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Authors: Xiaolin Liu, Shusong Zheng, Shuiquan Tian, Yaoqi Si, Shengwei Ma, Hong-Qing Ling and Jianqing Niu.
Theoretical and Applied Genetics (2024)
Key message: Discovery of Rht27, a dwarf gene in wheat, showed potential in enhancing grain yield by reducing plant height.
Abstract: "Plant height plays a crucial role in crop architecture and grain yield, and semi-dwarf Reduced Height (Rht) alleles contribute to lodging resistance and were important in “Green Revolution.” However, the use of these alleles is associated with some negative side effects in some environments, such as reduced coleoptile length, low nitrogen use efficiency, and reduced yield. Therefore, novel dwarf gene resources are needed to pave an alternative route to overcome these side effects. In this study, a super-dwarf mutant rht27 was obtained by the mutagenesis of G1812 (Triticum urartu, the progenitor of the A sub-genome of common wheat). Genetic analysis revealed that the dwarf phenotype was regulated by a single recessive genetic factor. The candidate region for Rht27 was narrowed to a 1.55 Mb region on chromosome 3, within which we found two potential candidate genes that showed polymorphisms between the mutant and non-mutagenized G1812. Furthermore, the natural variants and elite haplotypes of the two candidates were investigated in a natural population of common wheat. The results showed that the natural variants affect grain yield components, and the dwarf haplotypes show the potential in improving agronomic traits and grain yield. Although the mutation in Rht27 results in severe dwarf phenotype in T. urartu, the natural variants in common wheat showed desirable phenotype, which suggests that Rht27 has the potential to improve wheat yield by utilizing its weak allelic mutation or fine-tuning its expression level."
Authors: Barbora Ndreca, Alison Huttly, Sajida Bibi, Carlos Bayon, George Lund, Joshua Ham, Rocío Alarcón-Reverte, John Addy, Danuše Tarkowská, Stephen Pearce, Peter Hedden, Stephen G. Thomas and Andrew L. Phillips.
BMC Plant Biology (2024)
Abstract: Background - Semi-dwarfing alleles are used widely in cereals to confer improved lodging resistance and assimilate partitioning. The most widely deployed semi-dwarfing alleles in rice and barley encode the gibberellin (GA)-biosynthetic enzyme GA 20-OXIDASE2 (GA20OX2). The hexaploid wheat genome carries three homoeologous copies of GA20OX2, and because of functional redundancy, loss-of-function alleles of a single homoeologue would not be selected in wheat breeding programmes. Instead, approximately 70% of wheat cultivars carry gain-of-function mutations in REDUCED HEIGHT 1 (RHT1) genes that encode negative growth regulators and are degraded in response to GA. Semi-dwarf Rht-B1b or Rht-D1b alleles encode proteins that are insensitive to GA-mediated degradation. However, because RHT1 is expressed ubiquitously these alleles have pleiotropic effects that confer undesirable traits in some environments. Results - We have applied reverse genetics to combine loss-of-function alleles in all three homoeologues of wheat GA20OX2 and its paralogue GA20OX1 and evaluated their performance in three years of field trials. ga20ox1 mutants exhibited a mild height reduction (approximately 3%) suggesting GA20OX1 plays a minor role in stem elongation in wheat. ga20ox2 mutants have reduced GA1 content and are 12–32% shorter than their wild-type segregants, comparable to the effect of the Rht-D1b ‘Green Revolution’ allele. The ga20ox2 mutants showed no significant negative effects on yield components in the spring wheat variety ‘Cadenza’. Conclusions - Our study demonstrates that chemical mutagenesis can expand genetic variation in polyploid crops to uncover novel alleles despite the difficulty in identifying appropriate mutations for some target genes and the negative effects of background mutations. Field experiments demonstrate that mutations in GA20OX2 reduce height in wheat, but it will be necessary to evaluate the effect of these alleles in different genetic backgrounds and environments to determine their value in wheat breeding as alternative semi-dwarfing alleles.
Authors: Xumin Xiang, Hongli Yang, Xi Yuan, Xue Dong, Sihua Mai, Qianqian Zhang, Limiao Chen, Dong Cao, Haifeng Chen, Wei Guo and Li Li.
Plant Cell Reports (2024)
Key message: The study on the GmDWF1-deficient mutant dwf1 showed that GmDWF1 plays a crucial role in determining soybean plant height and yield by influencing the biosynthesis of brassinosteroids.
Abstract: "Soybean has not adopted the Green Revolution, such as reduced height for increased planting density, which have proven beneficial for cereal crops. Our research identified the soybean genes GmDWF1a and GmDWF1b, homologous to Arabidopsis AtDWF1, and found that they are widely expressed, especially in leaves, and linked to the cellular transport system, predominantly within the endoplasmic reticulum and intracellular vesicles. These genes are essential for the synthesis of brassinosteroids (BR). Single mutants of GmDWF1a and GmDWF1b, as well as double mutants of both genes generated through CRISPR/Cas9 genome editing, exhibit a dwarf phenotype. The single-gene mutant exhibits moderate dwarfism, while the double mutant shows more pronounced dwarfism. Despite the reduced stature, all types of mutants preserve their node count. Notably, field tests have shown that the single GmDWF1a mutant produced significantly more pods than wild-type plants. Spraying exogenous brassinolide (BL) can compensate for the loss in plant height induced by the decrease in endogenous BRs. Comparing transcriptome analyses of the GmDWF1a mutant and wild-type plants revealed a significant impact on the expression of many genes that influence soybean growth. Identifying the GmDWF1a and GmDWF1b genes could aid in the development of compact, densely planted soybean varieties, potentially boosting productivity."
Authors: Ángela María Sánchez-López, Abdellatif Bahaji, Samuel Gámez-Arcas, Nuria De Diego, Ondřej Vrobel, Petr Tarkowski, Edurne Baroja-Fernández, Francisco José Muñoz, Goizeder Almagro, Jose María Seguí-Simarro, Mercedes Tabernero-Mendoza, Lidia López-Serrano, Rafael J.L. Morcillo and Javier Pozueta-Romero.
Plant Physiology and Biochemistry (2024)
Highlights: • Vascular plastidial phosphoglucose isomerase (vPGI1) modulates the leaf proteome. • Vascular pentose phosphate pathway (vPPP) activity regulates photosynthesis. • Long-distance interplay between vPPP and photosynthesis in mesophyll cells. • vPGI1-mediated PPP activity modulates the metabolic flux to the MEP pathway.
Abstract: "In Arabidopsis, the plastidial isoform of phosphoglucose isomerase, PGI1, mediates growth and photosynthesis, likely due to its involvement in the vascular production of cytokinins (CK). To examine this hypothesis, we characterized pgi1-2 knockout plants impaired in PGI1 and pgi1-2 plants specifically expressing PGI1 in root tips and vascular tissues. Moreover, to investigate whether the phenotype of pgi1-2 plants is due to impairments in the plastidial oxidative pentose phosphate pathway (OPPP) or the glycolytic pathway, we characterized pgl3-1 plants with reduced OPPP and pfk4pfk5 knockout plants impaired in plastidial glycolysis. Compared with wild-type (WT) leaves, pgi1-2 leaves exhibited weaker expression of photosynthesis- and 2-C-methyl-D-erythritol 4-P (MEP) pathway-related proteins, and stronger expression of oxidative stress protection-related enzymes. Consistently, pgi1-2 leaves accumulated lower levels of chlorophyll, and higher levels of tocopherols, flavonols and anthocyanins than the WT. Vascular- and root tip-specific PGI1 expression countered the reduced photosynthesis, low MEP pathway-derived CK content, dwarf phenotype and the metabolic characteristics of pgi1-2 plants, reverting them to WT-like levels. Moreover, pgl3-1, but not pfk4pfk5 plants phenocopied pgi1-2. Histochemical analyses of plants expressing GUS under the control of promoter regions of genes encoding plastidial OPPP enzymes exhibited strong GUS activity in root tips and vascular tissues. Overall, our findings show that root tip and vascular PGI1-mediated plastidial OPPP activity affects photosynthesis and growth through mechanisms involving long-distance modulation of the leaf proteome by MEP pathway-derived CKs."
Authors: Xiu Fang, Hao Wu, Wanchang Huang, Zhongxian Ma, Yue Jia, Yongwei Min, Qing Ma and Ronghao Cai.
Plant Physiology and Biochemistry (2024)
Highlights: • Mutation of the ZmWRKY92 gene resulted in decreased plant height in maize. • ZmWRKY92 is a nuclear localized protein with transactivation activity in yeast. • ZmWRKY92 binds to the W-box element in the promoter of GA synthesis-related genes.
Abstract: "The plant height is a crucial agronomic trait in contemporary maize breeding. Appropriate plant height can improve crop lodging resistance, increase the planting density and harvest index of crops, and thus contribute to stable and increased yields. In this study, molecular characterization showed that ZmWRKY92 is a nuclear protein and has transcriptional activation in yeast. ZmWRKY92 can specifically bind to the W-box (TTGACC), which was confirmed by double LUC experiments and Yeast one-hybrid assays. Subsequently we screened wrky92 mutants from a library of ethyl methanesulfonate (EMS)-induced mutants. The mutation of a base in ZmWRKY92 leading to the formation of a truncated protein variant is responsible for the dwarfing phenotype of the mutant, which was further verified by allelic testing. Detailed phenotypic analysis revealed that wrky92 mutants have shorter internodes due to reduced internode cell size and lower levels of GA3 and IAA. Transcriptome analysis revealed that the ZmWRKY92 mutation caused significant changes in the expression of genes related to plant height in maize. Additionally, ZmWRKY92 was found to interact with the promoters of ZmGA20ox7 and ZmGID1L2, which are associated with GA synthesis. This study shows that ZmWRKY92 significantly affects the plants height in maize and is crucial in identifying new varieties suitable for growing in high-density conditions."
Authors: Jingye Cheng, Yong Jia, Camilla Hill, Tianhua He, Ke Wang, Ganggang Guo, Sergey Shabala, Meixue Zhou, Yong Han and Chengdao Li.
Journal of Advanced Research (2024)
Highlights • Genes concoding gibberellin 2-oxidase are expanded to ten copies in the barley genome and shown copy number variation in the barley pan genome. • The ten genes are transcriptionally expressed in a tissue-specific way, indicating divergent biological functions. • Functions of two genes of gibberellin 2-oxidase were validated by virus-induced gene silencing and CRISPR gene editing to control different agronomic traits. • A natural mutant for the gene was identified with semidwarf stature, early flowering and heavier seeds. • The results provide a promising strategy to minimise the adverse effects of the original Green Revolution semi-dwarf genes to develop the next generation of barley cultivars better adapted to a changing climate.
Abstract: "Introduction - Gibberellin (GA) is a vital phytohormone in regulating plant growth and development. During the “Green Revolution”, modification of GA-related genes created semi-dwarfing phenotype in cereal crops but adversely affected grain weight. Gibberellin 2-oxidases (GA2oxs) in barley act as key catabolic enzymes in deactivating GA, but their functions are still less known. Objectives - This study investigates the physiological function of two HvGA2ox genes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits. Methods - Virus-induced gene silencing and CRISPR/Cas9 technology were used to manipulate gene expression of HvGA2ox9 and HvGA2ox8a in barley and RNA-seq was conducted to compare the transcriptome between wild type and mutants. Also, field trials in multiple environments were performed to detect the functional haplotypes. Results - There were ten GA2oxs that distinctly expressed in shoot, tiller, inflorescence, grain, embryo and root. Knockdown of HvGA2ox9 did not affect plant height, while ga2ox8a mutants generated by CRISPR/Cas9 increased plant height and significantly altered seed width and weight due to the increased bioactive GA4 level. RNA-seq analysis revealed that genes involved in starch and sucrose metabolism were significantly decreased in the inflorescence of ga2ox8a mutants. Furthermore, haplotype analysis revealed one naturally occurring HvGA2ox8a haplotype was associated with decreased plant height, early flowering and wider and heavier seed. Conclusion - Our results demonstrate the potential of manipulating GA2ox genes to fine tune GA signalling and biofunctions in desired plant tissues and open a promising avenue for minimising the trade-off effects of Green Revolution semi-dwarfing genes on grain size and weight. The knowledge will promote the development of next generation barley cultivars with better adaptation to a changing climate."
Author: Ravi Gupta.
Plant Cell Reports (2024)
Abstract: "Key message - A recent study identified a natural deletion in the r-e-z haploblock which confers a semi-dwarf trait, higher nitrogen use efficiency, and improved yield in semi-dwarf wheat varieties by attenuating the brassinosteroid signaling."
Authors: Qin Song, Lingfei Kong, Jiarui Yang, Minghui Lin, Yuqian Zhang, Xuerui Yang, Xiaojing Wang, Zhengjie Zhao, Meng Zhang, Jiarui Pan, Shunqin Zhu, Bo Jiao, Changzheng Xu and Keming Luo.
The Plant Journal (2024)
Abstract: "Drought stress caused by global warming has resulted in significant tree mortality, driving the evolution of water conservation strategies in trees. Although phytohormones have been implicated in morphological adaptations to water deficits, the molecular mechanisms underlying these processes in woody plants remain unclear. Here, we report that overexpression of PtoMYB142 in Populus tomentosa results in a dwarfism phenotype with reduced leaf cell size, vessel lumen area, and vessel density in the stem xylem, leading to significantly enhanced drought resistance. We found that PtoMYB142 modulates gibberellin catabolism in response to drought stress by binding directly to the promoter of PtoGA2ox4, a GA2-oxidase gene induced under drought stress. Conversely, knockout of PtoMYB142 by the CRISPR/Cas9 system reduced drought resistance. Our results show that the reduced leaf size and vessel area, as well as the increased vessel density, improve leaf relative water content and stem water potential under drought stress. Furthermore, exogenous GA3 application rescued GA-deficient phenotypes in PtoMYB142-overexpressing plants and reversed their drought resistance. By suppressing the expression of PtoGA2ox4, the manifestation of GA-deficient characteristics, as well as the conferred resistance to drought in PtoMYB142-overexpressing poplars, was impeded. Our study provides insights into the molecular mechanisms underlying tree drought resistance, potentially offering novel transgenic strategies to enhance tree resistance to drought."
Authors: Xueya Zhao, Kunpeng Zhang, Huidong Zhang, Mengxi Bi, Yi He, Yiqing Cui, Changhua Tan, Jian Ma and Mingfang Qi.
Frontiers in Plant Science (2023)
Abstract: "Plant height is an important agronomic trait. Dwarf varieties present several advantages, such as lodging resistance, increased yield, and suitability for mechanized harvesting, which are crucial for crop improvement. However, limited research is available on dwarf tomato varieties suitable for production. In this study, we report a novel short internode mutant named “short internode and pedicel (sip)” in tomato, which exhibits marked internode and pedicel shortening due to suppressed cell elongation. This mutant plant has a compact plant structure and compact inflorescence, and has been demonstrated to produce more fruits, resulting in a higher harvest index. Genetic analysis revealed that this phenotype is controlled by a single recessive gene, SlSIP. BSA analysis and KASP genotyping indicated that ERECTA (ER) is the possible candidate gene for SlSIP, which encodes a leucine-rich receptor-like kinase. Additionally, we obtained an ER functional loss mutant using the CRISPR/Cas9 gene-editing technology. The 401st base A of ER is substituted with T in sip, resulting in a change in the 134th amino acid from asparagine (N) to isoleucine (I). Molecular dynamics(MD) simulations showed that this mutation site is located in the extracellular LRR domain and alters nearby ionic bonds, leading to a change in the spatial structure of this site. Transcriptome analysis indicated that the genes that were differentially expressed between sip and wild-type (WT) plants were enriched in the gibberellin metabolic pathway. We found that GA3 and GA4 decreased in the sip mutant, and exogenous GA3 restored the sip to the height of the WT plant. These findings reveal that SlSIP in tomatoes regulates stem elongation by regulating gibberellin metabolism. These results provide new insights into the mechanisms of tomato dwarfing and germplasm resources for breeding dwarfing tomatoes."
Authors: Shichen Li, Zhihui Sun, Qing Sang, Chao Qin, Lingping Kong, Xin Huang, Huan Liu, Tong Su, Haiyang Li, Milan He, Chao Fang, Lingshuang Wang, Shuangrong Liu, Bin Liu, Baohui Liu, Xiangdong Fu, Fanjiang Kong and Sijia Lu
Nature Communications (2023)
Editor's view: Many cereal crops have been bred to be more compact to allow high-density planting, but soybean has remained relatively overlooked. Here, the authors describe a compact soybean mutant, reduced internode 1, that significantly enhances grain yield under high-density planting conditions compared to an elite cultivar.
Abstract: "Major cereal crops have benefitted from Green Revolution traits such as shorter and more compact plants that permit high-density planting, but soybean has remained relatively overlooked. To balance ideal soybean yield with plant height under dense planting, shortening of internodes without reducing the number of nodes and pods is desired. Here, we characterized a short-internode soybean mutant, reduced internode 1 (rin1). Partial loss of SUPPRESSOR OF PHYA 105 3a (SPA3a) underlies rin1. RIN1 physically interacts with two homologs of ELONGATED HYPOCOTYL 5 (HY5), STF1 and STF2, to promote their degradation. RIN1 regulates gibberellin metabolism to control internode development through a STF1/STF2–GA2ox7 regulatory module. In field trials, rin1 significantly enhances grain yield under high-density planting conditions comparing to its wild type of elite cultivar. rin1 mutants therefore could serve as valuable resources for improving grain yield under high-density cultivation and in soybean–maize intercropping systems. Many cereal crops have been bred to be more compact to allow high-density planting, but soybean has remained relatively overlooked. Here, the authors describe a compact soybean mutant, reduced internode 1, that significantly enhances grain yield under high-density planting conditions compared to an elite cultivar."
Authors: Shuping Jiao, Sujan Mamidi, Mark A. Chamberlin, Mary Beatty, Shawn Thatcher, Kevin D. Simcox, Fanna Maina, Hu Wang-Nan, Gurmukh S. Johal, Lynn Heetland, Sandeep R. Marla, Robert B. Meeley, Jeremy Schmutz, Geoffrey P. Morris and Dilbag S. Multani.
New Phytologist (2023)
Abstract: "In the current genomic era, the search and deployment of new semi-dwarf alleles have continued to develop better plant types in all cereals. We characterized an agronomically optimal semi-dwarf mutation in Zea mays L. and a parallel polymorphism in Sorghum bicolor L. We cloned the maize brachytic1 (br1-Mu) allele by a modified PCR-based Sequence Amplified Insertion Flanking Fragment (SAIFF) approach. Histology and RNA-Seq elucidated the mechanism of semi-dwarfism. GWAS linked a sorghum plant height QTL with the Br1 homolog by resequencing a West African sorghum landraces panel. The semi-dwarf br1-Mu allele encodes an MYB transcription factor78 that positively regulates stalk cell elongation by interacting with the polar auxin pathway. Semi-dwarfism is due to differential splicing and low functional Br1 wild-type transcript expression. The sorghum ortholog, SbBr1, co-segregates with the major plant height QTL qHT7.1 and is alternatively spliced. The high frequency of the Sbbr1 allele in African landraces suggests that African smallholder farmers used the semi-dwarf allele to improve plant height in sorghum long before efforts to introduce Green Revolution-style varieties in the 1960s. Surprisingly, variants for differential splicing of Brachytic1 were found in both commercial maize and smallholder sorghum, suggesting parallel tuning of plant architecture across these systems."
Authors: Sunny Ahmar and Damian Gruszka.
Trends in Biochemical Sciences (2023)
Abstract: "A modern green revolution is needed to ensure global food security. Recently, Song et al. reported a new strategy to create high-yielding, semi-dwarf wheat varieties with improved nitrogen-use efficiency by inhibiting brassinosteroid (BR) signaling through clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9 (Cas9)-mediated knockout of the ZnF-B gene encoding a zinc-finger RING-type E3 ligase."
Author: Bhagirath Choudhary
In. Rural Voice - India
Excerpts: "Developed by Bayer Crop Science, the short corn contains a novel biotech trait of “altered plant architecture” for reduced plant height to less than 7 feet from 9 to 12 feet for a traditional corn hybrid, almost 33% reduction in plant height without compromising plant biomass."
"The short or semi-dwarf corn has resulted from the successful deployment of genetic modification technology that alters plant architecture either by partial or complete loss of expression of the GA20ox3 and GA20ox5 genes, which encode GA20-oxidase, an enzyme involved in the biosynthetic pathway of the plant hormone gibberellin, primarily responsible for plant height. The novel biotech trait approach powered by gene transfer and genome edited technology is distinct from the conventional breeding techniques, which introgress naturally occurring dwarf, semi-dwarf or short stature characteristic into elite germplasm. The introduction of the Green Revolution in the mid-1960s was based on GA-responsive naturally occurring dwarf mutants that saved the world, particularly India from a devastating famine and ensured food security. Rht gene of “Norin-10” variety of wheat and SD-1 gene of “Dee-geo-woo-gen” rice variety from Taiwan were used as the dwarf source for developing semi-dwarf and high-yielding wheat and rice varieties. Subsequently, agricultural science and research gained momentum and for the next five decades the semi-dwarf genes Rht and SD-1 were extensively used in developing countries to develop modern wheat and rice varieties for different agro-climatic zones."
"In continuation, the short or semi-dwarf trait is the next wave of technological advancement which would unleash the potential of gene transfer and genome editing in corn and other crops that bypassed the green revolution era....."
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Authors: Rui Yan, Tianle Zhang, Yuan Wang, Wenxiu Wang, Rahat Sharif, Jiale Liu, Qinglong Dong, Haoan Luan, Xuemei Zhang, Han Li, Suping Guo, Guohui Qi and Peng Jia.
Plant Physiology and Biochemistry (2024)
Highlights: • Seventeen GA2-oxidase genes identified in apple clustered into four clades. • MdGA2ox7 responded to cold and salt treatments. • MdGA2ox7 was activated during light-induced anthocyanin accumulation. • MdGA2ox7 alleviated cold and salt stress damage. • MdGA2ox7 promoted anthocyanin biosynthesis.
Abstract: "Apple (Malus domestica Borkh.) is a widely cultivated fruit crop worldwide but often suffers from abiotic stresses such as salt and cold. Gibberellic acid (GA) plays a pivotal in controlling plant development, environmental adaptability, and secondary metabolism. The GA2-oxidase (GA2ox) is responsible for the deactivation of bioactive GA. In this study, seventeen GA2-oxidase genes were identified in the apple genome, and these members could be clustered into four clades based on phylogenetic relationships and conserved domain structures. MdGA2ox7 exhibited robust expression across various tissues, responded to cold and salt treatments, and was triggered in apple fruit peels via light-induced anthocyanin accumulation. Subcellular localization prediction and experiments confirmed that MdGA2ox7 was located in the cytoplasm. Overexpression of MdGA2ox7 in Arabidopsis caused a lower level of active GA and led to GA-deficient phenotypes, such as dwarfism and delayed flowering. MdGA2ox7 alleviated cold and salt stress damage in both Arabidopsis and apple in concert with melatonin (MT). Additionally, MdGA2ox7 enhanced anthocyanin biosynthesis in apple calli and activated genes involved in anthocyanin synthesis. These findings provide new insights into the functions of apple GA2ox in regulating development, stress tolerance, and secondary metabolism."
Authors: Amanpreet Kaur, Norman B. Best, Thomas Hartwig, Josh Budka, Rajdeep Khangura, Steven McKenzie, Alejandro Aragón-Raygoza, Josh Strable, Burkhard Schulz and Brian P. Dilkes.
Plant Physiology (2023)
One-sentence summary: Molecular identity of a maize semidwarf mutant reveals a role for the maize GRAS domain transcription factor ortholog of DWARF AND LOW TILLERING in brassinosteroid signaling.
Abstract: "Brassinosteroids (BR) and gibberellins (GA) regulate plant height and leaf angle in maize (Zea mays). Mutants with defects in BR or GA biosynthesis or signaling identify components of these pathways and enhance our knowledge about plant growth and development. In this study, we characterized three recessive mutant alleles of GRAS transcription factor 42 (gras42) in maize, a GRAS transcription factor gene orthologous to the DWARF AND LOW TILLERING (DLT) gene of rice (Oryza sativa). These maize mutants exhibited semi-dwarf stature, shorter and wider leaves, and more upright leaf angle. Transcriptome analysis revealed a role for GRAS42 as a determinant of BR signaling. Analysis of the expression consequences from loss of GRAS42 in the gras42-mu1021149 mutant indicated a weak loss of BR signaling in the mutant, consistent with its previously demonstrated role in BR signaling in rice. Loss of BR signaling was also evident by the enhancement of weak BR biosynthetic mutant alleles in double mutants of nana plant1-1 and gras42-mu1021149. The gras42-mu1021149 mutant had little effect on GA-regulated gene expression, suggesting that GRAS42 is not a regulator of core GA signaling genes in maize. Single cell expression data identified gras42 expressed among cells in the G2/M phase of the cell cycle consistent with its previously demonstrated role in cell cycle gene expression in Arabidopsis (Arabidopsis thaliana). Cis-acting natural variation controlling GRAS42 transcript accumulation was identified by expression genome-wide association study (eGWAS) in maize. Our results demonstrate a conserved role for GRAS42/SCARECROW-LIKE 28 (SCL28)/DLT in BR signaling, clarify the role of this gene in GA signaling, and suggest mechanisms of tillering and leaf angle control by BR."
Authors: Barbora Ndreca, Alison Huttly, Sajida Bibi, Carlos Bayon, George Lund, Joshua Ham, Rocío Alarcón-Reverte, John Addy, Danuše Tarkowská, Stephen Pearce, Peter Hedden, Stephen G. Thomas and Andrew L. Phillips.
Research Square (2024)
Abstract: "Background - Semi-dwarfing alleles are used widely in cereals to confer improved lodging resistance and assimilate partitioning. The most widely deployed semi-dwarfing alleles in rice and barley encode the gibberellin (GA)-biosynthetic enzyme GA 20-OXIDASE2 (GA20OX2). The hexaploid wheat genome carries three homoeologous copies of GA20OX2, and because of functional redundancy, loss-of-function alleles of a single homoeologue would not be selected in wheat breeding programmes. Instead, approximately 70% of wheat cultivars carry gain-of-function mutations in REDUCED HEIGHT 1 (RHT1) genes that encode negative growth regulators and are degraded in response to GA. Semi-dwarf Rht-B1b or Rht-D1b alleles encode proteins that are insensitive to GA-mediated degradation. However, because RHT1 is expressed ubiquitously these alleles have pleiotropic effects that confer undesirable traits in some environments. Results - We have applied reverse genetics to combine loss-of-function alleles in all three homoeologues of wheat GA20OX2 and its paralogue GA20OX1 and evaluated their performance in three years of field trials. ga20ox1 mutants exhibited a mild height reduction (approximately 3%) suggesting GA20OX1 plays a minor role in stem elongation in wheat. ga20ox2 mutants have reduced GA1 content and are 12-32% shorter than their wild-type segregants, comparable to the effect of the Rht-D1b ‘Green Revolution’ allele. The ga20ox2 mutants showed no significant negative effects on yield components, although these alleles should be evaluated in different genetic backgrounds and environments. Conclusions - Our study demonstrates that induced mutagenesis can expand genetic variation in polyploid crops to uncover novel alleles and that mutations in GA20OX2 could have utility in wheat breeding as alternative semi-dwarfing alleles.
Authors: Jiahong Lv, Yi Feng, Longmei Zhai, Lizhong Jiang, Yue Wu, Yimei Huang, Runqi Yu, Ting Wu, Xinzhong Zhang, Yi Wang and Zhenhai Han.
Horticulture Research (2024)
Abstract: "Apple rootstock dwarfing and dense planting are common practices in apple farming. However, the dwarfing mechanisms are not understood. In this study, the expression of MdARF3 in the root system of dwarfing rootstock 'M9' was lower than in the vigorous rootstock from Malus micromalus due to the deletion of the WUSATAg element in the promoter of the 'M9' genotype. Notably, this deletion variation was significantly associated with dwarfing rootstocks. Subsequently, transgenic tobacco (Nicotiana tabacum) cv. Xanthi was generated with the ARF3 promoter from 'M9' and M. micromalus genotypes. The transgenic apple with 35S:: MdARF3 was also obtained. The transgenic tobacco and apple with the highly expressed ARF3 had a longer root system and a higher plant height phenotype. Furthermore, the yeast one-hybrid, luciferase, electrophoretic mobility shift assays, and Chip-qPCR identified MdWOX4-1 in apples that interacted with the pMm-ARF3 promoter but not the pM9-ARF3 promoter. Notably, MdWOX4-1 significantly increased the transcriptional activity of MdARF3 and MdLBD16-2. However, MdARF3 significantly decreased the transcriptional activity of MdLBD16-2. Further analysis revealed that MdARF3 and MdLBD16-2 were temporally expressed during different stages of lateral root development. pMdLBD16-2 was mainly expressed during the early stage of lateral root development, which promoted lateral root production. On the contrary, pMmARF3 was expressed during the late stage of lateral root development to promote elongation. The findings in this study will shed light on the genetic causes of apple plant dwarfism and provide strategies for molecular breeding of dwarfing apple rootstocks."
Authors: Haiqiang Zhang, Zichen Liu, Yunxiao Wang, Siyu Mu, Hongzhong Yue, Yanjie Luo, Zhengao Zhang, Yuhong Li and Peng Chen.
Theoretical and Applied Genetics (2024)
Key message A novel super compact mutant, scp-3, was identified using map-based cloning in cucumber. The CsDWF7 gene encoding a delta7 sterol C-5(6) desaturase was the candidate gene of scp-3.
Abstract: "Mining dwarf genes is important in understanding stem growth in crops. However, only a small number of dwarf genes have been cloned or characterized. Here, we characterized a cucumber (Cucumis sativus L.) dwarf mutant, super compact 3 (scp-3), which displays shortened internodes and dark green leaves with a wrinkled appearance. The photosynthetic rate of scp-3 is significantly lower than that of the wild type. The dwarf phenotype of scp-3 mutant can be partially rescued by the exogenous brassinolide (BL) application, and the endogenous brassinosteroids (BRs) levels in the scp-3 mutant were significantly lower compared to the wild type. Microscopic examination revealed that the reduced internode length in scp-3 resulted from a decrease in cell size. Genetic analysis showed that the dwarf phenotype of scp-3 was controlled by a single recessive gene. Combined with bulked segregant analysis and map-based cloning strategy, we delimited scp-3 locus into an 82.5 kb region harboring five putative genes, but only one non-synonymous mutation (A to T) was discovered between the mutant and its wild type in this region. This mutation occurred within the second exon of the CsGy4G017510 gene, leading to an amino acid alteration from Leu156 to His156. This gene encodes the CsDWF7 protein, an analog of the Arabidopsis DWF7 protein, which is known to be involved in the biosynthesis of BRs. The CsDWF7 protein was targeted to the cell membrane. In comparison to the wild type, scp-3 exhibited reduced CsDWF7 expression in different tissues. These findings imply that CsDWF7 is essential for both BR biosynthesis as well as growth and development of cucumber plants."
Authors: Guangyan Yang, Manyi Sun, Lester Brewer, Zikai Tang, Niels Nieuwenhuizen, Janine Cooney, Shaozhuo Xu, Jiawen Sheng, Christelle Andre, Cheng Xue, Ria Rebstock, Bo Yang, Wenjing Chang, Yueyuan Liu, Jiaming Li, Runze Wang, Mengfan Qin, Cyril Brendolise, Andrew C. Allan, Richard V. Espley, Kui Lin-Wang and Jun Wu.
Plant Biotechnology Journal (2024)
Abstract: "Variation in anthocyanin biosynthesis in pear fruit provides genetic germplasm resources for breeding, while dwarfing is an important agronomic trait, which is beneficial to reduce the management costs and allow for the implementation of high-density cultivation. Here, we combined bulked segregant analysis (BSA), quantitative trait loci (QTL), and structural variation (SV) analysis to identify a 14-bp deletion which caused a frame shift mutation and resulted in the premature translation termination of a B-box (BBX) family of zinc transcription factor, PyBBX24, and its allelic variation termed PyBBX24ΔN14. PyBBX24ΔN14 overexpression promotes anthocyanin biosynthesis in pear, strawberry, Arabidopsis, tobacco, and tomato, while that of PyBBX24 did not. PyBBX24ΔN14 directly activates the transcription of PyUFGT and PyMYB10 through interaction with PyHY5. Moreover, stable overexpression of PyBBX24ΔN14 exhibits a dwarfing phenotype in Arabidopsis, tobacco, and tomato plants. PyBBX24ΔN14 can activate the expression of PyGA2ox8 via directly binding to its promoter, thereby deactivating bioactive GAs and reducing the plant height. However, the nuclear localization signal (NLS) and Valine-Proline (VP) motifs in the C-terminus of PyBBX24 reverse these effects. Interestingly, mutations leading to premature termination of PyBBX24 were also identified in red sports of un-related European pear varieties. We conclude that mutations in PyBBX24 gene link both an increase in pigmentation and a decrease in plant height."
Authors: Xiujie Liu, Kai Huang and Chengcai Chu.
Plant Communications (2024)
Excerpts: "Very recently, Li et al. (2023) identified an ideal allele for compact plant architecture in soybean, reduced internode 1 (rin1), that downregulates plant height by reducing internode length and increases total yield per plot under dense planting conditions (Figure 1C). Li et al. have screened out a dwarf mutant from the mutant library in the background of Heinong 35 (HN35), an elite soybean cultivar in China. Interestingly, the reduced plant height of the mutant was mainly caused by the shortened internode, and the yield per plant of rin1 is higher than HN35 (Li et al., 2023). With F2 segregating population derived from the cross between rin1 and Heihe 43 (HH43), another elite cultivar, as well as a residual heterozygous inbred population from the F2 segregating population, the candidate gene of rin1 was cloned."
"In summary, the work of Li et al. (2023) that not only provides a potential elite allele, rin1, for soybean GR, but also uncovers the molecular mechanism of plant height and internode length regulation by RIN1, making a groundbreaking advance in soybean breeding for dense planting to enhance grain yield. Introducing rin1 into more elite soybean cultivars would be an effective strategy to promote the leap of soybean production, especially for China, which has a substantially lower soybean yield compared to USA, which has benefited from soybean varieties with enhanced lodging resistance to adapt to high-density planting (Figure 1B)."
Author: Carlisle Bascom, Jr.
The Plant Cell (2024)
Excerpts: "Myriad genes control plant size and development in Arabidopsis (A. thaliana), including those encoding the BASIC PENTACYSTEINE (BPC) class of transcription factors (Monfared et al. 2011). However, whether BPCs regulate development in woody plants is an open question. In this issue, Haiyan Zhao and colleagues (Zhao et al. 2024) reveal some details of the genetic regulation of dwarfism in apple trees, Malus domestica. Through genetics, bioinformatics, and biochemical assays, Zhao and colleagues elucidated a key molecular mechanism for plant dwarfism (see Figure)."
"Histone trimethylation (H3K27me3) results in repression of target genes (Cai et al. 2021). Here, the authors found that H3K27me3 enrichment was significantly increased at MdYUC2a and 6b loci in OX plants. H3K27me3 modifications are facilitated by a large complex of proteins known as the polycomb group. The author used biochemical techniques to demonstrate that MdBPC2 interacts with the polycomb group member LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Indeed, MdYUC2a and 6b loci are enriched with MdLHP1 (see Figure). With this result, the authors proposed a straight-forward model whereby MdBPC2 protein recruits LHP1 protein to the promoters of a subset of YUCCA genes to repress their expression, thereby reducing the amount of auxin produced. In dwarf rootstocks, increased MdBPC2 expression results in much less MdYUC2a and 6b enzymes, and shorter, auxin-deficient plants (see Figure). Moving forward, one can see BPCs as an attractive target for crop breeding programs where dwarf plants are the goal."
Authors: Canran Sun, Yang Liu, Guofang Li, Yanle Chen, Mengyuan Li, Ruihua Yang, Yongtian Qin, Yongqiang Chen, Jinpeng Cheng, Jihua Tang and Zhiyuan Fu.
The Crop Journal (2024)
Abstract: "Plant height (PH) is associated with lodging resistance and planting density, which is regulated by a complicated gene network. In this study, we identified a spontaneous dwarfing mutation in maize, m30, with decreased internode number and length but increased internode diameter. A candidate gene, ZmCYP90D1, which encodes a member of the cytochrome P450 family, was isolated by map-based cloning. ZmCYP90D1 was constitutively expressed and showed highest expression in basal internodes, and its protein was targeted to the nucleus. A G-to-A substitution was identified to be the causal mutation, which resulted in a truncated protein in m30. Loss of function of ZmCYP90D1 changed expression of hormone-responsive genes, in particular brassinosteroid (BR)-responsive genes which is mainly involved in cell cycle regulation and cell wall extension and modification in plants. The concentration of typhasterol (TY), a downstream intermediate of ZmCYP90D1 in the BR pathway, was reduced. A haplotype conferring dwarfing without reducing yield was identified. ZmCYP90D1 was inferred to influence plant height and stalk diameter via hormone-mediated cell division and cell growth via the BR pathway."
Authors: Haiyan Zhao, Shuyuan Wan, Yanni Huang, Xiaoqiang Li, Tiantian Jiao, Zhijun Zhang, Baiquan Ma, Lingcheng Zhu, Fengwang Ma and Mingjun Li.
The Plant Cell (2024)
Abstract: "Auxin plays important roles throughout plant growth and development. However, the mechanisms of auxin regulation of plant structure are poorly understood. In this study, we identified a transcription factor of the BARLEY B RECOMBINANT/BASIC PENTACYSTEINE (BBR/BPC) family in apple (Malus × domestica), MdBPC2. It was highly expressed in dwarf rootstocks and it negatively regulated auxin biosynthesis. Overexpression of MdBPC2 in apple decreased plant height, altered leaf morphology, and inhibited root system development. These phenotypes were due to reduced auxin levels and were restored reversed after exogenous IAA treatment. Silencing of MdBPC2 alone had no obvious phenotypic effect, while silencing both class I and class II BPCs in apple significantly increased auxin content in plants. Biochemical analysis demonstrated that MdBPC2 directly bound to the GAGA-rich element in the promoters of the auxin synthesis genes MdYUC2a and MdYUC6b, inhibiting their transcription and reducing auxin accumulation in MdBPC2 overexpression lines. Further studies established that MdBPC2 interacted with the polycomb group (PcG) protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) to inhibit MdYUC2a and MdYUC6b expression via methylation of histone 3 lysine 27 (H3K27me3). Silencing MdLHP1 reversed the negative effect of MdBPC2 on auxin accumulation. Our results reveal a dwarfing mechanism in perennial woody plants involving control of auxin biosynthesis by a BPC transcription factor, suggesting its use for genetic improvement of apple rootstock."
Authors: Yanzhao Yang, Chengcai Chu, Qian Qian and Hongning Tong.
Trends in Plant Science (2024)
Highlights: Brassinosteroids (BR) signaling pathway is believed to be largely conserved among different species, although some components, steps, or events may differ between rice and Arabidopsis thaliana. BRs play essential roles in regulating both yield and stress-related traits, as well as in environmental adaptability, and thus hold promise for producing high-yielding and stable crops with less input. BR genes have been shown to be valuable for crop improvement employing various approaches. One prevalent method is to enhance the planting density of rice, maize, and wheat. Strategies such as exploring function-specific genes, identifying beneficial alleles, inducing favorable mutations, and optimizing the spatial hormone distribution can facilitate the utilization of BR genes towards the next Green Revolution.
Abstract: "The use of gibberellin-related dwarfing genes significantly increased grain yield during the Green Revolution. Brassinosteroids (BRs) play a vital role in regulating agronomic traits and stress resistance. The potential of BR-related genes in crop improvement has been well demonstrated, positioning BRs as crucial targets for the next agricultural biotechnological revolution. However, BRs exert pleiotropic effects on plants, and thus present both opportunities and challenges for their application. Recent research suggests promising strategies for leveraging BR regulatory molecules for crop improvement, such as exploring function-specific genes, identifying beneficial alleles, inducing favorable mutations, and optimizing spatial hormone distribution. Advancing our understanding of the roles of BRs in plants is imperative to implement these strategies effectively."
Authors: XiangGuo Liu, Yang Liu, Ziqi Chen, Chuang Zhang, Jia Guo, Qing Liu, Yuejia Yin, Yang Hu, Hanchao Xia, Bingyang Li, Xiaopeng Sun and Yidan Li.
Research Square (2023)
Abstract: "Drought stress, a major plant abiotic stress, is capable of suppressing crop yield performance severely. However, the trade-off between crop drought tolerance and yield performance turns out to be significantly challenging in drought-resistant crop breeding. Several phytohormones (e.g., gibberellin (GA)) have been reported to play a certain role in plant drought response, which also take on critical significance in plant growth and development. In this study, the loss-of-function mutations of GA biosynthesis enzyme ZmGA20ox3 were produced using the CRISPR-Cas9 system in maize. As indicated by the result of two-year field trials, the above-mentioned mutants displayed semi-dwarfing phenotype with the decrease of GA1, and almost no yield loss was generated compared with wild-type (WT) plants. Interestingly, as revealed by the transcriptome analysis, differential expressed genes (DEGs) were notably enriched in abiotic stress progresses, and biochemical tests indicated the significantly increased ABA, JA, and DIMBOA levels in mutants, suggesting that ZmGA20ox3 may take on vital significance in stress response in maize. The in-depth analysis suggested that the loss function of ZmGA20ox3 can enhance drought tolerance in maize seedling, reduce Anthesis-Silking Interval (ASI) delay while decreasing the yield loss significantly in the field under drought conditions. The results of this study supported that regulating ZmGA20ox3 can improve plant height while enhancing drought resistance in maize, thus serving as a novel method for drought-resistant genetic improvement in maize."
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