SSR markers are useful tools in wheat varietal purity and genetic diversity assessment

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Different breeding programs worldwide have developed various cultivars that can cope with changing and increasingly unpredictable environments while meeting market needs. These developments have brought a new challenge: creating tools to distinguish such varieties and trace their genetic purity. Using 40 wheat cultivars grown in Romania, Vasile and collaborators show that Simple Sequence Repeat markers (SSRs; short base-pair sequences repeated several times in tandem) are promising tools to achieve that. Of the 22 motifs evaluated, all but one showed some variation, suggesting that they can indeed be used to assess varietal purity. Moreover, these sequences helped distinguish certified wheat materials from those of other crops and even other wheat varieties. This research shows the utility of SSRs and, as a result, expands the current toolbox that plant breeders and producers have for assessing wheat varietal purity. In fact, materials from harvests of different years showed high similarity for these markers, suggesting that current agricultural practices succeed in maintaining such purity. (Summary by Carlos A. Ordóñez-Parra @caordonezparra) Seed Sci. Technol. 10.15258/sst.2023.51.2.01

A unique photoinhibition protection mechanism in Chlorella ohadii that thrives in extreme high-light intensities

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In plants and algae, excessive light can damage the photosystem and lead to a decrease in photosynthetic capacity, a process called photoinhibition (PI). Levin et al. showed that Chlorella ohadii isolated from the Negev desert in Israel lacks or has limited capability of the usual photoprotection mechanisms seen in plants and model microalgae species including psbS, LHCSR, PSII protein phosphorylation and state-transitions. Instead, C. ohadii accumulates a high amount of carotene biosynthesis related protein (CBR) at high light intensity. These CBRs were suggested to bind to overexcited chlorophylls to dissipate energy, avoiding reactive oxygen species (ROS) formation and photoinhibition. In addition to CBRs, C. ohadii undergo major structural changes to the photosystem II antennae which lowers the amount of light entering the reaction center. Further studies of the high-light repsonses of C. ohadii and investigating CBR overexpression in plants could could contribute towards building resilient and high-yielding crops that can grow in desert environment. (Summary by Yen Peng (Apple) Chew @_applechew) Plant J. 10.1111/tpj.16241

Point mutations in the catalytic domain disrupt cellulose synthase vesicle trafficking and protein dynamics

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Cellulose is an important and useful biopolymer, present in plant cell walls and synthesized at the plasma membrane by protein complexes called cellulose synthase complexes (CSCs) composed of multimers of cellulose synthase (CESA). CESAs are embedded in the membrane and move along the membrane as they polymerize cellulose. In a new study, Huang et al. examined the properties of a suite of single-amino acid mutations in the catalytic domain of CESAs to determine how they impact not only the catalytic properties, but also the movement of CESAs and CSCs as the move from the endoplasmic reticulum through the Golgi, vesicles, and delivery to the plasma membrane. Their results suggest that most of these point mutations cause not only catalytic defects but also trafficking disruptions and disruptions in protein folding or complex assembly. This study sheds further light onto the structure and function of CESAs and provides information that can be used for engineering of modified CSCs. (Summary by Mary Williams @PlantTeaching) Plant Cell 10.1093/plcell/koad110

Natural variation of maize root hydraulic architecture underlies highly diverse water uptake capacities

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Water uptake by roots is controlled by two factors: the architecture of the root system, and its hydraulic capacity. The later property is largely determined by the anatomical and physiological properties of the root cells, which include things like suberization and the presence of aquaporins (regulated water channels). Rishmawi et al. characterized multiple parameters on more than 200 hydroponically-grown inbred Zea mays lines. Many of the measured parameters varied by more than 10-fold among the lines, and some traits were shown to vary independently (e.g., surface area of primary root and seminal roots) or conversely dependently (e.g., seed size and number of seminal roots) with others. The initial survey revealed that a subset of lines captured the full diversity and that were selected for further study. Further studies will include analysis of these traits under stress conditions and identification of their genetic underpinnings. (Summary by Mary Williams @PlantTeaching) Plant Physiol. 10.1093/plphys/kiad213

SIGMA FACTOR5 protects freezing plants

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Low temperatures quickly and reversibly inhibit photosynthesis, which is assumed to shield the photosynthetic system from a drop in metabolic activity brought about by cold. In a recent study, Cano-Ramirez et al. found that in Arabidopsis, a nuclear-encoded sigma factor (SIG5) controls chloroplast transcription and contributes to adaptation to low-temperature conditions. In prokaryotes, sigma factors contribute to promoter targeting of RNA polymerases, and this function is conserved in the plant plastid-encoded RNA polymerase. The sigma factor-encoding genes have been transferred to the nuclear genome from the plastid genome in plants, providing a mechanism for nucleus to plastid signaling. The authors showed that ELONGATED HYPOCOTYL5 (HY5) and HY5 HOMOLOG (HYH) influence SIG5 accumulation. Previous studies have indicated that both SIG5 and HY5 participate in circadian signaling, and that other responses to cold are gated (modulated) by the time of day. The authors showed that the time at which the cold treatment is applied affects the magnitude of SIG5 transcript level and transcriptional activity, mediated by HY5 and HYH. Because SIG5 regulates the transcription of the gene encoding the D2 protein (psbD) of photosystem II (PSII), its role in enhancing photosynthetic efficiency during long-term cold and freezing exposure via HY5/HYH and the circadian clock provides an interesting opportunity to increase crop yield under low-temperature stress. Furthermore, this study indicates that sigma factors are involved in cold-temperature responses in both prokaryotes and eukaryotes. (Summary by Rajarshi Sanyal, @rajarshi_sanyal. Nature Plants, 10.1038/s41477-023-01377-1)

Regulated and optimized control of insect pheromone biosynthesis in plants

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Insect sex pheromones, volatile molecules used to attract mates, are used commercially to disrupt breeding behavior of insect pests and can be a good alternative to harmful pesticides. These pheromones have been produced in plants at a low amount and shown to be released as volatiles, but their production levels can be improved and refined. Kallam et al. used metabolic engineering to improve pheromone production in tobacco plants six-fold by using yeast enzymes in the biosynthesis pathway. The authors also showed that a combination of a low-cost copper-inducible system on dead CRISPR-Cas9 (dCas9) fused to a transcriptional activation domain gave a tight upregulation on pheromone production, alleviating growth-inhibitory effects that can arise from consitutive production. Transient expression through Agrobacterium-infiltration yielded the highest amount of pheromone due to high copy number plasmids, outperforming stable lines that require the selection of high-yielding strains and overcoming regulatory barriers. This paper shows great potential of tunable insect sex pheromone production in plants. Furthermore, the modular genetic elements described here are more broadly useful to the design of constructs for plant metabolic engineering. (Summary by Yen Peng (Apple) Chew @_applechew)  Plant Biotechnol. J. 10.1111/pbi.14048

Plant Science Research Weekly: April 28, 2023

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Review: Resolving metabolic interaction mechanisms in plant microbiomes

Life is spurred forward by the power of metabolic interactions. Within the plant microbiome, microbial communities use diverse mechanisms to thrive, survive, and multiply. In this review, Pacheco & Vorholt describe the interplay of metabolic interactions within plant microbiomes and review current approaches. Plants host a wide range of microbes with various metabolic strategies, such as polysaccharide degraders on leaves and pathogens that feed on root exudates. These interactions can significantly impact plant growth, ecosystem productivity, and nutrient use. Despite the challenges posed by the complexity of plant microbiomes, methods have been developed to discover how specific microbe interactions affect the microbiome. The creation of co-occurrence networks via high throughout sequencing melded with microbial lifestyle characteristics can provide insight into the interplay of microbial interactions and metabolic reactions. As examples, some bacteria co-occur with others due to cross-feeding, and plant root exudates change upon interaction with some bacteria.  In addition, the authors examine how synthetic communities can reveal how the presence or behavior of one species affects the growth, survival, or reproduction of another species. Furthermore, predictive computational community modeling can be employed to understand community dynamics and integrate the previously described approaches to positively impact crop protection. (Summary by Eric Hobson @ehobs) Curr Opin Microbiol 10.1016/j.mib.2023.102317

Review: Why don’t genetically identical seeds germinate at the same time?

If you’ve ever conducted a germination experiment, you’ve probably asked yourself: what causes seeds to germinate at different times? The most obvious answer would be to point to genetic differences, but this phenomenon also occurs in genetically identical seeds. In this exciting paper, Sharma and Majee bring us a comprehensive review of the different physiological and molecular mechanisms that have been proposed, including transcriptional heterogeneity and noise, epigenetic diversity, and biomolecular condensates. All these mechanisms point out potential sources of variation in gene expression, phytohormone concentrations and the biochemical availability of these compounds that can lead to a seed germinating more or less quickly. The review also discusses the ecological advantages of seed germination variability and how modern techniques, such as seed priming, can reduce it and ensure higher synchronization in agricultural contexts. While there does not appear to be a definitive answer to explain germination heterogeneity, this review paves the way for future research to help us understand the mechanisms behind it. (Summary by Carlos A. Ordóñez-Parra @caordonezparra) J. Exp. Bot. 10.1093/jxb/erad101

Review: The role of ethylene in plant temperature stress response

The phytohormone ethylene is known for its importance in plant development and mostly for its role in fruit ripening. However, in this review Huang et al. summarize recent findings on ethylene’s role in temperature (hot and cold) stress response and ethylene crosstalk with other hormones. Interestingly, different plants respond to heat stress differently. For example, heat stress induces ethylene production in Arabidopsis, wheat, and pea whereas it inhibits ethylene production in tomato and lettuce. These effects are also tissue specific; in Arabidopsis, at 45°C ethylene levels in roots and shoot apices remain unchanged but are induced in leaves. Furthermore, thermotolerance of many plants is induced by external application of ACC (an ethylene precursor) or ethephon (converted to ethylene in the plant). Generally, the heat-stress responses are mediated by heat shock proteins, which are induced by heat shock transcription factors, and in Arabidopsis ethylene signaling activates some heat shock transcription factors. Ethylene also mediates freezing tolerance in a species-specific manner. Freezing tolerance in tomato, tobacco and Arabidopsis is increased by ACC application, whereas inhibitors of ethylene synthesis improve freezing tolerance in Medicago truncatula. Thus, effects of ethylene stress response can be positive or negative depending on plant species and developmental stages. Transcription factors in the AP2/ERFs family integrate BR, JA and ABA signaling and could provide targets for genetic efforts to enhance plant tolerance to heat or cold stress. (Summary by Indrani Kakati, @indranikb)  Trends Plant Sci. 10.1016/j.tplants.2023.03.001

SSR markers are useful tools in wheat varietal purity and genetic diversity assessment

Different breeding programs worldwide have developed various cultivars that can cope with changing and increasingly unpredictable environments while meeting market needs. These developments have brought a new challenge: creating tools to distinguish such varieties and trace their genetic purity. Using 40 wheat cultivars grown in Romania, Vasile and collaborators show that Simple Sequence Repeat markers (SSRs; short base-pair sequences repeated several times in tandem) are promising tools to achieve that. Of the 22 motifs evaluated, all but one showed some variation, suggesting that they can indeed be used to assess varietal purity. Moreover, these sequences helped distinguish certified wheat materials from those of other crops and even other wheat varieties. This research shows the utility of SSRs and, as a result, expands the current toolbox that plant breeders and producers have for assessing wheat varietal purity. In fact, materials from harvests of different years showed high similarity for these markers, suggesting that current agricultural practices succeed in maintaining such purity. (Summary by Carlos A. Ordóñez-Parra @caordonezparra) Seed Sci. Technol. 10.15258/sst.2023.51.2.01

A unique photoinhibition protection mechanism in Chlorella ohadii that thrives in extreme high-light intensities

In plants and algae, excessive light can damage the photosystem and lead to a decrease in photosynthetic capacity, a process called photoinhibition (PI). Levin et al. showed that Chlorella ohadii isolated from the Negev desert in Israel lacks or has limited capability of the usual photoprotection mechanisms seen in plants and model microalgae species including psbS, LHCSR, PSII protein phosphorylation and state-transitions. Instead, C. ohadii accumulates a high amount of carotene biosynthesis related protein (CBR) at high light intensity. These CBRs were suggested to bind to overexcited chlorophylls to dissipate energy, avoiding reactive oxygen species (ROS) formation and photoinhibition. In addition to CBRs, C. ohadii undergo major structural changes to the photosystem II antennae which lowers the amount of light entering the reaction center. Further studies of the high-light repsonses of C. ohadii and investigating CBR overexpression in plants could could contribute towards building resilient and high-yielding crops that can grow in desert environment. (Summary by Yen Peng (Apple) Chew @_applechew) Plant J. 10.1111/tpj.16241

Point mutations in the catalytic domain disrupt cellulose synthase vesicle trafficking and protein dynamics

Cellulose is an important and useful biopolymer, present in plant cell walls and synthesized at the plasma membrane by protein complexes called cellulose synthase complexes (CSCs) composed of multimers of cellulose synthase (CESA). CESAs are embedded in the membrane and move along the membrane as they polymerize cellulose. In a new study, Huang et al. examined the properties of a suite of single-amino acid mutations in the catalytic domain of CESAs to determine how they impact not only the catalytic properties, but also the movement of CESAs and CSCs as the move from the endoplasmic reticulum through the Golgi, vesicles, and delivery to the plasma membrane. Their results suggest that most of these point mutations cause not only catalytic defects but also trafficking disruptions and disruptions in protein folding or complex assembly. This study sheds further light onto the structure and function of CESAs and provides information that can be used for engineering of modified CSCs. (Summary by Mary Williams @PlantTeaching) Plant Cell 10.1093/plcell/koad110

Natural variation of maize root hydraulic architecture underlies highly diverse water uptake capacities

Water uptake by roots is controlled by two factors: the architecture of the root system, and its hydraulic capacity. The later property is largely determined by the anatomical and physiological properties of the root cells, which include things like suberization and the presence of aquaporins (regulated water channels). Rishmawi et al. characterized multiple parameters on more than 200 hydroponically-grown inbred Zea mays lines. Many of the measured parameters varied by more than 10-fold among the lines, and some traits were shown to vary independently (e.g., surface area of primary root and seminal roots) or conversely dependently (e.g., seed size and number of seminal roots) with others. The initial survey revealed that a subset of lines captured the full diversity and that were selected for further study. Further studies will include analysis of these traits under stress conditions and identification of their genetic underpinnings. (Summary by Mary Williams @PlantTeaching) Plant Physiol. 10.1093/plphys/kiad213

SIGMA FACTOR5 protects freezing plants

Low temperatures quickly and reversibly inhibit photosynthesis, which is assumed to shield the photosynthetic system from a drop in metabolic activity brought about by cold. In a recent study, Cano-Ramirez et al. found that in Arabidopsis, a nuclear-encoded sigma factor (SIG5) controls chloroplast transcription and contributes to adaptation to low-temperature conditions. In prokaryotes, sigma factors contribute to promoter targeting of RNA polymerases, and this function is conserved in the plant plastid-encoded RNA polymerase. The sigma factor-encoding genes have been transferred to the nuclear genome from the plastid genome in plants, providing a mechanism for nucleus to plastid signaling. The authors showed that ELONGATED HYPOCOTYL5 (HY5) and HY5 HOMOLOG (HYH) influence SIG5 accumulation. Previous studies have indicated that both SIG5 and HY5 participate in circadian signaling, and that other responses to cold are gated (modulated) by the time of day. The authors showed that the time at which the cold treatment is applied affects the magnitude of SIG5 transcript level and transcriptional activity, mediated by HY5 and HYH. Because SIG5 regulates the transcription of the gene encoding the D2 protein (psbD) of photosystem II (PSII), its role in enhancing photosynthetic efficiency during long-term cold and freezing exposure via HY5/HYH and the circadian clock provides an interesting opportunity to increase crop yield under low-temperature stress. Furthermore, this study indicates that sigma factors are involved in cold-temperature responses in both prokaryotes and eukaryotes. (Summary by Rajarshi Sanyal, @rajarshi_sanyal. Nature Plants, 10.1038/s41477-023-01377-1)

Controlling and optimizing insect pheromone biosynthesis in Nicotiana benthamiana

Insect sex pheromones, volatile molecules used to attract mates, are used commercially to disrupt breeding behavior of insect pests and can be a good alternative to harmful pesticides. These pheromones have been produced in plants at a low amount and shown to be released as volatiles, but their production levels can be improved and refined. Kallam et al. used metabolic engineering to improve pheromone production in tobacco plants six-fold by using yeast enzymes in the biosynthesis pathway. The authors also showed that a combination of a low-cost copper-inducible system on dead CRISPR-Cas9 (dCas9) fused to a transcriptional activation domain gave a tight upregulation on pheromone production, alleviating growth-inhibitory effects that can arise from consitutive production. Transient expression through Agrobacterium-infiltration yielded the highest amount of pheromone due to high copy number plasmids, outperforming stable lines that require the selection of high-yielding strains and overcoming regulatory barriers. This paper shows great potential of tunable insect sex pheromone production in plants. Furthermore, the modular genetic elements described here are more broadly useful to the design of constructs for plant metabolic engineering. (Summary by Yen Peng (Apple) Chew @_applechew)  Plant Biotechnol. J. 10.1111/pbi.14048

CsCRC regulates cucumber fruit length

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Che, Pan, Liu, Li et al. provide insight into fruit length variation in cucumber.

By Gen Chea,e, Yupeng Panb, Xiaolan Zhanga,*

aState Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China;

bHorticulture Department, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA;

cSchool of Life Science, Key Laboratory of Herbage ＆ Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot 010070, China

Background: Cucumber is an important vegetable crop cultivated worldwide. The fruit length in cucumber varies from 5 to 60 cm in different germplasms, and thus serves as a key domestication trait affecting yield and appearance quality. Although several regulators and multiple QTLs controlling fruit length have been identified, the natural variations and molecular mechanisms underlying fruit length divergence are largely unknown.

Question: How can cucumber vary so widely in its fruit length? FS5.2 was previously identified as a major-effect QTL specifying fruit length in cucumber, while the underlying controlling gene and its regulating mechanism are unclear.

Findings: A nonsynonymous SNP (G to A) in CsCRC was identified to control the fruit length variation caused by the FS5.2 locus. Allelic analysis of 165 cucumber accessions showed that the CsCRCA allele only exists in 7 Xishuangbanna cucumbers with short or round fruits, while the CsCRCG allele was shared by all the remaining wild and cultivated cucumbers. Replacing the CsCRCG allele with CsCRCA by backcrossing resulted in a 34~39% reduction in fruit length. Genetic transformation-based functional characterization revealed that CsCRCG is a positive regulator of fruit length elongation and cell size expansion. CsCRCG, but not CsCRCA, targets the downstream auxin-responsive protein gene CsARP1 (a positive mediator of fruit length), to promote its expression and stimulate fruit elongation in cucumber.

Next step: Manipulation of fruit length can be achieved by either modulating the expression levels of CsCRCG or utilizing different CsCRC alleles (CsCRCG or CsCRCA) in cucumber breeding practices. The regulatory mechanism of CsARP1 and its relation with auxin await further characterization in plants.

Gen Che, Yupeng Pan, Xiaofeng Liu, Min Li, Jianyu Zhao, ShuangshuangYan, Yuting He, Zhongyi Wang, Zhihua Cheng, Weiyuan Song, Zhaoyang Zhou, Tao Wu , Yiqun Weng, Xiaolan Zhang. (2023). Natural variation in CRABS CLAW contributes to fruit length divergence in cucumber https://doi.org/10.1093/plcell/koac335

Dan Yuan: The Plant Cell Author Profile

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Dan Yuan, co-first author of “INDETERMINATE1 autonomously regulates phosphate homeostasis upstream of the miR399-ZmPHO2 signaling module in maize”

Current Position: Postdoctoral Fellow, College of Life Sciences and Oceanography, Shenzhen University

Education: Ph.D. in Huazhong Agricultural University

Non-scientific Interests: Badminton, Music

Brief biography: In 2014, I joined the Lab of Prof. Lei Shi at Huazhong Agricultural University to pursue my Ph.D. study. During Ph.D. period, my research mainly focused on the regulation mechanism of boron efficient absorption in Brassica napus, and I received my Ph.D. degree in plant nutrition in Dec. 2020. Later, I joined the Lab of Prof. Lin Liu at Shenzhen University as a postdoctoral fellow to investigate the regulatory mechanisms of plant microRNAs. The maize transcription factor INDETERMINATE1 (ID1) was first reported to participate in the regulation of maize flowering. In this study, we further revealed that ID1 could modulate the transcription of ZmmiR399 family genes as a negative regulator, thus alleviating the targeted cleavage of ZmPHO2 at mRNA level and contributing to the maintenance of phosphate homeostasis in maize. Our study establishes a regulatory connection between Pi-deprivation sensing by the miR399-ZmPHO2 regulatory module and plant developmental regulation by ID1 in maize.

 姓名：袁丹

现在职位：深圳大学博士后

教育经历：华中农业大学，植物营养学，博士

兴趣爱好：羽毛球，音乐

个人简介：我于2014年进入华中农业大学硕博连读，师从石磊教授。博士期间从事甘蓝型油菜硼营养高效吸收的调控机制研究，于2020年12月获得植物营养学博士学位。之后，进入深圳大学刘琳教授组开展博士后研究，从事植物小RNA的调控机制研究。玉米转录因子INDETERMINATE1 (ID1)，首先被报道参与玉米的开花调控。在本研究中，我们进一步揭示ID1作为负调节因子参与ZmmiR399家族基因的转录调控，从而缓解ZmPHO2在mRNA水平上的靶向切割，并有助于维持玉米中磷酸盐的稳态。我们的研究建立了玉米缺磷响应调控模块miR399-ZmPHO2和ID1参与的植株发育调控之间的联系。