|
|
Analysis of the Development Trends in Global Agricultural Animal Gene Editing Fundamental Research |
ZHANG Meng-Meng*, JIANG Ying, LI Ning |
Beijing Capital Agribusiness Future Biotechnology Co., Ltd., Beijing100088, China |
|
|
Abstract Gene editing technology is a precise modification technique that can manipulate DNA sequences in living organisms. In order to understand the global development trends in this field, particularly with regard to agricultural animal gene editing, the present study utilized the bibliometric methods to analyze research data from 2015 to 2022 in the field of gene editing technology. In this study, we systematically examined the main research institutions, teams, research frontiers, and current status of agricultural animal gene editing technology research. The results showed that China is in a leading position internationally in gene editing technology research at the literature level, as it is ranked second in the world in terms of the number of gene editing technology-related papers published between 2015 and 2022. Eight of the top 20 institutions being in China, accounting for 40% of the total in the world. However, compared with developed countries, such as the United States, China still lags behind in terms of core technology innovation, gene editing system development, optimization and Cas protein discoveries, all of which are mainly being conducted overseas. Although China ranks second in the world in terms of the number of papers published in top international academic journals, however, it is far behind the United States. In the Nature Biotechnology, China accounts for only one-fifth of the total number of papers, with 31 papers published. The number of research reports on gene editing technology in agricultural animals is relatively small, but it is increasing year by year. The application of gene editing technology in animal breeding has immense potential in the field of agricultural animal breeding, particularly in developing disease-resistant breeds. Finally, we look forward to the prospect of gene editing technology and the development trends of agricultural animal breeding field based on the current situation and national conditions, in order to provide us with a reference for using gene editing technology to solve major problems in agricultural animal breeding, especially disease resistance breeding.
|
Received: 28 June 2023
|
|
Corresponding Authors:
* zhangmengmeng@sunlonbio.com
|
|
|
|
[1] 李国栋. 2010. 基于SCI论文产出的我国基础研究比较分析[J]. 北华航天工业学院学报, 20: 21-23+34. (Li G D.2010. SCI-E based literature productivity analysis of bioinformatics in China[J]. Journal of North China Institute of Aerospace Engineering, 20: 21-23+34.) [2] 徐嘉威, 贺花, 沈雪梅, 等. 2018. 基因编辑技术在家畜育种中的研究进展[J]. 基因组学与应用生物学, 37(4): 1423-1430. (Xu J W, He H, Shen X M, et al.2018. Research progress of gene editing technology in livestock breeding[J]. Genomics and Applied Biology, 37(4): 1423-1430.) [3] 许丽, 王玥, 姚驰远, 等. 2018. 基因编辑技术发展态势分析与建议[J]. 中国生物工程杂志, 38: 113-122. (Xu L, Wang Y, Yao C Y, et al.2018. Trends and development bottleneck analysis of gene editing technology[J]. China Biotechnology, 38: 113-122.) [4] Abudayyeh O O, Gootenberg J S, Konermann S, et al.2016. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector[J]. Science, 353: aaf5573. [5] Barrangou R, Fremaux C, Deveau H, et al.2007. CRISPR provides acquired resistance against viruses in prokaryotes[J]. Science, 315: 1709-1712. [6] Chavez A, Scheiman J, Vora S, et al.2015. Highly efficient Cas9-mediated transcriptional programming[J]. Nature Methods, 12: 326-328. [7] Chen C.2004. Searching for intellectual turning points: Progressive knowledge domain visualization[J]. Proceedings of the National Academy of Sciences of the USA, 101(Suppl 1): 5303-5310. [8] Cohen D R, Townsend C A.2018. A dual role for a polyketide synthase in dynemicin enediyne and anthraquinone biosynthesis[J]. Nature Chemistry, 10: 231-236. [9] Cong L, Ran F A, Cox D, et al.2013. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 339: 819-823. [10] Dever D P, Bak R O, Reinisch A, et al.2016. CRISPR/Cas9 beta-globin gene targeting in human haematopoietic stem cells[J]. Nature, 539: 384-389. [11] Dong O X, Yu S, Jain R, et al.2020. Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9[J]. Nature Communications, 11(1): 1178. [12] Eyquem J, Mansilla-Soto J, Giavridis T, et al.2017. Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection[J]. Nature, 543: 113-117. [13] Gaudelli N M, Komor A C, Rees H A, et al.2017. Programmable base editing of A• T to G• C in genomic DNA without DNA cleavage[J]. Nature, 551: 464-471. [14] Gilbert L A, Larson M H, Morsut L, et al.2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes[J]. Cell, 154: 442-451. [15] Gilpatrick T, Lee I, Graham J E, et al.2020. Targeted nanopore sequencing with Cas9-guided adapter ligation[J]. Nature Biotechnology, 38: 433-438. [16] Hsu P D, Lander E S, Zhang F.2014. Development and applications of CRISPR-Cas9 for genome engineering[J]. Cell, 157: 1262-1278. [17] Ishino Y, Shinagawa H, Makino K, et al.1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product[J]. Journal of Bacteriology, 169: 5429-5433. [18] Jansen R, Embden J D V, Gaastra W, et al.2002. Identification of genes that are associated with DNA repeats in prokaryotes[J]. Molecular Microbiology, 43: 1565-1575. [19] Jeong Y H, Kim Y J, Kim E Y, et al.2016. Knock-in fibroblasts and transgenic blastocysts for expression of human FGF2 in the bovine beta-casein gene locus using CRISPR/Cas9 nuclease-mediated homologous recombination[J]. Zygote, 24: 442-456. [20] Jia H, Zhang L, Wang T, et al.2017. Development of a CRISPR/Cas9-mediated gene-editing tool in Streptomyces rimosus[J]. Microbiology (Reading), 163: 1148-1155. [21] Jinek M, Chylinski K, Fonfara I, et al.2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 337: 816-821. [22] Keung A J, Bashor C J, Kiriakov S, et al.2014. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation[J]. Cell, 158: 110-120. [23] Kim G-D, Lee J H, Song S, et al.2020. Generation of myostatin-knockout chickens mediated by D10A-Cas9 nickase[J]. The FASEB Journal, 34: 5688-5696. [24] Komor A C, Kim Y B, Packer M S, et al.2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage[J]. Nature, 533: 420-424. [25] Li M, Li X, Zhou Z, et al.2016. Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 system[J]. Frontiers in Plant Science, 7: 377. [26] Li R, Zeng W, Ma M, et al.2020. Precise editing of myostatin signal peptide by CRISPR/Cas9 increases the muscle mass of Liang Guang Small Spotted pigs[J]. Transgenic Research, 29: 149-163. [27] Li X, Hao F, Hu X, et al.2019. Generation of Tbeta4 knock-in Cashmere goat using CRISPR/Cas9[J]. International Journal of Biological Sciences, 15: 1743-1754. [28] Liu X, Zhang Y, Cheng C, et al.2017. CRISPR-Cas9-mediated multiplex gene editing in CAR-T cells[J]. Cell Research, 27: 154-157. [29] Liu Y, Zou R, Nihongaki Y, et al.2020. Very fast CRISPR on demand[J]. Biophysical Journal, 118: 29a. [30] Maeder M L, Angstman J F, Richardson M E, et al.2013a. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins[J]. Nature Biotechnology, 31: 1137-1142. [31] Maeder M L, Linder S J, Cascio V M, et al.2013b. CRISPR RNA-guided activation of endogenous human genes[J]. Nature Methods, 10: 977-979. [32] Mali P, Yang L, Esvelt K M, et al.2013. RNA-guided human genome engineering via Cas9[J]. Science, 339: 823-826. [33] Mendenhall E M, Williamson K E, Reyon D, et al.2013. Locus-specific editing of histone modifications at endogenous enhancers[J]. Nature Biotechnology, 31: 1133-1136. [34] Miller J C, Holmes M C, Wang J, et al.2007. An improved zinc-finger nuclease architecture for highly specific genome editing[J]. Nature Biotechnology, 25: 778-785. [35] Miller J C, Tan S, Qiao G, et al.2011. A TALE nuclease architecture for efficient genome editing[J]. Nature Biotechnology, 29: 143-148. [36] Mojica F J, Díez‐Villaseñor C, Soria E, et al.2000. Biological significance of a family of regularly spaced repeats in the genomes of archaea, bacteria and mitochondria[J]. Molecular microbiology, 36: 244-246. [37] Morineau C, Bellec Y, Tellier F, et al.2017. Selective gene dosage by CRISPR-Cas9 genome editing in hexaploid Camelina sativa[J]. Plant Biotechnology Journal, 15: 729-739. [38] Park T S, Lee H J, Kim K H, et al.2014. Targeted gene knockout in chickens mediated by TALENs[J]. Proceedings of the National Academy of Sciences of the USA, 111: 12716-12721. [39] Park T S, Park J, Lee J H, et al.2019. Disruption of G0/G1 switch gene 2 (G0S2) reduced abdominal fat deposition and altered fatty acid composition in chicken[J]. The FASEB Journal, 33: 1188-1198. [40] Qi L S, Larson M H, Gilbert L A, et al.2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression[J]. Cell, 152: 1173-1183. [41] Soyk S, Muller N A, Park S J, et al.2017. Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato[J]. Nature Genetics, 49: 162-168. [42] Sun Y, Jiao G, Liu Z, et al.2017. Generation of high-amylose rice through CRISPR/Cas9-mediated targeted mutagenesis of starch branching enzymes[J]. Frontiers in Plant Science, 8: 298. [43] Tanihara F, Hirata M, Nguyen N T, et al.2021. Generation of CD163-edited pig via electroporation of the CRISPR/Cas9 system into porcine in vitro-fertilized zygotes[J]. Animal Biotechnology, 32: 147-154. [44] Taylor L, Carlson D F, Nandi S, et al.2017. Efficient TALEN-mediated gene targeting of chicken primordial germ cells[J]. Development, 144: 928-934. [45] Tong Y, Whitford C M, Robertsen H L, et al.2019. Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST[J]. Proceedings of the National Academy of Sciences of the USA, 116: 20366-20375. [46] Travis J.2015. Breakthrough of the Year: CRISPR makes the cut[J]. Science Magazine: 1456-1457. [47] Tu C F, Chuang C, Yang T S.2022. The application of new breeding technology based on gene editing in pig industry—A review[J]. Animal Bioscience, 35(6): 791. [48] Van Eck N J, Waltman L.2010. Software survey: VOSviewer, a computer program for bibliometric mapping[J]. Scientometrics, 84: 523-538. [49] Wang F, Wang C, Liu P, et al.2016. Enhanced rice blast resistance by CRISPR/Cas9-Targeted mutagenesis of the erf transcription factor gene OsERF922[J]. PLOS ONE, 11: e0154027. [50] Wang J Y, Doudna J A.2023. CRISPR technology: A decade of genome editing is only the beginning[J]. Science, 379(6629): eadd8643. [51] Whitworth K M, Lee K, Benne J A, et al.2014. Use of the CRISPR/Cas9 system to produce genetically engineered pigs from in vitro-derived oocytes and embryos[J]. Biology of Reproduction, 91: 78. [52] Wu H, Wang Y, Zhang Y, et al.2015. TALE nickase-mediated SP110 knockin endows cattle with increased resistance to tuberculosis[J]. Proceedings of the National Academy of Sciences of the USA, 112: E1530-1539. [53] Xu K, Zhou Y, Mu Y, et al.2020. CD163 and pAPN double-knockout pigs are resistant to PRRSV and TGEV and exhibit decreased susceptibility to PDCoV while maintaining normal production performance[J]. Elife, 9: e57132. [54] Xu L, Wang J, Liu Y, et al.2019. CRISPR-edited stem cells in a patient with HIV and acute lymphocytic leukemia[J]. The New England Journal of Medicine, 381: 1240-1247. [55] Xu R, Yang Y, Qin R, et al.2016. Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice[J]. Journal of Genetics and Genomics, 43: 529-532. [56] Yang H, Zhang J, Zhang X, et al.2018. CD163 knockout pigs are fully resistant to highly pathogenic porcine reproductive and respiratory syndrome virus[J]. Antiviral Research, 151: 63-70. [57] Young A E, Mansour T A, Mcnabb B R, et al.2020. Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull[J]. Nature Biotechnology, 38: 225-232. [58] Yu S, Luo J, Song Z, et al.2011. Highly efficient modification of beta-lactoglobulin (BLG) gene via zinc-finger nucleases in cattle[J]. Cell Research, 21: 1638-1640. [59] Zetsche B, Gootenberg J S, Abudayyeh O O, et al.2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system[J]. Cell, 163: 759-771. [60] Zhang J, Liu J, Yang W, et al.2019a. Comparison of gene editing efficiencies of CRISPR/Cas9 and TALEN for generation of MSTN knock-out cashmere goats[J]. Theriogenology, 132: 1-11. [61] Zhang X, Li W, Liu C, et al.2017. Alteration of sheep coat color pattern by disruption of ASIP gene via CRISPR Cas9[J]. Scientific Reports, 7: 8149. [62] Zhang Y, Wang J, Wang Z, et al.2019b. A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae[J]. Nature Communications, 10: 1053. |
|
|
|