Review
Plant Sciences
Mawuli K. Azameti, Wadzani Palnam Dauda
Summary: Genome editing technologies have revolutionized crop improvement research by creating targeted modifications in plant genomes. Base editing, a novel approach, has gained quick acceptance due to its precision, simplicity, and multiplex capabilities. This technology shows great potential in enhancing crop production.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Agronomy
Tingting Liu, Jinpeng Zou, Xi Yang, Kejian Wang, Yuchun Rao, Chun Wang
Summary: CRISPR/Cas-mediated genome editing and prime editing system have greatly advanced plant genetic research and agricultural breeding. Prime editing, with its precise capabilities, has been rapidly verified and applied in various plants, showing promising prospects in genetic improvement and precision molecular breeding.
Article
Plant Sciences
Syed Inzimam Ul Haq, Dianfeng Zheng, Naijie Feng, Xingyu Jiang, Feng Qiao, Jin-Sheng He, Quan-Sheng Qiu
Summary: This review summarizes the advances of CRISPR/Cas9 technology in plant genome editing and discusses its applications in forage breeding, as well as the potential and challenges.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Agronomy
Fangquan Wang, Yang Xu, Wenqi Li, Zhihui Chen, Jun Wang, Fangjun Fan, Yajun Tao, Yanjie Jiang, Qian-Hao Zhu, Jie Yang
Summary: The novel herbicide-tolerance allele (G628W) created in rice using CRISPR/Cas9-mediated gene editing proved to be valuable for developing elite rice varieties with strong herbicide tolerance. A DNA marker for the G628W allele was developed to accurately distinguish homozygous from heterozygous segregants, facilitating its use and introgression into elite alleles for crop breeding. This study further demonstrates the feasibility of CRISPR/Cas9-mediated gene editing in generating novel genetic variation for crop improvement.
Review
Microbiology
Yan Zhang, Shutong Chen, Long Yang, Qiang Zhang
Summary: Edible fungi are sought after for their delicious taste and rich nutritional and medicinal value. The cultivation of superior and innovative edible fungi strains plays a crucial role in the rapidly advancing edible fungi industry, particularly in China. CRISPR/Cas9 technology has proven to be a powerful tool for molecular breeding in edible fungi, enabling high-efficiency and high-precision genome modification. This review provides a summary of the working mechanism of the CRISPR/Cas9 system and discusses its application progress, limitations, challenges, and potential solutions in various edible fungi species.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Jingying Li, Chen Zhang, Yubing He, Shaoya Li, Lei Yan, Yucai Li, Ziwei Zhu, Lanqin Xia
Summary: Precise replacement of an allele with an elite allele controlling an important agronomic trait in a predefined manner by gene editing technologies is highly desirable in crop improvement. Base editing and prime editing are two newly developed precision gene editing systems which can introduce the substitution of a single base and install the desired short indels to the target loci in the absence of double-strand breaks and donor repair templates, respectively. Various strategies have been attempted to optimize both base editor (BE) and prime editor (PE) to improve their editing efficacy, specificity, and expand the targeting scopes. Based on the latest development, appropriate BEs and PEs are recommended for basic plant research and crop improvement, and further optimization of these editors is proposed. Both BEs and PEs are envisioned to become routine and customized precise gene editing tools for plant biological research and crop improvement in the near future.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jiyeon Kweon, Jung-Ki Yoon, An-Hee Jang, Ha Rim Shin, Ji-Eun See, Gayoung Jang, Jong-Il Kim, Yongsub Kim
Summary: The engineered prime editors leverage various PAM-flexible Cas9 variants to broaden the range of target sites and achieve high editing activity, successfully generating multiple types of mutations in cells. Additionally, they successfully introduce mutations such as BRAF V600E that cannot be induced by conventional prime editors, expanding the applicability of CRISPR-based prime editing technologies in biological research.
Review
Forestry
Renan Terassi Pinto, Chanaka Roshan Abeyratne, Luciano Vilela Paiva, Vagner Augusto Benedito
Summary: Breeding tree species to meet economic demands is challenging due to their long juvenile phase, reproductive difficulties, and scarcity of genetic resources. However, with advances in genome projects and gene editing technologies, it is now possible to design tree crops with optimized traits. This study explores the application of CRISPR-Cas-based systems in tree crops and highlights the opportunity to tailor the breeding of perennial crops in the face of environmental challenges and population demands.
TREE GENETICS & GENOMES
(2023)
Review
Biochemistry & Molecular Biology
Yizhen Li, Jing Liang, Bufang Deng, Yingli Jiang, Jingyan Zhu, Like Chen, Min Li, Juan Li
Summary: The CRISPR/Cas9 system has been extensively used to optimize germplasm resources. However, large-scale genomic research has shown that novel variations in crop plants are caused by single-nucleotide polymorphisms (SNPs). Substituting single bases in the plant genome can produce desired traits. Base editing techniques allow precise single-nucleotide changes without double-strand breaks (DSBs) and donor repair templates (DRTs), providing a new approach to genome editing.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Immunology
Huan Qin, Wenliang Zhang, Shiyao Zhang, Yuan Feng, Weihui Xu, Jia Qi, Qian Zhang, Chunxiu Xu, Shanshan Liu, Jia Zhang, Yushuang Lei, Wanqin Liu, Shuyu Feng, Jingjing Wang, Xuefei Fu, Zifen Xu, Ping Li, Kai Yao
Summary: The researchers developed a genome-editing tool called PESpRY, which combines the versatility of prime editors with the unconstrained PAM requirement of the SpRY Cas9 variant. Using this tool, they were able to successfully correct gene mutations in a mouse model of retinitis pigmentosa, leading to substantial restoration of vision.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Biotechnology & Applied Microbiology
Hui Kwon Kim, Goosang Yu, Jinman Park, Seonwoo Min, Sungtae Lee, Sungroh Yoon, Hyongbum Henry Kim
Summary: This study identified factors affecting PE2 efficiency through high-throughput evaluation and developed three computational models to predict pegRNA efficiency, which can be applied to edits of various types and positions. Spearman's correlations between 0.47 and 0.81 were found when testing the accuracy of the predictions using independent test data sets.
NATURE BIOTECHNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Ali Saber Sichani, Maryam Ranjbar, Maryam Baneshi, Farid Torabi Zadeh, Jafar Fallahi
Summary: In the field of medicine, the development of precise gene-editing tools, particularly CRISPR/Cas9, has revolutionized the potential for gene therapy in treating genetic diseases. This article discusses the different types of CRISPR/Cas-based gene-editing techniques, their functions, and the ongoing research studies that aim to improve their efficiency and reliability for future gene therapies. The article also compares the capabilities of these platforms and highlights their potential limitations.
MOLECULAR BIOTECHNOLOGY
(2023)
Review
Plant Sciences
Seungmin Son, Sang Ryeol Park
Summary: The development of CRISPR/Cas9-mediated genome editing technology has revolutionized plant breeding, allowing high-precision and high-efficiency editing in all plants. However, there are still challenges that limit the application of this technology in plants, despite improvements.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Fangning Zhang, Ting Xiang Neik, William J. W. Thomas, Jacqueline Batley
Summary: CRISPR-Cas is the most prevalent and promising genome editing tool, which plays a crucial role in ensuring global food security and achieving sustainable agricultural development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Shengyao Zhi, Yuxi Chen, Guanglan Wu, Jinkun Wen, Jinni Wu, Qianyi Liu, Yang Li, Rui Kang, Sihui Hu, Jiahui Wang, Puping Liang, Junjiu Huang
Summary: Prime editor (PE) is a new genome editing tool that has the potential to correct the majority of known human genetic disease-related mutations. In this study, split-PEs were constructed and delivered using dual adenoassociated viruses (AAVs), successfully mediating gene editing in human cells and adult mouse retina.
Article
Agronomy
Shuwei Chang, Guoqiang Huang, Duoxiang Wang, Wanwan Zhu, Jianxin Shi, Litao Yang, Wanqi Liang, Qi Xie, Dabing Zhang
Summary: This study identifies six rice SIAH-type E3 ligases and reveals their regulatory role in determining the stability of formin proteins. The study also highlights the redundancy between these six genes and provides insights into the importance of these genes in plant growth and development.
Article
Plant Sciences
Jihyun Kim, Jeniffer Silva, Chanwoo Park, Younghun Kim, Nayeon Park, Johan Sukweenadhi, Junping Yu, Jianxin Shi, Dabing Zhang, Keun Ki Kim, Hong-Joo Son, Hyeon Cheal Park, Chang-Oh Hong, Kwang Min Lee, Yu-Jin Kim
Summary: Cytochrome P450 (CYP) catalyzes monooxygenation reactions in plant metabolism, with CYP703 playing a key role in fatty acid hydroxylation in male reproductive tissues. PgCYP703A4 in Korean ginseng is conserved in function, affecting fruit size and cutin synthesis through fatty acid hydroxylation pathways.
Article
Plant Sciences
Gaodian Shen, Wenli Sun, Zican Chen, Lei Shi, Jun Hong, Jianxin Shi
Summary: This review summarizes the roles of plant GELPs in regulating plant development and plant-environment interactions, as well as the potential regulatory mechanisms.
Article
Multidisciplinary Sciences
Feng Mao, Depeng Wu, Fangfang Lu, Xin Yi, Yujuan Gu, Bin Liu, Fuxia Liu, Tang Tang, Jianxin Shi, Xiangxiang Zhao, Lei Liu, Lilian Ji
Summary: A genome-wide association study (GWAS) was conducted to identify genes associated with low temperature germination (LTG) in rice. A total of 37 quantitative trait loci (QTLs) were detected, including a novel QTL qLTG1-2. Two candidate genes, LOC_Os01g23580 and LOC_Os01g23620, showed significant differential expression between high and low LTG accessions.
Article
Plant Sciences
Jun Hong, Leah Rosental, Yang Xu, Dawei Xu, Isabel Orf, Wengsheng Wang, Zhiqiang Hu, Su Su, Shaoxing Bai, Mohammed Ashraf, Chaoyang Hu, Changquan Zhang, Zhikang Li, Jianlong Xu, Qiaoquan Liu, Hui Zhang, Fengli Zhang, Zhijing Luo, Mingjiao Chen, Xiaofei Chen, Natalie Betts, Alisdair Fernie, Wanqi Liang, Guanqun Chen, Yariv Brotman, Dabing Zhang, Jianxin Shi
Summary: This study revealed the genetic regulation of rice seed glycerolipids using metabolite-based approaches. Two genes were found to be involved in the variation of saturated triacylglycerol and lyso-phosphatidylcholine contents. The study also demonstrated the association of these genes with other traits such as heading date and flooding tolerance. The findings suggest that the diversity of rice seed glycerolipids may have been unintentionally shaped during natural and artificial selection.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Plant Sciences
Shaoxing Bai, Jun Hong, Su Su, Zhikang Li, Wensheng Wang, Jianxin Shi, Wanqi Liang, Dabing Zhang
Summary: Novel alleles of reported tiller angle genes and candidate genes for rice tiller angle were identified through a combination of GWAS with transcriptomic, qRT-PCR, and haplotype analysis. This study provides new insights into the genetic architecture of rice tiller angle and candidate genes for rice breeding.
PLANT CELL REPORTS
(2022)
Article
Agricultural Engineering
Feng Chen, Nianjun Xu, Kai Liu, Rongrong Lv, Jianxin Shi, Jianguo Liu, Xue Sun, Chaoyang Hu
Summary: This study presents a strategy to enhance the production and bio-accessibility of astaxanthin in Haematococcus pluvialis by screening and culturing specific cells under high light condition. The isolated strain RMS10 showed a 31.9% increase in biomass and a 53.3% increase in astaxanthin content after 9-day high light induction, which could be easily extracted and digested without cell disruption.
BIORESOURCE TECHNOLOGY
(2022)
Article
Plant Sciences
Yueya Zhang, Jin Shi, Chaoqun Shen, Vinh-Trieu To, Qi Shi, Lingzhen Ye, Jianxin Shi, Dabing Zhang, Weiwei Chen
Summary: This study utilized genome resequencing to uncover genome-wide DNA polymorphisms and develop high-density InDel markers in two barley cultivars. The findings provide valuable genetic resources for both basic and applied research in barley.
PLANT CELL REPORTS
(2022)
Article
Agronomy
Guochao Zhao, Shuifeng Xie, Shipeng Zong, Tong Wang, Chanjuan Mao, Jianxin Shi, Jianyue Li
Summary: This study cloned and characterized a novel C2H2 zinc finger protein TL1 that plays a positive role in regulating amylose synthesis in rice grains, thus improving the eating and cooking quality of rice. Loss of TL1 function resulted in reduced amylose content but increased viscosity and total lipid content in rice. In addition, the ratio of amylopectin A chains with a degree of polymerization (DP) 6-12 to B chains with DP 13-24 was altered, leading to enhanced grain quality. Knockout of TL1 in a high-yielding rice variety had no noticeable side effects on major agronomic traits.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Plant Sciences
Yu-Tong Jiang, Ji-Xuan Zheng, Rong-Han Li, Yu-Chen Wang, Jianxin Shi, Ali Ferjani, Wen-Hui Lin
Summary: Research has shown that tonoplast proton pumps play a crucial role in plant gametophyte development, with their absence leading to abnormal FG development and disruptions in auxin levels regulation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Jun Hong, Su Su, Li Wang, Shaoxing Bai, Jianlong Xu, Zhikang Li, Natalie Betts, Wanqi Liang, Wensheng Wang, Jianxin Shi, Dabing Zhang
Summary: Plant height in rice is an important trait, and this study identified multiple genes and genetic interactions involved in regulating this trait. The discovery of a structural variant in the SD1 gene and the identification of additional genes provide valuable resources for breeding semi-dwarf rice. These findings also contribute to our understanding of the genetic mechanisms underlying plant height regulation in rice.
PLANT CELL AND ENVIRONMENT
(2023)
Review
Plant Sciences
Jianxin Shi, Gynheung An, Andreas P. M. Weber, Dabing Zhang
Summary: To achieve the goals of the UN's 2030 Agenda for Sustainable Development, transformative change is needed in our agrifood systems to ensure food security in the face of climate change, population growth, urbanization, and natural resource depletion. Rice, a major staple cereal crop, has historically contributed to global food security and will continue to do so in the future. Advances in research and breeding practices have helped meet increasing demands, but the future of rice production depends on resilient cultivars that can adapt to changing environmental conditions. This Special Issue highlights the field of rice-environment interactions and proposes future directions for rice research, including the development of environment-resilient rice varieties.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Plant Sciences
Weihua Li, Duoxiang Wang, Xiaokun Hong, Jin Shi, Jun Hong, Su Su, Cristopher Reyes Loaiciga, Jing Li, Wanqi Liang, Jianxin Shi, Dabing Zhang
Summary: Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. These genes encode transcription factors that play essential roles in rice growth and development. The discovery of these genes in the rice pan-genome provides valuable genetic resources for rice improvement, overcoming the limitation of the existing identified MADS-box genes. The expression analysis confirms their presence in flower tissues and suggests their potential roles in seed development.
PLANT CELL REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Zican Chen, Weronika Jasinska, Muhammad Ashraf, Leah Rosental, Jung Hong, Dabing Zhang, Yariv Brotman, Jianxin Shi
Summary: Arabidopsis sepals coordinate flower opening in the morning as ambient temperature rises, but the underlying molecular mechanisms are poorly understood. This study explored the role of lipids in this process by comparing lipidomic changes in sepals of mutant plants under normal and mild heat stress temperatures. The findings revealed the impact of mild heat stress on sepal lipidome and the differential effects of HSP70-16 and VDAC3 on sepal lipidomic responses.
Review
Plant Sciences
Yueya Zhang, Chaoqun Shen, Jin Shi, Jianxin Shi, Dabing Zhang
Summary: One of the challenges for global food security is to improve the grain yield of cereal crops by modifying their inflorescence architecture. Recent advancements in understanding the genetic regulation of inflorescence architecture in crops like rice, maize, wheat, and barley have provided valuable insights. This knowledge can be utilized to optimize inflorescence architecture and ultimately enhance crop grain yield.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)