Bin Liu

Rice Research Institute

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Shaohong Zhang

Rice Research Institute

Junliang Zhao

Rice Research Institute

Jingfang Dong

Rice Research Institute

Tifeng Yang

Guangdong Academy of Agricultural Sciences

Yamei Ma

Rice Research Institute

Yang Wu

Sichuan University

Xingxue Mao

Rice Research Institute

Hua Fu

Ministry of Agriculture and Rural Affairs

Xiaoyuan Zhu

Jiangnan University

Lian Zhou

Shanghai Jiao Tong University

Cooperative Institutions

Ministry of Agriculture and Rural Affairs

Guangdong Academy of Agricultural Sciences

Rice Research Institute

Chinese Academy of Agricultural Sciences

Chinese Academy of Sciences

South China Agricultural University

Institute of Plant Protection

International Rice Research Institute

Institute of Crop Sciences

Shanghai Jiao Tong University

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The Function of SD1 on Shoot Length and its Pyramiding Effect on Shoot Length and Plant Height in Rice (Oryza sativa L.)

Rice (2024)

Jingfang Dong Yamei Ma Haifei Hu Jian Wang Yang Wu

Abstract Strong seedling vigor is imperative to achieve stable seedling establishment and enhance the competitiveness against weeds in rice direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor in rice, but few genes for SL have been cloned so far. In the previous study, we identified two tightly linked and stably expressed QTLs for SL, qSL-1f and qSL-1d by genome-wide association study, and cloned the causal gene ( LOC_Os01g68500 ) underlying qSL-1f . In the present study, we identify LOC_Os01g66100 (i.e. the semidwarf gene SD1 ), a well-known gene controlling plant height (PH) at the adult-plant stage, as the causal gene underlying qSL-1d through gene-based haplotype analysis and knockout transgenic verification. By measuring the phenotypes (SL and PH) of various haplotypes of the two genes and their knockout lines, we found SD1 and LOC_ Os01g68500 controlled both SL and PH, and worked in the same direction, which provided the directly genetic evidence for a positive correlation between SL and PH combined with the analysis of SL and PH in the diverse natural population. Moreover, the knockout transgenic experiments suggested that SD1 had a greater effect on PH compared with LOC_ Os01g68500 , but no significant difference in the effect on SL. Further investigation of the pyramiding effects of SD1 and LOC_Os01g68500 based on their haplotype combinations suggested that SD1 may play a dominant role in controlling SL and PH when the two genes coexist. In this study, the effect of SD1 on SL at the seedling stage is validated. In total, two causal genes, SD1 and LOC_ Os01g68500 , for SL are cloned in our studies, which controlled both SL and PH, and the suitable haplotypes of SD1 and LOC_ Os01g68500 are beneficial to achieve the desired SL and PH in different rice breeding objectives. These results provide a new clue to develop rice varieties for direct seeding and provide new genetic resources for molecular breeding of rice with suitable PH and strong seedling vigor.

Genetically modified rice

10.1186/s12284-024-00699-8

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Additional file 1 of Genome-Wide Association Mapping and Gene Expression Analysis Reveal the Negative Role of OsMYB21 in Regulating Bacterial Blight Resistance in Rice

Figshare (2021)

Yang Wu Junliang Zhao Shaohong Zhang Chen Luo Tifeng Yang

Additional file 1: Table S1. Information on the 313 diverse genotypes used in this study.

Genome-wide Association Study

10.6084/m9.figshare.14880465

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Additional file 8: of OsWRKY67 positively regulates blast and bacteria blight resistance by direct activation of PR genes in rice

Figshare (2018)

Qing Liu Xia Li Shijuan Yan Ting Yu Jianyuan Yang

Table S2. Differentially expressed genes in OsWRKY67 overexpressing plants by RNA-seq analysis. (XLSX 26 kb)

Sheath blight

10.6084/m9.figshare.7262507

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Mining candidate genes for rice cadmium accumulation in the shoot through a genome-wide association study and transcriptomic analysis

Frontiers in Genetics (2022)

Jian Wang Yang Wu Shaohong Zhang Jingfang Dong Tifeng Yang

High cadmium (Cd) accumulation in rice is a serious threat to human health. The genetic mechanism of Cd accumulation in rice is highly complicated. To identify the low Cd accumulation in rice germplasm, investigate the genetic mechanism underlying Cd accumulation, and mine the elite genes of significant importance for rice breeding of low Cd accumulation varieties, we performed a genome-wide association study (GWAS) for rice Cd concentration in the shoot. The rice accessions were 315 diverse indica rice accessions selected from the 1568 rice accessions with 700,000 SNPs. Within the high rate of linkage disequilibrium (LD) decay, eight QTLs related to rice Cd accumulation were identified. Transcriptomic analysis showed there were 799 differentially expressed genes (DEGs) in the root and 857 DEGs in the shoot, which are probably considered to be the cause of the significant difference in Cd accumulation between high and low Cd accumulation varieties. In qCd11-1, we detected a crucial candidate gene, LOC_Os11g11050, which encodes an initiation factor, expressed differently in the root between the high and low Cd accumulation varieties. Furthermore, under Cd treatment, the expression levels of LOC_Os11g11050 significantly decreased in both the high and low Cd accumulation varieties. Sequence comparison and qRT-PCR revealed that there were indel sequences and base substitutions in the promoter region of LOC_Os11g11050 correlated with the LOC_Os11g11050 expression level, as well as the phenotype of Cd concentration differences in shoot between the high and low Cd accumulation accessions. LOC_Os11g11050 might play important roles in Cd accumulation. The results of our study provide valuable resources for low Cd accumulation in indica varieties and the candidate functional gene, as well as molecular mechanisms for Cd accumulation in indica rice. The genetic architecture underlying Cd accumulation in indica can be used for further applying the low Cd gene existing in indica for decreasing Cd accumulation in rice.

Indel

Candidate gene

Linkage Disequilibrium

Germ plasm

10.3389/fgene.2022.944529

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A comparison of grain protein content QTLs and flour protein content QTLs across environments in cultivated wheat

Euphytica (2010)

Liang Zhao Kunpu Zhang Bin Liu Zhiying Deng Hou-lan QU

Epistasis

Doubled haploidy

10.1007/s10681-009-0109-z

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A Novel Function of GW5 on Controlling the Early Growth Vigor and its Haplotype Effect on Shoot Dry Weight and Grain Size in Rice (Oryza sativa L.)

Rice (2024)

Tifeng Yang Jingfang Dong Xijuan Xiong Longting Zhang Jian Wang

Strong early growth vigor is an essential target in both direct seeded rice breeding and high-yielding rice breeding for rice varieties with relatively short growth duration in the double-cropping region. Shoot dry weight (SDW) is one of the important traits associated with early growth vigor, and breeders have been working to improve this trait. Finding stable QTLs or functional genes for SDW is crucial for improving the early growth vigor by implementing molecular breeding in rice. Here, a genome-wide association analysis revealed that the QTL for SDW, qSDW-5, was stably detected in the three cultivation methods commonly used in production practice. Through gene-based haplotype analysis of the annotated genes within the putative region of qSDW-5, and validated by gene expression and knockout transgenic experiments, LOC_Os05g09520, which is identical to the reported GW5/GSE5 controlling grain width (GW) and thousand grain weight (TGW) was identified as the causal gene for qSDW-5. Five main haplotypes of LOC_Os05g09520 were identified in the diverse international rice collection used in this study and their effects on SDW, GW and TGW were analyzed. Phenotypic comparisons of the major haplotypes of LOC_Os05g09520 in the three subpopulations (indica, japonica and aus) revealed the same patterns of wider GW and higher TGW along with higher SDW. Furtherly, the haplotype analysis of 138 rice varieties/lines widely used in southern China showed that 97.8% of the cultivars/lines carry Hap2

Dry weight

10.1186/s12284-024-00728-6

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Overexpression of OsGF14f Enhances Quantitative Leaf Blast and Bacterial Blight Resistance in Rice

International Journal of Molecular Sciences (2022)

Yamei Ma Jianyuan Yang Jingfang Dong Shaohong Zhang Wu Yang

Although it is known that rice 14-3-3 family genes are involved in various defense responses, the functions of OsGF14f in response to diseases have not been reported. Here, we showed that the transcription of OsGF14f was significantly induced by leaf blast infection, and the overexpression of OsGF14f quantitatively enhanced resistance to leaf blast and bacterial blight in rice. Further analysis showed that the expression levels of salicylic acid (SA) pathway-associated genes (PAL1, NH1, PR1a and PR10) in the OsGF14f-overexpressing plants, were higher than those in wild-type plants after inoculation with the blast isolate (Magnaporthe oryzae Barr). In addition, the expression level of OsGF14f was significantly induced after SA treatment, and higher endogenous SA levels were observed in the OsGF14f-overexpressing plants compared with that in wild-type plants, especially after blast challenge. Taken together, these results suggest that OsGF14f positively regulates leaf blast and bacterial blight resistance in rice via the SA-dependent signaling pathway.

Systemic Acquired Resistance

10.3390/ijms23137440

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Citations (4)

Candidate Defense Genes as Predictors of Quantitative Blast Resistance in Rice

Molecular Plant-Microbe Interactions (2004)

Bin Liu Shaohong Zhang Xiaoyuan Zhu Qiyun Yang Wu ShangZhong

Although quantitative trait loci (QTL) underpin many desirable agronomic traits, their incorporation into crop plants through marker-assisted selection is limited by the low predictive value of markers on phenotypic performance. Here we used candidate defense response (DR) genes to dissect quantitative resistance in rice using recombinant inbred (RI) and advanced backcross (BC) populations derived from a blast-resistant cultivar, Sanhuangzhan 2 (SHZ-2). Based on DNA profiles of DR genes, RI lines were clustered into two groups corresponding to level of resistance. Five DR genes, encoding putative oxalate oxidase, dehydrin, PR-1, chitinase, and 14-3-3 protein, accounted for 30.0, 23.0, 15.8, 6.7, and 5.5% of diseased leaf area (DLA) variation, respectively. Together, they accounted for 60.3% of the DLA variation and co-localized with resistance QTL identified by interval mapping. Average phenotypic contributions of oxalate oxidase, dehydrin, PR-1, chitinase, and 14-3-3 protein in BC lines were 26.1, 19.0, 18.0, 11.5, and 10.6%, respectively, across environments. Advanced BC lines with four to five effective DR genes showed enhanced resistance under high disease pressure in field tests. Our results demonstrate that the use of natural variation in a few candidate genes can solve a long-standing problem in rice production and has the potential to address other problems involving complex traits.

Candidate gene

Chitinase

Inbred strain

Marker-Assisted Selection

10.1094/mpmi.2004.17.10.1146

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Citations (145)

Relationship between Blast Resistance and Amylose Content in a RIL Population Derived from Rice Crossed SHZ-2×LTH

Zhang Shao Bin Liu Zhu Xiao Yang Jian Wu Shang

Sanhuangzhan 2(SHZ-2) has been considered as a promising blast resistance source in rice breeding in South China because of its durable blast resistance and good agronomic traits.Three major genes responsible for qualitative resistance and five defense genes significantly associated with quantitative resistance to blast in SHZ-2 have been identified and mapped using the candidate resistance gene approach in our previous study.However,its edible quality of kernel is relatively poor because of high amylose content(AC),and most derived resistant cultivars have the similar shortcoming.To have an insight into the relationship between strong blast resistance and high AC in(SHZ-2),a RIL population derived from a cross between SHZ-2 and Lijiangxintuanheigu(LTH) was used to identify the blast resistance genes in SHZ-2 and QTL for AC in the study. Results revealed no significant(P0.05) correlation between blast resistance and AC in the RIL population(Table 2).t-test also indicated that there was no significant difference for average AC between highly blast-resistant RI lines and blast-susceptible RI lines(Table 3).Three QTLs for AC were identified when single-factor analysis of variance and interval mapping were performed.They were mapped on chromosome 5,6 and 7,respectively.All the three QTL were from LTH and contributed to the reduction of AC.Comparing the locations of QTL for AC identified in this study with the locations of previously identified genes(major genes and QTL) conferring blast resistance in SHZ-2,there was no close linkage among these genes for the two traits(Fig.2).These results suggested that the strong blast resistance are not linked with the higher AC in SHZ-2 and it is possible to combine the two traits and develop an elite cultivar with durable blast resistance and ideal AC by proper selection of parents and marker-assisted selection.

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Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa L.)

Research Square (Research Square) (2023)

Tifeng Yang Jingfang Dong Junliang Zhao Longting Zhang Lian Zhou

Abstract Strong seedling vigor is an important breeding target for rice varieties used in direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor characterized by rapid growth of seedling, which enhance seedling emergence. Therefore, mining genes for SL and conducting molecular breeding help to develop varieties for direct seeding. However, few QTLs for SL have been fine mapped or cloned so far. In this study, a genome-wide association study of SL was performed in a diverse rice collection consisting of 391 accessions in two years, using phenotypes generated by different cultivation methods according to the production practice, and a total of twenty-four QTLs for SL were identified. Among them, the novel QTL qSL-1f on chromosome 1 could be stably detected across all three cultivation methods in the whole population and indica subpopulation. Through gene-based haplotype analysis of the annotated genes within the putative region of qSL-1f, and validated by gene expression and knockout transgenic experiments, LOC_Os01g68500 was identified as the causal gene for SL, which has a single-base variation (C-to-A transversion) in its CDS region, resulting in the significant difference in SL of rice. LOC_Os01g68500 encodes a DUF538 (Domain of unknown function) containing protein, and the function of DUF538 protein gene on rice seedling growth is firstly reported in this study. These results provide a new clue for exploring the molecular mechanism regulating SL, and promising gene source for the molecular breeding in rice.

Candidate gene

Genetically modified rice

10.21203/rs.3.rs-2834086/v1

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