Reorganization of 3D genome architecture provides insights into pathogenesis of early fatty liver disease in laying hens

Background Fatty liver disease causes huge economic losses in the poultry industry due to its high occurrence and lethality rate.Three-dimensional(3D)chromatin architecture takes part in disease processing by regulating tran-scriptional reprogramming.The study is carried out to investigate the alterations of hepatic 3D genome and H3K27ac profiling in early fatty liver(FLS)and reveal their effect on hepatic transcriptional reprogramming in laying hens.Results Results show that FLS model is constructed with obvious phenotypes including hepatic visible lipid deposi-tion as well as higher total triglyceride and cholesterol in serum.A/B compartment switching,topologically associat-ing domain(TAD)and chromatin loop changes are identified by high-throughput/resolution chromosome conforma-tion capture(HiC)technology.Targeted genes of these alternations in hepatic 3D genome organization significantly enrich pathways related to lipid metabolism and hepatic damage.H3K27ac differential peaks and differential expres-sion genes(DEGs)identified through RNA-seq analysis are also enriched in these pathways.Notably,certain DEGs are found to correspond with changes in 3D chromatin structure and H3K27ac binding in their promoters.DNA motif analysis reveals that candidate transcription factors are implicated in regulating transcriptional reprogram-ming.Furthermore,disturbed folate metabolism is observed,as evidenced by lower folate levels and altered enzyme expression.Conclusion Our findings establish a link between transcriptional reprogramming changes and 3D chromatin struc-ture variations during early FLS formation,which provides candidate transcription factors and folate as targets for FLS prevention or treatment.

Multi-omics analysis reveals the pivotal role of phytohormone homeostasis in regulating maize grain water content

Grain water content(GWC)is a key determinant for mechanical harvesting of maize(Zea mays).In our previous research,we identified a quantitative trait locus,qGWC1,associated with GWC in maize.Here,we examined near-isogenic lines(NILs)NILL and NILH that differed at the qGWC1 locus.Lower GWC in NILL was primarily attributed to reduced grain water weight(GWW)and smaller fresh grain size,rather than the accumulation of dry matter.The difference in GWC between the NILs became more pronounced approximately 35 d after pollination(DAP),arising from a faster dehydration rate in NILL.Through an integrated analysis of the transcriptome,proteome,and metabolome,coupled with an examination of hormones and their derivatives,we detected a marked decrease in JA,along with an increase in cytokinin,storage forms of IAA(IAA-Glu,IAA-ASP),and IAA precursor IPA in immature NILL kernels.During kernel development,genes associated with sucrose synthases,starch biosynthesis,and zein production in NILL,exhibited an initial up-regulation followed by a gradual down-regulation,compared to those in NILH.This discovery highlights the crucial role of phytohormone homeostasis and genes related to kernel development in balancing GWC and dry matter accumulation in maize kernels.

Identification and characterization of the chalkiness endosperm gene CHALK-H in rice(Oryza sativa L.)

Chalkiness is one of the most important agronomic traits in rice breeding,which directly affects the quality of rice seed.In this study,we identified a chalkiness endosperm mutant,chalk-h,from N-methyl-N-nitrosourea(MNU)-induced japonica rice cultivar Hwacheong(HC).Compared with wild type(WT)-HC,chalk-h showed severe chalkiness in the endosperm,yellowish green leaves,as well as reduced plant height.Scanning electron microscopy(SEM)analysis showed that starch grains in the chalk-h mutant were irregular in size and loosely arranged,with large gaps between granules,forming ovoid or orbicular shapes.MutMap analysis revealed that the phenotype of chalk-h is controlled by a single recessive gene LOC_Os11g39670 encoding seryl-tRNA synthetase,which is renamed as CHALK-H.A point mutation occurs in chalk-h on the sixth exon(at nucleotide 791)of CHALK-H,in which adenine(A)is replaced by thymidine(T),resulting in an amino acid codon change from glutamine(Glu)to valine(Val).The chalk-h mutant exhibited a heat-sensitive phenotype from the 3-leaf stage,including yellow-green leaves and reduced pigment content.The transcriptional expression of starch synthesis-related genes was down-regulated in the chalk-h mutants compared to WT-HC at different grain-filling stages.With an increase in temperature,the expression of photosynthesis-related genes was down-regulated in the chalk-h mutant compared to WT-HC.Overexpression of CHALK-H rescued the phenotype of chalk-h,with endosperm and leaf color similar to those of WT-HC.Our findings reveal that CHALK-H is a causative gene controlling chalkiness and leaf color of the chalk-h mutant.CHALK-H is the same gene locus as TSCD11,which was reported to be involved in chloroplast development under high temperature.We suggest that CHALK-H/TSCD11 plays important roles not only in chloroplast development,but also in photosynthesis and starch synthesis during rice growth and development,so it has great application potential in rice breeding for high quality and yield.

Identification of quantitative trait loci for the dead leaf rate and the seedling dead rate under alkaline stress in rice

The quantitative trait loci （QTLs） for the dead leaf rate （DLR） and the dead seedling rate （DSR） at the different rice growing periods after transplanting under alkaline stress were identified using an F2：3 population, which included 200 individuals and lines derived from a cross between two japonica rice cultivars Gaochan 106 and Changbai 9 with microsatellite markers. The DLR detected at 20 days to 62 days after transplanting under alkaline stress showed continuous normal or near normal distributions in F3 lines, which was the quantitative trait controlled by multiple genes. The DSR showed a continuous distribution with 3 or 4 peaks and was the quantitative trait controlled by main and multiple genes when rice was grown for 62 days after transplanting under alkaline stress. Thirteen QTLs associated with DLR were detected at 20 days to 62 days after transplanting under alkaline stress. Among these, qDLR9-2 located in RM5786-RM160 on chromosome 9 was detected at 34 days, 41 days, 48 days, 55 days, and 62 days, respectively; qDLR4 located in RM3524-RM3866 on chromosome 4 was detected at 34 days, 41 days, and 48 days, respectively; qDLR7-1 located in RM3859-RM320 on chromosome 7 was detected at 20 days and 27 days; and qDLR6-2 in RM1340-RM5957 on chromosome 6 was detected at 55 days and 62 days, respectively. The alleles of both qDLR9-2 and qDLR4 were derived from alkaline sensitive parent ＂Gaochanl06＂. The alleles of both qDLR7-1 and qDLR6-2 were from alkaline tolerant parent Changbai 9. These gene actions showed dominance and over dominance primarily. Six QTLs associated with DSR were detected at 62 days after transplanting under alkaline stress. Among these, qDSR6-2 and qDSR8 were located in RM1340-RM5957 on chromosome 6 and in RM3752-RM404 on chromosome 8, respectively, which were associated with DSR and accounted for 20.32% and 18.86% of the observed phenotypic variation, respectively; qDSR11-2 and qDSR11-3 were located in RM536-RM479 and RM2596-RM286 on chromosome 11, respectively, which were associated with DSR explaining 25.85% and 15.41% of the observed phenotypic variation, respectively. The marker flanking distances of these QTLs were quite far except that of qDSR6-2, which should be researched further.

Differential Expression of Two Cytosolic Ascorbate Peroxidases and Two Superoxide Dismutase Genes in Response to Abiotic Stress in Rice

Superoxide dismutase (SOD) and ascorbate peroxidase (APX) play central roles in the pathway for scavenging reactive oxygen species in plants, thereby contributing to the tolerance against abiotic stress. Here we report the responses of cytosolic SOD (cSOD; sodCc1 and sodCc2) and cytosolic APX (cAPX; OsAPX1 and OsAPX2) genes to oxidative and abiotic stress in rice. RNA blot analyses revealed that methyl viologen treatment caused a more prominent induction of cAPXs compared with cSODs, and hydrogen peroxide treatment induced the expression of cAPXs whereas cSODs were not affected. These results suggest that cAPXs play more important roles in defense against oxidative stress compared with cSODs. It is noted that cSODs and cAPXs showed coordinate response to abscisic acid treatment which induced both sodCc1 and OsAPX2. However, cSODs and cAPXs responded differentially to drought, salt and chilling stress, which indicates that cSOD and cAPX genes are expressed differentially in response to oxidative and abiotic stress in rice.

A Microspore-derived Rice Transformation System and Dissection of the Complex RCg2 Promoter

Meaningful evaluation of promoter activity following dissection of various promoter elements requires the production of many transgenic rice plants. For such purposes, we have developed highly effective Agrobacterium-

Engineering Plants as Platforms for Production of Vaccines

Microbial pathogens have always posed serious threats and challenges to human existence. Pathogenic microbes causing epidemic and pandemic outbreaks have the potential of effacing life on earth. Vaccines are used as prophylactic as well as treatment measures against diseases and are effective in eradicating deadly pathogens. Conventional vaccines though effective, have high production costs, involve tedious purification processes and have biosafety issues, requiring time-consuming biosafety tests for commercial production. Plant-based vaccines offer several advantages over the conventional systems such as ease of production, storage, higher yields, stability and safety. The review discusses significance, advantages, comparisons, prospects and challenges or constraints in the production of plant-based vaccines and antibodies.

Changes in Anatomical Features and Protein Pattern of Sunflower Partially Resistant and Susceptible Lines During Infection By Virulence Factors of Sclerotinia Sclerotiorum

Helianthus annuus L.as an oil seed crop is widely grown throughout the world.One of the most destructive diseases of sunflower is stem rot caused by Sclerotinia sclerotiorum.Oxalic acid is the major virulence factor of this necrotrophic pathogen.It is important to further investigate plant responses to this non-specific toxin.Therefore,in the present study,we compared the patterns of total soluble proteins and xylem morphology of partially resistant and susceptible sunflower lines after treatment with Sclerotinia culture filtrate.The basal stems of both lines were treated with 40 mM oxalic acid(pH 3.7)of fungus culture filtrate and samples were collected at 24,48 and 72 hours post treatment.In SDS-PAGE protein pattern new protein bands appeared in both lines after treatment.These observations suggest induction of stress-related proteins upon culture filtrate treatment.The identities of these new proteins need to be more clarify in future investigations.The changes in xylem morphology and degree of lignification of both lines was studied by light microscopy and microtome sectioning techniques after treatment with S.sclerotiorum culture filtrate.Anatomical investigations revealed changes in xylem diameter and xylem lignification of treated lines at various time points.More lignin deposition in xylem vessels of partially resistant line has been observed after treatment.In addition,the size of xylem vessels in partially resistant line has been sharply decreased upon pathogen filtrate treatment.The results of this study will help us gain a more complete understanding of resistance mechanisms to this cosmopolitan and devastating pathogen.

Concomitant Increases of the Developing Seed Phosph<i>oenol</i>pyruvate Carboxylase Ac-tivity and the Seed Protein Content of Field-Grown Wheat with Nitrogen Supply

Wheat seed storage protein is of great importance for human food. To increase the contents of storage proteins effectively, nitrogen fertilizer at flowering stages is commonly applied. In our previous study, rice phosphoenolpyruvate carboxylase (PEPCase) activity in developing seeds was observed in response to nitrogen application at a flowering stage and was positively correlated to the response of the protein content in seeds of six cultivars. This observation might indicate that the seeds have a biological system for accepting nitrogen in seeds by using PEPCase. To test whether this physiological event occurs in wheat, we examined the PEPCase activity and protein content in field-grown wheat seeds under different nitrogen supply conditions. With only basal dressing, seeds showed lower PEPCase activity and protein content (both 0.90-fold) compared to seeds without basal fertilizer. With ammonium sulfate application at 8.3 and 25 g/m2 at a flowering stage, seeds showed higher PEPCase activity (1.08- and 1.17-fold, respectively) and protein content (1.15- and 1.42-fold, respectively), depending on the nitrogen level. We investigated the relationship between PEPCase activity and protein content in the seeds among four conditions. The effect of the nitrogen supply on PEPCase activity during grain-filling stages was validated by the results of a hydroponic culture experiment. Together the results demonstrate that our hypothesis seems to apply to field-grown wheat.

CIPK9: a calcium sensor-interacting protein kinase required for low-potassium tolerance in Arabidopsis

Potassium is one of the major macro-nutrients essential for a number of cellular processes in plants. Low potassium level in the soil represents a limiting factor for crop production. Recent studies have identified potassium transporters that are involved in potassium acquisition, and some of them are critical for potassium nutrition under low potassium conditions. However, little is understood on the molecular components involved in low potassium signaling and responses. We report here the identification ofa calcineurin B-like protein-interacting protein kinase （CIPK9） as a critical regulator of low potassium response in ,Arabidopsis. The CIPK9 gene was responsive to abiotic stress conditions, and its transcript was inducible in both roots and shoots by potassium deprivation. Disruption of CIPK9 function rendered the mutant plants hypersensitive to low potassium media. Further analysis indicated that K^＋ uptake and content were not affected in the mutant plants, implying CIPK9 in the regulation of potassium utilization or sensing processes.

Transgenic japonica rice expressing the cry1C gene is resistant to striped stem borers in Northeast China

Rice production and quality are seriously affected by the lepidopteran pest,striped stem borer(SSB),in Northeast China.In this study,a synthetic cry1 C gene encoding Bacillus thuringiensis(Bt)δ-endotoxin,which is toxic to lepidopteran pest,was transformed into a japonica rice variety(Jigeng 88)in Northeast China by Agrobacterium-mediated transformation.Through molecular detection and the Basta resistance germination assay,a total of 16 single-copy homozygous transgenic lines were obtained from 126 independent transformants expressing cry1 C.Finally,four cry1 C-transgenic lines(JL16,JL23,JL41,and JL42)were selected by evaluation of the Cry1 C protein level,insect-resistance and agronomic traits.The cry1 C-transgenic lines had higher resistance to SSB and higher yield compared with non-transgenic(NT)control plants.T-DNA flanking sequence analysis of the transgenic line JL42 showed that the cry1 C gene was inserted into the intergenic region of chromosome 11,indicating that its insertion may not interfere with the genes near insertion site.In summary,this study developed four cry1 C-transgenic japonica rice lines with high insect resistance and high yield.They can be used as insect-resistant germplasm materials to overcome the problem of rice yield reduction caused by SSB and reduce the use of pesticides in Northeast China.

Complex genetic architecture underlying the plasticity of maize agronomic traits

Phenotypic plasticity is the ability of a given genotype to produce multiple phenotypes in response to changing environmental conditions.Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant to future agriculture under a changing climate.Here we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a diverse maize population planted at five sites with distinct environmental conditions.We found that latituderelated environmental factors were the main drivers of across-site variation in flowering time traits but not in plant architecture or yield traits.For the 23 traits,we detected 109 quantitative trait loci(QTLs),29 for mean values,66 for plasticity,and 14 for both parameters,and 80%of the QTLs interacted with latitude.The effects of several QTLs changed in magnitude or sign,driving variation in phenotypic plasticity.We experimentally validated one plastic gene,ZmTPS14.1,whose effect was likely mediated by the compensation effect of ZmSPL6 from a downstream pathway.By integrating genetic diversity,environmental variation,and their interaction into a joint model,we could provide site-specific predictions with increased accuracy by as much as 9.9%,2.2%,and 2.6%for days to tassel,plant height,and ear weight,respectively.This study revealed a complex genetic architecture involving multiple alleles,pleiotropy,and genotype-byenvironment interaction that underlies variation in the mean and plasticity of maize complex traits.It provides novel insights into the dynamic genetic architecture of agronomic traits in response to changing environments,paving a practical way toward precision agriculture.

Identification and characterization of extrachromosomal circular DNA in the silk gland of Bombyx mori

The silk gland cells of silkworm are special cells which only replicate DNA in the nucleus without cell division throughout the larval stage. The extrachromosomal circular DNAs (eccDNAs) have not yet been reported in the silk gland of silkworms. Herein, we have explored the characterization of eccDNAs in the posterior silk gland of silkworms. A total of 35 346 eccDNAs were identified with sizes ranging from 30 to 13 569 549 bp. Motif analysis revealed that dual direct repeats are flanking the 5′ and 3′ breaking points of eccDNA. The sequences exceeding 1 kb length in eccDNAs present palindromic sequence characteristics flanking the 5′ and 3′ breaking points of the eccDNA. These motifs might support possible models for eccDNA generation. Genomic annotation of the eccDNA population revealed that most eccDNAs (58.6%) were derived from intergenic regions, whereas full or partial genes were carried by 41.4% of eccDNAs. It was found that silk protein genes fib-H, fib-L, and P25, as well as the transcription factors SGF and sage, which play an important regulatory role in silk protein synthesis, could be carried by eccDNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the genes carried by eccDNAs were mainly associated with the development and metabolism-related signaling pathways. Moreover, it was found that eccDNAfib-L could promote the transcription of fib-L gene. Overall, the results of the present study not only provide a novel perspective on the mechanism of silk gland development and silk protein synthesis but also complement previously reported genome-scale eccDNA data supporting that eccDNAs are common in eukaryotes.

Cas9-targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants

Transposable element insertions(TEIs) are an important source of genomic innovation by contributing to plant adaptation, speciation, and the production of new varieties. The often large,complex plant genomes make identifying TEIs from short reads difficult and expensive. Moreover, rare somatic insertions that refect mobilome dynamics are difficult to track using short reads.To address these challenges, we combined Cas9-targeted Nanopore sequencing(CANS) with the novel pipeline Nano Cas TE to trace both genetically inherited and somatic TEIs in plants. We performed CANS of the EVADé(EVD) retrotransposon in wild-type Arabidopsis thaliana and rapidly obtained up to 40× sequence coverage.Analysis of hemizygous T-DNA insertion sites and genetically inherited insertions of the EVD transposon in the ddm1(decrease in DNA methylation1) genome uncovered the crucial role of DNA methylation in shaping EVD insertion preference.We also investigated somatic transposition events of the ONSEN transposon family, finding that genes that are downregulated during heat stress are preferentially targeted by ONSENs. Finally, we detected hypomethylation of novel somatic insertions for two ONSENs. CANS and Nano Cas TE are effective tools for detecting TEIs and exploring mobilome organization in plants in response to stress and in different genetic backgrounds, as well as screening T-DNA insertion mutants and transgenic plants.

Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes,we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes.Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation.Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements.We identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101e52,172,397;278-bp DEL,chr18:23,840,143 e23,840,421)located in muscle-specific enhancers are associated with the expression of target genes related to meat quality(FSD2)and muscle fiber hypertrophy(LMOD2 and WASL)in pigs.Our results highlight the role of SVs in domestic porcine evolution,and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.

Calcineurin-B-Like Protein CBL9 Interacts with Target Kinase CIPK3 in the Regulation of ABA Response in Seed Germination

Calcium plays a vital role as a second messenger in many signaling pathways in plants. The calcineurin B-like proteins （CBLs） represent a family of plant calcium-binding proteins that function in calcium signaling by interacting with their interacting protein kinases （CIPKs）. In our previous study, we have reported a role for one of the CBLs （CBL9） and one of the CIPKs （CIPK3） in ABA signaling. Here, we have shown that CBL9 and CIPK3 physically and functionally interact with each other in regulating the ABA responses. The CBL9 and CIPK3 proteins interacted with each other in the yeast two- hybrid system and when expressed in plant cells. The double mutant cbl9cipk3 showed the similar hypersensitive response to ABA as observed in single mutants （cbl9 or cipk3）. The constitutively active form of CIPK3 genetically complemented the cbl9 mutant, indicating that CIPK3 function downstream of CBL9. Based on these findings, we conclude that CBL9 and CIPK3 act together in the same pathway for regulating ABA responses.

Genome-wide patterns of large-size presence/absence variants in sorghum

The presence/absence variants （PAVs） are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum （Sorghum bicolour L.） genomes, each 12？ coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size （＆gt;30 kb） PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode celldeath and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA trans-posons as the major components. The frequency and distribution of these PAVs differed substantial y across 96＆amp;nbsp;sorghum inbred lines, and the low-and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.

In vitro antitumor effect of cucurbitacin E on human lung cancer cell line and its molecular mechanism

Cucurbitacin E(CuE) is previously reported to exhibit antitumor effect by several means.In this study, CuE acted as a tyrosine kinase inhibitor interfering with the epidermal growth factor receptor/mitogen-activated protein kinase(EGFR/MAPK) signaling pathway and subsequently induced apoptosis and cell cycle arrest in non-small-cell lung cancer(NSCLC) cell line A549.The apoptosis regulators, cleaved Caspases-3 and Caspases-9, were observed to be increased with the treatment of CuE.The activated transcription factor STAT3 and the apoptosis inhibitor protein survivin were also observed to be reduced.The cell cycle regulators, CyclinA2, cylinB1, CyclinD1 and CyclinE, were also investigated and the results suggested that the cell cycle was arrested at G1/G0 phase.Treatment of CuE also altered the existence status of most of the participants in the EGFR/MAPK signaling.Phosphorylation of EGFR enhanced significantly, leading to the alteration of members downstream, either total amount or phosphorylation level, notably,MEK1/2 and ERK1/2.Moreover, the results of molecular simulation brought an insight on the interaction mechanism between CuE and EGFR.In summary, CuE exhibited anti-proliferative effect against A549 cells by targeting the EGFR/MAPK signaling pathway.

Early Transcriptomic Adaptation to Na_2CO_3 Stress Altered the Expression of a Quarter of the Total Genes in the Maize Genome and Exhibited Shared and Distinctive Profles with NaCl and High pH Stresses

Sodium carbonate （Na2CO3） presents a huge challenge to plants by the combined damaging effects of Na＋, high pH, and CO32. Little is known about the cellular responses to Na2CO3 stress. In this study, the transcriptome of maize （Zea mays L. cv. B73） roots exposed to Na2CO3 stress for 5 h was compared with those of NaCI and NaOH stresses. The expression of 8,319 genes, representing over a quarter of the total number of genes in the maize genome, was altered by Na2CO3 stress, and the downregulated genes （5,232） outnumbered the upregulated genes （3,087）. The effects of Na2CO3 differed from those of NaCI and NaOH, primarily by downregulating different categories of genes. Pathways commonly altered by Na2CO3, NaCI, and NaOH were enriched in phenylpropanoid biosynthesis, oxidation of unsaturated fatty acids, ATP- binding cassette （ABC） transporters, as well as the metabolism of secondary metabolites. Genes for brassinosteroid biosynthesis were specifically upregulated by Na2CO3, while genes involved in ascorbate and aldarate metabolism, protein processing in the endoplasmic reticulum and by N-glycosylation, fatty acid biosynthesis, and the circadian rhythm were downregulated. This work provides the first holistic picture of early transcriptomic adaptation to Na2CO3 stress, and highlights potential molecular pathways that could be manipulated to improve tolerance in maize.

Resequencing 250 Soybean Accessions:New Insights into Genes Associated with Agronomic Traits and Genetic Networks

The limited knowledge of genomic diversity and functional genes associated with the traits of soybean varieties has resulted in slow progress in breeding.In this study,we sequenced the genomes of 250 soybean landraces and cultivars from China,America,and Europe,and investigated their population structure,genetic diversity and architecture,and the selective sweep regions of these accessions.Five novel agronomically important genes were identified,and the effects of functional mutations in respective genes were examined.The candidate genes GSTT1,GL3,and GSTL3 associated with the isoflavone content,CKX3 associated with yield traits,and CYP85 A2 associated with both architecture and yield traits were found.The phenotype-gene network analysis revealed that hub nodes play a crucial role in complex phenotypic associations.This study describes novel agronomic trait-associated genes and a complex genetic network,providing a valuable resource for future soybean molecular breeding.