Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph co...Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph construction,and near-complete genome assemblies now allow accurate SV detection and genotyping.These innovations overcome the limitations of single-reference genomes,enabling the discovery of complex SVs,including nested and overlapping variants,and providing access to previously inaccessible genomic regions such as centromeres and telomeres.This review highlights the current landscape of cattle SV research,with emphasis on integrating longread sequencing and pangenome frameworks to uncover breed-specific and population-level variation.While many SVs are linked to economically important traits such as feed efficiency and disease resistance,their broader regulatory impacts remain an active area of investigation.Emerging functional genomics approaches,including transcriptomics,epigenomics,and genome editing,will clarify how SVs influence gene regulation and phenotype.Looking forward,the integration of SV catalogs with multi-omics data,imputation resources,and artificial intelligence-driven models will be essential for translating discoveries into breeding and conservation applications.Integrating structural variants into breeding pipelines promises to revolutionize livestock genomics,enabling precision selection and sustainable agriculture despite challenges in cost,data sharing,and functional validation.展开更多
IR64 is an elite Xian/indica variety developed by International Rice Research Institute(IRRl)in 1985,which has been the most widely grown variety and core breeding parent in South/Southeast Asia(Mackill and Khush,2018...IR64 is an elite Xian/indica variety developed by International Rice Research Institute(IRRl)in 1985,which has been the most widely grown variety and core breeding parent in South/Southeast Asia(Mackill and Khush,2018).IR64 has been utilized to develop stress-tolerant(such as drought-adapted and submergenceresistant)near-isogenic lines,underscoring its great potential in agricultural genomics(Tanaka et al.,2020).展开更多
Soybean(Glycine max L.)is a globally vital crop for oil production and food security.High-quality genomic resources are instrumental for both functional genomics and breeding.Here,we report a near-complete,high-qualit...Soybean(Glycine max L.)is a globally vital crop for oil production and food security.High-quality genomic resources are instrumental for both functional genomics and breeding.Here,we report a near-complete,high-quality genome assembly of the elite cultivar Tianlong 1(TL1),featuring fully resolved telomeres and centromeres,as well as a gap-free assembly of 14 of its 20 chromosomes.On the basis of the genome assembly,we generate an ethyl methanesulfonate(EMS)-mutagenized population comprising 2555 M7 plants.Whole-genome resequencing of 288 EMS mutants uncovers 1,163,869 high-confidence single-nucleotide polymorphisms(SNPs)and 542,709 insertions/deletions(InDels),achieving 91.89%coverage of predicted protein-coding genes.Phenotypic screening demonstrates robust genotype–phenotype associations,with two nonsynonymous mutants displaying pronounced defects in seed and leaf development.Collectively,the chromosome-scale TL1 genome assembly and the extensively characterized mutant population establish valuable resources for functional genomics and precision breeding in soybean and related legume species.展开更多
Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challengin...Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce.展开更多
Background Understanding the genetic basis of male reproduction in mammals remains challenging.Commercial pig populations offer a unique model for studying fertility,as semen traits are routinely recorded using high-t...Background Understanding the genetic basis of male reproduction in mammals remains challenging.Commercial pig populations offer a unique model for studying fertility,as semen traits are routinely recorded using high-throughput systems.Results In a large-scale GWAS of 15 semen traits based on 286,314 ejaculates collected from 2,954 boars of a purebred pig line,we identified 10 QTL,including four loci with recessive deleterious alleles.Several lead SNPs affected multiple semen traits.For example,a SNP on SSC6 was significantly associated with distal cytoplasmic droplets and with effects on tail abnormalities and sperm motility in a follow up analysis.The allele frequencies of some loci were different in older boar's,most likely due to culling based on poor semen quality.Using WGS,we identified six missense variants in high linkage disequilibrium(LD)with lead SNPs in genes related to sperm production(e.g.,MEIOB,CFAP74 and UBE2B).Remarkably,the frequency of some alleles with predicted deleterious effects on semen traits increased between 2013 and 2019.Conclusions Our results highlight loci with major effects on semen quality,some of which are linked to functional variants in key genes involved in spermatogenesis.The information from this study can be used to select against deleterious alleles affecting semen characteristics in pigs and provides valuable insight into the genetics of mammalian male fertility.展开更多
Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the...Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle.To comprehensively characterize the genomic variation within Bos indicus and,specifically,dairy breeds,we aim to identify non-reference sequences and construct a comprehensive pangenome.Results Five representative genomes of prominent dairy breeds,including Gir,Kankrej,Tharparkar,Sahiwal,and Red Sindhi,were sequenced using 10X Genomics‘linked-read’technology.Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to the Bos indicus Brahman reference genome.A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods,revealing 8 Mb and 17.7 Mb of novel sequence respectively.A confident set of 6,844 Non-reference Unique Insertions(NUIs)spanning 7.57 Mb was identified through both methods,representing the pange-nome of Indian Bos indicus breeds.Comparative analysis with previously published pangenomes unveiled 2.8 Mb(37%)commonality with the Chinese indicine pangenome and only 1%commonality with the Bos taurus pange-nome.Among these,2,312 NUIs encompassing~2 Mb,were commonly found in 98 samples of the 5 breeds and des-ignated as Bos indicus Common Insertions(BICIs)in the population.Furthermore,926 BICIs were identified within 682 protein-coding genes,54 long non-coding RNAs(lncRNA),and 18 pseudogenes.These protein-coding genes were enriched for functions such as chemical synaptic transmission,cell junction organization,cell-cell adhesion,and cell morphogenesis.The protein-coding genes were found in various prominent quantitative trait locus(QTL)regions,suggesting potential roles of BICIs in traits related to milk production,reproduction,exterior,health,meat,and carcass.Notably,63.21%of the bases within the BICIs call set contained interspersed repeats,predominantly Long Inter-spersed Nuclear Elements(LINEs).Additionally,70.28%of BICIs are shared with other domesticated and wild species,highlighting their evolutionary significance.Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India.The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.展开更多
Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its impor...Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its importance,the lack of a complete genome assembly has been a stumbling block in its biological breeding process.Therefore,we generated deep coverage ultralong Oxford Nanopore Technology(ONT)and PacBio HiFi reads to construct a telomere-to-telomere(T2T)genome assembly.The final assembly spans 537.27 Mb with no gaps,demonstrating a remarkable completeness of 98.1%.We utilized a combination of transcriptome data and homologous proteins to annotate the genome,identifying 36018 protein-coding genes.Furthermore,we profiled global cytosine DNA methylations using ONT sequencing data.Global methylome analysis revealed high methylation levels in transposable element(TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas.By integrating a detailed multi-omics data analysis,we obtained valuable insights into the mechanism underlying endopleura coloration.This investigation led to the identification of eight candidate genes(e.g.ANR)involved in anthocyanin biosynthesis pathways,which are crucial for the development of color in plants.The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.展开更多
Seedlessness has always been a valuable quality characteristic of edible grape varieties.Although the production of seedless grapes has been ongoing for decades,the genetic complexity of seedless grapes is not yet ful...Seedlessness has always been a valuable quality characteristic of edible grape varieties.Although the production of seedless grapes has been ongoing for decades,the genetic complexity of seedless grapes is not yet fully understood.Therefore,determining the genetic mechanisms and key regulatory genes of seedless grapes is of great significance for seedless grape breeding and meeting market demands.The emergence of high-throughput analysis software offers greater possibilities for mining genes related to plant organ development.Specifically,to mine a greater number of candidate genes related to grape seed traits,this study used the seed trait parameters analyzed by Tomato Analyzer as the target trait and then used a genome-wide association study(GWAS)to mine candidate genes.In the two-year analysis using principal component analysis(PCA),we extracted five principal components with a cumulative contribution rate of 96.586%.The cumulative contribution rate for component 1 reached 87.352%.Correlation analysis revealed correlation coefficients ranging from 0.54 to 0.98 among the seven basic traits.The GWAS results indicated that 370 SNP loci were significantly correlated with seed traits.These SNP loci were distributed on 18 chromosomes,except for chromosome 4,with most SNP loci distributed on chromosome 18.Based on the physical location of single nucleotide polymorphism(SNP)markers significantly associated with seed-related traits in the grape reference genome,candidate genes are screened within the range of linkage disequilibrium(LD)attenuation distance,both upstream and downstream of the significant SNP loci.These candidate genes were mainly transcription factor-related genes(VvMADS4 and VvMADS5),ubiquitin ligase-related genes(E3 ubiquitin ligase BIG BROTHER),serine/threonine protein kinase-related genes,and carbohydrate metabolism-related genes(Sucrose Synthase 2)and simultaneously controlled multiple(at least two or more)seed traits.These results indicate that seed traits are jointly regulated by some genes involved in seed morphology regulation.In this work,we identified new gene loci related to grape seed traits.Identifying molecular markers closely related to these seed traits is of great significance for breeding seedless grape varieties.展开更多
Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lac...Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.展开更多
Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into a...Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.展开更多
Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris,but their cytological and evolutionary consequences remain poorly understood.Here,we investigated chromosome numbers an...Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris,but their cytological and evolutionary consequences remain poorly understood.Here,we investigated chromosome numbers and genome sizes in 64 accessions representing the morphological diversity across the genus.Chromosome numbers ranged from 12 to 33,with seven accessions newly identified,including L.chunxiaoensis(2n=33),two putative L.guangxiensis(2n=19),and fivenatural hybrids(2n=16,18,29,33).Genome sizes varied from 18.03 Gb(L.wulingensis)to 32.62 Gb(L.caldwellii).Although no significantcorrelationwas found between genome size and chromosome number across all accessions,a strong correlation within ploidy-level groups(i.e.,diploid or aneuploid)suggested roles for post-polyploid diploidization,aneuploidy,and dysploidy in speciation.Phylogenetic analyses based on chloroplast genomes and nuclear DNA sequences revealed significantdiscordance,indicating a complex reticulate evolution and historical hybridization,which may complicate morphological classification.Chromosome number aligned more closely with morphological groups,underscoring the necessity of integrating cytological,molecular,and morphological data for accurate taxonomy,particularly in largegenome taxa.Based on this evidence,we propose a putative speciation pathway involving multiple hybridization and polyploidization events,with allopolyploidy playing a predominant role.Furthermore,our results indicate that the species L.insularis and L.longifolia are geographic populations of L.sprengeri and L.aurea,respectively,and confirmedthe distribution of L.traubii and L.albiflora in China' Mainland.These findingsoffer new insights into the mechanisms underlying speciation,interspecificrelationships,and the evolutionary history of Lycoris.展开更多
Resilience traits in pig populations allow animals to deal better with infectious disease and suboptimal production environments.The data on daily weight,feed intake and feed behaviors in pigs are collected in test pe...Resilience traits in pig populations allow animals to deal better with infectious disease and suboptimal production environments.The data on daily weight,feed intake and feed behaviors in pigs are collected in test period by automated feeding stations,which facilitate to evaluate the resilience traits.In this study,we adopted the root mean square error(RMSE)of ordinary least squares(OLS)and the negative residuals of quantile regression(QR)to generate four different novel resilience traits using daily records of feed intake and feed duration between 90 and 180 days of age in a population of commercial Duroc pigs.The genome-wide association studies(GWAS)based on single-and two-trait mixed models were carried out on 550 pigs using 48,603 single nucleotide polymorphisms(SNPs)to identify genomic regions associated with resilience traits in growing pigs.We further focused on the GWAS signals to conduct gene annotation,colocalization with multi-tissue eQTL summary statistics of PigGTEx project and identification of enhancers and promoters using the publicly available data.The genomic heritabilities of four novel resilience traits ranged from 0.09 to 0.41.The pairwise genetic and phenotypic correlations ranged from 0.16 to 0.95 and from 0.05 to 0.36,respectively.Twenty-seven SNPs were identified to be significantly associated with these resilience traits.They were distributed on nine chromosomes(SSC1,SSC2,SSC6,SSC7,SSC8,SSC12,SSC14,SSC16 and SSC17).After annotation,39 QTLs and 49 candidate genes were identified.Several of these are functionally relevant candidate genes including OTUD4,TIFA and CARD14,which are involved in the host immune response,disease susceptibility and signal transduction.Eight unique SNPs were found to be causal in both GWAS and eQTL analyses across 15 tissues.Notably,one SNP(rs80794541)was associated with eQTLs identified concurrently across seven tissues/cell types,including the macrophage cell type.Furthermore,four significant SNPs(rs81467127,rs81356029,rs80794541 and rs81305085)were linked to the function of the primed enhancer,active element,and poised promoter in five pig tissues.Using the porcine fibroblast HiC dataset,SNP(rs81356029)on SSC2 regulates the CARNS1 and SSH3,while SNP(rs80794541)on SSC7 regulates the H2AC6.In this study,we generated four novel resilience traits and identified SNPs significantly associated with these resilience traits in a Duroc pig population.GWAS signals were associated with candidate genes involving in the immune traits,and were linked to the crucial regulatory elements as well.Our findings will contribute to elucidating the genetic mechanism that can enhance genome-enabled breeding and inform further research on resilience in domestic pigs.展开更多
The Andaman Islands,part of the Indo-Burma biodiversity hotspot,holds unique florawith many endemic and threatened species.However,this fragile diversity is under increasing pressure from infrastructure expansion,clim...The Andaman Islands,part of the Indo-Burma biodiversity hotspot,holds unique florawith many endemic and threatened species.However,this fragile diversity is under increasing pressure from infrastructure expansion,climate change and habitat fragmentation.The recently announced Great Nicobar Island Development project by the Government of India,which includes an international transhipment terminal,airport,township and power plant,if implemented,would cause major habitat loss and fragmentation,possibly leading to species extinctions.展开更多
The genome tagging project(GTP)plays a pivotal role in addressing a critical gap in the understanding of protein functions.Within this framework,we successfully generated a human influenza hemagglutinin-tagged sperm-s...The genome tagging project(GTP)plays a pivotal role in addressing a critical gap in the understanding of protein functions.Within this framework,we successfully generated a human influenza hemagglutinin-tagged sperm-specific protein 411(HA-tagged Ssp411)mouse model.This model is instrumental in probing the expression and function of Ssp411.Our research revealed that Ssp411 is expressed in the round spermatids,elongating spermatids,elongated spermatids,and epididymal spermatozoa.The comprehensive examination of the distribution of Ssp411 in these germ cells offers new perspectives on its involvement in spermiogenesis.Nevertheless,rigorous further inquiry is imperative to elucidate the precise mechanistic underpinnings of these functions.Ssp411 is not detectable in metaphase Ⅱ(MⅡ)oocytes,zygotes,or 2-cell stage embryos,highlighting its intricate role in early embryonic development.These findings not only advance our understanding of the role of Ssp411 in reproductive physiology but also significantly contribute to the overarching goals of the GTP,fostering groundbreaking advancements in the f ields of spermiogenesis and reproductive biology.展开更多
Introduction Tibetan sheep,economically important animals on the Qinghai–Tibet Plateau,have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective ...Introduction Tibetan sheep,economically important animals on the Qinghai–Tibet Plateau,have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective breeding.However,most current research focuses on one or two breeds,and lacks a comprehensive representa-tion of the genetic diversity across multiple Tibetan sheep breeds.This study aims to fill this gap by investigating the genetic structure,diversity and high-altitude adaptation of 6 Tibetan sheep breeds using whole-genome rese-quencing data.Results Six Tibetan sheep breeds were investigated in this study,and whole-genome resequencing data were used to investigate their genetic structure and population diversity.The results showed that the 6 Tibetan sheep breeds exhibited distinct separation in the phylogenetic tree;however,the levels of differentiation among the breeds were minimal,with extensive gene flow observed.Population structure analysis broadly categorized the 6 breeds into 3 distinct ecological types:plateau-type,valley-type and Euler-type.Analysis of unique single-nucleotide polymor-phisms(SNPs)and selective sweeps between Argali and Tibetan sheep revealed that Tibetan sheep domestication was associated primarily with sensory and signal transduction,nutrient absorption and metabolism,and growth and reproductive characteristics.Finally,comprehensive analysis of selective sweep and transcriptome data sug-gested that Tibetan sheep breeds inhabiting different altitudes on the Qinghai–Tibet Plateau adapt by enhancing cardiopulmonary function,regulating body fluid balance through renal reabsorption,and modifying nutrient diges-tion and absorption pathways.Conclusion In this study,we investigated the genetic diversity and population structure of 6 Tibetan sheep breeds in Qinghai Province,China.Additionally,we analyzed the domestication traits and investigated the unique adapta-tion mechanisms residing varying altitudes in the plateau region of Tibetan sheep.This study provides valuable insights into the evolutionary processes of Tibetan sheep in extreme environments.These findings will also contribute to the preservation of genetic diversity and offer a foundation for Tibetan sheep diversity preservation and plateau animal environmental adaptation mechanisms.展开更多
Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been co...Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been conducted.Here,we reconstruct high-quality ancestral genomes for the most recent common ancestor(MRCA)of the Triticeae,and the MRCA of the wheat lineage(Triticum and Aegilops).The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060,respectively,which were arranged in their ancestral order.By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes,we revisit the rye chromosome structural evolution and propose alternative evolutionary routes.The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu is found to have occurred independently and is unlikely to be the result of chromosomal introgression following distant hybridization.We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event.Lastly,we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution,representing potential CR hotspots.This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.展开更多
Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(...Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete.In this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants.Based on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes.Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.展开更多
Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systema...Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systematically addressed how taxonomic complexity,especially in rapidly radiating lineages with intricate evolutionary histories,might influencethe efficacyof plastome-scale barcodes.Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains,and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus.Therefore,Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity.In this study,we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes.Our results revealed that the traditional standard barcode combination(nrITS+matK+rbcL+trnH-psbA)achieved the highest discrimination rates(81.25%),closely followed by the plastid large single copy(LSC)region(80.21%),then by full plastome,the supermatrix of proteincoding genes,and hypervariable regions(79.17%).Notably,the matK and ycf1 gene alone could discriminate 78.13%of species.Key determinants of species discrimination by integrating alignment length(AL)and the proportion of parsimony-informative sites(PPIS),as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity.Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes,this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’specificbiological habits and potentially reflectingunique evolutionary patterns in the plastid genome.展开更多
Polyembryony has posed a significant impediment to the advancement of citrus hybrid breeding.FhRWP is widely regarded as a pivotal factor governing asexual reproduction in citrus,and prior research has demonstrated th...Polyembryony has posed a significant impediment to the advancement of citrus hybrid breeding.FhRWP is widely regarded as a pivotal factor governing asexual reproduction in citrus,and prior research has demonstrated that FhARID1,acting as an upstream regulator,modulates FhRWP expression.In this study,we performed a genome-wide characterization of the ARID-HMG-related genes using the short juvenile minicitrus Fortunella hindsii.A total of 20 ARID-HMG-related genes were identified.Protein interaction network and enrichment analysis suggested that ARID-HMG-related proteins might might be involved in chromatin remodeling complexes.Knockout of FhARID1 in F.hindsii did not induce the conversion from polyembryony to monoembryony.However,fharid1 plants in T1 generation exhibited abnormal proliferation at axillary buds,which is similar to phenotype of fhrwp plants.Expression analysis of fharid1 ovary tissues revealed the downregulation of FhRWP.The results indicated that FhARID1,as an upstream regulator of FhRWP,has an effect on the development of citrus axillary buds.Expression analysis of overexpressed leaves of FhARID1 lines showed that no significant up-regulation of FhRWP,indicating that FhARID1 is not the sole upstream regulatory factor of FhRWP.Only FhARID2 showed a correlation in expression with FhARID1 among the ARID-related genes,further supporting the notion that this gene may be involved in complex formation rather than acting alone.Yeast two-hybrid and MS/MS spectra further indicated that FhARID1 function requires casein kinase II-mediated post-transcriptional phosphorylation.This study elucidated the function of FhARID1 in citrus apomixis and axillary bud development,providing a fundamental basis for understanding the role of ARID-HMG-related genes.展开更多
基金supported in part by AFRI grant numbers 2019-7015-29321 and 2021-67015-33409 from the USDA National Institute of Food and Agriculture(NIFA)the SCINet project of the USDA ARS project number 0500-00093-001-00-D。
文摘Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph construction,and near-complete genome assemblies now allow accurate SV detection and genotyping.These innovations overcome the limitations of single-reference genomes,enabling the discovery of complex SVs,including nested and overlapping variants,and providing access to previously inaccessible genomic regions such as centromeres and telomeres.This review highlights the current landscape of cattle SV research,with emphasis on integrating longread sequencing and pangenome frameworks to uncover breed-specific and population-level variation.While many SVs are linked to economically important traits such as feed efficiency and disease resistance,their broader regulatory impacts remain an active area of investigation.Emerging functional genomics approaches,including transcriptomics,epigenomics,and genome editing,will clarify how SVs influence gene regulation and phenotype.Looking forward,the integration of SV catalogs with multi-omics data,imputation resources,and artificial intelligence-driven models will be essential for translating discoveries into breeding and conservation applications.Integrating structural variants into breeding pipelines promises to revolutionize livestock genomics,enabling precision selection and sustainable agriculture despite challenges in cost,data sharing,and functional validation.
基金supported by the Natural Science Foundation of Anhui Province(2408085MC058 and 2308085QC91)National Natural Science Foundation of China(32301783and U21A20214)+5 种基金Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS CSIAF-202303)Nanfan special project,CAAS(YYLH2309,YBXM2322,YYLH2401)Scientific Innovation 2030 Project(2022ZD0401703)CAAS Innovative Team Award,Science and Technology of Innovative research program of Anhui Province(202423m1005002)National Key Research and Development Program of China(2023YFD1200900)the Natural Science Foundation General Program of Hebei Province(C2024204242).
文摘IR64 is an elite Xian/indica variety developed by International Rice Research Institute(IRRl)in 1985,which has been the most widely grown variety and core breeding parent in South/Southeast Asia(Mackill and Khush,2018).IR64 has been utilized to develop stress-tolerant(such as drought-adapted and submergenceresistant)near-isogenic lines,underscoring its great potential in agricultural genomics(Tanaka et al.,2020).
基金supported by the National Natural Science Foundation of China(31970344)Joint Funds of the Natural Science Foundation of Hainan Province,China(2021JJLH0065).
文摘Soybean(Glycine max L.)is a globally vital crop for oil production and food security.High-quality genomic resources are instrumental for both functional genomics and breeding.Here,we report a near-complete,high-quality genome assembly of the elite cultivar Tianlong 1(TL1),featuring fully resolved telomeres and centromeres,as well as a gap-free assembly of 14 of its 20 chromosomes.On the basis of the genome assembly,we generate an ethyl methanesulfonate(EMS)-mutagenized population comprising 2555 M7 plants.Whole-genome resequencing of 288 EMS mutants uncovers 1,163,869 high-confidence single-nucleotide polymorphisms(SNPs)and 542,709 insertions/deletions(InDels),achieving 91.89%coverage of predicted protein-coding genes.Phenotypic screening demonstrates robust genotype–phenotype associations,with two nonsynonymous mutants displaying pronounced defects in seed and leaf development.Collectively,the chromosome-scale TL1 genome assembly and the extensively characterized mutant population establish valuable resources for functional genomics and precision breeding in soybean and related legume species.
基金supported by Central Public-interest Scientific Institution Basal Research Fund(CATAS-Nos.1630152023007,1630152023011,1630152023012,1630152023013)the National Natural Science Foundation of China(Grant No.32071805).
文摘Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce.
基金the GEroNIMO(Genome and Epigenome Enabled Breeding in Monogastics)project.The GEroNIMO project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No 101000236。
文摘Background Understanding the genetic basis of male reproduction in mammals remains challenging.Commercial pig populations offer a unique model for studying fertility,as semen traits are routinely recorded using high-throughput systems.Results In a large-scale GWAS of 15 semen traits based on 286,314 ejaculates collected from 2,954 boars of a purebred pig line,we identified 10 QTL,including four loci with recessive deleterious alleles.Several lead SNPs affected multiple semen traits.For example,a SNP on SSC6 was significantly associated with distal cytoplasmic droplets and with effects on tail abnormalities and sperm motility in a follow up analysis.The allele frequencies of some loci were different in older boar's,most likely due to culling based on poor semen quality.Using WGS,we identified six missense variants in high linkage disequilibrium(LD)with lead SNPs in genes related to sperm production(e.g.,MEIOB,CFAP74 and UBE2B).Remarkably,the frequency of some alleles with predicted deleterious effects on semen traits increased between 2013 and 2019.Conclusions Our results highlight loci with major effects on semen quality,some of which are linked to functional variants in key genes involved in spermatogenesis.The information from this study can be used to select against deleterious alleles affecting semen characteristics in pigs and provides valuable insight into the genetics of mammalian male fertility.
基金the project “Genomics for Conservation of Indigenous Cattle Breeds and for Enhancing Milk Yield, Phase-I” [BT/ PR26466/AAQ/1/704/2017], funded by the Department of Biotechnology (DBT ), Indiathe project “Identification of key molecular factors involved in resistance/susceptibility to paratuberculosis infection in indigenous breeds of cows” [BT/PR32758/AAQ/1/760/2019], which was also funded by Department of Biotechnology (DBT ), India。
文摘Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle.To comprehensively characterize the genomic variation within Bos indicus and,specifically,dairy breeds,we aim to identify non-reference sequences and construct a comprehensive pangenome.Results Five representative genomes of prominent dairy breeds,including Gir,Kankrej,Tharparkar,Sahiwal,and Red Sindhi,were sequenced using 10X Genomics‘linked-read’technology.Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to the Bos indicus Brahman reference genome.A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods,revealing 8 Mb and 17.7 Mb of novel sequence respectively.A confident set of 6,844 Non-reference Unique Insertions(NUIs)spanning 7.57 Mb was identified through both methods,representing the pange-nome of Indian Bos indicus breeds.Comparative analysis with previously published pangenomes unveiled 2.8 Mb(37%)commonality with the Chinese indicine pangenome and only 1%commonality with the Bos taurus pange-nome.Among these,2,312 NUIs encompassing~2 Mb,were commonly found in 98 samples of the 5 breeds and des-ignated as Bos indicus Common Insertions(BICIs)in the population.Furthermore,926 BICIs were identified within 682 protein-coding genes,54 long non-coding RNAs(lncRNA),and 18 pseudogenes.These protein-coding genes were enriched for functions such as chemical synaptic transmission,cell junction organization,cell-cell adhesion,and cell morphogenesis.The protein-coding genes were found in various prominent quantitative trait locus(QTL)regions,suggesting potential roles of BICIs in traits related to milk production,reproduction,exterior,health,meat,and carcass.Notably,63.21%of the bases within the BICIs call set contained interspersed repeats,predominantly Long Inter-spersed Nuclear Elements(LINEs).Additionally,70.28%of BICIs are shared with other domesticated and wild species,highlighting their evolutionary significance.Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India.The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.
基金supported by the Yunnan Seed Laboratory,China(202205AR070001-15)the National Natural Science Foundation of China,China(Grant No.32160697)。
文摘Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its importance,the lack of a complete genome assembly has been a stumbling block in its biological breeding process.Therefore,we generated deep coverage ultralong Oxford Nanopore Technology(ONT)and PacBio HiFi reads to construct a telomere-to-telomere(T2T)genome assembly.The final assembly spans 537.27 Mb with no gaps,demonstrating a remarkable completeness of 98.1%.We utilized a combination of transcriptome data and homologous proteins to annotate the genome,identifying 36018 protein-coding genes.Furthermore,we profiled global cytosine DNA methylations using ONT sequencing data.Global methylome analysis revealed high methylation levels in transposable element(TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas.By integrating a detailed multi-omics data analysis,we obtained valuable insights into the mechanism underlying endopleura coloration.This investigation led to the identification of eight candidate genes(e.g.ANR)involved in anthocyanin biosynthesis pathways,which are crucial for the development of color in plants.The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.
基金supported by grants from the Basic Research Business Fees for Public Welfare in Xinjiang Autonomous Region(Mining candidate genes related to grape seed traits based on GWAS,KY2023028)the Xinjiang Uygur Autonomous Region Tianchi Talent-Young Doctor for Chuan Zhang(Revealing the domestication history of Xinjiang native grape varieties and genetic analysis of important agronomic traits)the Xinjiang Academy of Agricultural Sciences Youth Science and Technology Backbone Innovation Ability Training Project(xjnkq-2023006).
文摘Seedlessness has always been a valuable quality characteristic of edible grape varieties.Although the production of seedless grapes has been ongoing for decades,the genetic complexity of seedless grapes is not yet fully understood.Therefore,determining the genetic mechanisms and key regulatory genes of seedless grapes is of great significance for seedless grape breeding and meeting market demands.The emergence of high-throughput analysis software offers greater possibilities for mining genes related to plant organ development.Specifically,to mine a greater number of candidate genes related to grape seed traits,this study used the seed trait parameters analyzed by Tomato Analyzer as the target trait and then used a genome-wide association study(GWAS)to mine candidate genes.In the two-year analysis using principal component analysis(PCA),we extracted five principal components with a cumulative contribution rate of 96.586%.The cumulative contribution rate for component 1 reached 87.352%.Correlation analysis revealed correlation coefficients ranging from 0.54 to 0.98 among the seven basic traits.The GWAS results indicated that 370 SNP loci were significantly correlated with seed traits.These SNP loci were distributed on 18 chromosomes,except for chromosome 4,with most SNP loci distributed on chromosome 18.Based on the physical location of single nucleotide polymorphism(SNP)markers significantly associated with seed-related traits in the grape reference genome,candidate genes are screened within the range of linkage disequilibrium(LD)attenuation distance,both upstream and downstream of the significant SNP loci.These candidate genes were mainly transcription factor-related genes(VvMADS4 and VvMADS5),ubiquitin ligase-related genes(E3 ubiquitin ligase BIG BROTHER),serine/threonine protein kinase-related genes,and carbohydrate metabolism-related genes(Sucrose Synthase 2)and simultaneously controlled multiple(at least two or more)seed traits.These results indicate that seed traits are jointly regulated by some genes involved in seed morphology regulation.In this work,we identified new gene loci related to grape seed traits.Identifying molecular markers closely related to these seed traits is of great significance for breeding seedless grape varieties.
基金supported by the National Key Research and Development Program of China(2023YFF1000100 and 2023YFA0914601)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District(PT202101-01).
文摘Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.
基金supported by the Shenzhen Science and Technology Program,China(Grant No.KCXFZ20211020163808012)the Nanfan Special Project,Chinese Academy of Agricultural Sciences,China(Grant No.YBXM2426).
文摘Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.
基金supported by the ScientificFund of Nanjing Botanical Garden Men.Sun Yat-Sen(JSPKLB202519)Jiangsu Provincial Crop Germplasm Resource Bank(Lycoris)(JS-ZW-K04)Forestry Science and Technology Popularization Demonstration Project of the Central Finance[Su(2024)TG06].
文摘Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris,but their cytological and evolutionary consequences remain poorly understood.Here,we investigated chromosome numbers and genome sizes in 64 accessions representing the morphological diversity across the genus.Chromosome numbers ranged from 12 to 33,with seven accessions newly identified,including L.chunxiaoensis(2n=33),two putative L.guangxiensis(2n=19),and fivenatural hybrids(2n=16,18,29,33).Genome sizes varied from 18.03 Gb(L.wulingensis)to 32.62 Gb(L.caldwellii).Although no significantcorrelationwas found between genome size and chromosome number across all accessions,a strong correlation within ploidy-level groups(i.e.,diploid or aneuploid)suggested roles for post-polyploid diploidization,aneuploidy,and dysploidy in speciation.Phylogenetic analyses based on chloroplast genomes and nuclear DNA sequences revealed significantdiscordance,indicating a complex reticulate evolution and historical hybridization,which may complicate morphological classification.Chromosome number aligned more closely with morphological groups,underscoring the necessity of integrating cytological,molecular,and morphological data for accurate taxonomy,particularly in largegenome taxa.Based on this evidence,we propose a putative speciation pathway involving multiple hybridization and polyploidization events,with allopolyploidy playing a predominant role.Furthermore,our results indicate that the species L.insularis and L.longifolia are geographic populations of L.sprengeri and L.aurea,respectively,and confirmedthe distribution of L.traubii and L.albiflora in China' Mainland.These findingsoffer new insights into the mechanisms underlying speciation,interspecificrelationships,and the evolutionary history of Lycoris.
基金funded by the National Key Research and Development Program of China(2024YFF1000100 and 2021YFD1301102)the National Natural Science Foundations of China(32172702)the National Agricultural Science and Technology Innovation Program,Chinese Academy of Agricultural Sciences(ASTIP-IAS02).
文摘Resilience traits in pig populations allow animals to deal better with infectious disease and suboptimal production environments.The data on daily weight,feed intake and feed behaviors in pigs are collected in test period by automated feeding stations,which facilitate to evaluate the resilience traits.In this study,we adopted the root mean square error(RMSE)of ordinary least squares(OLS)and the negative residuals of quantile regression(QR)to generate four different novel resilience traits using daily records of feed intake and feed duration between 90 and 180 days of age in a population of commercial Duroc pigs.The genome-wide association studies(GWAS)based on single-and two-trait mixed models were carried out on 550 pigs using 48,603 single nucleotide polymorphisms(SNPs)to identify genomic regions associated with resilience traits in growing pigs.We further focused on the GWAS signals to conduct gene annotation,colocalization with multi-tissue eQTL summary statistics of PigGTEx project and identification of enhancers and promoters using the publicly available data.The genomic heritabilities of four novel resilience traits ranged from 0.09 to 0.41.The pairwise genetic and phenotypic correlations ranged from 0.16 to 0.95 and from 0.05 to 0.36,respectively.Twenty-seven SNPs were identified to be significantly associated with these resilience traits.They were distributed on nine chromosomes(SSC1,SSC2,SSC6,SSC7,SSC8,SSC12,SSC14,SSC16 and SSC17).After annotation,39 QTLs and 49 candidate genes were identified.Several of these are functionally relevant candidate genes including OTUD4,TIFA and CARD14,which are involved in the host immune response,disease susceptibility and signal transduction.Eight unique SNPs were found to be causal in both GWAS and eQTL analyses across 15 tissues.Notably,one SNP(rs80794541)was associated with eQTLs identified concurrently across seven tissues/cell types,including the macrophage cell type.Furthermore,four significant SNPs(rs81467127,rs81356029,rs80794541 and rs81305085)were linked to the function of the primed enhancer,active element,and poised promoter in five pig tissues.Using the porcine fibroblast HiC dataset,SNP(rs81356029)on SSC2 regulates the CARNS1 and SSH3,while SNP(rs80794541)on SSC7 regulates the H2AC6.In this study,we generated four novel resilience traits and identified SNPs significantly associated with these resilience traits in a Duroc pig population.GWAS signals were associated with candidate genes involving in the immune traits,and were linked to the crucial regulatory elements as well.Our findings will contribute to elucidating the genetic mechanism that can enhance genome-enabled breeding and inform further research on resilience in domestic pigs.
基金supported by the Global Genome Initiative for Gardens(GGI-Gardens Award),United States Botanic Garden and Botanic Gardens Conservation International,United Kingdom(Grant No.GGI/2024/1).
文摘The Andaman Islands,part of the Indo-Burma biodiversity hotspot,holds unique florawith many endemic and threatened species.However,this fragile diversity is under increasing pressure from infrastructure expansion,climate change and habitat fragmentation.The recently announced Great Nicobar Island Development project by the Government of India,which includes an international transhipment terminal,airport,township and power plant,if implemented,would cause major habitat loss and fragmentation,possibly leading to species extinctions.
基金the support from the National Natural Science Foundation of China(No.32070849)The Foundation of Science and Technology Commission of Shanghai Municipality(No.22DX1900400)+1 种基金Science and Technology Commission of Shanghai Municipality(No.23JC1403803)Shanghai Municipal Science and Technology Commission Targeted Funding Project(No.22DX1900400).
文摘The genome tagging project(GTP)plays a pivotal role in addressing a critical gap in the understanding of protein functions.Within this framework,we successfully generated a human influenza hemagglutinin-tagged sperm-specific protein 411(HA-tagged Ssp411)mouse model.This model is instrumental in probing the expression and function of Ssp411.Our research revealed that Ssp411 is expressed in the round spermatids,elongating spermatids,elongated spermatids,and epididymal spermatozoa.The comprehensive examination of the distribution of Ssp411 in these germ cells offers new perspectives on its involvement in spermiogenesis.Nevertheless,rigorous further inquiry is imperative to elucidate the precise mechanistic underpinnings of these functions.Ssp411 is not detectable in metaphase Ⅱ(MⅡ)oocytes,zygotes,or 2-cell stage embryos,highlighting its intricate role in early embryonic development.These findings not only advance our understanding of the role of Ssp411 in reproductive physiology but also significantly contribute to the overarching goals of the GTP,fostering groundbreaking advancements in the f ields of spermiogenesis and reproductive biology.
基金supported by the Natural Science Foundation of Qinghai Province(No.2022-ZJ-901)the National Breeding Joint Research Project。
文摘Introduction Tibetan sheep,economically important animals on the Qinghai–Tibet Plateau,have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective breeding.However,most current research focuses on one or two breeds,and lacks a comprehensive representa-tion of the genetic diversity across multiple Tibetan sheep breeds.This study aims to fill this gap by investigating the genetic structure,diversity and high-altitude adaptation of 6 Tibetan sheep breeds using whole-genome rese-quencing data.Results Six Tibetan sheep breeds were investigated in this study,and whole-genome resequencing data were used to investigate their genetic structure and population diversity.The results showed that the 6 Tibetan sheep breeds exhibited distinct separation in the phylogenetic tree;however,the levels of differentiation among the breeds were minimal,with extensive gene flow observed.Population structure analysis broadly categorized the 6 breeds into 3 distinct ecological types:plateau-type,valley-type and Euler-type.Analysis of unique single-nucleotide polymor-phisms(SNPs)and selective sweeps between Argali and Tibetan sheep revealed that Tibetan sheep domestication was associated primarily with sensory and signal transduction,nutrient absorption and metabolism,and growth and reproductive characteristics.Finally,comprehensive analysis of selective sweep and transcriptome data sug-gested that Tibetan sheep breeds inhabiting different altitudes on the Qinghai–Tibet Plateau adapt by enhancing cardiopulmonary function,regulating body fluid balance through renal reabsorption,and modifying nutrient diges-tion and absorption pathways.Conclusion In this study,we investigated the genetic diversity and population structure of 6 Tibetan sheep breeds in Qinghai Province,China.Additionally,we analyzed the domestication traits and investigated the unique adapta-tion mechanisms residing varying altitudes in the plateau region of Tibetan sheep.This study provides valuable insights into the evolutionary processes of Tibetan sheep in extreme environments.These findings will also contribute to the preservation of genetic diversity and offer a foundation for Tibetan sheep diversity preservation and plateau animal environmental adaptation mechanisms.
基金CAs Youth Interdisciplinary Team(JCTD-2022-06)the National Nature Science Foundation of China(31870209).
文摘Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been conducted.Here,we reconstruct high-quality ancestral genomes for the most recent common ancestor(MRCA)of the Triticeae,and the MRCA of the wheat lineage(Triticum and Aegilops).The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060,respectively,which were arranged in their ancestral order.By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes,we revisit the rye chromosome structural evolution and propose alternative evolutionary routes.The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu is found to have occurred independently and is unlikely to be the result of chromosomal introgression following distant hybridization.We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event.Lastly,we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution,representing potential CR hotspots.This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.
基金supported by grants from the National Natural Science Foundation of China(32170238,32400191)Guangdong Basic and Applied Basic Research Foundation(2023A1515111029)+2 种基金the Science,Technology and Innovation Commission of Shenzhen Municipality(RCYX20200714114538196)the Chinese Academy of Agricultural Sciences Elite Youth Program(grant 110243160001007)the Guangdong Pearl River Talent Program(2021QN02N792)。
文摘Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete.In this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants.Based on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes.Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.
基金supported by the National Natural Science Foundation of China(32371700,32071670 and 31870196)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)+4 种基金the Science and Technology Basic Resources Investigation Program of China(2021FY100200)Yunnan Revitalization Talent Support Program“Young Talent”and“Innovation Team”Projects(202405AS350019)the 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy of Science(XTBG-1450101)the Key R&D program of Yunnan Province,China(202103AC100003)the Key Basic Research program of Yunnan Province,China(202101BC070003).
文摘Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systematically addressed how taxonomic complexity,especially in rapidly radiating lineages with intricate evolutionary histories,might influencethe efficacyof plastome-scale barcodes.Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains,and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus.Therefore,Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity.In this study,we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes.Our results revealed that the traditional standard barcode combination(nrITS+matK+rbcL+trnH-psbA)achieved the highest discrimination rates(81.25%),closely followed by the plastid large single copy(LSC)region(80.21%),then by full plastome,the supermatrix of proteincoding genes,and hypervariable regions(79.17%).Notably,the matK and ycf1 gene alone could discriminate 78.13%of species.Key determinants of species discrimination by integrating alignment length(AL)and the proportion of parsimony-informative sites(PPIS),as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity.Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes,this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’specificbiological habits and potentially reflectingunique evolutionary patterns in the plastid genome.
基金funded by the National Key Research and Development Program of China(Grant No.2022YFF1003100)Modern Citrus Industry Technology System of China(Grant No.CARS-26).
文摘Polyembryony has posed a significant impediment to the advancement of citrus hybrid breeding.FhRWP is widely regarded as a pivotal factor governing asexual reproduction in citrus,and prior research has demonstrated that FhARID1,acting as an upstream regulator,modulates FhRWP expression.In this study,we performed a genome-wide characterization of the ARID-HMG-related genes using the short juvenile minicitrus Fortunella hindsii.A total of 20 ARID-HMG-related genes were identified.Protein interaction network and enrichment analysis suggested that ARID-HMG-related proteins might might be involved in chromatin remodeling complexes.Knockout of FhARID1 in F.hindsii did not induce the conversion from polyembryony to monoembryony.However,fharid1 plants in T1 generation exhibited abnormal proliferation at axillary buds,which is similar to phenotype of fhrwp plants.Expression analysis of fharid1 ovary tissues revealed the downregulation of FhRWP.The results indicated that FhARID1,as an upstream regulator of FhRWP,has an effect on the development of citrus axillary buds.Expression analysis of overexpressed leaves of FhARID1 lines showed that no significant up-regulation of FhRWP,indicating that FhARID1 is not the sole upstream regulatory factor of FhRWP.Only FhARID2 showed a correlation in expression with FhARID1 among the ARID-related genes,further supporting the notion that this gene may be involved in complex formation rather than acting alone.Yeast two-hybrid and MS/MS spectra further indicated that FhARID1 function requires casein kinase II-mediated post-transcriptional phosphorylation.This study elucidated the function of FhARID1 in citrus apomixis and axillary bud development,providing a fundamental basis for understanding the role of ARID-HMG-related genes.
