分子编写育种——动物育种的发展方向

doi:10.3864/j.issn.0578-1752.2018.12.016

Abstract

Abstract: With the rapid development of genomics and genome editing techniques, and the extensive application of techniques such as microinjection and somatic cell nuclear transfer, a new set of breeding strategies and methods has gradually formed, which we named breeding by molecular writing (BMW). Using BMW, directional breeding of new varieties can be achieved by molecular-level genome editing, which can not only break down reproductive barriers separating different taxa, allowing the cross-species introduction of new traits, but also enable single-nucleotide insertion, deletion, and substitution in individual genomes. This can include the precise integration of exogenous genes; precise deletion and substitution of endogenous genes; and replication, deletion, and substitution of SNP loci. The main advantage of BMW is the rapid and efficient gathering of several beneficial traits into one species, while significantly reducing unintended effects. Molecular writing can be used for the following tasks: (1) identification and verification of new breeding markers; (2) cross-species molecular writing; (3) base sequence deletion in genomes; and (4) molecular writing within species. The BMW technique allows the introduction of only one or several target genes or SNPs and the rapid acquisition of new stable genetic varieties with pronounced target characters without sexual hybridization, and can then create new varieties in combination with conventional breeding methods. BMW can achieve genetic (or molecular) hybridization breeding at the individual and group levels, acquiring molecular heterosis, efficiently resolving several long-standing difficulties in breeding, and significantly improving breeding efficiency. It has strong potential for application in livestock and poultry breeding, and is a key part of the future of breeding. This paper discusses the basic concepts, research methods, research contents, and current research status of breeding by molecular writing in detail, and presents the prospects of applying BMW, providing references for researchers and practitioners in fields such as animal breeding and livestock and poultry reproduction.

Key words: breeding, breeding by molecular writing, gene editing, somatic cell nuclear transfer, gene knockout

LIU ZhiGuo, WANG BingYuan, MU YuLian, WEI Hong, CHEN JunHai, LI Kui. Breeding by Molecular Writing (BMW): the Future Development of Animal Breeding[J].Scientia Agricultura Sinica, 2018, 51(12): 2398-2409.

References

[1] MUSUNURU K. The hope and hype of CRISPR-Cas9 genome editing: A review. JAMA Cardiology, 2017, 2(8): 914-919.

[2] 刘志国. CRISPR/Cas9系统介导基因编辑的研究进展.畜牧兽医学报, 2014, 45(10): 1567-1583.

LIU Z G. Research progress on CRISPR/Cas9 mediated genome editing. Acta Veterinaria et Zootechnica Sinica, 2014, 45(10): 1567-1583.(in Chinese)

[3] RUAN J X, XU J, CHEN-TSAI R Y, LI K. Genome editing in livestock: Are we ready for a revolution in animal breeding industry? Transgenic Research, 2017, 26(6): 715-726.

[4] TELUGU B P, PARK K-E,PARK C-H. Genome editing and genetic engineering in livestock for advancing agricultural and biomedical applications. Mammalian Genome, 2017, 28(7-8): 338-347.

[5] M NORET S, TESSON L, REMY S, USAL C, OUISSE L-H, BRUSSELLE L, CHENOUARD V,ANEGON I. Advances in transgenic animal models and techniques. Transgenic Research, 2017, 26(5): 703-708.

[6] DEKELVER R, OU L, LAOHARAWEE K, TOM S, RADEKE R, ROHDE M, SPROUL S, PRZYBILLA M, KONIAR B L, PODETZ-PEDERSEN K, COOKSLEY R D, HOLMES M C, MCIVOR R S, WHITLEY C B,WECHSLER T. ZFN-mediated in vivo genome editing results in phenotypic correction in murine MPS I and MPS II models. Molecular Genetics And Metabolism, 2017, 120(1): S41.

[7] TAYLOR L, CARLSON D F, NANDI S, SHERMAN A, FAHRENKRUG S C,MCGREW M J. Efficient TALEN-mediated gene targeting of chicken primordial germ cells. Development, 2017, 144(5): 928.

[8] CHEN Y, YU J, NIU Y, QIN D, LIU H, LI G, HU Y, WANG J, LU Y, KANG Y, JIANG Y, WU K, LI S, WEI J, HE J, WANG J, LIU X, LUO Y, SI C, BAI R, ZHANG K, LIU J, HUANG S, CHEN Z,

WANG S, CHEN X, BAO X, ZHANG Q, LI F, GENG R, LIANG A, SHEN D, JIANG T, HU X, MA Y, JI W,SUN Y E. Modeling rett syndrome using TALEN-edited MECP2 mutant cynomolgus monkeys. Cell, 2017, 169(5): 945-955.e10.

[9] LI X P, YANG Y, BU L, GUO X G, TANG C C, SONG J, FAN N N, ZHAO B T, OUYANG Z, LIU Z M, ZHAO Y, YI X L, QUAN L Q, LIU S C, YANG Z G, OUYANG H, CHEN Y E, WANG Z, LAI L X. Rosa26-targeted swine models for stable gene over-expression and Cre-mediated lineage tracing. Cell Research, 2014, 24(4): 501-504.

[10] RUAN J, LI H, XU K, WU T, WEI J, ZHOU R, LIU Z, MU Y, YANG S, OUYANG H, CHEN-TSAI R Y,LI K. Highly efficient CRISPR/Cas9-mediated transgene knockin at the H11 locus in pigs. Scientific Reports, 2015, 5: 14253.

[11] GAO Y, WU H, WANG Y, LIU X, CHEN L, LI Q, CUI C, LIU X, ZHANG J,ZHANG Y. Single Cas9 nickase induced generation of NRAMP1 knockin cattle with reduced off-target effects. Genome Biology, 2017, 18(1): 13-13.

[12] WELLS K D, BARDOT R, WHITWORTH K M, TRIBLE B R, FANG Y, MILEHAM A, KERRIGAN M A, SAMUEL M S, PRATHER R S,ROWLAND R R. Replacement of porcine CD163 scavenger receptor cysteine-rich domain 5 with a CD163-like homolog confers resistance of pigs to genotype 1 but not genotype 2 porcine reproductive and respiratory syndrome virus. Journal of Virology, 2017, 91(2):e01521.

[13] GROBET L, ROYO MARTIN L J, PONCELET D, PIROTTIN D, BROUWERS B, RIQUET J, SCHOEBERLEIN A, DUNNER S, MENISSIER F, MASSABANDA J, FRIES R, HANSET R,GEORGES M. A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nature Genetics, 1997, 17(1): 71-74.

[14] LILLICO S G, PROUDFOOT C, KING T J, TAN W, ZHANG L, MARDJUKI R, PASCHON D E, REBAR E J, URNOV F D, MILEHAM A J, MCLAREN D G,WHITELAW C B A. Mammalian interspecies substitution of immune modulatory alleles by genome editing. Scientific Reports, 2016, 6: 21645.

[15] YANG L H, G ELL M, NIU D, GEORGE H, LESHA E, GRISHIN D, AACH J, SHROCK E, XU W, POCI J, CORTAZIO R, WILKINSON R A, FISHMAN J A,CHURCH G. Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science, 2015, 350(6264): 1101.

[16] NIU D, WEI H-J, LIN L, GEORGE H, WANG T, LEE I H, ZHAO H-Y, WANG Y, KAN Y, SHROCK E, LESHA E, WANG G, LUO Y, QING Y, JIAO D, ZHAO H, ZHOU X, WANG S, WEI H, G ELL M, CHURCH G M,YANG L. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science, 2017.

[17] DAVID C. Super-muscly pigs created by small genetic tweak. Nature, 2015, (523): 13-14.

[18] WANG K K, OUYANG H, XIE Z C, YAO C G, GUO N N, LI M J, JIAO H P,PANG D X. Efficient generation of myostatin mutations in pigs using the CRISPR/Cas9 system. Scientific Reports, 2015, 5: 16623.

[19] BI Y, HUA Z, LIU X, HUA W, REN H, XIAO H, ZHANG L, LI L, WANG Z, LAIBLE G, WANG Y, DONG F,ZHENG X. Isozygous and selectable marker-free MSTN knockout cloned pigs generated by the combined use of CRISPR/Cas9 and Cre/LoxP. Scientific Reports, 2016, 6: 31729.

[20] YU S, LUO J, SONG Z, DING F, DAI Y, LI N. Highly efficient modification of beta-lactoglobulin (BLG) gene via zinc-finger nucleases in cattle. Cell Research, 2011, 21(11): 1638-1640.

[21] KUROIWA Y, KASINATHAN P, MATSUSHITA H, SATHIYASELAN J, SULLIVAN E J, KAKITANI M, TOMIZUKA K, ISHIDA I,ROBL J M. Sequential targeting of the genes encoding immunoglobulin- mu and prion protein in cattle. Nature Genetics, 2004, 36(7): 775-780.

[22] DENNING C, BURL S, AINSLIE A, BRACKEN J, DINNYES A, FLETCHER J, KING T, RITCHIE M, RITCHIE W A, ROLLO M, DE SOUSA P, TRAVERS A, WILMUT I,CLARK A J. Deletion of the alpha(1,3)galactosyl transferase (GGTA1) gene and the prion protein (PrP) gene in sheep. Nature Biotechnology, 2001, 19(6): 559-562.

[23] YU G, CHEN J, YU H, LIU S, CHEN J, XU X, SHA H, ZHANG X, WU G, XU S,CHENG G. Functional disruption of the prion protein gene in cloned goats. Journal of General Virology, 2006, 87(4): 1019-1027.

[24] ZHU C, LI B, YU G, CHEN J, YU H, CHEN J, XU X, WU Y, ZHANG A,CHENG G. Production of Prnp-/- goats by gene targeting in adult fibroblasts. Transgenic Research, 2009, 18(2): 163-171.

[25] WHITWORTH K M, ROWLAND R R, EWEN C L, TRIBLE B R, KERRIGAN M A, CINO-OZUNA A G, SAMUEL M S, LIGHTNER J E, MCLAREN D G, MILEHAM A J, WELLS K D,PRATHER R S. Gene-edited pigs are protected from porcine reproductive and respiratory syndrome virus. Nature Biotechnology, 2015, 34(1): 20-22.

[26] BURKARD C, LILLICO S G, REID E, JACKSON B, MILEHAM A J, AIT-ALI T, WHITELAW C B, ARCHIBALD A L. Precision engineering for PRRSV resistance in pigs: Macrophages from genome edited pigs lacking CD163 SRCR5 domain are fully resistant to both PRRSV genotypes while maintaining biological function. Plos Pathogens, 2017, 13(2): e1006206.

[27] WHITWORTH K M, LEE K, BENNE J A, BEATON B P, SPATE L D, MURPHY S L, SAMUEL M S, MAO J, O'GORMAN C, WALTERS E M, MURPHY C N, DRIVER J, MILEHAM A, MCLAREN D, WELLS K D,PRATHER R S. Use of the CRISPR/Cas9 system to produce genetically engineered pigs from in vitro-derived oocytes and embryos. Biology of Reproduction, 2014, 91(3): 1-13.

[28] 魏迎辉, 刘志国, 徐奎, EVANNA HUYHN, PAUL DYCE, 李继良, 周伟良, 董树仁, 冯保亮, 牟玉莲, JULANG LI, 李奎. CD163双等位基因编辑猪的制备及传代. 中国农业科学, 2018, 51(4): 770-777.

WEI Y H, LIU Z G, XU K, EVANNA H, PAUL D, LI J L, ZHOU W L, DONG S R, FENG B L, MU Y L, LI J, LI K. Generation and propagation of cluster of differentiation 163 biallelic gene editing pigs. Scientia Agricultura Sinica, 2018, 51(4): 770-777.（in Chinese）

[29] VAN LAERE A S, NGUYEN M, BRAUNSCHWEIG M, NEZER C, COLLETTE C, MOREAU L, ARCHIBALD A L, HALEY C S, BUYS N, TALLY M, ANDERSSON G, GEORGES M, ANDERSSON L. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature, 2003, 425(6960): 832-836.

[30] GRAF B, SENN M. Behavioural and physiological responses of calves to dehorning by heat cauterization with or without local anaesthesia. Applied Animal Behaviour Science, 1999, 62(2): 153-171.

[31] LONG C R, GREGORY K E. Inheritance of the horned, scurred, and polled condition in cattle. Journal of Heredity, 1978, 69(6): 395-400.

[32] MEDUGORAC I, SEICHTER D, GRAF A, RUSS I, BLUM H, G PEL K H, ROTHAMMER S, F RSTER M, KREBS S. Bovine polledness – An autosomal dominant trait with allelic heterogeneity. Plos One, 2012, 7(6): e39477.

[33] TAN W F, CARLSON D F, LANCTO C A, GARBE J R, WEBSTER D A, HACKETT P B, FAHRENKRUG S C. Efficient nonmeiotic allele introgression in livestock using custom endonucleases. Proceedings of the National Academy of Sciences, 2013, 110(41): 16526-16531.

[34] LYALL J, IRVINE R M, SHERMAN A, MCKINLEY T J, NUNEZ A, PURDIE A, OUTTRIM L, BROWN I H, ROLLESTON-SMITH G, SANG H, TILEY L. Suppression of avian influenza transmission in genetically modified chickens. Science, 2011, 331(6014): 223-226.

[35] RUIZ-HERNANDEZ R, MWANGI W, PEROVAL M, SADEYEN J R, ASCOUGH S, BALKISSOON D, STAINES K, BOYD A, MCCAULEY J, SMITH A, BUTTER C. Host genetics determine susceptibility to avian influenza infection and transmission dynamics. Scientific Reports, 2016, 6: 26787.

[36] LEDFORD H, Salmon is first transgenic animal to win US approval for food. Nature. 2015.

[37] 王大元. 美国转基因三文鱼商业化的启示.科学通报, 2016, 61(3): 289-295.

Wang D Y. Implications of US GMO salmon approved for commercial food use. Chinese Science Bulletin, 2016, 61(3):289-295. (in Chinese)

[38] WALTZ E. First genetically engineered salmon sold in Canada. Nature, 2017, 548: 148.

[39] LIN S, STAAHL B T, ALLA R K, DOUDNA J A. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. eLife, 2014, 3: e04766.

[40] MA Y, CHEN W, ZHANG X, YU L, DONG W, PAN S, GAO S, HUANG X, ZHANG L. Increasing the efficiency of CRISPR/Cas9- mediated precise genome editing in rats by inhibiting NHEJ and using Cas9 protein. RNA Biology, 2016, 13(7): 605-612.

[41] YANG D, SCAVUZZO M A, CHMIELOWIEC J, SHARP R, BAJIC A, BOROWIAK M. Enrichment of G2/M cell cycle phase in human pluripotent stem cells enhances HDR-mediated gene repair with customizable endonucleases. Scientific Reports, 2016, 6: 21264.

[42] RICHARDSON C D, RAY G J, DEWITT M A, CURIE G L, CORN J E. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nature Biotechnology, 2016, 34(3): 339-344.

[43] HENDEL A, BAK R O, CLARK J T, KENNEDY A B, RYAN D E, ROY S, STEINFELD I, LUNSTAD B D, KAISER R J, WILKENS A B, BACCHETTA R, TSALENKO A, DELLINGER D, BRUHN L, PORTEUS M H. Chemically modified guide RNAs enhance CRISPR- Cas genome editing in human primary cells. Nature Biotechnology, 2015, 33(9): 985-989.

[44] YU C, LIU Y, MA T, LIU K, XU S, ZHANG Y, LIU H, LA RUSSA M, XIE M, DING S, QI LEIS. Small molecules enhance CRISPR genome editing in pluripotent stem cells. Cell Stem Cell, 2015, 16(2): 142-147.

[45] NISHIDA K, ARAZOE T, YACHIE N, BANNO S, KAKIMOTO M, TABATA M, MOCHIZUKI M, MIYABE A, ARAKI M, HARA K Y, SHIMATANI Z, KONDO A. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science, 2016. Doi:10.1126/Science.aaf8729.

[46] KOMOR A C, KIM Y B, PACKER M S, ZURIS J A, LIU D R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature, 2016, 533(7603): 420-424.

[47] PAN Y, SHEN N, JUNG-KLAWITTER S, BETZEN C, HOFFMANN G F, HOHEISEL J D, BLAU N. CRISPR RNA-guided FokI nucleases repair a PAH variant in a phenylketonuria model. Scientific Reports, 2016, 6: 35794.

[48] TERAO M, TAMANO M, HARA S, KATO T, KINOSHITA M, TAKADA S. Utilization of the CRISPR/Cas9 system for the efficient production of mutant mice using crRNA/tracrRNA with Cas9 nickase and FokI-dCas9. Experimental Animals, 2016, 65(3): 275-283.

[49] SLAYMAKER I M, GAO L, ZETSCHE B, SCOTT D A, YAN W X, ZHANG F. Rationally engineered Cas9 nucleases with improved specificity. Science, 2015, 351(6268): 84.

[50] KLEINSTIVER B P, PATTANAYAK V, PREW M S, TSAI S Q, NGUYEN N T, ZHENG Z, JOUNG J K. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature, 2016, 529: 490-495.

[51] FU Y, SANDER J D, REYON D, CASCIO V M, JOUNG J K. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nature Biotechnology, 2014, 32(3): 279-284.

[52] CHO S W, KIM S, KIM Y, KWEON J, KIM H S, BAE S, KIM J S. Analysis of off-target effects of CRISPR/Cas-derived RNA- guided endonucleases and nickases. Genome Research, 2014, 24(1): 132-141.

[53] HUANG S, WEIGEL D, BEACHY R N, LI J. A proposed regulatory framework for genome-edited crops. Nature Genetics, 2016, 48(2): 109-111.

[54] WALTZ E. Gene-edited CRISPR mushroom escapes US regulation. Nature, 2016, 532: 158-159.

[55] GAO C. The future of CRISPR technologies in agriculture. Nature Reviews Molecular Cell Biology, 2018. Doi:10.1038/nrm.2018.2

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