• Wang K, Yu H, Zhang X, Ye D, Huang H, Wang Y, Zheng Z, Li T. (2021) A transcriptomic view of cadmium retention in roots of cadmium-safe rice line (Oryza sativa L.). Journal of Hazardous Materials 418, 126379.

A better understanding of the mechanisms controlling cadmium (Cd) accumulation in rice will benefit the development of strategies to minimize Cd accumulation in grains. A Cd-safe rice line designated D62B accumulated less than 0.2 mg Cd kg–1 in brown rice due to its strong capacity for Cd retention in roots. Here transcriptomic was used to clarify the underlying mechanisms of Cd response in roots of D62B compared with a high Cd-accumulating line (Wujin4B). There were 777, 1058 differentially expressed genes (DEGs) in D62B and Wujin4B, respectively, when exposed to Cd. The functions of DEGs were clearly line-specific. Cell wall biosynthesis responded more intensively to Cd stress in D62B, facilitating Cd restriction. Meanwhile, more glutathione (GSH) and phytochelatins synthesized in D62B with the upregulation of sulphur and GSH metabolism. Besides, membrane proteins played critical roles in Cd response in D62B, whereas 18 terms involved in regulation were enriched in Wujin4B. Exogenous GSH further induced the expression of genes related to GSH metabolism and cell wall biosynthesis, leading to the retention of more Cd. Great responsiveness of cell wall biosynthesis and GSH metabolism could be considered the most important specific mechanisms for Cd retention in the roots of Cd-safe rice line.

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• Verstraeten B, Atighi M, Reza R, Virginia E, Carolina D, Meyer T, Kyndt T. (2021) Non-coding RNAs in the interaction between rice and Meloidogyne graminicola. BMC Genomics 22(1), 560.

Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues.

We found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data.

To our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies.

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• Zhong M, Huang F, Luo R, Lv Y, Ali U, Sheng Z, Tang S, Wei X, Hu P. (2019) The effect of cadmium on the microRNAome, degradome and transcriptome of rice seedlings. Plant Growth Regulation 90(1), 15-27.

The damage induced by the uptake of cadmium (Cd) into the rice plant is of growing concern. Although many micro-RNAs (miRNAs) and their target genes have been identified in experiments designed to elucidate the molecular impact of exposure to Cd, as yet there has been no attempt to integrate data from sequencing the microRNAome, the degradome and the transcriptome of rice plants exposed to Cd. Here, the abundance of 40 miRNAs was shown to be substantially altered as response to Cd exposure. Of those, 38 (belonging to 22 known miRNA families) were already documented in rice and two (PC-3p-38247_129 and PC-3p-102187_26) are novel. The abundance of 18 genes differentially transcribed as a result of Cd exposure was found to be inversely correlated to that of 18 of the Cd-responsive miRNAs. The majority of the target genes encoded transcription factors, including ARF13, SCL6, various SPLs, NFYA6, GAMYB, and various NACs which encode proteins that participate in signal transduction and abiotic stress resistance. In all, the present study established a fundamental basis for evaluating the regulatory role of miRNA and their targets in plant exposure to Cd stress.

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• Zhao C. (2019) A 3-bp deletion of WLS5 gene leads to weak growth and early leaf senescence in rice. Rice 12(1), 26.

In rice (Oryza sativa) and other grains, weak growth (dwarfism, short panicle length, and low seed-setting rate) and early senescence lead to reduced yield. The molecular mechanisms behind these processes have been widely studied; however, the complex genetic regulatory networks controlling growth and senescence require further elucidation.

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• Huang X. (2019) Comparative analysis of microRNAs and their targets in the roots of two cultivars with contrasting salt tolerance in rice (Oryza sativa L.). Plant Growth Regulation 87(1), 139-148.

MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress responses. Rice cultivars IR26 (sub. xian) and Jiucaiqing (sub. geng) exhibit significant salt tolerance differences during their growth. This study performed a genome-wide discovery of salt responsive miRNAs in rice roots, and in particular, the differentially expressed miRNAs between two cultivars. Specifically- and commonly-regulated miRNAs involved in salt stress between two cultivars were identified. The genes targeted by these miRNAs were involved in multiple biological processes including transcriptional regulation and response to stimulus. This preliminary characterization provides a framework for future analysis of miRNAs and their roles in rice salt stress response and describes the possible mechanisms for miRNA mediated salt tolerance by comparative analysis of miRNAs and their targets in salt-resistant and -sensitive cultivars.

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• Chen J. (2018) Multiple Regression Analysis Reveals MicroRNA Regulatory Networks in Oryza sativa under Drought Stress. International Journal of Genomics 2018, 9395261.

Drought is a major abiotic stress that reduces rice development and yield. miRNAs (microRNAs) are known to mediate posttranscriptional regulation under drought stress. Although the importance of individual miRNAs has been established, the crosstalks between miRNAs and mRNAs remain unearthed. Here we performed microarray analysis of miRNAs and matched mRNA expression profiles of drought-treated rice cultivar Nipponbare. Drought-responsive miRNA-mRNA regulations were identified by a combination of a partial least square (PLS) regression approach and sequence-based target prediction. A drought-induced network with 13 miRNAs and 58 target mRNAs was constructed, and four miRNA coregulatory modules were revealed. Functional analysis suggested that drought-response miRNA targets are enriched in hormone signaling, lipid and carbohydrate metabolism, and antioxidant defense. 13 candidate miRNAs and target genes were validated by RT-qPCR, hierarchical clustering, and ROC analysis. Two target genes (DWARF-3 and P0651G05.2) of miRNA coregulatory modules were further verified by RLM-5′ RACE. Together, our integrative study of miRNA-mRNA interaction provided attractive candidates that will help elucidate the drought-response mechanisms in Oryza sativa.

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• Miao Y, Ye C, Shen L, Cao Y, Tu J, Yu J. (2018) Unique miRNome in heat tolerant indica rice var. HT54 seedlings. Ecological Genetics and Genomics 7(8), 13-22.

As the most important major food crop, rice (Oryza sativa) often suffers from heat stress in tropical and subtropical regions. Thus, to investigate the mechanisms of responses and tolerance to heat stress (HS) at the miRNA level is important for breeding new rice varieties with HS tolerance. In this study, six miRNA libraries (with duplicates for each of the 0 h, 12 h and 24 h HS treatment) for HT54, an indica heat tolerant line, were sequenced. Based on this, a set of HS-responsive miRNAs and their target genes were identified by using the next-generation sequencing (NGS) and degradome sequencing (DS). A total of 419 conserved and 77 novel miRNAs were identified, of which 39 conserved and 2 novel miRNAs were found to be significantly differentially expressed (p < 0.05). As the most up-regulated miRNA, the expression of miR396 family members were verified by qRT-PCR. In addition, one down-regulated miR162b and one novel miRNA (pc-5p-93188_29) were experimentally validated. These results inferred that these loci were responsive to HS. Moreover, a total of 1364 target transcripts were identified for 114 conserved miRNAs and a total of 65 were identified for 22 novel miRNA families. GO and pathway enrichment analyses showed that these genes most likely play vital roles in rice HS tolerance. Taken together, a set of HS-responsive conserved and novel miRNAs were firstly characterized and identified in rice seedlings, which would lay a solid foundation for clarifying rice HS response and tolerance mechanisms.

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• He L, Zhang S, Qiu Z, Zhao J, Nie W, Lin H, Zhu Z, Zeng D, Qian Q, Zhu L. (2018) FRUCTOKINASE-LIKE PROTEIN 1 interacts with TRXz to regulate chloroplast development in rice. Journal of Integrative Plant Biology 60(2), 94-111.

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.

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• Fang C, Dou L, Liu Y, Yu J, Tu J. (2018) Heat stress-responsive transcriptome analysis in heat susceptible and tolerant rice by high-throughput sequencing. Ecological Genetics and Genomics 6(1), 33-40.

As one of the most vital major food crops feeding almost half the earth’s population, rice often suffers from heat stress in tropical and subtropical regions. To study rice heat stress tolerance mechanism is critical for breeding new heat tolerant rice varieties. We performed RNA-Seq analysis to check rice transcriptomic differences responsive to heat stress in both heat-tolerant (HT, HT54) and heat-sensitive (HS, HT13) lines. A sum of 0.603 billion reads were acquired on behalf of 32,391 unique genes. Compared with 0 h, a sum of 2275 genes showed enhanced regulation while 2270 genes showed inhibited regulation in the HS line at 12 h, contrarily 2603 genes showed enhanced regulation and 2900 genes showed inhibited regulation in the HT line. A sum of 1438 genes showed enhanced regulation and 1237 genes showed inhibited regulation in the HS line at 24 h, contrarily 1599 genes showed enhanced regulation and 1754 genes showed inhibited regulation in the HT line. About 22,490 genes were assigned to gene ontology (GO) term in terms of biological process, cellular component and molecular function categories. Compared with 0 h, a sum of 8 and 4 genes showed different expression (RFC ≥ 2.0) between the HT and HS rice lines at 12 and 24 h, respectively. This work most probably set a solid foundation for elucidating the heat stress tolerance mechanisms and crop genetic improvement in rice.

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• Lv Y, Shao G, Qiu J, Jiao G, Sheng Z, Xie L, Wu Y, Tang S, Wei X, Hu P. (2017) White Leaf and Panicle 2, encoding a PEP-associated protein, is required for chloroplast biogenesis under heat stress in rice. Journal of Experimental Botany 68(18), 5147-5160.

The plastid-encoded RNA polymerase (PEP) plays an important role in the transcription machinery of mature chloroplasts, yet details of its function remain elusive in rice. Here, we identified a novel PEP-associated protein (PAP), WLP2, based on its two allelic white leaf and panicle mutants, wlp2s and wlp2w. The two mutants were albino lethal at high temperatures and showed decreased chlorophyll accumulation, abnormal chloroplast ultrastructure, and attenuated photosynthetic activity. Map-based cloning suggested that WLP2 encodes a putative pfkB-type carbohydrate kinase family protein, which is homologous to fructokinase-like 1 (AtFLN1) in Arabidopsis. WLP2 is mainly expressed in green tissues and its protein localizes in chloroplasts. Expression levels of PEP-encoded genes, chloroplast development genes and photosynthesis-related genes were compromised in wlp2 mutants, indicating that WLP2 is essential for normal chloroplast biogenesis. Moreover, WLP2 and its paralog OsFLN2 can physically interact with thioredoxin OsTRXz to form a TRX-FLN regulatory module, which not only regulates transcription of the PEP-encoded genes but also maintains the redox balance in chloroplasts under heat stress. Furthermore, the wlp2w mutant gene represents a potential advantage in enhancing seed purity and high-throughput breeding. Our results strongly indicate that WLP2 protects chloroplast development from heat stress via a TRX-FLN regulatory module in rice.

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