Cassava Me RS40 is required for the regulation of plant salt tolerance

Soil salinity affects the expression of serine/arginine-rich(SR) genes and isoforms by alternative splicing, which in turn regulates the adaptation of plants to stress.We previously identified the cassava spliceosomal component 35 like(SCL) and SR subfamilies, belonging to the SR protein family, which are extensively involved in responses to abiotic stresses.However, the post-transcriptional regulatory mechanism of cassava arginine/serine-rich(RS) subfamily in response to salt stress remains to be explored.In the current study, we identified 37 genes of the RS subfamily from 11 plant species and systematically investigated the transcript levels of the RS40 and RS31 genes under diverse abiotic stress conditions.Subsequently, an analysis of the conserved protein domains revealed that plant RS subfamily genes were likely to preserve their conserved molecular functions and played critical functional roles in responses to abiotic stresses.Importantly, we found that overexpression of MeRS40 in Arabidopsis enhanced salt tolerance by maintaining reactive oxygen species homeostasis and up-regulating the salt-responsive genes.However,overexpression of MeRS40 gene in cassava reduced salt tolerance due to the depression of its endogenous gene expression by negative autoregulation of its own pre-mRNA.Moreover, the MeRS40 protein interacted with MeU1-70Ks(MeU1-70Ka and MeU1-70Kb) in vivo and in vitro, respectively.Therefore, our findings highlight the critical role of cassava SR proteins in responses to salt stress in plants.

A Novel Mechanism Underlying the Coordination of Plant Growth and Salt Stress Response

Salt stress is a major environmental stress that threats crop growth and yield.It is of great significance to study the molecular genetic network of plants in response to salt stress and to cultivate salt-tolerant crop varieties for national food security.A study published in Nature Plants,Dr.ZHAO Chunzhao’s group from the CAS Center for Excellence in Molecular Plant Sciences(CEMPS),Chinese Academy of Science,uncovers a novel mechanism underlying the coordination of plant growth and salt tolerance in plants.

Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen (Populus rotundifolia) in the Hengduan Mountains

Biogeographical barriers to gene flow are central to plant phylogeography.In East Asia,plant distribution is greatly influenced by two phylogeographic breaks,the Mekong-Salween Divide and Tanaka-Kaiyong Line,however,few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both.Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia,a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China.Demographic and migration hypotheses were tested using coalescent-based approaches.Limited historical gene flow was observed between the western and eastern groups of P.rotundifolia,but substantial flow occurred across both the Mekong-Salween Divide and Tanaka-Kaiyong Line,manifesting in clear admixture and high genetic diversity in the central group.Wind-borne pollen and seeds may have facilitated the dispersal of P.rotundifolia following prevalent northwest winds in the spring.We also found that the Hengduan Mountains,where multiple genetic barriers were detected,acted on the whole as a barrier between the western and eastern groups of P.rotundifolia.Ecological niche modeling suggested that P.rotundifolia has undergone range expansion since the last glacial maximum,and demographic reconstruction indicated an earlier population expansion around 600 Ka.The phylogeographic pattern of P.rotundifolia reflects the interplay of biological traits,wind patterns,barriers,niche differentiation,and Quaternary climate history.This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.

Conservation genomic investigation of an endangered conifer,Thuja sutchuenensis,reveals low genetic diversity but also low genetic load

Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.

Global characterization of OsPIP aquaporins reveals that the H_(2)O_(2)transporter OsPIP2;6 increases resistance to rice blast

Plasma membrane intrinsic proteins(PIPs)are conserved plant aquaporins that transport small molecules across the plasma membrane to trigger instant stress responses and maintain cellular homeostasis under biotic and abiotic stress.To elucidate their roles in plant immunity to pathogen attack,we characterized the expression patterns,subcellular localizations,and H_(2)O_(2)-transport ability of 11 OsPIPs in rice(Oryza sativa),and identified OsPIP2;6 as necessary for rice disease resistance.OsPIP2;6 resides on the plasma membrane and facilitates cytoplasmic import of the immune signaling molecule H_(2)O_(2).Knockout of OsPIP2;6 increases rice susceptibility to Magnaporthe oryzae,indicating a positive function in plant immunity.OsPIP2;6 interacts with OsPIP2;2,which has been reported to increase rice resistance to pathogens via H_(2)O_(2)transport.Our findings suggest that OsPIP2;6 cooperates with OsPIP2;2 as a defense signal transporter complex during plant–pathogen interaction.

Molecular regulation and genetic control of rice thermal response

Global warming threatens food security.Rice(Oryza sativa L.),a vital food crop,is vulnerable to heat stress,especially at the reproductive stage.Here we summarize putative mechanisms of high-temperature perception(via RNA secondary structure,the phyB gene,and phase separation)and response(membrane fluidity,heat shock factors,heat shock proteins,and ROS(reactive oxygen species)scavenging)in plants.We describe how rice responds to heat stress at different cell-component levels(membrane,endoplasmic reticulum,chloroplasts,and mitochondria)and functional levels(denatured protein elimination,ROS scavenging,stabilization of DNA and RNA,translation,and metabolic flux changes).We list temperature-sensitive genetic male sterility loci available for use in rice hybrid breeding and explain the regulatory mechanisms associated with some of them.Breeding thermotolerant rice species without yield penalties via natural alleles mining and transgenic editing should be the focus of future work.

Effects of taxon sampling on molecular dating for within-genus divergence events,when deep fossils are used for calibration

A universal method of molecular dating that can be applied to all families and genera regardless of their fossil records, or lack thereof, is highly desirable. A possible method for eudicots is to use a large phylogeny calibrated using deep fossils including tricolpate pollen as a fixed （124 mya） calibration point. This method was used to calculate node ages within three species-poor disjunct basal eudicot genera, Caulophyllum, Podophyllum and Pachysandra, and sensitivity of these ages to effects such as taxon sampling were then quantified. By deleting from one to three accessions related to each genus in 112 different combinations, a confidence range describing variation due only to taxon sampling was generated. Ranges for Caulophyllum, Podophyllum and Pachysandra were 8.4-10.6, 7.6-20.0, and 17.6-25.0 mya, respectively. However, the confidence ranges calculated using bootstrapping were much wider, at 3-19, 0-32 and 11-32 mya, respectively. Furthermore, deleting 10 adjacent taxa had a large effect in Pachysandra only, indicating that undersampling effects are significant among Buxales. Changes to sampling density in neighboring clades, or to the position of the fixed fossil calibration point had small to negligible effects. Non-parametric rate smoothing was more sensitive to taxon sampling effects than was penalized likelihood. The wide range for Podophyllum, compared to the other two genera, was probably due to a high degree of rate heterogeneity within this genus. Confidence ranges calculated by this method could be narrowed by sampling more individuals within the genus of interest, and by sequencing multiple DNA regions from all species in the phylogeny.

Plant regeneration via protoplast electrofusion in cassava

Protoplast electrofusion between callus protoplasts of cultivar TMS60444 and mesophyll protoplasts of cultivar SC8 was performed as an approach for the genetic improvement of cassava.The fusion products were subsequently cultured in protoplast culture medium(TM2 G) with gradual dilution for approximately 1-2 months.Then the protoplast-derived compact calli were transferred to suspension culture medium(SH) for suspension culture.The cultured products developed successively into embryos,mature embryos,and shoots on somatic embryo emerging medium(MSN),embryo maturation medium(CMM),and shoot elongation medium(CEM),respectively.And the shoots were then rooted on Murashige and Skoog(1962) medium(MS).Sixty-six cell lines were obtained and 12 of them developed into plantlets.Based on assessment of ploidy level and chromosome counting,four of these plantlets were tetraploid and the remaining eight were diploid.Based on assessment of ploidy level and simple sequence repeat(SSR) analysis,nine tetraploid cell lines,one diploid variant plant line and nine variant cell lines were obtained.The diploid variant plant line and the nine variant cell lines all showed partial loss of genetic material compared to that of the parent TMS60444,based on SSR patterns.These results showed that some new germplasm of cassava were created.In this study,a protocol for protoplast electrofusion was developed and validated.Another important conclusion from this work is the confirmation of a viable protocol for the regeneration of plants from cassava protoplasts.Going forward,we hope to provide technical guidance for cassava tissue culture,and also provide some useful inspiration and reference for further genetic improvement of cassava.

Molecular understanding of wood formation in trees

Trees convert and store the majority of their photosynthetic products in wood which is an essential renewable resource much in demand by human society.Formation of wood follows a process of consecutive cell developmental stages,from vascular cambium proliferation,cell expansion and differentiation,secondary cell wall deposition to programmed cell death,which is controlled by the functionality of complex molecular networks.What are the molecular networks involved in wood formation?How do the molecular networks act in a way to generate wood tissue during tree growth?What are the regulatory modules that lead to the formation of various wood characteristics?The answers to these questions are fundamental to understanding how trees grow,as well as how we can genetically engineer trees with desired properties of wood for human needs.In recent years,a great deal of interest has been invested in the elucidation of wood formation at the molecular level.This review summarizes the current state of understanding of the molecular process that guides wood formation in trees.

Extrafloral nectary-the sleeping beauty of plant science

Cotton is one of the most important cash crops,its growth season coincides with a high incidence of diverse groups of pests,leading to heavy use of pesticides.Recent identification of a signaling protein as a candidate regulator of cotton extrafloral nectary provides a new insight into the formation of sophisticated defense mechanisms in plants.

Medicinal Plant Biology:A new era for medicinal plant research

Plants are amazing chemical factories,and medicinal plants provide a myriad of pharmaceutically active compounds that have been commonly used as traditional medicines for thousands of years.The practice of traditional medicine in China dates back at least 4,500 years.The Shen Nong Ben Cao Jing("Shen Nong's Herbal Classic"in 770−475 BC)has been considered the oldest list of medicinal plants.Recent rapid economic development has enabled China to invest substantially in science and technology research.In many ethnic groups worldwide,herbal medicines are,in the same way as traditional Chinese medicines,still commonly used today.A wide array of plant-extract health supplements has become increasingly popular in Western societies.Numerous drugs derived from a broad range of plant species have been discoveried,such as taxol and artemisinin and their derivatives.

SbMYB3 transcription factor promotes root-specific f lavone biosynthesis in Scutellaria baicalensis

Scutellaria baicalensis Georgi produces abundant root-specific f lavones(RSFs),which provide various benefits to human health.We have elucidated the complete biosynthetic pathways of baicalein and wogonin.However,the transcriptional regulation of f lavone biosynthesis in S.baicalensis remains unclear.We show that the SbMYB3 transcription factor functions as a transcriptional activator involved in the biosynthesis of RSFs in S.baicalensis.Yeast one-hybrid and transcriptional activation assays showed that SbMYB3 binds to the promoter of flavone synthase II-2(SbFNSII-2)and enhances its transcription.In S.baicalensis hairy roots,RNAi of SbMYB3 reduced the accumulation of baicalin and wogonoside,and SbMYB3 knockout decreased the biosynthesis of baicalein,baicalin,wogonin,and wogonoside,whereas SbMYB3 overexpression enhanced the contents of baicalein,baicalin,wogonin,and wogonoside.Transcript profiling by qRT–PCR demonstrated that SbMYB3 activates SbFNSII-2 expression directly,thus leading to more abundant accumulation of RSFs.This study provides a potential target for metabolic engineering of RSFs.

Natural variation in SlSOS2 promoter hinders salt resistance during tomato domestication

Increasing soil salinization seriously impairs plant growth and development,resulting in crop loss.The Salt-Overly-Sensitive(SOS)pathway is indispensable to the mitigation of Na+toxicity in plants under high salinity.However,whether natural variations of SOS2 contribute to salt tolerance has not been reported.Here a natural variation in the SlSOS2 promoter region was identified to be associated with root Na+/K+ratio and the loss of salt resistance during tomato domestication.This natural variation contains an ABI4-binding cis-element and plays an important role in the repression of SlSOS2 expression.Genetic evidence revealed that SlSOS2 mutations increase root Na+/K+ratio under salt stress conditions and thus attenuate salt resistance in tomato.Together,our findings uncovered a critical but previously unknown natural variation of SOS2 in salt resistance,which provides valuable natural resources for genetic breeding for salt resistance in cultivated tomatoes and other crops.

GA Associated Dwarf 5 encodes an ent-kaurenoic acid oxidase required for maize gibberellin biosynthesis and morphogenesis

Gibberellin(GA)functions in plant growth and development.However,genes involved in the biosynthesis and regulation of GA in crop plants are poorly understood.We isolated the mutant gad5-1(GAAssociated Dwarf 5),characterized by dwarfing,short internodes,and dark green and short leaves.Map-based gene cloning and allelic verification confirmed that ZmGAD5 encodes ent-kaurenoic acid oxidase(KAO),which catalyzes KA(ent-kaurenoic acid)to GA12 conversion during GA biosynthesis in maize.ZmGAD5 is localized to the endoplasmic reticulum and is present in multiple maize organs.In gad5-1,the expression of ZmGAD5 is severely reduced,and the levels of the direct substrate of KAO,KA,is increased,leading to a reduction in GA content.The abnormal phenotype of gad5-1 was restored by exogenous application of GA3.The biomass,plant height,and levels of GA12 and GA3 in transgenic Arabidopsis overexpressing ZmGAD5 were increased in comparison with the corresponding controls Col-0.These findings deepen our understanding of genes involved in GA biosynthesis,and could lead to the development of maize lines with improved architecture and higher planting-density tolerance.

The molecular basis of heat stress responses in plants

Global warming impacts crop production and threatens food security.Elevated temperatures are sensed by different cell components.Temperature increases are classified as either mild warm temperatures or excessively hot temperatures,which are perceived by distinct signaling pathways in plants.Warm temperatures induce thermomorphogenesis,while high-temperature stress triggers heat acclimation and has destructive effects on plant growth and development.In this review,we systematically summarize the heat-responsive genetic networks in Arabidopsis and crop plants based on recent studies.In addition,we highlight the strategies used to improve grain yield under heat stress from a source-sink perspective.We also discuss the remaining issues regarding the characteristics of thermosensors and the urgency required to explore the basis of acclimation under multifactorial stress combination.

Gap-free genome assembly and CYP450 gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis

Scutellaria baicalensis Georgi,a member of the Lamiaceae family,is a widely utilized medicinal plant.The flavones extracted from S.baicalensis contribute to numerous health benefits,including anti-inflammatory,antiviral,and anti-tumor activities.However,the incomplete genome assembly hinders biological studies on S.baicalensis.This study presents the first telomere-to-telomere(T2T)gap-free genome assembly of S.baicalensis through the integration of Pacbio HiFi,Nanopore ultra-long and Hi-C technologies.A total of 384.59 Mb of genome size with a contig N50 of 42.44 Mb was obtained,and all sequences were anchored into nine pseudochromosomes without any gap or mismatch.In addition,we analysed the major cyanidin-and delphinidin-based anthocyanins involved in the determination of blue-purple flower using a widely-targeted metabolome approach.Based on the genome-wide identification of Cytochrome P450(CYP450)gene family,three genes(SbFBH1,2,and 5)encoding flavonoid 3′-hydroxylases(F3′Hs)and one gene(SbFBH7)encoding flavonoid 3′5′-hydroxylase(F3′5′H)were found to hydroxylate the B-ring of flavonoids.Our studies enrich the genomic information available for the Lamiaceae family and provide a toolkit for discovering CYP450 genes involved in the flavonoid decoration.

Genome-Wide Dissection of Quan 9311A Breeding Process and Application Advantages

Germplasm resource innovation is a crucial factor for cultivar development,particularly within the context of hybrid rice breeding based on the three-line system.Quan 9311A,a cytoplasmic male sterile(CMS)line,has been successfully cultivated using rice restoration materials and extensively employed as a female parent in hybrid breeding program in China.This line was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11,with the intention of eliminating the restoring ability of 93-11 while retaining the sterility gene WA352c from Zhong 9A.Quan 9311A effectively amalgamates the most favorable agronomic traits from both parental lines.In this study,the relationship between phenotypic characteristics and the known functional genes of Quan 9311A were analyzed using the rice genome navigation technology based on whole-genome sequencing.The findings revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A,providing exceptional agronomic traits that are unavailable in earlier CMS lines.Despite the removal of the fertility restorer gene Rf3 from 93-11,numerous chromosomal segments from 93-11 persist in the Quan 9311A genome.Furthermore,the hybrid rice Quanyousimiao(QYSM)and the restorer line Wushansimiao(WSSM)were used as examples to illustrate the important role of Quan 9311A as the female parent in heterosis.It was found that QYSM carries a great number of superior alleles,which accounts for its high grain yield and wide adaptability.These insights not only advanced the utilization of hybrid rice pairing groups but also provided guidance for future breeding endeavors.The study introduced innovative concepts to further integrate genomics with traditional breeding techniques.Ultimately,Quan 9311A signified a significant milestone in rice breeding technology,opening up novel avenues for hybrid rice development.

TCD5 Enhances the Photosynthesis Capacity,Increases the Panicle Number and the Yield in Rice

Improvement of photosynthetic efficiency is a major approach to increase crop yield potential.Previously,we cloned a gene encoding the chloroplast-located putative monooxygenase TCD5,which is essential in plastid development under low temperature in rice(Oryza sativa L.).In this study,the effects of TCD5 on the photosynthesis and the yields were investigated in rice.Two sets of genetic materials with three levels of TCD5 expression,including tcd5 mutant or TCD5 RNAi transgenic lines and TCD5 over-expression transgenic lines in Jiahua1 and Nipponbare backgrounds,were used in the field trails of multi-locations and multi-years.TCD5 positively affected the panicle number and the yield at dosage.Compared with the wild-types,the panicle numbers were 12.4%-14.6%less in tcd5 mutant and 8.3%-38.6%less in TCD5 RNAi lines,but 26.2%-61.8%more in TCD5 over-expression lines.The grain yields per plant were 9.1%-18.4%less in tcd5 mutant and 14.3%-56.7%less in TCD5 RNAi lines,but 6.9%-56.5%more in TCD5 over-expression lines.The measurements of net photosynthetic rate indicated that mutation or knock down of TCD5 decreased the net photosynthetic rate by 10.4%and 15.6%,respectively,while increasing it by 8.9%and 8.7%in the TCD5 over-expression lines in Jiahua1 and Nipponbare backgrounds,respectively.Accordingly,the measurements of chlorophyll fluorescence parameters showed that the electron transport rate and quantum yield decreased in tcd5 mutant or TCD5 RNAi lines but increased in TCD5 overexpression lines,both in Jiahua1 and Nipponbare backgrounds.IP-MS screening revealed that TCD5 interacts with 29 chloroplast proteins involved in chlorophyll synthesis,photo-reactions of the photosynthesis,carbon assimilation and metabolism,energy metabolism,redox balance,protein synthesis and transportation.Two TCD5 interacted proteins,D1 and FBA were effective targets for improving photosynthesis.These results suggest a potentially new strategy for increasing rice yield by enhancing photosynthesis.

DNA cytosine methylation dynamics and functional roles in horticultural crops

Methylation of cytosine is a conserved epigenetic modification that maintains the dynamic balance of methylation in plants under the regulation of methyltransferases and demethylases.In recent years,the study of DNA methylation in regulating the growth and development of plants and animals has become a key area of research.This review describes the regulatory mechanisms of DNA cytosine methylation in plants.It summarizes studies on epigenetic modifications of DNA methylation in fruit ripening,development,senescence,plant height,organ size,and under biotic and abiotic stresses in horticultural crops.The review provides a theoretical basis for understanding the mechanisms of DNA methylation and their relevance to breeding,genetic improvement,research,innovation,and exploitation of new cultivars of horticultural crops.

Increasing grain weight and yield stability by increasing pre-heading non-structural carbohydrate reserves per spikelet in short-growth duration rice

Rice yield stability is a breeding goal,particularly for short-growth duration rice,but its underlying mechanisms remain unclear.In an attempt to identify the relationship between yield stability and source–sink characteristics in short-growth duration rice,a field experiment was conducted at three sites(Yueyang,Liuyang,and Hengyang)in 2021 and 2022.This study compared yield,yield components,source–sink characteristics,and their stability between two stable-yielding short-growth duration rice cultivars,Zhongzao 39(Z-39)and Lingliangyou 268(L-268),and two unstable-yielding short-growth duration rice cultivars,Zhongjiazao 17(Z-17)and Zhuliangyou 819(Z-819).The stability of agronomic parameters was represented by the coefficient of variation(CV).The respective CVs of yield in Z-17,Z-819,Z-39,and L-268 were 10.2%,10.1%,4.5%,and 5.7%in 2021 and 19.7%,15.0%,5.4%,and 6.5%in 2022.The respective CVs of grain weight were 6.3%,5.7%,3.4%,and 4.5%in Z-17,Z-819,Z-39,and L-268 in 2021,and 8.1%,6.3%,1.5%,and 0.8%in 2022.The mean source capacity per spikelet and pre-heading non-structural carbohydrate reserves per spikelet(NSC_(pre))were 7%–43%and7%–72%lower in Z-819 and Z-17than in L-268 and Z-39 in 2021 and 2022.The mean quantum yield of photosystem II photochemistry of leaf,leaf area index,and specific leaf weight of L-268 and Z-39 were higher than those of Z-819 and Z-17 at the heading stage.This study suggests that high NSC_(pre),caused by great leaf traits before heading,increases source capacity per spikelet and its stability,thereby increasing the stability of grain weight and yield.Increasing NSC_(pre)is critical for achieving grain weight and yield stability in short-growth duration rice.