Special Issue: Genomics-assisted Germplasm Improvement in Rice   

February 2018, Volume 60 Issue 2, Pages 81每188.

Cover Caption: Genomics-assisted germplasm improvement in rice
Germplasm innovation is critical for crop improvement. In this issue, Shen et al. (89-93) demonstrated the feasibility of improving rice yield using genome editing (the scissors in the cover) and bioinformatic (the numbers in the river) tools. The sun rising above the rice field represents the bright future of the field (Cover design: Kejian Wang and Lan Shen).


Genomics-assisted germplasm improvement  
Author: Qian Qian
Journal of Integrative Plant Biology 2018 60(2): 82每84
Published Online: January 4, 2018
DOI: 10.1111/jipb.12629
Abstract (Browse 205)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Letters to the Editor
Ectopic expression of fungal EcGDH improves nitrogen assimilation and grain yield in rice  
Author: Dongying Tang, Yuchong Peng, Jianzhong Lin, Changqing Du, Yuanzhu Yang, Dan Wang, Cong Liu, Lu Yan, Xiaoying Zhao, Xia Li, Liangbi Chen and Xuanming Liu
Journal of Integrative Plant Biology 2018 60(2): 85每88
Published Online: January 6, 2017
DOI: 10.1111/jipb.12519

NADP(H)-dependent glutamate dehydrogenases (GDH) in lower organisms have stronger ammonium affinity than those in higher plants. Here we report that transgenic rice overexpressing the EcGDH from Eurotium cheralieri exhibited significantly enhanced aminating activities. Hydroponic and field tests showed that nitrogen assimilation efficiency and grain yields were markedly increased in these transgenic plants, especially at the low nitrogen conditions. These results suggest that EcGDH may have potential to be used to improve nitrogen assimilation and grain yield in rice.

Abstract (Browse 800)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Owing to the higher affinity for ammonium, NADP(H)-dependent glutamate dehydrogenase (EcGDH) from Eurotium cheralieri can more efficiently assimilate nitrogen than OsGDH from rice. Ectopic expression of EcGDH significantly enhanced the nitrogen assimilation efficiency, and especially improved grain yield in rice at low nitrogen fertility.
QTL editing confers opposing yield performance in different rice varieties  
Author: Lan Shen, Chun Wang, Yaping Fu, Junjie Wang, Qing Liu, Xiaoming Zhang, Changjie Yan, Qian Qian and Kejian Wang
Journal of Integrative Plant Biology 2018 60(2): 89每93
Published Online: September 15, 2016
DOI: 10.1111/jipb.12501

Grain yield is one of the most important and complex trait for genetic improvement in crops; it is known to be controlled by a number of genes known as quantitative trait loci (QTLs). In the past decade, many yield-contributing QTLs have been identified in crops. However, it remains unclear whether those QTLs confer the same yield performance in different genetic backgrounds. Here, we performed CRISPR/Cas9-mediated QTL editing in five widely-cultivated rice varieties and revealed that the same QTL can have diverse, even opposing, effects on grain yield in different genetic backgrounds.

Abstract (Browse 766)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Grain yield is one of the most important and complex traits for genetic improvement in crops. This study utilized CRISPR/Cas9-mediated QTL editing in five widely-cultivated rice varieties, and revealed that the same QTL can have diverse, even opposing, effects on grain yield in different genetic backgrounds.
          Research Articles
FRUCTOKINASE-LIKE PROTEIN 1 interacts with TRXz to regulate chloroplast development in rice  
Author: Lei He, Sen Zhang, Zhennan Qiu, Juan Zhao, Wendan Nie, Haiyan Lin, Zhengge Zhu, Dali Zeng, Qian Qian and Li Zhu
Journal of Integrative Plant Biology 2018 60(2): 94每111
Published Online: January 10, 2018
DOI: 10.1111/jipb.12631

Chloroplast genes are transcribed by the plastid-encoded RNA polymerase (PEP) or nucleus-encoded RNA polymerase. FRUCTOKINASE-LIKE PROTEINS (FLNs) are phosphofructokinase-B (PfkB)-type carbohydrate kinases that act as part of the PEP complex; however, the molecular mechanisms underlying FLN activity in rice remain elusive. Previously, we identified and characterized a heat-stress sensitive albino (hsa1) mutant in rice. Map-based cloning revealed that HSA1 encodes a putative OsFLN2. Here, we further demonstrated that knockdown or knockout of the OsFLN1, a close homolog of HSA1/OsFLN2, considerably inhibits chloroplast biogenesis and the fln1 knockout mutants, created by clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associate protein 9, exhibit severe albino phenotype and seedling lethality. Moreover, OsFLN1 localizes to the chloroplast. Yeast two-hybrid, pull-down and bimolecular fluorescence complementation experiments revealed that OsFLN1 and HSA1/OsFLN2 interact with THIOREDOXINZ (OsTRXz) to regulate chloroplast development. In agreement with this, knockout of OsTRXz resulted in a similar albino and seedling lethality phenotype to that of the fln1 mutants. Quantitative reverse transcription polymerase chain reaction and immunoblot analysis revealed that the transcription and translation of PEP-dependent genes were strongly inhibited in fln1 and trxz mutants, indicating that loss of OsFLN1, HSA1/OsFLN2, or OsTRXz function perturbs the stability of the transcriptionally active chromosome complex and PEP activity. These results show that OsFLN1 and HSA1/OsFLN2 contribute to chloroplast biogenesis and plant growth.

Abstract (Browse 230)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
We demonstrated that knockout of OsFLN1 strongly inhibited chloroplast biogenesis, resulting in severe albino phenotype and seedling lethality. FLN1 and HSA1 interact with the OsTRXz, while knockout of OsTRXz resulted in a similar albino seedling lethality phenotype to fln1. Loss function of FLN1, FLN2, or OsTRXz perturbs chloroplast gene expression.
TSC1 enables plastid development under dark conditions, contributing to rice adaptation to transplantation shock  
Author: Xiaoliang Shi, Sunlu Chen, Yu Peng, Yufeng Wang, Jiugeng Chen, Zhanghua Hu, Baohe Wang, Aihong Li, Daiyin Chao, Yuhong Li and Sheng Teng
Journal of Integrative Plant Biology 2018 60(2): 112每129
Published Online: December 6, 2017
DOI: 10.1111/jipb.12621

Since its domestication from wild rice thousands of years ago, rice has been cultivated largely through transplantation. During transplantation from the nursery to the paddy field, rice seedlings experience transplantation shock which affects their physiology and production. However, the mechanisms underlying transplantation shock and rice adaptation to this shock are largely unknown. Here, we isolated a transplant-sensitive chloroplast-deficient (tsc1) rice mutant that produces albino leaves after transplantation. Blocking light from reaching the juvenile leaves and leaf primordia caused chloroplast deficiencies in transplanted tsc1 seedlings. TSC1 encodes a noncanonical adenosine triphosphate-binding cassette (ABC) transporter homologous to AtNAP14 and is of cyanobacterial origin. We demonstrate that TSC1 controls plastid development in rice under dark conditions, and functions independently of light signaling. However, light rescued the tsc1 mutant phenotype in a spectrum-independent manner. TSC1 was upregulated following transplantation, and modulated the iron and copper levels, thereby regulating prolamellar body formation during the early P4 stage of leaf development. Therefore, TSC1 is indispensable for plastid development in the absence of light, and contributes to adaptation to transplantation shock. Our study provides insight into the regulation of plastid development and establishes a framework for improving recovery from transplantation shock in rice.

Abstract (Browse 378)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Rice has been cultivated largely through transplantation. We examined a transplant-sensitive chloroplast-deficient mutant, and found that transplantation blocks light from reaching the juvenile leaves and leaf primordia. TSC1, a noncanonical ATP-binding cassette transporter, controls plastid development under dark conditions. Consequently, TSC1 contributes to rice adaptation to transplantation shock.
OsIDD2, a zinc finger and INDETERMINATE DOMAIN protein, regulates secondary cell wall formation  
Author: Peng Huang, Hideki Yoshida, Kenji Yano, Shunsuke Kinoshita, Kyosuke Kawai, Eriko Koketsu, Masako Hattori, Sayaka Takehara, Ji Huang, Ko Hirano, Reynante Lacsamana Ordonio, Makoto Matsuoka and Miyako Ueguchi-Tanaka
Journal of Integrative Plant Biology 2018 60(2): 130每143
Published Online: June 2, 2017
DOI: 10.1111/jipb.12557

Previously, we found 123 transcription factors (TFs) as candidate regulators of secondary cell wall (SCW) formation in rice by using phylogenetic and co-expression network analyses. Among them, we examined in this work the role of OsIDD2, a zinc finger and indeterminate domain (IDD) family TF. Its overexpressors showed dwarfism, fragile leaves, and decreased lignin content, which are typical phenotypes of plants defective in SCW formation, whereas its knockout plants showed slightly increased lignin content. The RNA-seq and quantitative reverse transcription polymerase chain reaction analyses confirmed that some lignin biosynthetic genes were downregulated in the OsIDD2-overexpressing plants, and revealed the same case for other genes involved in cellulose synthesis and sucrose metabolism. The transient expression assay using rice protoplasts revealed that OsIDD2 negatively regulates the transcription of genes involved in lignin biosynthesis, cinnamyl alcohol dehydrogenase 2 and 3 (CAD2 and 3), and sucrose metabolism, sucrose synthase 5 (SUS5), whereas an AlphaScreen assay, which can detect the interaction between TFs and their target DNA sequences, directly confirmed the interaction between OsIDD2 and the target sequences located in the promoter regions of CAD2 and CAD3. Based on these observations, we conclude that OsIDD2 is negatively involved in SCW formation and other biological events by downregulating its target genes.

Abstract (Browse 513)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Secondary cell wall, which plants make after maturing to reinforce the primary cell wall, is known to be under control of several transcription factors. We added a member of the indeterminate domain family, OsIDD2, to the list of the factors as a negative regulator of lignin biosynthesis in rice.
Chromatin-remodeling factor OsINO80 is involved in regulation of gibberellin biosynthesis and is crucial for rice plant growth and development  
Author: Chao Li, Yuhao Liu, Wen-Hui Shen, Yu Yu and Aiwu Dong
Journal of Integrative Plant Biology 2018 60(2): 144每159
Published Online: October 17, 2017
DOI: 10.1111/jipb.12603

The phytohormone gibberellin (GA) plays essential roles in plant growth and development. Here, we report that OsINO80, a conserved ATP-dependent chromatin-remodeling factor in rice (Oryza sativa), functions in both GA biosynthesis and diverse biological processes. OsINO80-knockdown mutants, derived from either T-DNA insertion or RNA interference, display typical GA-deficient phenotypes, including dwarfism, reduced cell length, late flowering, retarded seed germination and impaired reproductive development. Consistently, transcriptome analyses reveal that OsINO80 knockdown results in downregulation by more than two-fold of over 1,000 genes, including the GA biosynthesis genes CPS1 and GA3ox2, and the dwarf phenotype of OsINO80-knockdown mutants can be rescued by the application of exogenous GA3. Chromatin immunoprecipitation (ChIP) experiments show that OsINO80 directly binds to the chromatin of CPS1 and GA3ox2 loci. Biochemical assays establish that OsINO80 specially interacts with histone variant H2A.Z and the H2A.Z enrichments at CPS1 and GA3ox2 are decreased in OsINO80-knockdown mutants. Thus, our study identified a rice chromatin-remodeling factor, OsINO80, and demonstrated that OsINO80 is involved in regulation of the GA biosynthesis pathway and plays critical functions for many aspects of rice plant growth and development.

Abstract (Browse 279)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
This study characterized a novel chromatin remodeling factor, OsINO80, which is directly involved in GA biosynthesis pathway, and affects many aspects of rice growth and development.
A substitution mutation in OsPELOTA confers bacterial blight resistance by activating the salicylic acid pathway  
Author: Xiao-Bo Zhang, Bao-Hua Feng, Hui-Mei Wang, Xia Xu, Yong-Feng Shi, Yan He, Zheng Chen, Atul Prakash Sathe, Lei Shi and Jian-Li Wu
Journal of Integrative Plant Biology 2018 60(2): 160每172
Published Online: November 29, 2017
DOI: 10.1111/jipb.12613

We previously reported a spotted-leaf mutant pelota (originally termed HM47) in rice displaying arrested growth and enhanced resistance to multiple races of Xanthomonas oryzae pv. oryzae. Here, we report the map-based cloning of the causal gene OsPELOTA (originally termed splHM47). We identified a single base substitution from T to A at position 556 in the coding sequence of OsPELOTA, effectively mutating phenylalanine to isoleucine at position 186 in the translated protein sequence. Both functional complementation and over-expression could rescue the spotted-leaf phenotype. OsPELOTA, a paralogue to eukaryotic release factor 1 (eRF1), shows high sequence similarity to Drosophila Pelota and also localizes to the endoplasmic reticulum and plasma membrane. OsPELOTA is constitutively expressed in roots, leaves, sheaths, stems, and panicles. Elevated levels of salicylic acid and decreased level of jasmonate were detected in the pelota mutant. RNA-seq analysis confirmed that genes responding to salicylic acid were upregulated in the mutant. Our results indicate that the rice PELOTA protein is involved in bacterial leaf blight resistance by activating the salicylic acid metabolic pathway.

Abstract (Browse 357)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Compared to its ancestor, the lesion mimic rice pelota gains a new ability to protect itself from the attack of bacterial leaf blight pathogens caused by a single base nucleotide mutation. Enhanced resistance of pelota is achieved by activating a set of genes associated with the increasing level of salicylic acid.
The calcium-dependent kinase OsCPK24 functions in cold stress responses in rice  
Author: Yu Liu, Chunjue Xu, Yanfen Zhu, Lina Zhang, Taiyu Chen, Fei Zhou, Hao Chen and Yongjun Lin
Journal of Integrative Plant Biology 2018 60(2): 173每188
Published Online: November 29, 2017
DOI: 10.1111/jipb.12614

Calcium-dependent protein kinases (CPKs) are serine/threonine protein kinases that function in plant stress responses. Although CPKs are recognized as key messengers in signal transduction, the specific roles of CPKs and the molecular mechanisms underlying their activity remain largely unknown. Here, we characterized the function of OsCPK24, a cytosol-localized calcium-dependent protein kinase in rice. OsCPK24 was universally and highly expressed in rice plants and was induced by cold treatment. Whereas OsCPK24 knockdown plants exhibited increased sensitivity to cold compared to wild type (WT), OsCPK24-overexpressing plants exhibited increased cold tolerance. Plants overexpressing OsCPK24 exhibited increased accumulation of proline (an osmoprotectant) and glutathione (an antioxidant) and maintained a higher GSH/GSSG (reduced glutathione to oxidized glutathione) ratio during cold stress compared to WT. In addition to these effects in response to cold stress, we observed the kinase activity of OsCPK24 varied under different calcium concentrations. Further, OsCPK24 phosphorylated OsGrx10, a glutathione-dependent thioltransferase, at rates modulated by changes in calcium concentration. Together, our results support the hypothesis that OsCPK24 functions as a positive regulator of cold stress tolerance in rice, a process mediated by calcium signaling and involving phosphorylation and the inhibition of OsGrx10 to sustain higher glutathione levels.

Abstract (Browse 450)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
CPKs are serine/threonine protein kinases that function in plant stress responses. This study demonstrated that OsCPK24 is induced by cold treatments. It promotes cold tolerance when over-expressed and reduces cold tolerance when down-regulated, indicating that OsCPK24 is a positive regulator of cold stress tolerance in rice.
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