A transcriptional regulator that boosts grain yields and shortens the growth duration of rice

Wei, Shaobo; Li, Xia; Lu, Zefu; Zhang, Hui; Ye, Xiangyuan; Zhou, Yujie; Li, Jing; Yan, Yanyan; Pei, Hongcui; Duan, Fengying; Wang, Danying; Chen, Song; Wang, Peng; Zhang, Chao; Shang, Lianguang; Zhou, Yue; Yan, Peng; Zhao, Ming; Huang, Jirong; Bock, Ralph; Qian, Qian; Zhou, Wen

doi:10.1126/science.abi8455

Cited by 172 publications

(93 citation statements)

References 67 publications

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“…It has been identified in rice that an OsDREB1C can drive a transcription program with diverse functions, determining photosynthetic capacity, nitrogen utilization, and flowering time. The yield of rice overexpressing OsDREB1C has increased by 41.3%~68.3% [ 53 ]. In this study, we preliminarily explored the relative expression levels of 13 representative PdAP2/ERF genes in four tissues of ‘Wanfeng’ almond and six freezing stress temperature treatments in annual dormant branches based on qRT–PCR technology.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the Almond AP2/ERF Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress

Zhang²,

Hu³

et al. 2022

Biology

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The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays an important role in regulating plant growth and development and the response to biotic and abiotic stresses. However, there is no report on the AP2/ERF gene family in almond (Prunus dulcis). In this study, a total of 136 PdAP2/ERF genes were identified from the almond genome, and their protein physicochemical properties were analyzed. The PdAP2/ERF members were divided into five subgroups: AP2, RAV, ERF, DREB, and Soloist. The PdAP2/ERF members in each subgroup had conserved motif types and exon/intron numbers. PdAP2/ERFS members are distributed on eight chromosomes, with 22 pairs of segmental duplications and 28 pairs of tandem duplications. We further explored the colinear relationship between almond and Arabidopsis thaliana, Oryza sativa, Malus domestica, and Prunus persica AP2/ERF genes and their evolution. The results of cis-acting elements showed that PdAP2/ERF members are widely involved in various processes, such as growth and development, hormone regulation, and stress response. The results based on transcriptome expression patterns showed that PdAP2/ERF genes had significant tissue-specific expression characteristics and were involved in the response of annual dormant branches of almond to low-temperature freezing stress. In addition, the fluorescence quantitative relative expression results of 13 representative PdAP2/ERF genes in four tissues of ‘Wanfeng’ almond and under six low-temperature freezing treatments of annual dormant branches were consistent with the transcriptome results. It is worth noting that the fluorescence quantitative expression level showed that the PdERF24 gene was extremely significant at −30 °C, suggesting that this gene may play an important role in the response of almond dormancy to ultralow temperature freezing stress. Finally, we identified 7424 and 6971 target genes based on AP2 and ERF/DREB DNA-binding sites, respectively. The GO and KEGG enrichment results showed that these target genes play important roles in protein function and multiple pathways. In summary, we conducted bioinformatics and expression pattern studies on PdAP2/ERF genes, including 13 PdAP2/ERF genes, and performed fluorescence quantitative analysis of annual dormant shoots under different low-temperature freezing stress treatments to understand the tolerance of almond dormancy to freezing stress and suggest future improvements.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the Almond AP2/ERF Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress

Zhang²,

Hu³

et al. 2022

Biology

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“…ERF TFs, the last step of the ethylene signaling pathway, regulate the response of plants to environmental changes (Xie et al, 2019). Recently, one intronless ERF TF was reported to simultaneously modulate photosynthesis and nitrogen utilization in rice (Wei et al, 2022). ERF TFs showed remarkable changes to low CO 2 stress in all five Flaveria species (Supplemental Note 15).…”

Section: Discussionmentioning

confidence: 99%

Born with intronless ERF transcriptional factors: C₄photosynthesis inherits a legacy dating back 450 million years

Lyu

Yao

et al. 2022

Preprint

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The genus Flaveria, containing species at different evolutionary stages of the progression from C3 to C4 photosynthesis, is used as a model system to study the evolution of C4 photosynthesis. Here, we report chromosome-scale genome sequences for five Flaveria species, including C3, C4, and intermediate species. Our analyses revealed that both acquiring additional gene copies and recruiting ethylene responsive factor (ERF) cis-regulatory elements (CREs) contributed to the emergence of C4 photosynthesis. ERF transcriptional factors (TFs), especially intronless ERF TFs, were co-opted in dicotyledonous C4 species and monocotyledonous C4 species in parallel. These C4 species co-opted intronless ERF TFs originated from the Late Ordovician mass extinction that occurred ~450 million years ago in coping with environmental stress. Therefore, this study demonstrated that intronless ERF TFs were acquired during the early evolution of plants and provided the molecular toolbox facilitating multiple subsequent independent evolutions of C4 photosynthesis.

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“…The expression of OsDREB1C is induced by light and low-nitrogen levels. Overexpression lines of OsDREB1C (OsDREB1C-OE) exhibited higher grain yield by increasing the grain number per panicle ( Wei et al., 2022 ). Moreover, the increase in yield was due to improved nitrogen-use efficiency conferred by OsDREB1C-OE by stimulating nitrogen uptake of roots.…”

Section: Discussionmentioning

confidence: 99%

Response of Southeast Asian rice root architecture and anatomy phenotypes to drought stress

Siangliw

Thunnom²,

Natividad³

et al. 2022

Front. Plant Sci.

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Drought stress in Southeast Asia greatly affects rice production, and the rice root system plays a substantial role in avoiding drought stress. In this study, we examined the phenotypic and genetic correlations among root anatomical, morphological, and agronomic phenotypes over multiple field seasons. A set of >200 rice accessions from Southeast Asia (a subset of the 3000 Rice Genomes Project) was characterized with the aim to identify root morphological and anatomical phenotypes related to productivity under drought stress. Drought stress resulted in slight increases in the basal metaxylem and stele diameter of nodal roots. Although few direct correlations between root phenotypes and grain yield were identified, biomass was consistently positively correlated with crown root number and negatively correlated with stele diameter. The accessions with highest grain yield were characterized by higher crown root numbers and median metaxylem diameter and smaller stele diameter. Genome-wide association study (GWAS) revealed 162 and 210 significant SNPs associated with root phenotypes in the two seasons which resulted in identification of 59 candidate genes related to root development. The gene OsRSL3 was found in a QTL region for median metaxylem diameter. Four SNPs in OsRSL3 were found that caused amino acid changes and significantly associated with the root phenotype. Based on the haplotype analysis for median metaxylem diameter, the rice accessions studied were classified into five allele combinations in order to identify the most favorable haplotypes. The candidate genes and favorable haplotypes provide information useful for the genetic improvement of root phenotypes under drought stress.

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A transcriptional regulator that boosts grain yields and shortens the growth duration of rice

Cited by 172 publications

References 67 publications

Genome-Wide Analysis of the Almond AP2/ERF Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress

Genome-Wide Analysis of the Almond AP2/ERF Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress

Born with intronless ERF transcriptional factors: C₄photosynthesis inherits a legacy dating back 450 million years

Response of Southeast Asian rice root architecture and anatomy phenotypes to drought stress

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A transcriptional regulator that boosts grain yields and shortens the growth duration of rice

Cited by 172 publications

References 67 publications

Genome-Wide Analysis of the Almond AP2/ERF Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress

Genome-Wide Analysis of the Almond AP2/ERF Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress

Born with intronless ERF transcriptional factors: C4photosynthesis inherits a legacy dating back 450 million years

Response of Southeast Asian rice root architecture and anatomy phenotypes to drought stress

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Born with intronless ERF transcriptional factors: C₄photosynthesis inherits a legacy dating back 450 million years