Auxin Regulator OsGRF4 Simultaneously Regulates Rice Grain Shape and Blast Resistance

doi:10.16819/j.1001-7216.2021.210206

Abstract

Abstract:

【Objective】Rice grain shape is a complex quantitative trait controlled by multiple genes, which affects rice yield, rice appearance and milling quality simultaneously. It is of great significance to explore the genes related to grain shape and elucidate its genetic basis. Previously, a gene, namely GS2.2, which controls rice grain size, was mapped on the chromosome 2, by using a set of near isogenic lines derived from the small-grain japonica rice variety Nipponbare (NPB) as the recurrent parent, and an indica rice variety Tedaxian(TDX) as the donor parent. 【Method】In this study, fine mapping of GS2.2 and identification of candidate functional genes were carried out. 【Result】 GS2.2 was fine mapped to the 160.6 kb interval between the makers of 2M-7-1 and 2M-9, by using a BC₄F₂ population with 2887 small grain size plants and a BC₄F₃population with 70 large grain size plants. Bioinformatics analysis showed that the 160.6 kb chromosome interval encodes 18 open reading frames (termed as ORF1-18, respectively). Sequence analysis showed that there were five SNP differences in ORF18 between the large grain near isogenic line and Nipponbare. ORF18 encoded an auxin regulatory factor protein OsGRF4. The grain length of ORF18 knockout lines, whose ORF18 was knocked out in large grain near isogenic lines by using CRISPR/CAS9 gene editing technology, became smaller. The above results confirmed that ORF18 was a functional gene of GS2.2. Further identification of ORF18 near isogenic lines (ORF18-NIL) and gene editing knockout lines by in vitro inoculation and disease nursery inoculation showed that the rice blast resistance of ORF18-NIL increased, while that of gene editing knockout lines decreased, indicating that ORF18 also positively regulates rice blast resistance. 【Conclusion】The auxin regulator OsGRF4 found in this study simultaneously regulates rice grain shape and blast resistance, which provides an important gene for breeding rice variety with high yield in coordination with enhanced resistance.

Key words: rice, grain shape, GS2.2, OsGRF4, rice blast disease resistance

摘要：

【目的】水稻粒形为多基因控制的复杂数量性状,同时影响稻谷产量和稻米外观及碾磨品质,挖掘粒形相关基因并解析其遗传机制,对于水稻高产和优质品种选育具有重要意义。【方法】以前期利用大粒籼稻品种特大籼(TDX)为供体亲本、小粒粳稻品种日本晴(Nipponbare,NPB)为轮回亲本获得的一个大粒近等基因系,在水稻第2染色体上初定位粒形调控基因GS2.2(grain size 2.2)的基础上,对GS2.2基因进行了精细定位和候选功能基因的克隆鉴定。【结果】利用BC₄F₂群体中2887份极小粒单株及该群体中70份基因型杂合的大粒单株自交获得的BC₄F₃群体,将GS2.2基因精细定位在2M-7-1与2M-9之间的160.6 kb的区间内。该区间编码18个基因开放阅读框(ORF1-18)。测序发现ORF18基因在大粒近等基因系与小粒日本晴等位基因间存在5个SNP差异,ORF18编码生长素调控因子蛋白OsGRF4。采用CRISPR/Cas9基因编辑技术对大粒近等基因系中ORF18进行敲除,发现ORF18敲除株系粒长变短,证实ORF18是GS2.2的功能基因。进一步对ORF18大粒近等基因系和基因编辑敲除株系进行稻瘟菌室内离体和病圃接种鉴定,发现ORF18大粒近等基因系稻瘟病抗性增强,而基因编辑敲除株系稻瘟病抗性减弱,表明ORF18正调控水稻稻瘟病抗性。【结论】本研究发现的生长素调控因子OsGRF4协同调控水稻粒形和稻瘟病抗性,为协调水稻高产和抗性育种提供了重要的基因资源。

关键词: 水稻, 粒形性状, GS2.2, OsGRF4, 稻瘟病抗性

Yudong CAO, Xiangyi XIAO, Naizhong YE, Xiaowen DING, Xiaoxuan YI, Jinling LIU, Yinghui XIAO. Auxin Regulator OsGRF4 Simultaneously Regulates Rice Grain Shape and Blast Resistance[J]. Chinese Journal OF Rice Science, 2021, 35(6): 629-638.

曹煜东, 肖湘谊, 叶乃忠, 丁晓雯, 易晓璇, 刘金灵, 肖应辉. 生长素调控因子OsGRF4协同调控水稻粒形和稻瘟病抗性[J]. 中国水稻科学, 2021, 35(6): 629-638.

Figures/Tables 11

Table 1 Primers for construction and identification of CRISPR/Cas9 vectors.

引物用途 Primer usage	引物名称 Primer name	引物序列 Primer sequence
CRISPR/Cas9载体构建 Constriction of CRISPR/Cas9 vector	CRS-GRF4-F	GCCGCAGCTCCTCGTACTGCGCCG
CRISPR/Cas9载体构建 Constriction of CRISPR/Cas9 vector	CRS-GRF4-R	AAACCGGCGCAGTACGAGGAGCTG
敲除转基因植株鉴定 Identification of knockout transgenic plants	GRF4-CRSJD-F	AACCCATTTTCTTGGCTC
敲除转基因植株鉴定 Identification of knockout transgenic plants	GRF4-CRSJD-R	CGCCTGATCGGAATAAAC

Fig. 1. Construction of genetic map and physical map of GS2.2. A, Genetic map of GS2.2; B, BAC clone contig and physical map of GS2.2 locus; C, The GS2.2 physical interval was determined by overlapping recombinant lines. NIL, Near-isogenic line with large grains; NPB, Nipponbare; “L+Number” represents a recombinant strain with large grains, and the “S+Number” represents a recombinant strain with small grains. The phenotype of grain length and width for NPB, NIL and recombinant lines was presented on the right.

Table 2 Prediction and analysis of GS2.2 candidate genes.

候选基因 Candidate gene		蛋白编码结构 Protein coding structure
ORF1	Probable WRKY transcription factor 14
ORF2	Protein NRT1/ PTR FAMILY 8.3
ORF3	ADP-ribosylation factor
ORF4	Uncharacterized LOC4330423
ORF5	Putative surface protein SACOL0050
ORF6	60S ribosomal protein L12-1
ORF7	DNA topoisomerase 2
ORF8	Protein-coding
ORF9	Os02g0699800
ORF10	Transcription initiation factor TFIID subunit 8
ORF11	Uncharacterized protein At1g51745
ORF12	Cell division cycle 20.2, cofactor of APC complex
ORF13	Myb family transcription factor APL
ORF14	Ubiquinol oxidase 2, mitochondrial
ORF15	Polyamine transporter PUT1
ORF16	Cyclin-dependent kinase F-4
ORF17	Protein Brevis radix-like 2
ORF18	Growth-regulating factor 4

Fig. 2. OsGRF4 structure and natural variation in alleles from NIL and NPB.

Fig. 3. Sequence of target site for OsGRF4 CRISPR / Cas9 gene editing and genotype of OsGRF4 CRISPR / Cas9 gene editing lines in NIL background. A, Sequence of target site for OsGRF4 CRISPR / Cas9 gene editing; B, Genotype of OsGRF4 CRISPR / Cas9 gene editing lines in NIL.

Table 3 OsGRF4 CRISPR / Cas9 gene editing knockout mutation types.

转基因株系 Transgenic lines	基因型 Genotype	基因编辑类型 Gene editing type
Reference	GCTGCCGCCGTTCACCGCGGCGCAGTACGAGGAGC
CR-NIL-15	GCTGCCGCCGTTCACCGCGGTCGCAGTACGAGGAGC	+1
CR-NIL-16	GCTGCCGCCGTTCACCGCGGACGCAGTACGAGGAG	+1
CR-NIL-16	GCTGCCGCCGTTCACCGCGGCCGCAGTACGAGGAG	+1
CR-NIL-17	AGGCTGCCGCCGTTCACCGC-(46 bp del)CTGGTGGCAGGCGTG	-46
CR-NIL-17	AGGCTGCCGCCGTTCACCGCGGGCGCAGTACGAGG	+1
CR-NIL-19	GGCTGCCGCCGTTCACCGCGGCGCAGTACGAGGAG (WT)	+0
CR-NIL-19	GGCTGCCGCCGTTCACCGCGTACGCAGTACGAGGA	+1
CR-NIL-20	GCTGCCGCCGTTCACCGCGGTCGCAGTACGAGGAG	+1
CR-NIL-23	GCTGCCGCCGTTCACCGCGGACGCAGTACGAGGAG	+1
CR-NIL-22	GCTGCCGCCGTTCACCGCGGGCGCAGTACGAGGAG	+1
CR-NIL-22	GCTGCCGCCGTTCACCGCGGTCGCAGTACGAGGAG	+1

Fig. 4. Grain shape of gene editing lines in GS2.2-NIL background. A and B, Phenotype of grain length and width. C-F, Statistic data of grain length, width, thickness and 1000-grain weight. *P<0.05; **P<0.01(t-test). Error bar indicated the SD value (n=30). NIL, GS2.2-NIL; CR20, CR-NIL-20; CR23, CR-NIL-23.

Fig. 5. Phenotype of agronomic traits of OsGRF4 gene editing lines in NIL background. A, Plant architecture for gene editing lines. B-G, Plant height, panicle length, tiller number, total grains per panicle, number of full grains per panicle and seed setting rate for gene editing lines. The t-test was used for significance analysis. Error bar indicated the SD value (n=3). **P<0.01.NIL, GS2.2-NIL; CR20, CR-NIL-20; CR23, CR-NIL-23.

Fig. 6. Symptoms of GS2.2-NIL and Nipponbare(NPB) after infected by rice blast fungal in natural disease nurse. A, Symptoms of leaf after rice blast fungal infection in the natural disease nurse; B, Leaf blast rating after rice blast fungal infection in the natural disease nurse. The t-test was used for significance analysis. Error bar indicated the SD(n=10). **P<0.01。

Fig. 7. Symptoms of GS2.2-NIL and Nipponbare(NPB) after in vitro inoculation with rice blast fungus. A, Leaf disease phenotype; B, Relative blast fungal biomass in the infected leaf; C, Area of leaf infected by blast fungal. The t-test was used for significance analysis, error bar indicated the SD value(n=3). **P<0.01(t-test).

Fig. 8. Symptoms of GS2.2-NIL, Nipponbare(NPB) and CRISPR/Cas9 editing lines after in vitro inoculation with rice blast fungus. A, Phenotype of infection; B, Infected leaf area; C, The relative fungal biomass. The t-test was used for significance analysis, error bar indicated the SD value (n=3). *P<0.05; **P<0.01(t-test). NIL-15, CR-NIL-15.

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