Research Progress and Prospect in Molecular Biology of Rice in China in recent Years

doi:10.3969/j.issn.1006-8082.2023.06.003

Abstract

Abstract:

The paper overall reviewed the research progress of rice molecular biology in 2020-2022 in China, briefly comparied the research difference in China and abroad, prospected the research trend and direction. In recent 3 years, a rice pangenome and genome navigation system, RiceNavi,has been developed for QTN polymerizationand breeding route optimization. The Oryza super pangenome with the largest population size in plantsand fully annotated genomes has been constructed. Several nitrogen efficient genes have been identified and their molecular mechanism of nitrogen efficiency has been dissected. Expression of some genes can significantly increase rice yield under experimental conditions. Significant progress has also been made in the mechanism research of rice broad-spectrum disease resistance, temperature response, and salt-alkali resistance. In gene editing, a new polynucleotide targeted deletion system AFIDs (APOBEC-Cas9 fusion induced deletion systems) has been established, successfully achieving accurate and predictable polynucleotide deletion in rice and wheat genomes. Using CRISPR/Cas9 technology,gene editing has produced many practical new materials. The rice apomixis material Fix2 (Fixation of hybrids 2) edited by a new gene increased the seed setting rate from 3.2% to 82%. The rice material knocked out the homologous gene GS3/AT1 can increase yield by about 22.4% in the field.

Key words: rice, adversity biology, high nitrogen efficiency, pangenome

摘要：

综述了2020—2022年我国水稻分子生物学研究上的重要进展，简要比较了国内外的研究进展差异，提出了研究趋势和展望。近3年来，我国开发了水稻泛基因组、用于QTN聚合和育种路线优化的基因组导航系统RiceNavi，构建了目前植物中群体规模最大的、基因组充分注释的稻属超级泛基因组；鉴定到多个氮高效基因，研究了氮高效的分子机制，一些基因的表达可使实验条件下水稻产量大幅增加；在水稻广谱抗性、温度反应、抗盐碱耐逆机制研究上亦取得明显的进展；基因编辑上，建立了新型多核苷酸靶向删除系统AFIDs（APOBEC-Cas9 fusion-induced deletion systems），成功在水稻和小麦基因组中实现了精准、可预测的多核苷酸删除，利用 CRISPR/Cas9 技术，基因编辑出许多实用的新材料；新基因编辑的水稻无融合生殖材料Fix2 (Fixation of hybrids 2)结实率从原来的3.2%提高至82.0%；敲除水稻同源基因GS3/AT1的水稻材料田间能增产约22.4%。

关键词: 水稻, 逆境生物学, 氮高效, 泛基因组

CLC Number:

S511

CUI Yuanjiang, LV Yang, HU Haitao, WU Shiqiang, GUO Longbiao. Research Progress and Prospect in Molecular Biology of Rice in China in recent Years[J]. China Rice, 2023, 29(6): 10-15.

崔元江, 吕阳, 胡海涛, 吴世强, 郭龙彪. 近年我国水稻分子生物学研究进展[J]. 中国稻米, 2023, 29(6): 10-15.

References 63

[1]	GAO M J, HE Y, YIN X, et al. Ca²⁺ sensor-mediated ROS scavenging suppresses rice immunity and is exploited by a fungal effector[J]. Cell, 2021, 184(21): 5 391-5 404.
[2]	ZHAI K R, LIANG D, LI H L, et al. NLRs guard metabolism to coordinate pattern- and effector-triggered immunity[J]. Nature, 2022, 601(7892): 245-251.
[3]	LIN H, WANG M Y, CHEN Y, et al. An MKP-MAPK protein phosphorylation cascade controls vascular immunity in plants[J]. Science Advance, 2022, 8(10): eabg8723.
[4]	MATSUMOTO H, FAN X, WANG Y, et al. Bacterial seed endophyte shapes disease resistance in rice[J]. Nature Plants, 2021, 7(1): 60-72.
[5]	LI L L, ZHANG H H, YANG Z H, et al. Independently evolved viral effectors convergently suppress DELLA protein SLR1-mediated broad-spectrum antiviral immunity in rice[J]. Nature Communication, 2022, 13(1): 6 920.
[6]	HU X H, SHEN S, WU J L, et al. A natural allele of proteasome maturation factor improves rice resistance to multiple pathogens[J]. Nature Plants, 2023, 9(2): 228-237.
[7]	ZHAN C H, LEI L, LIU Z X, et al. Selection of a subspecies-specific diterpene gene cluster implicated in rice disease resistance[J]. Nature Plants, 2020, 6(12): 1 447-1 454.
[8]	XU G J, ZHONG X H, SHI Y L, et al. A fungal effector targets a heat shock-dynamin protein complex to modulate mitochondrial dynamics and reduce plant immunity[J]. Science Advance, 2020, 6(48): eabb7719.
[9]	YANG C, LIU R, PANG J H, et al. Poaceae-specific cell wall-derived oligosaccharides activate plant immunity via OsCERK1 during Magnaporthe oryzae infection in rice[J]. Nature Communication, 2021, 12(1): 2 178.
[10]	LIU Y, ZHANG X, YUAN G X, et al. A designer rice NLR immune receptor confers resistance to the rice blast fungus carrying noncorresponding avirulence effectors[J]. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118(44): e2110751118.
[11]	LI G B, HE J X, WU J L, et al. Overproduction of OsRACK1A, an effector-targeted scaffold protein promoting OsRBOHB-mediated ROS production, confers rice floral resistance to false smut disease without yield penalty[J]. Molecular Plant, 2022, 15(11): 1 790-1 806.
[12]	MENG F W, ZHAO Q Q, ZHAO X, et al. A rice protein modulates endoplasmic reticulum homeostasis and coordinates with a transcription factor to initiate blast disease resistance[J]. Cell Reporter, 2022, 39(11): 110 941.
[13]	KAN Y, MU X R, ZHANG H, et al. TT2 controls rice thermotolerance through SCT1-dependent alteration of wax biosynthesis[J]. Nature Plants, 2022, 8(1): 53-67.
[14]	ZHANG H, ZHOU J F, KAN Y, et al. A genetic module at one locus in rice protects chloroplasts to enhance thermotolerance[J]. Science, 2022, 376(6599): 1 293-1 300.
[15]	WANG J C, REN Y L, LIU X, et al. Transcriptional activation and phosphorylation of OsCNGC9 confer enhanced chilling tolerance in rice[J]. Molecular Plant, 2021, 14(2): 315-329.
[16]	TANG J Q, TIAN X J, MEI E Y, et al. WRKY53 negatively regulates rice cold tolerance at the booting stage by fine-tuning anther gibberellin levels[J]. Plant Cell, 2022, 34(11): 4 495-4 515.
[17]	XU Y F, ZHANG L, OU S J, et al. Natural variations of SLG1 confer high-temperature tolerance in indica rice[J]. Nature Communication, 2020, 11(1): 5 441.
[18]	TANG Y, GAO C C, GAO Y, et al. OsNSUN2-mediated 5-methylcytosine mRNA modification enhances rice adaptation to high temperature[J]. Developmental Cell, 2020, 53(3): 272-286.
[19]	JIA M R, MENG X B, SONG X G, et al. Chilling-induced phosphorylation of IPA1 by OsSAPK6 activates chilling tolerance responses in rice[J]. Cell Discovery, 2022, 8(1):71.
[20]	GUO X Y, ZHANG D J, WANG Z L, et al. Cold-induced calreticulin OsCRT3 conformational changes promote OsCIPK7 binding and temperature sensing in rice[J]. The EMBO Journal, 2023, 42(1): e110518.
[21]	LI Z T, WANG B, LUO W, et al. Natural variation of codon repeats in COLD11 endows rice with chilling resilience[J]. Science Advance, 2023, 9(1): eabq5506.
[22]	ZHANG H L, YU F F, XIE P, et al. A Gγ protein regulates alkaline sensitivity in crops[J]. Science, 2023, 379(6638): eade8416.
[23]	SUN X M, XIONG H Y, JIANG C H, et al. Natural variation of DROT1 confers drought adaptation in upland rice[J]. Nature Communication, 2022, 13(1): 4 265.
[24]	LV J, HUANG L Y, ZHANG S L, et al. Neo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice[J]. Nature Communication, 2020, 11(1): 725.
[25]	YIN W B, XIAO Y H, NIU M, et al. ARGONAUTE2 enhances grain length and salt tolerance by activating BIG GRAIN3 to modulate cytokinin distribution in rice[J]. Plant Cell, 2020, 32(7): 2 292-2 306.
[26]	WEI H, WANG X L, HE Y Q, et al. Clock component OsPRR73 positively regulates rice salt tolerance by modulating OsHKT2;1-mediated sodium homeostasis[J]. The EMBO Journal, 2021, 40(3): e105086.
[27]	WANG L F, CAO S, WANG P T, et al. DNA hypomethylation in tetraploid rice potentiates stress-responsive gene expression for salt tolerance[J]. Proceedings of National Academy Sciences of the United States of America, 2021, 118(13): e2023981118.
[28]	LI Q Q, XU F, CHEN Z, et al. Synergistic interplay of ABA and BR signal in regulating plant growth and adaptation[J]. Nature Plants, 2021, 7(8):1108-1 118.
[29]	XIANG Y H, YU J J, LIAO B, et al. An α/β hydrolase family member negatively regulates salt tolerance but promotes flowering through three distinct functions in rice[J]. Molecular Plant, 2022, 15(12): 1 908-1 930.
[30]	DENG P, JING W, CAO C Q, et al. Transcriptional repressor RST1 controls salt tolerance and grain yield in rice by regulating gene expression of asparagine synthetase[J]. Proceedings of National Academy Sciences of the United States of America, 2022, 119(50): e2210338119.
[31]	QIN P, LU H W, DU H L, et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations[J]. Cell, 2021, 184(13): 3 542-3 558.
[32]	WEI X, QIU J, YONG K C, et al. A quantitative genomics map of rice provides genetic insights and guides breeding[J]. Nature Genetics, 2021, 53(2): 243-253.
[33]	ZHANG F, XUE H Z, DONG X R, et al. Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes[J]. Genome Research, 2022, 32(5): 853-863.
[34]	ZHANG F, HU Z Q, WU Z C, et al. Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: Cross-species two-dimensional GWAS reveals the underlying genetics[J]. Plant Cell, 2021, 33(8): 2 538-2 561.
[35]	SHANG L Q, LI X X, HE H Y, et al. A super pan-genomic landscape of rice[J]. Cell Research, 2022, 32(10): 878-896.
[36]	LIU Y Q, WANG H R, JIANG Z M, et al. Genomic basis of geographical adaptation to soil nitrogen in rice[J]. Nature, 2021, 590(7847): 600-605.
[37]	CAI S Y, ZHAO X, PITTELKOW C M, et al. Optimal nitrogen rate strategy for sustainable rice production in China[J]. Nature, 2023, 615(7950): 73-79.
[38]	WU K, WANG S S, SONG W Z, et al. Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice[J]. Science, 2020, 367 (6478): 641.
[39]	WEI S B, LI X, LU Z F, et al. A transcriptional regulator that boosts grain yields and shortens the growth duration of rice[J]. Science, 2022, 377(6604): 386.
[40]	ZHANG S, ZHANG Y Y, LI K N, et al. Nitrogen mediates flowering time and nitrogen use efficiency via floral regulators in rice[J]. Current Biology, 2021, 31(4): 671-683.
[41]	WANG Q, SU Q, NIAN J Q, et al. The Ghd7 transcription factor represses ARE1 expression to enhance nitrogen utilization and grain yield in rice[J]. Molecular Plant, 2021, 14(6): 1 012-1 023.
[42]	ZHANG M X, WANG Y, CHEN X, et al. Plasma membrane H⁺-ATPase overexpression increases rice yield via simultaneous enhancement of nutrient uptake and photosynthesis[J]. Nature Communication, 2021, 12(1): 735.
[43]	YANG H, LI Y F, CAO Y W, et al. Nitrogen nutrition contributes to plant fertility by affecting meiosis initiation[J]. Nature Communication, 2022, 13(1): 485.
[44]	HAN M L, LV Q Y, ZHANG J, et al. Decreasing nitrogen assimilation under drought stress by suppressing DST-mediated activation of nitrate reductase 1.2 in rice[J]. Molecular Plant, 2022, 15(1): 167-178.
[45]	KHANDAY I, SKINNER D, YANG B, et al. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds[J]. Nature, 2019, 565(7 737): 91-95.
[46]	WANG C, LIU Q, SHEN Y, et al. Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes[J]. Nature Biotechnology, 2019, 37(3): 283-286.
[47]	WEI X, LIU C, CHEN X, et al. Synthetic apomixis with normal hybrid rice seed production[J]. Molecular Plant, 2023, 16(3): 489-492.
[48]	VERNET A, MEYNARD D, LIAN Q C, et al. High-frequency synthetic apomixis in hybrid rice[J]. Nature Communication, 2022, 13(1): 7 963.
[49]	SONG X G, MENG X B, GUO H Y, et al. Targeting a gene regulatory element enhances rice grain yield by decoupling panicle number and size[J]. Nature Biotechnology, 2022, 40(9): 1 403-1 411.
[50]	LIN Q P, ZONG Y, XUE C X, et al. Prime genome editing in rice and wheat[J]. Nature Biotechnology, 2020, 38(5): 582-585.
[51]	LIN Q P, JIN S, ZONG Y, et al. High-efficiency prime editing with optimized, paired pegRNAs in plants[J]. Nature Biotechnology, 2021, 39(8): 923-927.
[52]	CHEN W K, CHEN L, ZHANG X, et al. Convergent selection of a WD40 protein that enhances grain yield in maize and rice[J]. Science, 2022, 375(6587): 1 372.
[53]	XU F, TANG J Y, WANG S X, et al. Antagonistic control of seed dormancy in rice by two bHLH transcription factors[J]. Nature Genetics, 2022, 54(12): 1 972-1 982.
[54]	MA B, ZHANG L, GAO Q F, et al. A plasma membrane transporter coordinates phosphate reallocation and grain filling in cereals[J]. Nature Genetics, 2021, 53(6): 906-915.
[55]	LI J, YOKOSHO K, LIAO H, et al. Diel magnesium fluctuations in chloroplasts contribute to photosynthesis in rice[J]. Nature Plants, 2020, 6(7): 848-859.
[56]	SUN J, ZHANG G C, CUI Z B, et al. Regain flood adaptation in rice through a 14-3-3 protein OsGF14h[J]. Nature Communication, 2022, 13(1): 5 664.
[57]	GUAN Z Y, ZHANG Q X, ZHANG Z F, et al. Mechanistic insights into the regulation of plant phosphate homeostasis by the rice SPX2 - PHR2 complex[J]. Nature Communication, 2022, 13(1): 1 581.
[58]	HUANG H J, WANG Y Z, LI L L, et al. Planthopper salivary sheath protein LsSP1 contributes to manipulation of rice plant defenses[J]. Nature Communication, 2023, 14(1): 737.
[59]	LI H X, YOU C J, YOSHIKAWA M, et al. A spontaneous thermo-sensitive female sterility mutation in rice enables fully mechanized hybrid breeding[J]. Cell Research, 2022, 32(10): 931-945.
[60]	YU H, LIN T, MENG X B, et al. A route to de novo domestication of wild allotetraploid rice[J]. Cell, 2021, 184(5): 1 156-1 170.
[61]	GUTAKER R M, GROEN S C, BELLIS E S, et al. Genomic history and ecology of the geographic spread of rice[J]. Nature Plants, 2020, 6(5): 492-502.
[62]	NAGAI K, MORI Y, ISHIKAWA S, et al. Antagonistic regulation of the gibberellic acid response during stem growth in rice[J]. Nature, 2020, 584(7819): 109-114.
[63]	SHIN D, LEE S, KIM T H, et al. Natural variations at the Stay-Green gene promoter control lifespan and yield in rice cultivars[J]. Nature Communication, 2020, 11(1): 2 819.