Chinese wisdom and modern innovation of aquaculture

Aquaculture originates from ancient Chinese wisdom,and is considered the most efficient food-producing industry.About 70 years ago,New China proposed an industrial approach to fish production and made a policy decision to begin modern aquaculture development.As one of lucky persons since the early 1980s,I have committed my scholarly career to the studies on genetics and breeding biotechnology of polyploid gibel carp(Carassius gibelio).Here,several significant recent innovations,such as the proposition of the amphitriploid concept,the association of ploidy changes with reproduction transition,the finding of a unique ameiofusiongenesis mode,the establishment of a controllable fertility approach,the creation of intermuscular bonefree mutants,as well as the recreation of desirable goldfish,are introduced and emphasized from an active participant of these innovations.Additionally,some modern innovations and contributions are also highlighted in other aspects of aquaculture including feed development,disease control,facilities and equipment upgrading,as well as paradigm and mode changes.This comprehensive synthesis of ancient Chinese wisdom and modern innovations seeks to provide valuable insights into the field from a historical basis.

Corrigendum to“Root-derived long-distance signals trigger ABA synthesis and enhance drought resistance in Arabidopsis”[Journal of Genetics and Genomics(2024)51,749e761]

This corrigendum clarifies to supplement the“Data availability”session.Data availability The raw sequence data reported in this paper have been deposited in the National Genomics Data Center,China National Center for Bioinformation/Beijing Institute of Genomics,Chinese Academy of Sciences(GSA:CRA017487 and iProx:IPX0009175000).

A method for custom measurement of fish dimensions using the improved YOLOv5-keypoint framework with multi-attention mechanisms

Dimensional data directly reflects the growth rate of individual fish,an important economic trait of interest to fish researchers.Efficiently obtaining large-scale fish dimension data would be valuable for both selective breeding and production.To address this,our study proposes a custom dimension measurement method for fish using the YOLOv5-keypoint framework with multi-attention mechanisms.We optimized the YOLOv5 framework,incorporated the SimAM attention mechanism to achieve more accurate and faster fish detection,and added customizable landmarks to the network structure,enabling flexible configuration of the number and location of feature points in the training dataset.This method is applicable to various aquacultural species and other objects.We tested the effectiveness of the method using the economically important grass carp(Ctenopharyngodon idella).The proposed method outperforms pure YOLOv5,Faster R-CNN,and SSD in terms of precision and recall rates,achieving an impressive average precision of 0.9781.Notably,field trials confirmed the method's exceptional measurement accuracy,exceeding 97%compatibility with manual measurements,while demonstrating a realtime speed of 38 frames per second on the NVIDIA RTX A4000.This enables efficient and accurate large-scale surface dimension measurements of economic fish.To facilitate massive measurements in agricultural research,we have implemented this method as an online platform,called Mode-recognition Ruler(MrRuler,http://bioinf o.ihb.ac.cn/mrruler).The platform identifies objects in a single image at an average speed of 0.486±0.005 s,based on a dataset of 10,000 images.MrRuler includes two preset carp models and allows users to upload training datasets for custom models of their targets of interest.

Evolutionary mechanisms and practical significance of reproductive success and clonal diversity in unisexual vertebrate polyploids

Unisexual reproduction is generally relevant to polyploidy, and unisexual vertebrates are often considered an evolutionary “dead end” due to the accumulation of deleterious mutations and absence of genetic diversity. However, some unisexual polyploids have developed strategies to avoid genomic decay, and thus provide ideal models to unveil unexplored evolutionary mechanisms, from the reproductive success to clonal diversity creation. This article reviews the evolutionary mechanisms for overcoming meiotic barrier and generating genetic diversity in unisexual vertebrates, and summarizes recent research advancements in the polyploid Carassius complex. Gynogenetic gibel carp(Carassius gibelio) is a unique amphitriploid that has undergone a recurrent autotriploidy and has overcome the bottleneck of triploid sterility via gynogenesis. Recently, an efficient strategy in which ploidy changes, including from amphitriploid to amphitetraploid, then from amphitetraploid to novel amphitriploid, drive unisexual-sexual-unisexual reproduction transition and clonal diversity has been revealed.Based on this new discovery, multigenomic reconstruction biotechnology has been used to breed a novel strain with superior growth and stronger disease resistance. Moreover, a unique reproduction mode that combines both abilities of ameiotic oogenesis and sperm-egg fusion,termed as ameio-fusiongensis, has been discovered, and it provides an efficient approach to synthesize sterile allopolyploids. In order to avoid ecological risks upon escape and protect the sustainable property rights of the aquaculture seed industry, a controllable fertility biotechnology approach for precise breeding is being developed by integrating sterile allopolyploid synthesis and gene-editing techniques.This review provides novel insights into the origin and evolution of unisexual vertebrates and into the attempts being made to exploit new breeding biotechnologies in aquaculture.

Root-derived long-distance signals trigger ABA synthesis and enhance drought resistance in Arabidopsis

Vascular plants have evolved intricate long-distance signaling mechanisms to cope with environmental stress,with reactive oxygen species(ROS)emerging as pivotal systemic signals in plant stress responses.However,the exact role of ROS as root-to-shoot signals in the drought response has not been determined.In this study,we reveal that compared with wild-type plants,ferric reductase defective 3(frd3)mutants exhibit enhanced drought resistance concomitant with elevated NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3(NCED3)transcript levels and abscisic acid(ABA)contents in leaves as well as increased hydrogen peroxide(H_(2)O_(2))levels in roots and leaves.Grafting experiments distinctly illustrate that drought resistance can be conferred by the frd3 rootstock regardless of the scion genotype,indicating that long-distance signals originating from frd3 roots promote an increase in ABA levels in leaves.Intriguingly,the drought resistance conferred by the frd3 mutant rootstock is weakened by the CAT2-overexpressing scion,suggesting that H_(2)O_(2)may be involved in long-distance signaling.Moreover,the results of comparative transcriptome and proteome analyses support the drought resistance phenotype of the frd3 mutant.Taken together,our findings substantiate the notion that frd3 root-derived long-distance signals trigger ABA synthesis in leaves and enhance drought resistance,providing new evidence for root-to-shoot long-distance signaling in the drought response of plants.

Knockout of OsSPL10 confers enhanced glufosinate resistance in rice

Dear Editor,Rice(Oryza sativa L.)is one of the world’s major food crops,feeding more than half of the global population.To reduce labor and production costs,direct seeding is becoming popular for rice cultivation,but weeds have become a serious problem(Jin et al.,2022).Chemical herbicides are one of the most effective ways to control weeds.Therefore,the development of herbicide-resistant rice has great significance for modern rice production.

The innovative safe herbicide dienediamine saves paraquat

Throughout the history of agriculture,the challenge of weed management has endured,necessitating significant investments to facilitate ideal crop growth and maximize yields.Strategies for weed control mainly involve manual and chemical methodologies.While manual weeding persists in certain regions,chemical herbicides notably represent the primary approach.

A novel cell line established from skin tissue of gibel carp(Carassius gibelio)is susceptible to Carassius auratus herpesvirus infection

Frequent outbreaks of emerging infectious diseases in fish,such as Carassius auratus herpesvirus(CaHV)infection has caused great economic losses in China.However,the lack of a sensitive cell culture system has limited studies of CaHV.In the present study,a new cell line(gibel carp skin cell,GiCS)derived from gibel carp(Carassius gibelio)skin tissue was established to create a valuable tool for research of the virus.The GiCS cells consisted mainly of epithelial-like cells,which grew well at 25℃in L-15 medium supplemented with 10–20%fetal bovine serum.Chromosomal analysis revealed that the skin cell line remained amphitriploid,with most chromosome counts being 156(54%).The GiCS cells can be efficiently transfected and expressed exogenous genes.In particular,the GiCS cells showed high susceptibility to CaHV infection,which was confirmed by virus infection tests,detection of viral gene expression,and ultrastructural observation.To our knowledge,it is the first cell line that is highly permissive to CaHV infection.In addition,the cells also showed susceptibility to several aquatic animal viruses from different families including Iridoviridae,Rhabdoviridae,and Reoviridae.In conclusion,these results indicated that the establishment of the GiCS cell line is a significant advance that will be beneficial to future studies of CaHV and other aquatic animal viruses.

A gain-of-function mutation of the MATE family transporter DTX6 confers paraquat resistance in Arabidopsis

Paraquat is one of the most widely used nonselective herbicides and has elicited the emergence of para-quat-resistant weeds.However,the molecular mechanisms of paraquat resistance are not completely un-derstood.Here we report the Arabidopsis gain-of-function mutant pqt15-D with significantly enhanced resistance to paraquat and the corresponding gene PQT15,which encodes the Multidrug and Toxic Extru-sion(MATE)transporter DTX6.A point mutation at+932 bp in DTX6 causes a G311E amino acid substitution,enhancing the paraquat resistance ofpqt15-D,and overexpression of DTX6/PQT15 in the wild-type plants also results in strong paraquat resistance.Moreover,heterologous expression of DTX6 and DTX6-D in Es-cherichia coil significantly enhances bacterial resistance to paraquat.Importantly,overexpression of DTX6-D enables Arabidopsis plants to tolerate 4 mM paraquat,a near-commercial application level.DTX6/PQT15 is localized in the plasma membrane and endomembrane,and functions as a paraquat efflux transporter as demonstrated by paraquat efflux assays with isolated protoplasts and bacterial cells.Taken together,our results demonstrate that DTX6/PQT15 is an efflux transporter that confers paraquat resis-tance by exporting paraquat out of the cytosol.These findings reveal a molecular mechanism of paraquat resistance in higher plants and provide a promising candidate gene for engineering paraquat-resistant crops.

Understanding paraquat resistance mechanisms in Arabidopsis thaliana to facilitate the development of paraquat-resistant crops

Paraquat(PQ)is the third most used broad-spectrum nonselective herbicide around the globe after glyphosate and glufosinate.Repeated usage and overreliance on this herbicide have resulted in the emergence of PQ-resistant weeds that are a potential hazard to agriculture.It is generally believed that PQ resistance in weeds is due to increased sequestration of the herbicide and its decreased translocation to the target site,as well as an enhanced ability to scavenge reactive oxygen species.However,little is known about the genetic bases and molecular mechanisms of PQ resistance in weeds,and hence no PQ-resistant crops have been developed to date.Forward genetics of the model plant Arabidopsis thaliana has advanced our understanding of the molecular mechanisms of PQ resistance.This review focuses on PQ resistance loci and resistance mechanisms revealed in Arabidopsis and examines the possibility of developing PQ-resistant crops using the elucidated mechanisms.

Loss of OsARF18 function confers glufosinate resistance in rice

Dear Editor,Weeds are one of the most common biotic stresses causing severe crop yield decline(Jin et al.,2022).Chemical herbicides are an economical and effective method for weed control and are widely used in modern agriculture(Amna et al.,2019).However,the improper use of herbicides can impede crop growth,ultimately leading to reduced crop yields.Therefore,it is of great significance to develop herbicide-resistant crops to alleviate weed infestations and maintain sustainable crop production.

A finTRIM member 100 (FTR100) is unique to Otomorpha fish for constitutive regulation of IFN response

Vertebrate interferon(IFN)expression is fine-tuned in order to avoid excessive tissue injury under normal conditions and during virus infection.FinTRIM(fish novel TRIM,FTR)proteins are reported to regulate the fish IFN response.Here,we identify a novel finTRIM gene from yellow catfish(Pelteobagrus fulvidraco),which is sequentially named PfFTR100 according to the nomenclature rule in zebrafish.Genome-wide analyses reveal that FTR100 is unique to Otomorpha fish,with a single copy in spite of additional genome duplication in some fish species.Considering that few of the 99 finTRIM genes identified in zebrafish are conserved in main fish branches and most,such as FTR100,are unique to distinct branches due to lineage-specific expansion of finTRIM genes,we develop a nomenclature for newly cloned finTRIM genes from different fish species.PfFTR100 mRNA is not induced by virus infection,with a relatively high expression level comparable to that of cellular IFN and some IFN-stimulated genes(ISGs)in virally-infected tissues.However,ectopically-expressed PfFTR100 protein is attenuated in virally-infected cells through the proteasomal-dependent pathway.Overexpression of PfFTR100 promotes SVCV replication by downregulating the constitutive and inducible IFN response via a mechanism by which PfFTR100 targets IRF3 and IRF7 to attenuate their mRNA levels rather than their protein levels.Our results indicate that yellow catfish FTR100 is essential for homeostatic regulation of fish tonic IFN response.

OsNLP3 enhances grain weight and reduces grain chalkiness in rice

Grain weight,a key determinant of yield in rice(Oryza sativa L.),is governed primarily by genetic factors,whereas grain chalkiness,a detriment to grain quality,is intertwined with environmental factors such as mineral nutrients.Nitrogen(N)is recognized for its effect on grain chalkiness,but the underlying molecular mechanisms remain to be clarified.This study revealed the pivotal role of rice NODULE INCEPTION-LIKE PROTEIN 3(OsNLP3)in simultaneously regulating grain weight and grain chalkiness.Our investigation showed that loss of OsNLP3 leads to a reduction in both grain weight and dimension,in contrast to the enhancement observed with OsNLP3 overexpression.OsNLP3 directly suppresses the expression of OsCEP6.1 and OsNF-YA8,which were identified as negative regulators associated with grain weight.Consequently,two novel regulatory modules,OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8,were identified as key players in grain weight regulation.Notably,the OsNLP3-OsNF-YA8 module not only increases grain weight but also mitigates grain chalkiness in response to N.This research clarifies the molecular mechanisms that orchestrate grain weight through the OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8 modules,highlighting the pivotal role of the OsNLP3-OsNF-YA8 module in alleviating grain chalkiness.These findings reveal potential targets for simultaneous enhancement of rice yield and quality.

Rethinking fish biology and biotechnologies in the challenge era for burgeoning genome resources and strengthening food security

Fish biology has been developed for more than 100 years,but some important breakthroughs have been made in the last decade.Early studies commonly concentrated on morphology,phylogenetics,development,growth,reproduction manipulation,and disease control.Recent studies have mostly focused on genetics,molecular biology,genomics,and genome biotechnologies,which have provided a solid foundation for enhancing aquaculture to ensure food security and improving aquatic environments to sustain ecosystem health.Here,we review research advances in five major areas:(1)biological innovations and genomic evolution of four significant fish lineages including non-teleost ray-finned fishes,northern hemisphere sticklebacks,East African cichlid fishes,and East Asian cyprinid fishes;(2)evolutionary fates and consequences of natural polyploid fishes;(3)biological consequences of fish domestication and selection;(4)development and innovation of fish breeding biotechnologies;and(5)applicable approaches and potential of fish genetic breeding biotechnologies.Moreover,five precision breeding biotechniques are examined and discussed in detail including gene editing for the introgression or removal of beneficial or detrimental alleles,use of sex-specific markers for the production of mono-sex populations,controllable primordial germ cell on-off strategy for producing sterile offspring,surrogate broodstock-based strategies to accelerate breeding,and genome incorporation and sexual reproduction regainbased approach to create synthetic polyploids.Based on these scientific and technological advances,we propose a blueprint for genetic improvement and new breed creation for aquaculture species and analyze the potential of these new breeding strategies for improving aquaculture seed industry and strengthening food security.

Genomic Epidemiology of SARS-CoV-2 in Pakistan

COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,2020.We identified a total of 347 mutated positions,31 of which were over-represented in Pakistan.Meanwhile,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or coevolution.Some of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying selections.The genomic epidemiology revealed five distinctive spreading clusters.The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF1ab)of this cluster.Furthermore,28 putative international introductions were identified,several of which are consistent with the epidemiological investigations.In all,this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control.

一种独特的无减数融合生殖方式的发现及一条合成不育异源多倍体高效路径的创建

多倍化与生殖方式转换之间的联系作为进化遗传学的热点,能被开拓为农业生物遗传改良的新路径.最近我们通过整合雌核生殖银鲫和有性生殖鲫的基因组,创制了一个新双三倍体群体,发现它们中的大部分雌性恢复了单性雌核生殖能力.在本研究中,我们发现少数雌性获得了一种定义为“无减数融合生殖”的独特生殖方式.具有这种生殖方式的新双三倍体雌性不仅从单性雌核生殖银鲫遗传了无减数分裂产生不减数卵子的能力,还从有性生殖鲫遗传了卵核与精核融合形成受精卵的能力.随后我们将这种新双三倍体与二倍体团头鲂进行交配,直接创制了一个合成异源七倍体群体.它们的染色体组由来自其母本新双三倍体鲫的全套染色体组和来自父本二倍体团头鲂的一套染色体组构成.此外,我们还在一尾异源七倍体的部分体细胞中,检测到鲫与团头鲂染色体间相互易位的现象.随后我们追踪了异源七倍体生殖细胞在减数分裂过程中的染色体行为,揭示了它们不育的细胞学机制.结果表明,在减数第一次分裂(减Ⅰ)前期,染色体联会异常以及DNA双链断裂无法被完全修复,导致异源七倍体初级卵母细胞严重凋亡.尽管其初级精母细胞在减Ⅰ前期表现出与初级卵母细胞相似的染色体行为,但它们可以发育到减Ⅰ中期,并最终由于同源染色体分离失败而发生凋亡.最后,我们建立了一个可持续大规模生产具有无减数融合生殖能力的新双三倍体克隆系,还将其与多种鲤科鱼类进行交配快速创制出多种整合有不同鲤科鱼类基因组的不育异源多倍体群体,由此研发出一条高效的育种技术路径.本研究不仅拓宽了我们对脊椎动物生殖方式转换的认识,还为多倍体育种和杂种优势固定提供了一个可行的策略.

Balanced nitrogen–iron sufficiency boosts grain yield and nitrogen use efficiency by promoting tillering

Crop yield plays a critical role in global food security.For optimal plant growth and maximal crop yields,nutrients must be balanced.However,the potential significance of balanced nitrogen-iron(N-Fe)for improving crop yield and nitrogen use efficiency(NUE)has not previously been addressed.Here,we show that balanced N-Fe sufficiency significantly increases tiller number and boosts yield and NUE in rice and wheat.NIN-like protein 4(OsNLP4)plays a pivotal role in maintaining the N-Fe balance by coordinately regulating the expression of multiple genes involved in N and Fe metabolism and signaling.OsNLP4 also suppresses OsD3 expression and strigolactone(SL)signaling,thereby promoting tillering.Balanced N-Fe sufficiency promotes the nuclear localization of OsNLP4 by reducing H_(2)O_(2) levels,reinforcing the functions of OsNLP4.Interestingly,we found that OsNLP4 upregulates the expression of a set of H2O2-scavenging genes to promote its own accumulation in the nucleus.Furthermore,we demonstrated that foliar spraying of balanced N-Fe fertilizer at the tillering stage can effectively increase tiller number,yield,and NUE of both rice and wheat in the field.Collectively,these findings reveal the previously unrecognized effects of N-Fe balance on grain yield and NUE as well as the molecular mechanism by which the OsNLP4-OsD3 module integrates N-Fe nutrient signals to downregulate SL signaling and thereby promote rice tillering.Our study sheds light on how N-Fe nutrient signals modulate rice tillering and provide potential innovative approaches that improve crop yield with reduced N fertilizer input for benefitting sustainable agriculture worldwide.

Nitrate-responsive OsMADS27 promotes salt tolerance in rice

Salt stress is a major constraint on plant growth and yield.Nitrogen(N)fertilizers are known to alleviate salt stress.However,the underlying molecular mechanisms remain unclear.Here,we show that nitratedependent salt tolerance is mediated by OsMADS27 in rice.The expression of OsMADS27 is specifically induced by nitrate.The salt-inducible expression of OsMADS27 is also nitrate dependent.OsMADS27 knockout mutants are more sensitive to salt stress than the wild type,whereas OsMADS27 overexpression lines are more tolerant.Transcriptomic analyses revealed that OsMADS27 upregulates the expression of a number of known stress-responsive genes as well as those involved in ion homeostasis and antioxidation.We demonstrate that OsMADS27 directly binds to the promoters of OsHKT1.1 and OsSPL7 to regulate their expression.Notably,OsMADS27-mediated salt tolerance is nitrate dependent and positively correlated with nitrate concentration.Our results reveal the role of nitrate-responsive OsMADS27 and its downstream target genes in salt tolerance,providing a molecular mechanism for the enhancement of salt tolerance by nitrogen fertilizers in rice.OsMADS27 overexpression increased grain yield under salt stress in the presence of sufficient nitrate,suggestingthatOsMADS27 is a promising candidate for the improvementof salt tolerance inrice.

GCRV NS38 counteracts SVCV proliferation by intracellular antagonization during co-infection

Viral co-infection has been found in animals;however,the mechanisms of co-infection are unclear.The abundance and diversity of viruses in water make fish highly susceptible to co-infection.Here,we reported a coinfection in fish,which resulted in reduced host lethality and illustrated the intracellular molecular mechanism of viral co-infection.The spring viremia of carp virus(SVCV)is a highly lethal virus that infects Cyprinidae,such as zebrafish.The mortality of SVCV infection was significantly reduced when co-infected with the grass carp reovirus(GCRV).The severity of tissue damage and viral proliferation of SVCV was also reduced in co-infection with GCRV.The transcriptome bioinformatics analysis demonstrated that the effect on the host transcripts in response to SVCV infection was significantly reduced in co-infection.After excluding the extracellular interactions of these two viruses,the intracellular mechanisms were studied.We found that the GCRV NS38 remarkably decreased SVCV infection and viral proliferation.The interaction between GCRV NS38 and SVCV nucleoprotein(N)and phosphoprotein(P)proteins was identified,and NS38 downregulated both N and P proteins.Further analysis demonstrated that the N protein was degraded by NS38 indispensable of the autophagy receptor,sequestosome 1(p62).Meanwhile,K63-linked ubiquitination of the P protein was reduced by NS38,leading to ubiquitinated degradation of the P protein.These results reveal that the intracellular viral protein interactions are a crucial mechanism of co-infection and influence the host pathology and expand our understanding in intracellular viral interactions co-infection.

Causal gene identification and desirable trait recreation in goldfish

Goldfish(Carassius auratus) have long fascinated evolutionary biologists and geneticists because of their diverse morphological and color variations.Recent genome-wide association studies have provided a clue to uncover genomic basis underlying these phenotypic variations,but the causality between phenotypic and genotypic variations have not yet been confirmed.Here,we edited proposed candidate genes to recreate phenotypic traits and developed a rapid biotechnology approach which combines gene editing with high-efficiency breeding,artificial gynogenesis,and temperature-induced sex reversal to establish homozygous mutants within two generations(approximately eight months).We first verified that low-density lipoprotein receptorrelated protein 2B(lrp2a B) is the causal gene for the dragon-eye variation and recreated the dragon-eye phenotype in side-view Pleated-skirt Lion-head goldfish.Subsequently,we demonstrated that the albino phenotype was determined by both homeologs of oculocutaneous albinism type II(oca2),which has subfunctionalized to differentially govern melanogenesis in the goldfish body surface and pupils.Overall,we determined two causal genes for dragon-eye and albino phenotypes,and created four stable homozygous strains and more appealing goldfish with desirable traits.The developed biotechnology approach facilitates precise genetic breeding,which will accelerate re-domestication and recreation of phenotypically desirable goldfish.