基因编辑及全基因组选择技术在水稻育种中的应用展望

doi:10.16819/j.1001-7216.2024.230503

摘要/Abstract

摘要：

水稻是我国主要的粮食作物。由于我国人多地少的现状，长期以来水稻的育种目标是以产量为导向。我国科研人员通过协同攻关实现了水稻育种技术突破，矮化育种和杂交水稻育种技术的利用促进了水稻产量两次大的飞跃。随着我国消费者生活水平的提高以及极端天气出现的频次上升，水稻育种对品质、抗性与耐逆等也提出了更高要求。目前，生物技术正在不断革新，特别是基因编辑和全基因组选择育种技术的迅速发展，为高产优质多抗耐逆的水稻新品种选育提供强有力支持，推动着我国水稻生产向绿色可持续发展。本文就基因编辑技术和全基因组选择技术在水稻高产优质、抗病虫、耐逆及杂种优势育种应用中的新进展进行简述，旨在为高效培育能够满足市场需求的水稻新品种提供一些育种思路。

关键词: 水稻, 育种技术, 基因编辑, 全基因组选择

Abstract:

Rice is the main grain crop in China. Due to large population and limited land resources in China, rice breeding goals have long been yield oriented. Chinese researchers have continuously achieved breakthroughs in rice breeding technology, and the adoption of dwarf breeding and hybrid rice breeding technology has resulted in two significant leaps in rice yield in China. However, with the improvement of living standards and the increasing frequency of extreme weather events, higher demands have been placed on rice in terms of yield, quality, and resistance. At present, biotechnology is undergoing constant innovation, particularly with the rapid development of gene editing and genomic selection breeding technology. This progress is expected to provide robust support for the development of new rice varieties with high yield, superior quality, and resistance to multiple factors. It helps promote the green and sustainable development of rice production. This paper reviews the recent advancements in gene editing technology and genomic selection technology in rice breeding for high yield, superior quality, disease and insect resistance, stress tolerance, and heterosis. The goal is to provide breeding strategies for the efficient development of new varieties to meet demands.

Key words: rice, breeding techniques, gene editing, genomic selection

梁楚炎, 巫明明, 黄凤明, 翟荣荣, 叶靖, 朱国富, 俞法明, 张小明, 叶胜海. 基因编辑及全基因组选择技术在水稻育种中的应用展望[J]. 中国水稻科学, 2024, 38(1): 1-12.

LIANG Chuyan, WU Mingming, HUANG Fengming, ZHAI Rongrong, YE Jing, ZHU Guofu, YU Faming, ZHANG Xiaoming, YE Shenghai. Prospects for the Application of Gene Editing and Genomic Selection in Rice Breeding[J]. Chinese Journal OF Rice Science, 2024, 38(1): 1-12.

图/表 2

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基因名称 Gene name			表型 Phenotype		参考文献 Reference
IPA1	敲除Knockout	顺式调控区 Cis-regulatory element	产量提高15.9% 15.9% increase in yield		[21]
SD8	敲除Knockout	外显子Exon	密植条件下增产10% 10% increase in yield		[22]
OsKRN2	敲除Knockout	外显子Exon	增产8% 8% increase in yield		[23]
OsMADS17	敲除Knockout	5′UTR	穗粒数、粒重增加Grain number and weight increased		[24]
GW2, GW5, TGW6	敲除Knockout	外显子Exon	粒重增加Grain weight increased		[25]
OsPIN56, GS3, OsMYB30	敲除Knockout	外显子Exon	高产、耐冷High yield and cold resistance increased		[26]
Dull	敲除Knockout	外显子Exon	直链淀粉含量下降Decreased amylose content		[30]
Wx^b	敲除Knockout	TATA box	微调直链淀粉含量Fine-tune amylose content		[32]
Wx^a	敲除Knockout	5′UTR	直链淀粉含量下降Decreased amylose content		[33]
Wx^b	敲除Knockout	N-末端结构域 N-terminal domain	低淀粉含量Low starch content		[34]
SS3a, SS3b	敲除Knockout	外显子Exon	抗性淀粉增加Resistant starch increased		[35]
OsBADH2	敲除Knockout	外显子Exon	稻米香味增加Aroma of rice increased		[35]
OsGlus	敲除Knockout	外显子Exon	稻米蛋白质含量下降Decreased protein content		[37]
DEP1	敲除Knockout	蛋白质C端 C-terminus	提高产量和稻米品质Improved yield and rice quality		[38]
Bsr-d1, Pi21, ERF922	敲除Knockout	外显子Exon	稻瘟病及白叶枯病抗性增强Resistance to rice blast and rice bacterial blight was enhanced		[44]
OsS5H1, OsS5H2	敲除Knockout	外显子Exon	稻瘟病及白叶枯病抗性增强Resistance to rice blast and rice bacterial blight was enhanced		[45]
OsMPK5	敲除Knockout	磷酸化位点Phosphorylation site	产量及稻瘟病抗性提高Yield and blast resistance improved		[46]
Xa13	敲除Knockout	启动子Promoter	产量不变、强白叶枯病抗性Unchanged yield and stronger resistance to rice bacterial blight		[47]
OsSWEET11, 13, 14	敲除Knockout	启动子Promoter	广谱白叶枯病抗性Broad-spectrum rice bacterial blight resistance		[48]
OsSWEET14	敲除Knockout	启动子Promoter	白叶枯病抗性增加Increased resistance to rice bacterial blight		[49]
FAS	HIGS		二化螟存活率下降Survival rate of C. suppressalis decreased		[50]
OsWRKY53	iRNA		二化螟抗性增加C. suppressalis resistance increased		[51]
OsHPP04	敲除Knockout	外显子Exon	对拟禾本科根结线虫抗性增加Resistance to Meloidogyne graminicola increased		[52]
OsWRKY71, OsSKC1	敲入Knock-in	增强子Enhancer	非生物胁迫抗性增加Increased resistance to abiotic stresses		[54]
OsHYPK	敲除Knockout	外显子Exon	抗旱耐盐Increased drought and salt tolerant		[55]
AFP1	敲除Knockout	外显子Exon	耐旱耐热Increased drought and heat tolerant		[57]
SCT1	敲除Knockout	外显子Exon	耐热性增加Increased heat resistance		[58]
SCT2	敲除Knockout	外显子Exon	耐热性增加Increased heat resistance		[58]
OsRR22	敲除Knockout	外显子Exon	耐盐性增加Increased salt tolerance		[60]
PP01, HPPD	敲除Knockout	启动子Promoter	抗除草剂Herbicide resistance		[61]
PAIR1, REC8, OSD1	敲除Knockout	外显子Exon	高效无性繁殖, 自留种 Efficient vegetative propagation, self-retaining seeds		[67]
PAIR1, REC8, OSD1, MTL	敲除Knockout	外显子Exon	无融合生殖Apomixis		[68]
PAIR1, OsPO11.1, OSD1, MTL	敲除Knockout	外显子Exon	无融合生殖Apomixis	[69]
GS3, GS9, GW8	敲除Knockout	外显子Exon	雄性不育柱头外露率和异交结实率提高Increased exposure rate of male sterile stigma and outcrossing seed setting	[70]
DFOT1	敲除Knockout	外显子Exon	促进开花Promoted flowering	[71]
OsSWEET11a, 11b	敲除Knockout	外显子Exon	雄配子不育Sterile male gametes	[72]
OsWRKY53	敲除Knockout	外显子Exon	结实率、孕穗期耐冷性和花粉活力增加Increased seed setting rate, cold tolerance at booting stage and pollen viability	[59]
TMS5	敲除Knockout	外显子Exon	不育Infertility	[73]
TMS5	敲除Knockout	外显子Exon	致使四倍体不育Causing tetraploid infertility	[74]

基因名称 Gene name			表型 Phenotype		参考文献 Reference
IPA1	敲除Knockout	顺式调控区 Cis-regulatory element	产量提高15.9% 15.9% increase in yield		[21]
SD8	敲除Knockout	外显子Exon	密植条件下增产10% 10% increase in yield		[22]
OsKRN2	敲除Knockout	外显子Exon	增产8% 8% increase in yield		[23]
OsMADS17	敲除Knockout	5′UTR	穗粒数、粒重增加Grain number and weight increased		[24]
GW2, GW5, TGW6	敲除Knockout	外显子Exon	粒重增加Grain weight increased		[25]
OsPIN56, GS3, OsMYB30	敲除Knockout	外显子Exon	高产、耐冷High yield and cold resistance increased		[26]
Dull	敲除Knockout	外显子Exon	直链淀粉含量下降Decreased amylose content		[30]
Wx^b	敲除Knockout	TATA box	微调直链淀粉含量Fine-tune amylose content		[32]
Wx^a	敲除Knockout	5′UTR	直链淀粉含量下降Decreased amylose content		[33]
Wx^b	敲除Knockout	N-末端结构域 N-terminal domain	低淀粉含量Low starch content		[34]
SS3a, SS3b	敲除Knockout	外显子Exon	抗性淀粉增加Resistant starch increased		[35]
OsBADH2	敲除Knockout	外显子Exon	稻米香味增加Aroma of rice increased		[35]
OsGlus	敲除Knockout	外显子Exon	稻米蛋白质含量下降Decreased protein content		[37]
DEP1	敲除Knockout	蛋白质C端 C-terminus	提高产量和稻米品质Improved yield and rice quality		[38]
Bsr-d1, Pi21, ERF922	敲除Knockout	外显子Exon	稻瘟病及白叶枯病抗性增强Resistance to rice blast and rice bacterial blight was enhanced		[44]
OsS5H1, OsS5H2	敲除Knockout	外显子Exon	稻瘟病及白叶枯病抗性增强Resistance to rice blast and rice bacterial blight was enhanced		[45]
OsMPK5	敲除Knockout	磷酸化位点Phosphorylation site	产量及稻瘟病抗性提高Yield and blast resistance improved		[46]
Xa13	敲除Knockout	启动子Promoter	产量不变、强白叶枯病抗性Unchanged yield and stronger resistance to rice bacterial blight		[47]
OsSWEET11, 13, 14	敲除Knockout	启动子Promoter	广谱白叶枯病抗性Broad-spectrum rice bacterial blight resistance		[48]
OsSWEET14	敲除Knockout	启动子Promoter	白叶枯病抗性增加Increased resistance to rice bacterial blight		[49]
FAS	HIGS		二化螟存活率下降Survival rate of C. suppressalis decreased		[50]
OsWRKY53	iRNA		二化螟抗性增加C. suppressalis resistance increased		[51]
OsHPP04	敲除Knockout	外显子Exon	对拟禾本科根结线虫抗性增加Resistance to Meloidogyne graminicola increased		[52]
OsWRKY71, OsSKC1	敲入Knock-in	增强子Enhancer	非生物胁迫抗性增加Increased resistance to abiotic stresses		[54]
OsHYPK	敲除Knockout	外显子Exon	抗旱耐盐Increased drought and salt tolerant		[55]
AFP1	敲除Knockout	外显子Exon	耐旱耐热Increased drought and heat tolerant		[57]
SCT1	敲除Knockout	外显子Exon	耐热性增加Increased heat resistance		[58]
SCT2	敲除Knockout	外显子Exon	耐热性增加Increased heat resistance		[58]
OsRR22	敲除Knockout	外显子Exon	耐盐性增加Increased salt tolerance		[60]
PP01, HPPD	敲除Knockout	启动子Promoter	抗除草剂Herbicide resistance		[61]
PAIR1, REC8, OSD1	敲除Knockout	外显子Exon	高效无性繁殖, 自留种 Efficient vegetative propagation, self-retaining seeds		[67]
PAIR1, REC8, OSD1, MTL	敲除Knockout	外显子Exon	无融合生殖Apomixis		[68]
PAIR1, OsPO11.1, OSD1, MTL	敲除Knockout	外显子Exon	无融合生殖Apomixis	[69]
GS3, GS9, GW8	敲除Knockout	外显子Exon	雄性不育柱头外露率和异交结实率提高Increased exposure rate of male sterile stigma and outcrossing seed setting	[70]
DFOT1	敲除Knockout	外显子Exon	促进开花Promoted flowering	[71]
OsSWEET11a, 11b	敲除Knockout	外显子Exon	雄配子不育Sterile male gametes	[72]
OsWRKY53	敲除Knockout	外显子Exon	结实率、孕穗期耐冷性和花粉活力增加Increased seed setting rate, cold tolerance at booting stage and pollen viability	[59]
TMS5	敲除Knockout	外显子Exon	不育Infertility	[73]
TMS5	敲除Knockout	外显子Exon	致使四倍体不育Causing tetraploid infertility	[74]

统计模型 Statistical model	预测的表型 Predicted phenotype	参考文献 Reference
GBLUP	每穗颖花数、分蘖数、千粒重、粒长粒宽、单株干质量、株高、杂种优势 Number of spikelets per panicle, number of tillers, 1000-grain weight, grain length and width, dry weight per plant, plant height, and heterosis	[39]
RR-BLUP, Convolutional neural network(CNN)	粒长、抽穗期、穗长Grain length, heading date, panicle length	[40]
RR-BLUP, Bayesian LASSO(BL), Reproducing Kernel Hilbert Spaces(RKHS), Ran-dom Forest(RF), Multiple Linear Regression (MLR), Pedigree-BLUP(PED)	产量、株高、开花时间 Yield, plant height, flowering time	[41]
GBLUP	产量Yield	[42]
GBLUP	产量、秸秆生物量、抽穗期 Yield, straw biomass, heading date	[43]
BayesB, GBLUP	纹枯病抗性Sheath blight resistance	[63]
GBLUP, fgBLUP, sgBLUP, mgBLUP, BayesA, BayesC, ML	稻瘟病抗性Rice blast resistance	[64]
BLUP	杂交优势Heterosis	[75]
GBLUP	杂交优势Heterosis	[76]

统计模型 Statistical model	预测的表型 Predicted phenotype	参考文献 Reference
GBLUP	每穗颖花数、分蘖数、千粒重、粒长粒宽、单株干质量、株高、杂种优势 Number of spikelets per panicle, number of tillers, 1000-grain weight, grain length and width, dry weight per plant, plant height, and heterosis	[39]
RR-BLUP, Convolutional neural network(CNN)	粒长、抽穗期、穗长Grain length, heading date, panicle length	[40]
RR-BLUP, Bayesian LASSO(BL), Reproducing Kernel Hilbert Spaces(RKHS), Ran-dom Forest(RF), Multiple Linear Regression (MLR), Pedigree-BLUP(PED)	产量、株高、开花时间 Yield, plant height, flowering time	[41]
GBLUP	产量Yield	[42]
GBLUP	产量、秸秆生物量、抽穗期 Yield, straw biomass, heading date	[43]
BayesB, GBLUP	纹枯病抗性Sheath blight resistance	[63]
GBLUP, fgBLUP, sgBLUP, mgBLUP, BayesA, BayesC, ML	稻瘟病抗性Rice blast resistance	[64]
BLUP	杂交优势Heterosis	[75]
GBLUP	杂交优势Heterosis	[76]