Fahim Samadi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Takuya Yamaguchi
- Toyama Prefectural Tonami Agriculture and Forestry Promotion Center, 1-7 Saiwai-cho, Tonami, Toyama, 939-1386, Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Keisuke Katsura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Takashi Motobayashi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
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15
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Kouhen M, García-Caparrós P, Twyman RM, Abdelly C, Mahmoudi H, Schillberg S, Debez A. Improving environmental stress resilience in crops by genome editing: insights from extremophile plants. Crit Rev Biotechnol 2022; 43:559-574. [PMID: 35606905 DOI: 10.1080/07388551.2022.2042481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In basic and applied sciences, genome editing has become an indispensable tool, especially the versatile and adaptable CRISPR/Cas9 system. Using CRISPR/Cas9 in plants has enabled modifications of many valuable traits, including environmental stress tolerance, an essential aspect when it comes to ensuring food security under climate change pressure. The CRISPR toolbox enables faster and more precise plant breeding by facilitating: multiplex gene editing, gene pyramiding, and de novo domestication. In this paper, we discuss the most recent advances in CRISPR/Cas9 and alternative CRISPR-based systems, along with the technical challenges that remain to be overcome. A revision of the latest proof-of-concept and functional characterization studies has indeed provided more insight into the quantitative traits affecting crop yield and stress tolerance. Additionally, we focus on the applications of CRISPR/Cas9 technology in regard to extremophile plants, due to their significance on: industrial, ecological and economic levels. These still unexplored genetic resources could provide the means to harden our crops against the threat of climate change, thus ensuring food security over the next century.
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Affiliation(s)
- Mohamed Kouhen
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia.,Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Pedro García-Caparrós
- Agronomy Department of Superior School Engineering, University of Almeria, CIAIMBITAL, Almería, Spain
| | | | - Chedly Abdelly
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia
| | - Henda Mahmoudi
- International Center for Biosaline Agriculture, Academic City, Near Zayed University, Dubai, United Arab Emirates
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Ahmed Debez
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia
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16
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Li Q, Feng Q, Snouffer A, Zhang B, Rodríguez GR, van der Knaap E. Increasing Fruit Weight by Editing a Cis-Regulatory Element in Tomato KLUH Promoter Using CRISPR/Cas9. FRONTIERS IN PLANT SCIENCE 2022; 13:879642. [PMID: 35481139 PMCID: PMC9037380 DOI: 10.3389/fpls.2022.879642] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/07/2022] [Indexed: 06/01/2023]
Abstract
CRISPR/Cas-mediated genome editing is a powerful approach to accelerate yield enhancement to feed growing populations. Most applications focus on "negative regulators" by targeting coding regions and promoters to create nulls or weak loss-of-function alleles. However, many agriculturally important traits are conferred by gain-of-function alleles. Therefore, creating gain-of-function alleles for "positive regulators" by CRISPR will be of great value for crop improvement. CYP78A family members are the positive regulators of organ weight and size in crops. In this study, we engineered allelic variation by editing tomato KLUH promoter around a single-nucleotide polymorphism (SNP) that is highly associated with fruit weight. The SNP was located in a conserved putative cis-regulatory element (CRE) as detected by the homology-based prediction and the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). Twenty-one mutant alleles with various insertion and deletion sizes were generated in the LA1589 background. Five mutant alleles (m2+4bp , m3+1bp , m5-1bp , m13-8bp , and m14-9bp ) showed a consistent increase in fruit weight and a significant decrease in the proportion of small fruits in all experimental evaluations. Notably, m2+4bp and m3+1bp homozygote significantly increase fruit weight by 10.7-15.7 and 8.7-16.3%, respectively. Further analysis of fruit weight based on fruit position on the inflorescence indicated that the five beneficial alleles increase the weight of all fruits along inflorescence. We also found that allele types and transcriptional changes of SlKLUH were poor predictors of the changes in fruit weight. This study not only provides a way of identifying conserved CRE but also highlights enormous potential for CRISPR/Cas-mediated cis-engineering of CYP78A members in yield improvement.
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Affiliation(s)
- Qiang Li
- College of Horticulture, Hebei Agricultural University, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Qian Feng
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Ashley Snouffer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Biyao Zhang
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Gustavo Rubén Rodríguez
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Cátedra de Genética, Facultad de Ciencias Agrarias UNR, Santa Fe, Argentina
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
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17
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Matres JM, Hilscher J, Datta A, Armario-Nájera V, Baysal C, He W, Huang X, Zhu C, Valizadeh-Kamran R, Trijatmiko KR, Capell T, Christou P, Stoger E, Slamet-Loedin IH. Genome editing in cereal crops: an overview. Transgenic Res 2021; 30:461-498. [PMID: 34263445 PMCID: PMC8316241 DOI: 10.1007/s11248-021-00259-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/15/2021] [Indexed: 02/06/2023]
Abstract
Genome-editing technologies offer unprecedented opportunities for crop improvement with superior precision and speed. This review presents an analysis of the current state of genome editing in the major cereal crops- rice, maize, wheat and barley. Genome editing has been used to achieve important agronomic and quality traits in cereals. These include adaptive traits to mitigate the effects of climate change, tolerance to biotic stresses, higher yields, more optimal plant architecture, improved grain quality and nutritional content, and safer products. Not all traits can be achieved through genome editing, and several technical and regulatory challenges need to be overcome for the technology to realize its full potential. Genome editing, however, has already revolutionized cereal crop improvement and is poised to shape future agricultural practices in conjunction with other breeding innovations.
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Affiliation(s)
- Jerlie Mhay Matres
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Akash Datta
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Victoria Armario-Nájera
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Can Baysal
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Wenshu He
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Xin Huang
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Rana Valizadeh-Kamran
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Kurniawan R Trijatmiko
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Teresa Capell
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Inez H Slamet-Loedin
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines.
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18
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Huang X, Hilscher J, Stoger E, Christou P, Zhu C. Modification of cereal plant architecture by genome editing to improve yields. PLANT CELL REPORTS 2021; 40:953-978. [PMID: 33559722 DOI: 10.1007/s00299-021-02668-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
We summarize recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement. Plant architecture is defined as the three-dimensional organization of the entire plant. Shoot architecture refers to the structure and organization of the aboveground components of a plant, reflecting the developmental patterning of stems, branches, leaves and inflorescences/flowers. Root system architecture is essentially determined by four major shape parameters-growth, branching, surface area and angle. Interest in plant architecture has arisen from the profound impact of many architectural traits on agronomic performance, and the genetic and hormonal regulation of these traits which makes them sensitive to both selective breeding and agronomic practices. This is particularly important in staple crops, and a large body of literature has, therefore, accumulated on the control of architectural phenotypes in cereals, particularly rice due to its twin role as one of the world's most important food crops as well as a model organism in plant biology and biotechnology. These studies have revealed many of the molecular mechanisms involved in the regulation of tiller/axillary branching, stem height, leaf and flower development, root architecture and the grain characteristics that ultimately help to determine yield. The advent of genome editing has made it possible, for the first time, to introduce precise mutations into cereal crops to optimize their architecture and close in on the concept of the ideotype. In this review, we consider recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement.
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Affiliation(s)
- Xin Huang
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain.
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19
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Liu L, Lindsay PL, Jackson D. Next Generation Cereal Crop Yield Enhancement: From Knowledge of Inflorescence Development to Practical Engineering by Genome Editing. Int J Mol Sci 2021; 22:5167. [PMID: 34068350 PMCID: PMC8153303 DOI: 10.3390/ijms22105167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
Artificial domestication and improvement of the majority of crops began approximately 10,000 years ago, in different parts of the world, to achieve high productivity, good quality, and widespread adaptability. It was initiated from a phenotype-based selection by local farmers and developed to current biotechnology-based breeding to feed over 7 billion people. For most cereal crops, yield relates to grain production, which could be enhanced by increasing grain number and weight. Grain number is typically determined during inflorescence development. Many mutants and genes for inflorescence development have already been characterized in cereal crops. Therefore, optimization of such genes could fine-tune yield-related traits, such as grain number. With the rapidly advancing genome-editing technologies and understanding of yield-related traits, knowledge-driven breeding by design is becoming a reality. This review introduces knowledge about inflorescence yield-related traits in cereal crops, focusing on rice, maize, and wheat. Next, emerging genome-editing technologies and recent studies that apply this technology to engineer crop yield improvement by targeting inflorescence development are reviewed. These approaches promise to usher in a new era of breeding practice.
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Affiliation(s)
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (L.L.); (P.L.L.)
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20
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Srivastava AK, Suresh Kumar J, Suprasanna P. Seed 'primeomics': plants memorize their germination under stress. Biol Rev Camb Philos Soc 2021; 96:1723-1743. [PMID: 33961327 DOI: 10.1111/brv.12722] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/28/2022]
Abstract
Seed priming is a pre-germination treatment administered through various chemical, physical and biological agents, which induce mild stress during the early phases of germination. Priming facilitates synchronized seed germination, better seedling establishment, improved plant growth and enhanced yield, especially in stressful environments. In parallel, the phenomenon of 'stress memory' in which exposure to a sub-lethal stress leads to better responses to future or recurring lethal stresses has gained widespread attention in recent years. The versatility and realistic yield gains associated with seed priming and its connection with stress memory make a critical examination useful for the design of robust approaches for maximizing future yield gains. Herein, a literature review identified selenium, salicylic acid, poly-ethylene glycol, CaCl2 and thiourea as the seed priming agents (SPRs) for which the most studies have been carried out. The average priming duration for SPRs generally ranged from 2 to 48 h, i.e. during phase I/II of germination. The major signalling events for regulating early seed germination, including the DOG1 (delay of germination 1)-abscisic acid (ABA)-heme regulatory module, ABA-gibberellic acid antagonism and nucleus-organelle communication are detailed. We propose that both seed priming and stress memory invoke a 'bet-hedging' strategy in plants, wherein their growth under optimal conditions is compromised in exchange for better growth under stressful conditions. The molecular basis of stress memory is explained at the level of chromatin reorganization, alternative transcript splicing, metabolite accumulation and autophagy. This provides a useful framework to study similar mechanisms operating during seed priming. In addition, we highlight the potential for merging findings on seed priming with those of stress memory, with the dual benefit of advancing fundamental research and boosting crop productivity. Finally, a roadmap for future work, entailing identification of SPR-responsive varieties and the development of dual/multiple-benefit SPRs, is proposed for enhancing SPR-mediated agricultural productivity worldwide.
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Affiliation(s)
- Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.,Homi Bhabha National Institute, Mumbai, 400094, India
| | - Jisha Suresh Kumar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
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21
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Zeng Z, Han N, Liu C, Buerte B, Zhou C, Chen J, Wang M, Zhang Y, Tang Y, Zhu M, Wang J, Yang Y, Bian H. Functional dissection of HGGT and HPT in barley vitamin E biosynthesis via CRISPR/Cas9-enabled genome editing. ANNALS OF BOTANY 2020; 126:929-942. [PMID: 32575125 PMCID: PMC7539355 DOI: 10.1093/aob/mcaa115] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Vitamin E (tocochromanol) is a lipid-soluble antioxidant and an essential nutrient for human health. Among cereal crops, barley (Hordeum vulgare) contains a high level of vitamin E, which includes both tocopherols and tocotrienols. Although the vitamin E biosynthetic pathway has been characterized in dicots, such as Arabidopsis, which only accumulate tocopherols, knowledge regarding vitamin E biosynthesis in monocots is limited because of the lack of functional mutants. This study aimed to obtain gene knockout mutants to elucidate the genetic control of vitamin E composition in barley. METHODS Targeted knockout mutations of HvHPT and HvHGGT in barley were created with CRISPR/Cas9-enabled genome editing. High-performance liquid chromatography (HPLC) was performed to analyse the content of tocochromanol isomers in transgene-free homozygous Hvhpt and Hvhggt mutants. KEY RESULTS Mutagenesis efficiency among T0 regenerated plantlets was 50-65 % as a result of two simultaneously expressed guide RNAs targeting each gene; most of the mutations were stably inherited by the next generation. The transgene-free homozygous mutants of Hvhpt and Hvhggt exhibited decreased grain size and weight, and the HvHGGT mutation led to a shrunken phenotype and significantly lower total starch content in grains. HPLC analysis revealed that targeted mutation of HvHPT significantly reduced the content of both tocopherols and tocotrienols, whereas mutations in HvHGGT completely blocked tocotrienol biosynthesis in barley grains. Transient overexpression of an HvHPT homologue in tobacco leaves significantly increased the production of γ- and δ-tocopherols, which may partly explain why targeted mutation of HvHPT in barley grains did not eliminate tocopherol production. CONCLUSIONS Our results functionally validated that HvHGGT is the only committed gene for the production of tocotrienols, whereas HvHPT is partly responsible for tocopherol biosynthesis in barley.
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Affiliation(s)
- Zhanghui Zeng
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ning Han
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Cuicui Liu
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - B Buerte
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chenlu Zhou
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jianshu Chen
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Mengyao Wang
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuhong Zhang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yawei Tang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Muyuan Zhu
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Junhui Wang
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yinong Yang
- Department of Plant Pathology and Environment Microbiology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Hongwu Bian
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
- For correspondence. E-mail
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22
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Applications of CRISPR-Cas in agriculture and plant biotechnology. Nat Rev Mol Cell Biol 2020; 21:661-677. [PMID: 32973356 DOI: 10.1038/s41580-020-00288-9] [Citation(s) in RCA: 302] [Impact Index Per Article: 75.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2020] [Indexed: 12/26/2022]
Abstract
The prokaryote-derived CRISPR-Cas genome editing technology has altered plant molecular biology beyond all expectations. Characterized by robustness and high target specificity and programmability, CRISPR-Cas allows precise genetic manipulation of crop species, which provides the opportunity to create germplasms with beneficial traits and to develop novel, more sustainable agricultural systems. Furthermore, the numerous emerging biotechnologies based on CRISPR-Cas platforms have expanded the toolbox of fundamental research and plant synthetic biology. In this Review, we first briefly describe gene editing by CRISPR-Cas, focusing on the newest, precise gene editing technologies such as base editing and prime editing. We then discuss the most important applications of CRISPR-Cas in increasing plant yield, quality, disease resistance and herbicide resistance, breeding and accelerated domestication. We also highlight the most recent breakthroughs in CRISPR-Cas-related plant biotechnologies, including CRISPR-Cas reagent delivery, gene regulation, multiplexed gene editing and mutagenesis and directed evolution technologies. Finally, we discuss prospective applications of this game-changing technology.
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Kawai K, Ueguchi-Tanaka M, Matsuoka M. Future Strategy of Breeding: Learn by Two Important Genes of Miracle Rice. MOLECULAR PLANT 2020; 13:823-824. [PMID: 32387736 DOI: 10.1016/j.molp.2020.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/02/2020] [Accepted: 05/02/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Kyosuke Kawai
- Bioscience and Biotechnology Center, Nagoya University, 464-8601 Nagoya, Japan
| | | | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, 464-8601 Nagoya, Japan.
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