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Genome editing technologies and applications

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Advances in genome editing technology and its promising applications have had a great impact on basic science and clinical research. A number of approaches to genome editing have been developed. Particularly the CRISPR/Cas system, has given scientists the ability to make precise changes in the genomes ranging from plants to animals. In addition, CRISPR-based base editing and epigenetic editing greatly expand the genome editing toolbox. 

Here we present a collection of articles on genome editing in plant and animal cell systems that have been pulled together from manuscripts published in BMC Biotechnology and BMC Plant Biology submitted to a thematic series call for papers that drew to a close in late 2019. This collection highlights the latest in genome editing technologies and tools available to manipulate genomes to affect change to cellular behavior as well as whole organism phenotypes.  

  1. Peanut is an important legume crop growing worldwide. With the published allotetraploid genomes, further functional studies of the genes in peanut are very critical for crop improvement. CRISPR/Cas9 system is ...

    Authors: Hongmei Shu, Ziliang Luo, Ze Peng and Jianping Wang
    Citation: BMC Plant Biology 2020 20:417
    Content type: Research article Published on:

  2. The non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. However, whether the tRFs and phasiRNAs respond ...

    Authors: Wei Luan, Ya Dai, Xin-Yu Li, Yan Wang, Xiang Tao, Cai-Xia Li, Ping Mao and Xin-Rong Ma
    Citation: BMC Plant Biology 2020 20:320
    Content type: Research article Published on:

  3. The development of CRISPR/Cas9 technology has facilitated targeted mutagenesis in an efficient and precise way. Previously, RNAi silencing of the susceptibility (S) gene PowderyMildewResistance 4 (PMR4) in tomato...

    Authors: Miguel I. Santillán Martínez, Valentina Bracuto, Eleni Koseoglou, Michela Appiano, Evert Jacobsen, Richard G. F. Visser, Anne-Marie A. Wolters and Yuling Bai
    Citation: BMC Plant Biology 2020 20:284
    Content type: Research article Published on:

  5. Tobacco seed oil could be used as an appropriate feedstock for biodiesel production. However, the high linoleic acid content of tobacco seed oil makes it susceptible to oxidation. Altering the fatty acid profi...

    Authors: Yinshuai Tian, Kai Chen, Xiao Li, Yunpu Zheng and Fang Chen
    Citation: BMC Plant Biology 2020 20:233
    Content type: Research article Published on:

  6. CRISPR/Cas has recently become a widely used genome editing tool in various organisms, including plants. Applying CRISPR/Cas often requires delivering multiple expression units into plant and hence there is a ...

    Authors: Florian Hahn, Andrey Korolev, Laura Sanjurjo Loures and Vladimir Nekrasov
    Citation: BMC Plant Biology 2020 20:179
    Content type: Methodology article Published on:

  7. Shoot branching is an important trait of plants that allows them to adapt to environment changes. Strigolactones (SLs) are newly identified plant hormones that inhibit shoot branching in plants. The SL biosynt...

    Authors: Chong Ren, Yuchen Guo, Junhua Kong, Fatma Lecourieux, Zhanwu Dai, Shaohua Li and Zhenchang Liang
    Citation: BMC Plant Biology 2020 20:47
    Content type: Research article Published on:

  8. Soybean (Glycine max) is an economically important oil and protein crop. Plant height is a key trait that significantly impacts the yield of soybean; however, research on the molecular mechanisms associated with ...

    Authors: Qun Cheng, Lidong Dong, Tong Su, Tingyu Li, Zhuoran Gan, Haiyang Nan, Sijia Lu, Chao Fang, Lingping Kong, Haiyang Li, Zhihong Hou, Kun Kou, Yang Tang, Xiaoya Lin, Xiaohui Zhao, Liyu Chen…
    Citation: BMC Plant Biology 2019 19:562
    Content type: Research article Published on:

  9. The invasive fruit pest Drosophila suzukii was reported for the first time in Europe and the USA in 2008 and has spread since then. The adoption of type II clustered regularly interspaced short palindromic repeat...

    Authors: Hassan M. M. Ahmed, Luisa Hildebrand and Ernst A. Wimmer
    Citation: BMC Biotechnology 2019 19:85
    Content type: Research article Published on:

  10. Application of the CRISPR/Cas9 system or its derived base editors enables targeted genome modification, thereby providing a programmable tool to exploit gene functions and to improve crop traits.

    Authors: Wen Xu, Wei Song, Yongxing Yang, Ying Wu, Xinxin Lv, Shuang Yuan, Ya Liu and Jinxiao Yang
    Citation: BMC Plant Biology 2019 19:511
    Content type: Research article Published on:

  11. Genetic mutations cause severe human diseases, and suitable animal models to study the regulatory mechanisms involved are required. The CRISPR/Cas9 system is a powerful, highly efficient and easily manipulated...

    Authors: Guoxing Zheng, Qingqing Zhu, Junchao Dong, Xin Lin and Chengming Zhu
    Citation: BMC Biotechnology 2019 19:74
    Content type: Research article Published on:

  12. PDX1.2 has recently been shown to be a regulator of vitamin B6 biosynthesis in plants and is implicated in biotic and abiotic stress resistance. PDX1.2 expression is strongly and rapidly induced by heat stress. I...

    Authors: Elisa Dell’Aglio, Ivan Dalvit, Sylvain Loubéry and Teresa B. Fitzpatrick
    Citation: BMC Plant Biology 2019 19:464
    Content type: Research article Published on:

  13. The CRISPR-Cas9 system is a powerful and versatile tool for crop genome editing. However, achieving highly efficient and specific editing in polyploid species can be a challenge. The efficiency and specificity...

    Authors: Taj Arndell, Niharika Sharma, Peter Langridge, Ute Baumann, Nathan S. Watson-Haigh and Ryan Whitford
    Citation: BMC Biotechnology 2019 19:71
    Content type: Research article Published on:

  14. Wheat grains contain gluten proteins, which harbour immunogenic epitopes that trigger Coeliac disease in 1–2% of the human population. Wheat varieties or accessions containing only safe gluten have not been id...

    Authors: Aurélie Jouanin, Jan G. Schaart, Lesley A. Boyd, James Cockram, Fiona J. Leigh, Ruth Bates, Emma J. Wallington, Richard G. F. Visser and Marinus J. M. Smulders
    Citation: BMC Plant Biology 2019 19:333
    Content type: Research article Published on:

  15. CRISPR/Cas9 gene editing is now revolutionizing the ability to effectively modify plant genomes in the absence of efficient homologous recombination mechanisms that exist in other organisms. However, soybean i...

    Authors: Phat T. Do, Cuong X. Nguyen, Hien T. Bui, Ly T. N. Tran, Gary Stacey, Jason D. Gillman, Zhanyuan J. Zhang and Minviluz G. Stacey
    Citation: BMC Plant Biology 2019 19:311
    Content type: Research article Published on:

  16. The oilseed Camelina sativa is grown for a range of applications, including for biofuel, biolubricants, and as a source of omega-3 fatty acids for the aquaculture feed industry. The seed meal co-product is used a...

    Authors: Wendy J. Lyzenga, Myrtle Harrington, Diana Bekkaoui, Merek Wigness, Dwayne D. Hegedus and Kevin L. Rozwadowski
    Citation: BMC Plant Biology 2019 19:292
    Content type: Research article Published on:

  17. Natural variations in a genome can drastically alter the CRISPR-Cas9 off-target landscape by creating or removing sites. Despite the resulting potential side-effects from such unaccounted for sites, current of...

    Authors: Laurence O. W. Wilson, Sara Hetzel, Christopher Pockrandt, Knut Reinert and Denis C. Bauer
    Citation: BMC Biotechnology 2019 19:40
    Content type: Software Published on:

  18. CRISPR/Cas9 is widely used for precise genetic editing in various organisms. CRISPR/Cas9 editing may in many plants be hampered by the presence of complex and high ploidy genomes and inefficient or poorly cont...

    Authors: Bent Larsen Petersen, Svenning Rune Möller, Jozef Mravec, Bodil Jørgensen, Mikkel Christensen, Ying Liu, Hans H. Wandall, Eric Paul Bennett and Zhang Yang
    Citation: BMC Biotechnology 2019 19:36
    Content type: Research article Published on:

  19. Classical plant breeding was extremely successful in generating high yielding crop varieties. Yet, in modern crops, the long domestication process has impoverished the genetic diversity available for breeding....

    Authors: Felix Wolter, Patrick Schindele and Holger Puchta
    Citation: BMC Plant Biology 2019 19:176
    Content type: Review Published on:

  20. Increasing the content of oleic acid in peanut seeds is one of the major goals in peanut breeding due to consumer and industry benefits, such as anti-oxidation and long shelf-life. Homeologous ahFAD2A and ahFAD2B

    Authors: Mei Yuan, Jun Zhu, Limin Gong, Liangqiong He, Crystal Lee, Suoyi Han, Charles Chen and Guohao He
    Citation: BMC Biotechnology 2019 19:24
    Content type: Research article Published on:

  21. Gossypium hirsutum L. is grown worldwide and is the largest source of natural fiber crop. We focus on exploring the favorable alleles (FAs) for upland cotton varieties improvement, and further understanding the h...

    Authors: Panhong Dai, Yuchen Miao, Shoupu He, Zhaoe Pan, Yinhua Jia, Yingfan Cai, Junling Sun, Liru Wang, Baoyin Pang, Mi Wang and Xiongming Du
    Citation: BMC Plant Biology 2019 19:138
    Content type: Research article Published on:

  22. The plant architecture has significant effects on grain yield of various crops, including soybean (Glycine max), but the knowledge on optimization of plant architecture in order to increase yield potential is sti...

    Authors: Aili Bao, Haifeng Chen, Limiao Chen, Shuilian Chen, Qingnan Hao, Wei Guo, Dezhen Qiu, Zhihui Shan, Zhonglu Yang, Songli Yuan, Chanjuan Zhang, Xiaojuan Zhang, Baohui Liu, Fanjiang Kong, Xia Li, Xinan Zhou…
    Citation: BMC Plant Biology 2019 19:131
    Content type: Research article Published on:

  23. Two-line hybrid rice with high yield potential is increasingly popular and the photo- and temperature-sensitive male sterile line is one of the basic components for two-line hybrid rice breeding. The developme...

    Authors: Hirendra Nath Barman, Zhonghua Sheng, Sajid Fiaz, Min Zhong, Yawen Wu, Yicong Cai, Wei Wang, Guiai Jiao, Shaoqing Tang, Xiangjin Wei and Peisong Hu
    Citation: BMC Plant Biology 2019 19:109
    Content type: Research article Published on:

  24. Recent innovation in the field of genome engineering encompasses numerous levels of plant genome engineering which attract the substantial excitement of plant biologist worldwide. RNA-guided CRISPR Cas9 system...

    Authors: Noor al Amin, Naveed Ahmad, Nan Wu, Xiumin Pu, Tong Ma, Yeyao Du, Xiaoxue Bo, Nan Wang, Rahat Sharif and Piwu Wang
    Citation: BMC Biotechnology 2019 19:9
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Biotechnology 2020 20:42

  25. NPR1, nonexpressor of pathogenesis-related gene 1, is a master regulator involved in plant defense response to pathogens, and its regulatory mechanism in the defense pathway has been relatively clear. However, in...

    Authors: Rui Li, Chunxue Liu, Ruirui Zhao, Liu Wang, Lin Chen, Wenqing Yu, Shujuan Zhang, Jiping Sheng and Lin Shen
    Citation: BMC Plant Biology 2019 19:38
    Content type: Research article Published on:

  26. Genetic engineering technology such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system provides a powerful tool for developing disease models and determining gene functions. Rece...

    Authors: Kiyoung Eun, Min Gi Park, Yeon Woo Jeong, Yeon Ik Jeong, Sang-Hwan Hyun, Woo Suk Hwang, Sung-Hak Kim and Hyunggee Kim
    Citation: BMC Biotechnology 2019 19:1
    Content type: Research article Published on:

  27. CRISPR/Cas9 technology is one of the most powerful and useful tools for genome editing in various living organisms. In higher plants, the system has been widely exploited not only for basic research, such as g...

    Authors: Masahiro Nishihara, Atsumi Higuchi, Aiko Watanabe and Keisuke Tasaki
    Citation: BMC Plant Biology 2018 18:331
    Content type: Research article Published on:

  28. Recently, the CRISPR/Cas9 system has been widely used to precisely edit plant genomes. Due to the difficulty in Agrobacterium-mediated genetic transformation of wheat, the reported applications in CRISPR/Cas9 sys...

    Authors: Shujuan Zhang, Rongzhi Zhang, Guoqi Song, Jie Gao, Wei Li, Xiaodong Han, Mingli Chen, Yulian Li and Genying Li
    Citation: BMC Plant Biology 2018 18:302
    Content type: Research article Published on: