Unveiling the distinctive traits of functional rye centromeres:minisatellites,retrotransposons,and R-loop formation

Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle attachments.Despite their conserved functionality,centromeric DNA sequences exhibit rapid evolution,presenting diverse sizes and compositions across species.The functional significance of rye centromeric DNA sequences,particularly in centromere identity,remains unclear.In this study,we comprehensively characterized the sequence composition and organization of rye centromeres.Our findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons(LTR-RTs)and interspersed minisatellites.We systematically classified LTR-RTs into five categories,highlighting the prevalence of younger CRS1,CRS2,and CRS3 of CRSs(centromeric retrotransposons of Secale cereale)were primarily located in the core centromeres and exhibited a higher association with CENH3 nucleosomes.The minisatellites,mainly derived from retrotransposons,along with CRSs,played a pivotal role in establishing functional centromeres in rye.Additionally,we observed the formation of R-loops at specific regions of CRS1,CRS2,and CRS3,with both rye pericentromeres and centromeres exhibiting enrichment in R-loops.Notably,these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres,suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere specification.Our work provides insights into the DNA sequence composition,distribution,and potential function of R-loops in rye centromeres.This knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres,offering implications for the development of synthetic centromeres in future plant modifications and beyond.

抑制性频谱整合对大棕蝠下丘神经元声强敏感性的影响(英文)

自由声场条件下 ,采用特定双声刺激方法研究了不同频率通道之间的非线性整合对下丘神经元声强敏感性的调制作用。实验在 1 2只麻醉与镇定的大棕蝠 (Eptesicusfuscus)上进行 ,双电极同步记录 2个配对神经元的声反应动作电位。主要结果如下 :1 )所获 1 1 0个 (5 5对 )配对神经元中 ,85 5 %表现为抑制性频谱整合作用 ,其余 1 4 5 %为易化性频谱整合 ;2 )阈上 1 0dB (SPL)放电率抑制百分比与神经元最佳频率 (BF)及记录深度呈负相关 ;3)抑制效率随声刺激强度升高而逐步下降 ;4 )当掩蔽声分别位于神经元兴奋性频率调谐曲线(FTC)内 (MSin) /外 (MSout)时 ,其抑制效率存在差异。前者的放电率抑制百分比及声反应动力学范围(DR)下降百分比均显著高于后者 ;5 )抑制性频谱整合导致 3类DR改变 :6 1 6 %为下降、 1 0 9%增加、另有2 7 5 %变化小于 1 0 %。本结果进一步支持如下设想

TWISTED DWARF 1 Associates with BRASSINOSTEROID-INSENSITIVE 1 to Regulate Early Events of the Brassinosteroid Signaling Pathway

A genome-wide screen for mutants showing altered brassinosteroid （BR） sensitivity or bril-like phenotypes resulted in the identification of two new mutant alleles of TWISTED DWARF 1 （TWD1）, twd1-4, and twdl-5. Pre- vious studies indicated that TWD1, also named as ULTRACURVATA 2 or FKBP42, associates with auxin efflux transporters and is essential for their biological functions. Although earlier reports showed that BR signaling is downregulated in twdl, how TWD1 is integrated in BR signaling has not been elucidated. Here, we provide ge- netic and biochemical evidence demonstrating that TWD1 interacts with the BR receptor BRI1 in vivo in a BR- independent manner. Further analyses indicated that TWD1 modulates the BR signal transduction not by altering ER quality control or protein abundance of BRI1; instead, TWD1 appears to be critical in BR- induced interaction of BRI1 and its co-receptor BAK1, as well as BR-induced phosphorylation of these two proteins. These results provide better understanding of the early events of the BR signaling pathway.

Overlapping functions of YDA and MAPKKK3/MAPKKK5 upstream of MPK3/MPK6 in plant immunity and growth/development

Arabidopsis MITOGEN-ACTIVATED PROTEIN KINASE3(MAPK3 or MPK3)and MPK6 play important signaling roles in plant immunity and growth/development.MAPK KINASE4(MKK4)and MKK5 function redundantly upstream of MPK3 and MPK6 in these processes.YODA(YDA),also known as MAPK KINASE KINASE4(MAPKKK4),is upstream of MKK4/MKK5 and forms a complete MAPK cascade(YDA–MKK4/MKK5–MPK3/MPK6)in regulating plant growth and development.In plant immunity,MAPKKK3 and MAPKKK5 function redundantly upstream of the same MKK4/MKK5–MPK3/MPK6 module.However,the residual activation of MPK3/MPK6 in the mapkkk3 mapkkk5 double mutant in response to flg22 pathogen-associated molecular pattern(PAMP)treatment suggests the presence of additional MAPKKK(s)in this MAPK cascade in signaling plant immunity.To investigate whether YDA is also involved in plant immunity,we attempted to generate mapkkk3 mapkkk5 yda triple mutants.However,it was not possible to recover one of the double mutant combinations(mapkkk5 yda)or the triple mutant(mapkkk3 mapkkk5 yda)due to a failure of embryogenesis.Using the clustered regularly interspaced short palindromic repeats(CRISPR)–CRISPRassociated protein 9(Cas9)approach,we generated weak,N-terminal deletion alleles of YDA,yda-del,in a mapkkk3 mapkkk5 background.PAMP-triggered MPK3/MPK6 activation was further reduced in the mapkkk3 mapkkk5 yda-del mutant,and the triple mutant was more susceptible to pathogen infection,suggesting YDA also plays an important role in plant immune signaling.In addition,MAPKKK5 and,to a lesser extent,MAPKKK3 were found to contribute to gamete function and embryogenesis,together with YDA.While the double homozygous mapkkk3 yda mutant showed the same growth and development defects as the yda single mutant,mapkkk5 yda double mutant and mapkkk3 mapkkk5 yda triple mutants were embryo lethal,similar to the mpk3 mpk6 double mutants.These results demonstrate that YDA,MAPKKK3,and MAPKKK5 have overlapping functions upstream of the MKK4/MKK5–MPK3/MPK6 module in both plant immunity and growth/development.

Sporophytic nondisjunction of the maize B chromosome at high copy numbers

It has been known for decades that the maize B chromosome undergoes nondisjunction at the second pollen mitosis.Fluorescence in-situ hybridization （FISH） was used to undertake a quantitative study of maize plants with differing numbers of B chromosomes to observe if instability increases by increasing B dosage in root tip tissue.B chromosome nondisjunction was basically absent at low copy number,but increased at higher B numbers.Thus,B nondisjunction rates are dependent on the dosage of B＇s in the sporophyte.Differences in nondisjunction were also documented between odd and even doses of the B.In plants that have inherited odd numbered doses of the B chromosome,B loss is nearly twice as likely as B gain in a somatic division.When comparing plants with even doses of B＇s to plants with odd doses of B＇s,plants with even numbers had a significantly higher chance to increase in number.Therefore,the B＇s nondisjunctive capacity,previously thought to be primarily restricted to the gametophyte,is present in sporophytic cells.

Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance

Aneuploidy has profound effects on an organism,typically more so than polyploidy,and the basis of this contrast is not fully understood.A dosage series of the maize long arm of chromosome 1(1L)was used to compa re relative global gene expression in diffe rent types and degrees of aneuploidy to gain insights into how the magnitude of genomic imbalance as well as hypoploidy affects global gene expression.While previously available methods require a selective examination of specific genes,RNA sequencing provides a whole-genome view of gene expression in aneuploids.Most studies of global aneuploidy effects have concentrated on individual types of aneuploids because multiple dose aneuploidies of the same genomic region are difficult to produce in most model genetic organisms.The genetic toolkit of maize allows the examination of multiple ploidies and 1-4 doses of chromosome arms.Thus,a detailed examination of expression changes both on the varied chromosome arms and elsewhere in the genome is possible,in both hypoploids and hyperploids,compared with euploid controls.Previous studies observed the inverse trans effect,in which genes not varied in DNA dosage were expressed in a negative relationship to the varied chromosomal region.This response was also the major type of changes found globally in this study.Many genes varied in dosage showed proportional expression changes,though some were seen to be partly or fully dosage compensated.It was also found that the effects of aneuploidy were progressive,with more severe aneuploids producing effects of greater magnitude.

Visual ＂playback＂ of colorful signals in the field supports sensory drive for signal detectability

Colorful visual signals are important systems for investigating the effects of signaling environ ments and receiver physiology on signal evolution as predicted by the sensory drive hypothesis. Support for the sensory drive hypothesis on color signal evolution is mostly based on document ing correlations between the properties of signals and habitat conditions under which the signals are given （i.e., a correlational approach） and less commonly on the use of mathematical models that integrate representations of visual environments, signal properties, and sensory systems （i.e., a functional approach）. Here, we used an experimental approach in the field to evaluate signal efficacy of colorful lizard throat fans called dewlaps that show geographic variation in the lizard Anolis cristatellus. We used a remote controlled apparatus to display ＂fake dewlaps＂ to wild lizards to test for adaptive divergence in dewlap brightness （i.e., perceived intensity） among populations in situ. We found evidence of local adaptation in dewlap brightness consistent with the sensory drive hypothesis. Specifically, dewlaps that had the brightness characteristics of local lizards were more likely to be detected than those with the brightness characteristics of nonlocal lizards. Our findings indicate that simplified mathematical representations of visual environments may allow robust estimates of relative detectability or conspicuousness in natural habitats. We have shown the feasibility of evaluating color signal efficacy experimentally under natural conditions and dem onstrate the potential advantages of presenting isolated components of signals to an intended re ceiver to measure their contribution to signal function.

Genomic Rearrangement in Endogenous Long Terminal Repeat Retrotransposons of Rice Lines Introgressed by Wild Rice （Zizania latifolia Griseb.）

Stochastic introgression of alien DNA may impose a genomic stress to the recipient genome. Herein, we report that apparent de novo genomic rearrangements in 10 of 13 selected endogenous, lowcopy, and potentially active long terminal repeat （LTR） retrotransposons occurred in one or more of three rice lines studied that were introgressed by wild rice （Zizania latifolia Griseb.）. For nine retrotransposons in which both the reverse-transcriptase （RT） region and the LTR region were available, largely concordant rearrangements occurred at both regions in five elements and at the RT region only in the remaining four elements. A marked proportion of the genomic changes was shared by two or all three introgression lines that were derived from a single F~ plant. This indicates that most of the genomic changes occurred at early developmental stages of the F~ somatic cells, which then gave rise to germline cells, and, hence, ensured inheritance of the changes to later generations. Possible causes and potential implications of the introgression-induced genomic rearrangements in LTR retrotransposons are discussed in the context of plant genome evolution and breeding.

An overview of rice genetics research in China

Congratulations to the Genetics Society of China on their 40;anniversary! Genetics has expanded in scope in that time frame and has penetrated into many areas of biology, medicine and agriculture. Genetics is poised to continue that trajectory into the future with promises of new understanding and new technologies for the benefit to society. Here, we will highlight some of the

The adaptive value of increasing pulse repetition rate during hunting by echolocating bats

During hunting, bats of suborder Microchiropetra emit intense ultrasonic pulses and analyze the weak returning echoes with their highly developed auditory system to extract the information about insects or obstacles. These bats progressively shorten the duration, lower the frequency, decrease the intensity and increase the repetition rate of emitted pulses as they search, approach, and finally intercept insects or negotiate obstacles. This dynamic variation in multiple parameters of emitted pulses predicts that analysis of an echo parameter by the bat would be inevitably affected by other co-varying echo parameters. The progressive increase in the pulse repetition rate throughout the entire course of hunting would presumably enable the bat to extract maximal information from the increasing number of echoes about the rapid changes in the target or obstacle position for successful hunting. However, the increase in pulse repetition rate may make it difficult to produce intense short pulse at high repetition rate at the end of long-held breath. The increase in pulse repetition rate may also make it difficult to produce high frequency pulse due to the inability of the bat laryngeal muscles to reach its full extent of each contraction and relaxation cycle at a high repetition rate. In addition, the increase in pulse repetition rate increases the minimum threshold （i.e. decrease auditory sensitivity） and the response latency of auditory neurons. In spite of these seemingly physiological disadvantages in pulse emission and auditory sensitivity, these bats do progressively increase pulse repetition rate throughout a target approaching sequence. Then, what is the adaptive value of increasing pulse repetition rate during echolocation？ What are the underlying mechanisms for obtaining maximal information about the target features during increasing pulse repetition rate？ This article reviews the electrophysiological studies of the effect of pulse repetition rate on multiple- parametric selectivity of neurons in the central nucleus of the inferior colliculus of the big brown bat, Eptesicusfuscus using single repetitive sound pulses and temporally patterned trains of sound pulses. These studies show that increasing pulse repetition rate improves multiple-parametric selectivity of inferior collicular neurons. Conceivably, this improvement of multiple-parametric selectivity of collicular neurons with increasing pulse repetition rate may serve as the underlying mechanisms for obtaining maximal information about the prey features for successful hunting by bats.

Implications of the gene balance hypothesis for dosage compensation

Dosage compensation refers to the equal expression between the sexes despite the fact that the dosage of the X chromosome is different in males and females.In Drosophila there is a twofold upregulation of the single male X.In triple X metafemales,there is also dosage compensation,which occurs by a two-thirds downregulation.There is a concomitant reduction in expression of many autosomal genes in metafemales.The male specific lethal(MSL)complex is present on the male X chromosome.Evidence is discussed showing that the MSL complex sequesters a histone acetyltransferase to the X chromosome to mute an otherwise increased expression by diminishing the histone acetylation on the autosomes.Several lines of evidence indicate that a constraining activity occurs from the MSL complex to prevent overcompensation on the X that might otherwise occur from the high level of acetylation present.Together,the evidence suggests that dosage compensation is a modification of a regulatory inverse dosage effect that is a reflection of intrinsic gene regulatory mechanisms and that the MSL complex has evolved in reaction in order to equalize the expression on both the X and autosomes of males and females.

Using detection dogs and genetic analyses of scat to expand knowledge and assist felid conservation in Misiones, Argentina

Many carnivores require large ranges to meet their ecological and energetic needs;however,anthropogen­ic changes threaten species and their habitats.Camera traps have been used to effectively collect data on car­nivores in a variety of habitat types;however,a single survey effort is typically limited to species that have similar body size,habitat use and movement patterns,and individual identification of animals is not always pos­sible.We evaluated whether scat detection dogs could effectively survey for 4 wide-ranging felids that vary in these characteristics:jaguars(Panthera onca),pumas(Puma concolor),ocelots(Leopardus pardalis)and oncil­las(Leopardus tigrinus).From June to October 2009 and May to August 2011,a detection dog-handler team de­tected 588 scats,from which 176 unique genotypes were detected.We assigned sex to 84.7%of the genotyped scats and identified 55 individuals multiple times.The effectiveness of these noninvasive techniques(detection dogs and genetic analyses of scat)not only opens the door for additional studies in areas that were previous­ly difficult or impossible with standard survey techniques,but also provides conservationists with a set of tools that overcome some of the limitations associated with the use of camera traps alone.

Efficient Targeted Genome Modification in Maize Using CRISPR/Cas9 System

CRISPR （clustered regularly interspaced short palindromic repeats）/Cas9 system, which is a newly developed technology for targeted genome modification, has been successfully used in a number of species. In this study, we applied this technology to carry out targeted genome modification in maize. A marker gene Zmzb7 was chosen for targeting. The sgRNA-Cas9 construct was transformed into maize protoplasts, and indel （insertion and deletion） mutations could be detected. A mutant seedling with an expected albino phenotype was obtained from screening 120 seedlings generated from 10 callus events. Mutation efficiency in maize heterochromatic regions was also investigated. Twelve sites with different expression levels in maize centromeres or pericentromere regions were selected. The sgRNA- Cas9 constructs were transformed into protoplasts followed by sequencmg the transformed protoplast genomic DNA. The results show that the genes in heterochromatic regions could be targeted by the CRISPR/Cas9 system efficiently, no matter whether they are expressed or not. Meanwhile, off-target mutations were not found in the similar sites having no PAM （protospacer adjacent motif） or having more than two mismatches. Together. our results show that the CRISPR/Cas9 system is a robust and efficient tool for genome modification in both euchromatic and heterochromatic regions in maize.

A viral protein orchestrates rice ethylene signaling to coordinate viral infection and insect vector-mediated transmission

Arthropod-borne viruses cause serious threats to human health and global agriculture by rapidly spreading via insect vectors. Southern rice black-streaked dwarf virus (SRBSDV) is the most damaging rice-infecting virus that is frequently transmitted by planthoppers. However, the molecular mechanisms underlying its propagation in the host plants and epidemics in the field are largely unknown. Here, we showed that the SRBSDV-encoded P6 protein is a key effector that regulates rice ethylene signaling to coordinate viral infection and transmission. In early SRBSDV infection, P6 interacts with OsRTH2 in the cytoplasm to activate ethylene signaling and enhance SRBSDV proliferation;this also repels the insect vector to reduce infestation. In late infection, P6 enters the nucleus, where it interacts with OsEIL2, a key transcription factor of ethylene signaling. The P6-OsEIL2 interaction suppresses ethylene signaling by preventing the dimerization of OsEIL2, thereby facilitating viral transmission by attracting the insect vector. Collectively, these findings reveal a novel molecular mechanism by which an arbovirus modulates the host defense system to promote viral infection and transmission.

Letting Go is Never Easy:Abscission and Receptor- Like Protein Kinases

Abscission is the process by which plants discard organs in response to environmental cues/stressors, or as part of their normal development. Abscission has been studied throughout the history of the plant sciences and in numerous species. Although long studied at the anatomical and physiological levels, abscission has only been elucidated at the molecular and genetic levels within the last two decades, primarily with the use of the model plant Arabidopsis thaliana. This has led to the discovery of numerous genes involved at all steps of abscission, including key pathways involving receptor-like protein kinases （RLKs）. This review covers the current knowledge of abscission research, highlighting the role of RLKs.

Progressive heterosis in genetically defined tetraploid maize

Progressive heterosis, i.e., the additional hybrid vigor in double-cross tetraploid hybrids not found in their single-cross tetraploid parents, has been documented in a number of species including alfalfa,potato, and maize. In this study, four artificially induced maize tetraploids, directly derived from standard inbred lines, were crossed in pairs to create two single-cross hybrids. These hybrids were then crossed to create double-cross hybrids containing genetic material from all four original lines. Replicated fieldbased phenotyping of the materials over four years indicated a strong progressive heterosis phenotype in tetraploids but not in their diploid counterparts. In particular, the above ground dry weight phenotype of double-cross tetraploid hybrids was on average 34% and 56% heavier than that of the single-cross tetraploid hybrids and the double-cross diploid counterparts, respectively. Additionally,whole-genome resequencing of the original inbred lines and further analysis of these data did not show the expected spectrum of alleles to explain tetraploid progressive heterosis under the complementation of complete recessive model. These results underscore the reality of the progressive heterosis phenotype,its potential utility for increasing crop biomass production, and the need for exploring alternative hypothesis to explain it at a molecular level.

Phototropism in land plants： Molecules and mechanism from light perception to response

BACKGROUND： Phototropism is the response a plant exhibits when it is faced with a directional blue light stimulus. Though a seemingly simple differential cell elongation response within a responding tissue that results in organ curvature, phototropism is regulated through a complex set of signal perception and transduction events that move from the plasma membrane to the nucleus. In nature phototropism is one of several plant responses that have evolved to optimize photosynthesis and growth. OBJECTIVE： In the present work we will review the state of the field with respect to the molecules and mechanisms associated with phototropism in land plants. METHODS： A systematic literature search was done to identify relevant advances in the field. Though we tried to focus on literature within the past decade （1998-present）, we have discussed and cited older literature where appropriate because of context or its significant impact to the present field. Several previous review articles are also cited where appropriate and readers should seek those out. RESULTS： A total of 199 articles are cited that fulfill the criteria listed above. CONCLUSIONS： Though important numerous and significant advances have been made in our understanding of the molecular, biochemical, cell biological and physiologic mechanisms underlying phototropism in land plants over the past decade, there are many remaining unanswered questions. The future is indeed bright for researchers in the field and we look forward to the next decade worth of discoveries.

Disruptions in AUXl-Dependent Auxin Influx Alter Hypocotyl Phototropism in Arabidopsis

Phototropism represents a differential growth response by which plant organs can respond adaptively to changes in the direction of incident light to optimize leaf/stem positioning for photosynthetic light capture and root growth orientation for water/nutrient acquisition. Studies over the past few years have identified a number of compo- nents in the signaling pathway（s） leading to development of phototropic curvatures in hypocotyls. These include the pho- totropin photoreceptors （photl and phot2） that perceive directional blue-light （BL） cues and then stimulate signaling, leading to relocalization of the plant hormone auxin, as well as the auxin response factor NPH4/ARF7 that responds to changes in local auxin concentrations to directly mediate expression of genes likely encoding proteins necessary for development of phototropic curvatures, While null mutations in NPH4/ARF7 condition an aphototropic response to unidirectional BL, seedlings carrying the same mutations recover BL-dependent phototropic responsiveness if coirradiated with red light （RL） or pre-treated with either ethylene. In the present study, we identify second-site enhancer mutations in the nph4 background that abrogate these recovery responses. One of these mutations-mapl （modifier of arf7 phenotypes 1）-was found to represent a missense allele of AUX1-a gene encoding a high-affinity auxin influx carrier previously associated with a number of root responses. Pharmocological studies and analyses of additional auxl mutants confirmed that AUX1 functions as a modulator of hypocotyl phototropism. Moreover, we have found that the strength of dependence of hypocotyl phototropism on AUX1-mediated auxin influx is directly related to the auxin responsiveness of the seedling in question.

X chromosome inactivation and active X upregulation in therian mammals: facts, questions, and hypotheses

X chromosome inactivation is a mechanism that modulates the expression of X-linked genes in eutherian females(XX).Ohno proposed that to achieve a proper balance between X-linked and autosomal genes,those on the active X should also undergo a 2-fold upregula-tion.Although some support for Ohno's hypothesis has been provided through the years,recent genomic studies testing this hypoth-esis have brought contradictory results and fueled debate.Thus far,there are as many results in favor as against Ohno's hypothesis,depending on the nature of the datasets and the various assumptions and thresholds involved in the analyses.However,they have con-firmed the importance of dosage balance between X-linked and autosomal genes involved in stoichiometric relationships.These facts as well as questions and hypotheses are discussed below.

The Psb32 Protein Aids in Repairing Photodamaged Photosystem II in the Cyanobacterium Synechocystis 6803

Photosystem II （PSII）, a membrane protein complex, catalyzes the photochemical oxidation of water to molecular oxygen. This enzyme complex consists of approximately 20 stoichiometric protein components. However, due to the highly energetic reactions it catalyzes as part of its normal activity, PSII is continuously damaged and repaired. With advances in protein detection technologies, an increasing number of sub-stoichiometric PSII proteins have been identified, many of which aid in the biogenesis and assembly of this protein complex. Psb32 （SII1390） has previously been identified as a protein associated with highly active purified PSII preparations from the cyanobacterium Synechocystis sp. PCC 6803. To investigate its function, the subcellular localization of Psb32 and the impact of deletion of the psb32 gene on PSII were analyzed. Here, we show that Psb32 is an integral membrane protein, primarily located in the thylakoid membranes. Al- though not required for cell viability, Psb32 protects cells from oxidative stress and additionally confers a selective fitness advantage in mixed culture experiments. Specifically, Psb32 protects PSII from photodamage and accelerates its repair. Thus, the data suggest that Psb32 plays an important role in minimizing the effect of photoinhibition on PSII.