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
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
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
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
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
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
Genetic improvement of meat production traits has always been the primary goal of pig breeding.Geographical isolation,natural and artificial selection led to significant differences in the phenotypes of meat productio...Genetic improvement of meat production traits has always been the primary goal of pig breeding.Geographical isolation,natural and artificial selection led to significant differences in the phenotypes of meat production traits between Chinese local pigs and Western commercial pigs.Comparative genomics and transcriptomics analysis provided powerful tools to identify genetic variants and genes associated with skeletal muscle growth.However,the number of available genetic variants and genes are still limited.In this study,a comprehensive comparison of transcriptomes showed that ribosomal protein S27-like(RPS27L)gene was highly expressed in skeletal muscle and up-regulated in Chinese local pigs when compared with Western commercial pigs.Functional analysis revealed that overexpression of RPS27L promoted myoblast proliferation and repressed differentiation in pig skeletal muscle cells.Conversely,the knockdown of RPS27L led to the inhibition of myoblast proliferation and the promotion of differentiation.Notably,a 13-bp insertion-deletion(InDel)mutation was identified within the RPS27L promoter,inserted in Chinese local breeds and predominantly deleted in Western commercial breeds.Luciferase reporter assay suggested this InDel modulated RPS27L expression by influencing transcription factor 3(TCF3)and myogenic differentiation antigen(MYOD)binding to the promoter.Furthermore,a positive correlation was observed between RPS27L expression and backfat thickness.Association studies demonstrated this InDel was significantly associated with the body weight of pigs at the age of 240 d.Together,our results suggested that RPS27L was a regulator of skeletal muscle development and growth,and was a candidate marker for improving meat production traits in pigs.This study not only provided a biomarker for animal breeding,but also was helpful for understanding skeletal muscle development and muscular disease in humans.展开更多
Highlights OsCAX2 is localized to tonoplast,and cadmium induces its expression.OsCAX2 overexpression reduces cadmium concentration in indica rice grains by 49.1%.Cadmium(Cd)exposure poses significant health risks to h...Highlights OsCAX2 is localized to tonoplast,and cadmium induces its expression.OsCAX2 overexpression reduces cadmium concentration in indica rice grains by 49.1%.Cadmium(Cd)exposure poses significant health risks to humans,and the International Agency for Research on Cancer has classified it as a Group I carcinogen.Cadmium undergoes minimal metabolism in the human body;consequently,prolonged Cd^(2+)exposure can cause severe damage to multiple organs including the liver,kidneys,lungs,bones,and immune system(Shao et al.2024).Rice,one of the three global staple crops,and Cd exposure in humans primarily occurs the consumption of contaminated rice grains.The contribution of rice to the total dietary Cd intake is over 50% for non-smoking Asian populations(Chen et al.2018;Shi et al.2020).展开更多
The genetic basis of early-stage salt tolerance in alfalfa(Medicago sativa L.),a key factor limiting its productivity,remains poorly understood.To dissect this complex trait,we integrate genome-wide association studie...The genetic basis of early-stage salt tolerance in alfalfa(Medicago sativa L.),a key factor limiting its productivity,remains poorly understood.To dissect this complex trait,we integrate genome-wide association studies(GWAS)and transcriptomics from 176 accessions within a machine learning based genomic prediction framework.Analysis reveals weak genetic correlations among four salt-tolerance traits and a gradual decline in performance under increasing salt stress.GWAS identify 60 significant associated SNPs,with the highest number detected under 100 mM salt stress.Salt tolerance exhibits an additive effect from favorable haplotypes,which are most abundant in Chinese accessions.GWAS-associated genes are related to key regulators of hormone signaling and osmotic adjustment,while transcriptome analysis indicates a global repression of stress-responsive transcription factors.Integrating these multi-omics datasets allows us to identify 14 candidate genes,including MsHSD1(seed dormancy)and MsMTATP6(energy metabolism).Crucially,incorporating these markers into genomic prediction models improve cross-population predictive accuracy to an average of 54.4%.This study provides insights into the genetic architecture of salt tolerance in alfalfa and offers valuable markers to facilitate molecular breeding.展开更多
Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a...Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data.To dissect this classic cyto-nuclear conflict,we developed the‘PhyloForensics’framework,a novel diagnostic approach to systematically identify sources of phylogenetic instability.This framework revealed that signal heterogeneity(topological entropy variance)and information content(the proportion of informative sites)are the primary drivers of gene-tree conflict.Empirically validating this,we show that removing a small subset of“loudly conflicted”genes resolves deep-level incongruence,yielding a single,highly-supported topology previously obscured by noise.Finally,complementing this sequence-based resolution,we demonstrate that mitogenome architecture provides powerful phylogenetic signals,revealing predictable,mitogenome-wide evolutionary patterns,such as a significant negative correlation between branch length and both GC content and RNA editing sites.By integrating a validated conflict-resolution framework with architectural genomics,our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.展开更多
Nondestructive measurement technology of phenotype can provide substantial phenotypic data support for applications such as seedling breeding,management,and quality testing.The current method of measuring seedling phe...Nondestructive measurement technology of phenotype can provide substantial phenotypic data support for applications such as seedling breeding,management,and quality testing.The current method of measuring seedling phenotypes mainly relies on manual measurement which is inefficient,subjective and destroys samples.Therefore,the paper proposes a nondestructive measurement method for the canopy phenotype of the watermelon plug seedlings based on deep learning.The Azure Kinect was used to shoot canopy color images,depth images,and RGB-D images of the watermelon plug seedlings.The Mask-RCNN network was used to classify,segment,and count the canopy leaves of the watermelon plug seedlings.To reduce the error of leaf area measurement caused by mutual occlusion of leaves,the leaves were repaired by CycleGAN,and the depth images were restored by image processing.Then,the Delaunay triangulation was adopted to measure the leaf area in the leaf point cloud.The YOLOX target detection network was used to identify the growing point position of each seedling on the plug tray.Then the depth differences between the growing point and the upper surface of the plug tray were calculated to obtain plant height.The experiment results show that the nondestructive measurement algorithm proposed in this paper achieves good measurement performance for the watermelon plug seedlings from the 1 true-leaf to 3 true-leaf stages.The average relative error of measurement is 2.33%for the number of true leaves,4.59%for the number of cotyledons,8.37%for the leaf area,and 3.27%for the plant height.The experiment results demonstrate that the proposed algorithm in this paper provides an effective solution for the nondestructive measurement of the canopy phenotype of the plug seedlings.展开更多
Lizards usually exhibit frequent turnovers and a much greater diversity of sex determination mechanisms compared to birds and mammals,with the conserved ZW sex chromosomes of anguimorph lizards originating over 115 mi...Lizards usually exhibit frequent turnovers and a much greater diversity of sex determination mechanisms compared to birds and mammals,with the conserved ZW sex chromosomes of anguimorph lizards originating over 115 million years ago a seeming exception.We previously discovered in an anguimorph lizard Varanus acanthurus(Vac)whose entire chrW,but not chrZ is homologous to part of the chr2 by cytogenetic mapping,suggesting its complex history of sex chromosome evolution yet to be elucidated.To address this,we assemble a chromosome-level genome,and provide evidence that the Vac sex chromosome pair has undergone at least two times of recombination loss,producing a pattern of evolutionary strata like that of birds and mammals.Comparison to other lizard genomes date the stepwise propagation of specific retrotransposon subfamilies enriched near the duplicated gene pairs on the chrW and chr2 to the varanid ancestor.These retrotransposons probably have mediated the recruitment and amplification of autosomal genes on the chrW,including members of a large vomeronasal chemosensory receptor gene family V2R.Our results suggest that the W or Y chromosome as a refugium of repetitive elements,may recurrently recruit short-lived functional genes responsible for sexual dimorphisms during its long-term course of degeneration.展开更多
The past two years have witnessed remarkable progress in perovskite solar cells(PSCs),marked by breakthroughs in power conversion efficiency and strides in addressing long-term operational stability.At present,the cer...The past two years have witnessed remarkable progress in perovskite solar cells(PSCs),marked by breakthroughs in power conversion efficiency and strides in addressing long-term operational stability.At present,the certified power conversion efficiencies of singlejunction PSCs and silicon/perovskite tandem cells have surpassed 27%and 34%,respectively.Regarding stability,researchers begun to focus their attention on the challenges faced by PSCs when operated in outdoor environments.Furthermore,breakthroughs in the utilization of green solvents,fabrication in ambient air conditions,aqueous-phase synthesis of perovskite raw materials at kilogram scale,vacuum flash evaporation,and machine learning-assisted design are accelerating the commercialization of PSCs.The review summarizes the key advancements of PSCs during 2024-2025.It identifies a critical performance discrepancy between small-area devices and perovskite solar modules and delves into strategies aimed at bridging this gap.Finally,perspectives on the future directions of PSCs are presented,with a particular emphasis on improving photocurrent and environmental sustainability.展开更多
ATP-binding cassette transporter C2(ABCC2)is known to be a receptor for Bacillus thuringiensis(Bt)toxins in several lepidopteran insects.Mutations in the ABCC2 gene have been genetically linked to field-evolved resist...ATP-binding cassette transporter C2(ABCC2)is known to be a receptor for Bacillus thuringiensis(Bt)toxins in several lepidopteran insects.Mutations in the ABCC2 gene have been genetically linked to field-evolved resistance to the Cry1 F toxin from Bt in Spodoptera frugiperda.Here we generated a SfABCC2 knockout strain of S.frugiperda using the CRISPR/Cas9 system to provide further functional evidence of the role of this gene in susceptibility and resistance to Cry1 F.Results from bioassays showed that the SfABCC2 knockout S.frugiperda strain displayed 118-fold resistance to Cry1 F compared with the parental DH19 strain,but no resistance to Vip3 A toxin from Bt.These results provide the first reverse genetic evidence for SfABCC2 as a functional receptor for Cry1 F.展开更多
With the rapid development of sequencing technologies,especially the maturity of third-generation sequencing technologies,there has been a significant increase in the number and quality of published genome assemblies....With the rapid development of sequencing technologies,especially the maturity of third-generation sequencing technologies,there has been a significant increase in the number and quality of published genome assemblies.The emergence of these high-quality genomes has raised higher requirements for genome evaluation.Although numerous computational methods have been developed to evaluate assembly quality from various perspectives,the selective use of these evaluation methods can be arbitrary and inconvenient for fairly comparing the assembly quality.To address this issue,we have developed the Genome Assembly Evaluating Pipeline(GAEP),which provides a comprehensive assessment pipeline for evaluating genome quality from multiple perspectives,including continuity,completeness,and correctness.Additionally,GAEP includes new functions for detecting misassemblies and evaluating the assembly redundancy,which performs well in our testing.GAEP is publicly available at https://github.com/zyoptimistic/GAEP under the GPL3.0 License.With GAEP,users can quickly obtain accurate and reliable evaluation results,facilitating the comparison and selection of high-quality genome assemblies.展开更多
The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative...The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative trait loci(QTL)associated with sink capacity(total spikelet number per panicle and thousand-grain weight),source leaf(flag leaf length,flag leaf width and flag leaf area),source-sink relationship(total spikelet number to flag leaf area ratio)and yield-related traits(filled grain number per panicle,panicle number per plant,grain yield per plant,biomass per plant,and harvest index)by genome-wide association analysis using 272 Xian(indica)accessions.The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations.A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers.Five QTL were detected consistently in four chromosomal regions in both environments.Five QTL clusters simultaneously affected source,sink,source–sink relationship,and grain yield traits,probably explaining the genetic basis of significant correlations of grain yield with source and sink traits.We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium(LD)blocks associated with significant SNPs and performing haplotype analysis.The genes included one cloned gene(NOG1)and three newly identified QTL(qHI6,qTGW7,and qFLA8).These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source–sink relationships using marker-assisted selection.展开更多
The MYB transcription factor is one of the largest gene families in plants,playing an important role in regulating plant growth,development,response to stress,senescence,and especially the anthocyanin biosynthesis.In ...The MYB transcription factor is one of the largest gene families in plants,playing an important role in regulating plant growth,development,response to stress,senescence,and especially the anthocyanin biosynthesis.In this study,A total of 217 MYB genes,including 901R-MYBs,124 R2R3-MYBs,and 3 R1R2R3-MYBs have been identified from the potato genome.The 1R-MYB and R2R3-MYB family members could be divided into 20 and 35 subgroups respectively.Analysis of gene structure and protein motifs revealed that members within the same subgroup presented similar exon/intron and motif organization,further supporting the results of phylogenetic analysis.Potato is an ideal plant to reveal the tissue-specific anthocyanins biosynthesis regulated by MYB,as the anthocyanins could be accumulated in different tissues,showing colorful phenotypes.Five pairs of colored and colorless tissues,stigma,petal,stem,leaf,and tuber flesh,were applied to the transcriptomic analysis.A total of 70 MYB genes were found to be differentially expressed between colored and colorless tissues,and these differentially expressed genes were suspected to regulate the biosynthesis of anthocyanin of different tissues.Co-expression analysis identified numerous potential interactive regulators of anthocyanins biosynthesis,involving 39 MYBs,24 bHLHs,2 WD-repeats,and 29 biosynthesis genes.Genome-wide association study(GWAS)of tuber flesh color revealed amajor signal at the end of Chromosome 10,which was co-localized with reported I gene(StMYB88),controlling tuber peel color.Analyses of DEGs(Differentially Expression Genes)revealed that both StMYB88 and StMYB89 were closely related to regulating anthocyanin biosynthesis of tuber flesh.This work offers a comprehensive overview of the MYB family in potato and will lay a foundation for the functional validation of these genes in the tissue-specific regulation of anthocyanin biosynthesis.展开更多
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.
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 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 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 Sustainable Development Special Project from Shenzhen,China(KCXFZ20201221173213037)the National Natural Science Foundation of China(32172697 and U23A20229)+1 种基金the Guangdong Provincial Natural Science Foundation(2021A1515011336)the Agricultural Science and Technology Innovation Program,China(CAASZDRW202406)。
文摘Genetic improvement of meat production traits has always been the primary goal of pig breeding.Geographical isolation,natural and artificial selection led to significant differences in the phenotypes of meat production traits between Chinese local pigs and Western commercial pigs.Comparative genomics and transcriptomics analysis provided powerful tools to identify genetic variants and genes associated with skeletal muscle growth.However,the number of available genetic variants and genes are still limited.In this study,a comprehensive comparison of transcriptomes showed that ribosomal protein S27-like(RPS27L)gene was highly expressed in skeletal muscle and up-regulated in Chinese local pigs when compared with Western commercial pigs.Functional analysis revealed that overexpression of RPS27L promoted myoblast proliferation and repressed differentiation in pig skeletal muscle cells.Conversely,the knockdown of RPS27L led to the inhibition of myoblast proliferation and the promotion of differentiation.Notably,a 13-bp insertion-deletion(InDel)mutation was identified within the RPS27L promoter,inserted in Chinese local breeds and predominantly deleted in Western commercial breeds.Luciferase reporter assay suggested this InDel modulated RPS27L expression by influencing transcription factor 3(TCF3)and myogenic differentiation antigen(MYOD)binding to the promoter.Furthermore,a positive correlation was observed between RPS27L expression and backfat thickness.Association studies demonstrated this InDel was significantly associated with the body weight of pigs at the age of 240 d.Together,our results suggested that RPS27L was a regulator of skeletal muscle development and growth,and was a candidate marker for improving meat production traits in pigs.This study not only provided a biomarker for animal breeding,but also was helpful for understanding skeletal muscle development and muscular disease in humans.
基金financially supported by the National Key R&D Program of China(2024YFD1200800)the Guangdong Basic and Applied Basic Research Foundation,China(2024A1515030094)。
文摘Highlights OsCAX2 is localized to tonoplast,and cadmium induces its expression.OsCAX2 overexpression reduces cadmium concentration in indica rice grains by 49.1%.Cadmium(Cd)exposure poses significant health risks to humans,and the International Agency for Research on Cancer has classified it as a Group I carcinogen.Cadmium undergoes minimal metabolism in the human body;consequently,prolonged Cd^(2+)exposure can cause severe damage to multiple organs including the liver,kidneys,lungs,bones,and immune system(Shao et al.2024).Rice,one of the three global staple crops,and Cd exposure in humans primarily occurs the consumption of contaminated rice grains.The contribution of rice to the total dietary Cd intake is over 50% for non-smoking Asian populations(Chen et al.2018;Shi et al.2020).
基金supported by the National Key Research and Development Program of China(2022YFF1003203)Biological Breeding-National Science and Technology Major Project(2022ZDo4011)+2 种基金the Central Public-interest Scientific Institution Basal Research Fund(Y2025YC44)the Central Public-interest Scientific Institution Basal Research Fund(2025-YWF-ZYSQ-04)the China Postdoctoral Science Foundation(2023M733832).
文摘The genetic basis of early-stage salt tolerance in alfalfa(Medicago sativa L.),a key factor limiting its productivity,remains poorly understood.To dissect this complex trait,we integrate genome-wide association studies(GWAS)and transcriptomics from 176 accessions within a machine learning based genomic prediction framework.Analysis reveals weak genetic correlations among four salt-tolerance traits and a gradual decline in performance under increasing salt stress.GWAS identify 60 significant associated SNPs,with the highest number detected under 100 mM salt stress.Salt tolerance exhibits an additive effect from favorable haplotypes,which are most abundant in Chinese accessions.GWAS-associated genes are related to key regulators of hormone signaling and osmotic adjustment,while transcriptome analysis indicates a global repression of stress-responsive transcription factors.Integrating these multi-omics datasets allows us to identify 14 candidate genes,including MsHSD1(seed dormancy)and MsMTATP6(energy metabolism).Crucially,incorporating these markers into genomic prediction models improve cross-population predictive accuracy to an average of 54.4%.This study provides insights into the genetic architecture of salt tolerance in alfalfa and offers valuable markers to facilitate molecular breeding.
基金funded by the Shenzhen Science and Technology Program(Grant No.JCYJ20241202130723030)the National Natural Science Foundation of China(Grant No.32170238)+2 种基金the Guangdong Pearl River Talent Program(Grant No.2021QN02N792)the Shenzhen Fundamental Research Program(Grant No.JCYJ20220818103212025)the Chinese Academy of Agricultural Sciences Elite Youth Program(110243160001007)to Z.W.
文摘Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data.To dissect this classic cyto-nuclear conflict,we developed the‘PhyloForensics’framework,a novel diagnostic approach to systematically identify sources of phylogenetic instability.This framework revealed that signal heterogeneity(topological entropy variance)and information content(the proportion of informative sites)are the primary drivers of gene-tree conflict.Empirically validating this,we show that removing a small subset of“loudly conflicted”genes resolves deep-level incongruence,yielding a single,highly-supported topology previously obscured by noise.Finally,complementing this sequence-based resolution,we demonstrate that mitogenome architecture provides powerful phylogenetic signals,revealing predictable,mitogenome-wide evolutionary patterns,such as a significant negative correlation between branch length and both GC content and RNA editing sites.By integrating a validated conflict-resolution framework with architectural genomics,our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.
基金funded by the National Key Research and Development Program of China(Grant No.2019YFD1001900)the HZAU-AGIS Cooperation Fund(Grant No.SZYJY2022006).
文摘Nondestructive measurement technology of phenotype can provide substantial phenotypic data support for applications such as seedling breeding,management,and quality testing.The current method of measuring seedling phenotypes mainly relies on manual measurement which is inefficient,subjective and destroys samples.Therefore,the paper proposes a nondestructive measurement method for the canopy phenotype of the watermelon plug seedlings based on deep learning.The Azure Kinect was used to shoot canopy color images,depth images,and RGB-D images of the watermelon plug seedlings.The Mask-RCNN network was used to classify,segment,and count the canopy leaves of the watermelon plug seedlings.To reduce the error of leaf area measurement caused by mutual occlusion of leaves,the leaves were repaired by CycleGAN,and the depth images were restored by image processing.Then,the Delaunay triangulation was adopted to measure the leaf area in the leaf point cloud.The YOLOX target detection network was used to identify the growing point position of each seedling on the plug tray.Then the depth differences between the growing point and the upper surface of the plug tray were calculated to obtain plant height.The experiment results show that the nondestructive measurement algorithm proposed in this paper achieves good measurement performance for the watermelon plug seedlings from the 1 true-leaf to 3 true-leaf stages.The average relative error of measurement is 2.33%for the number of true leaves,4.59%for the number of cotyledons,8.37%for the leaf area,and 3.27%for the plant height.The experiment results demonstrate that the proposed algorithm in this paper provides an effective solution for the nondestructive measurement of the canopy phenotype of the plug seedlings.
基金supported by the National Key Research and Development Program of China(2023YFA1800500,2024YFA1802500)the National Natural Science Foundation of China(32170415)+1 种基金supported by the Australian Government Research Training Program(RTP)stipend scholarship.supported by the Australian Research Council Discovery Project grant(ARC DP200101406).
文摘Lizards usually exhibit frequent turnovers and a much greater diversity of sex determination mechanisms compared to birds and mammals,with the conserved ZW sex chromosomes of anguimorph lizards originating over 115 million years ago a seeming exception.We previously discovered in an anguimorph lizard Varanus acanthurus(Vac)whose entire chrW,but not chrZ is homologous to part of the chr2 by cytogenetic mapping,suggesting its complex history of sex chromosome evolution yet to be elucidated.To address this,we assemble a chromosome-level genome,and provide evidence that the Vac sex chromosome pair has undergone at least two times of recombination loss,producing a pattern of evolutionary strata like that of birds and mammals.Comparison to other lizard genomes date the stepwise propagation of specific retrotransposon subfamilies enriched near the duplicated gene pairs on the chrW and chr2 to the varanid ancestor.These retrotransposons probably have mediated the recruitment and amplification of autosomal genes on the chrW,including members of a large vomeronasal chemosensory receptor gene family V2R.Our results suggest that the W or Y chromosome as a refugium of repetitive elements,may recurrently recruit short-lived functional genes responsible for sexual dimorphisms during its long-term course of degeneration.
基金the financial support of the National Natural Science Foundation of China(Nos.U21A20171,12074245,52102281)National Key R&D Program of China(Nos.2021YFB3800068 and 2020YFB1506400)+1 种基金Shanghai Sailing Program(No.21YF1421600)Young Elite Scientists Sponsorship Program by China Association for Science and Technology(No.2021QNRC001)。
文摘The past two years have witnessed remarkable progress in perovskite solar cells(PSCs),marked by breakthroughs in power conversion efficiency and strides in addressing long-term operational stability.At present,the certified power conversion efficiencies of singlejunction PSCs and silicon/perovskite tandem cells have surpassed 27%and 34%,respectively.Regarding stability,researchers begun to focus their attention on the challenges faced by PSCs when operated in outdoor environments.Furthermore,breakthroughs in the utilization of green solvents,fabrication in ambient air conditions,aqueous-phase synthesis of perovskite raw materials at kilogram scale,vacuum flash evaporation,and machine learning-assisted design are accelerating the commercialization of PSCs.The review summarizes the key advancements of PSCs during 2024-2025.It identifies a critical performance discrepancy between small-area devices and perovskite solar modules and delves into strategies aimed at bridging this gap.Finally,perspectives on the future directions of PSCs are presented,with a particular emphasis on improving photocurrent and environmental sustainability.
基金supported by the Key Project for Breeding Genetic Modified Organisms of China(2016ZX08012004003)。
文摘ATP-binding cassette transporter C2(ABCC2)is known to be a receptor for Bacillus thuringiensis(Bt)toxins in several lepidopteran insects.Mutations in the ABCC2 gene have been genetically linked to field-evolved resistance to the Cry1 F toxin from Bt in Spodoptera frugiperda.Here we generated a SfABCC2 knockout strain of S.frugiperda using the CRISPR/Cas9 system to provide further functional evidence of the role of this gene in susceptibility and resistance to Cry1 F.Results from bioassays showed that the SfABCC2 knockout S.frugiperda strain displayed 118-fold resistance to Cry1 F compared with the parental DH19 strain,but no resistance to Vip3 A toxin from Bt.These results provide the first reverse genetic evidence for SfABCC2 as a functional receptor for Cry1 F.
基金supported by the National Key Research and Development Project Program of China(2022YFC3400300,2019YFE0109600)the China Postdoctoral Science Foundation(2021M701584).
文摘With the rapid development of sequencing technologies,especially the maturity of third-generation sequencing technologies,there has been a significant increase in the number and quality of published genome assemblies.The emergence of these high-quality genomes has raised higher requirements for genome evaluation.Although numerous computational methods have been developed to evaluate assembly quality from various perspectives,the selective use of these evaluation methods can be arbitrary and inconvenient for fairly comparing the assembly quality.To address this issue,we have developed the Genome Assembly Evaluating Pipeline(GAEP),which provides a comprehensive assessment pipeline for evaluating genome quality from multiple perspectives,including continuity,completeness,and correctness.Additionally,GAEP includes new functions for detecting misassemblies and evaluating the assembly redundancy,which performs well in our testing.GAEP is publicly available at https://github.com/zyoptimistic/GAEP under the GPL3.0 License.With GAEP,users can quickly obtain accurate and reliable evaluation results,facilitating the comparison and selection of high-quality genome assemblies.
基金funded by the National Key Research and Development Program of China(2016YFD0100301)the National Natural Science Foundation of China(31671602)the Agricultural Science and Technology Innovation Program and the Cooperation and Innovation Mission(CAASZDXT2018001)
文摘The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative trait loci(QTL)associated with sink capacity(total spikelet number per panicle and thousand-grain weight),source leaf(flag leaf length,flag leaf width and flag leaf area),source-sink relationship(total spikelet number to flag leaf area ratio)and yield-related traits(filled grain number per panicle,panicle number per plant,grain yield per plant,biomass per plant,and harvest index)by genome-wide association analysis using 272 Xian(indica)accessions.The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations.A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers.Five QTL were detected consistently in four chromosomal regions in both environments.Five QTL clusters simultaneously affected source,sink,source–sink relationship,and grain yield traits,probably explaining the genetic basis of significant correlations of grain yield with source and sink traits.We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium(LD)blocks associated with significant SNPs and performing haplotype analysis.The genes included one cloned gene(NOG1)and three newly identified QTL(qHI6,qTGW7,and qFLA8).These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source–sink relationships using marker-assisted selection.
基金the National Natural Science Foundation of China(Grant No.31601756)the National Science Fund of Yunnan for Distinguished Young Scholars(Grant No.202001AV070003)。
文摘The MYB transcription factor is one of the largest gene families in plants,playing an important role in regulating plant growth,development,response to stress,senescence,and especially the anthocyanin biosynthesis.In this study,A total of 217 MYB genes,including 901R-MYBs,124 R2R3-MYBs,and 3 R1R2R3-MYBs have been identified from the potato genome.The 1R-MYB and R2R3-MYB family members could be divided into 20 and 35 subgroups respectively.Analysis of gene structure and protein motifs revealed that members within the same subgroup presented similar exon/intron and motif organization,further supporting the results of phylogenetic analysis.Potato is an ideal plant to reveal the tissue-specific anthocyanins biosynthesis regulated by MYB,as the anthocyanins could be accumulated in different tissues,showing colorful phenotypes.Five pairs of colored and colorless tissues,stigma,petal,stem,leaf,and tuber flesh,were applied to the transcriptomic analysis.A total of 70 MYB genes were found to be differentially expressed between colored and colorless tissues,and these differentially expressed genes were suspected to regulate the biosynthesis of anthocyanin of different tissues.Co-expression analysis identified numerous potential interactive regulators of anthocyanins biosynthesis,involving 39 MYBs,24 bHLHs,2 WD-repeats,and 29 biosynthesis genes.Genome-wide association study(GWAS)of tuber flesh color revealed amajor signal at the end of Chromosome 10,which was co-localized with reported I gene(StMYB88),controlling tuber peel color.Analyses of DEGs(Differentially Expression Genes)revealed that both StMYB88 and StMYB89 were closely related to regulating anthocyanin biosynthesis of tuber flesh.This work offers a comprehensive overview of the MYB family in potato and will lay a foundation for the functional validation of these genes in the tissue-specific regulation of anthocyanin biosynthesis.
