SYNTHESIS OF MACROPOROUS POLYACRYLAMIDE AND POLY(NISOPROPYLACRYLAMIDE) MONOLITHS VIA FRONTAL POLYMERIZATION AND INVESTIGATION OF PORE STRUCTURE VARIATION OF MONOLITHS

A novelty method,frontal polymerization(FP),was employed to directly produce a series of polyacrylamide (PAM),poly(N-isopropylacrylamide)(PNIPAM) and acrylamide-N-isopropylacrylamide copolymer macroporous monoliths. Field emission scanning electronic microscope and mercury intrusion method were adopted to measure some parameters of these monoliths,such as frame,pore size distribution as well as porosity.Effects of types of monomer,thicker and surfactant on porous structure of monoliths were studied.A variet...

Analysis of Intraspecies Diversity of Rice Reveals Variation Patterns of Oryza sativa Basic Leucine Zippers

The basic leucine zipper(bZIP)is an important class of transcription factors in plants,playing a critical role in plant growth and development and responses to biotic and abiotic stress.Due to gene presence/absence variations,it is limited to identify bZIP genes based on the reference genome.Therefore,we performed the bZIP gene family analysis in the rice pan-genome.By employing a rice pan-genome,ninety-four OsbZIPs(72 core genes and 22 variable genes)were identified and divided into 11 groups in a phylogenetic tree.Based upon Ka/Ks values in 33 accessions,OsbZIPs were subjected to different selection pressures during domestication.The analysis of the effects of structural variations(SVs)on gene expression,gene structure,and conserved domains showed that SVs could significantly alter the expression levels of certain OsbZIPs,leading to gene truncation and the emergence of numerous atypical genes.Thirty-four differentially expressed OsbZIPs were identified by analyzing RNA-seq data of the Xanthomonas oryzae pv.oryzae(Xoo)infection susceptible(IR24)and resistant(IRBB67)lines under high temperature,and by counting the number of differentially expressed OsbZIPs in different subgroups.These Osb-ZIPs were found to respond to Xoo infection at an early stage and may not be involved in the mechanism of Xa4 and Xa7 resistance to Xoo.The multiple variation patterns of OsbZIP genes provide new insights into the OsbZIP genes in rice.These results provide new resources and offer new directions for functional studies of OsbZIPs.

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

The occurrence,inheritance,and segregation of complex genomic structural variation in synthetic Brassica napus

"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.

An improved proximal-based decomposition method for structured monotone variational inequalities

The proximal-based decomposition method was originally proposed by Chen and Teboulle （Math. Programming, 1994, 64：81-101 for solving corrvex minimization problems. This paper extends it to solving monotone variational inequalities associated with separable structures with the improvements that the restrictive assumptions on the involved parameters are much relaxed, and thus makes it practical to solve the subproblems easily. Without additional assumptions, global convergence of the new method is proved under the same mild assumptions on the problem＇s data as the original method.

Seasonal Variations in Phytoplankton Community Structure in the Sanggou,Ailian,and Lidao Bays

The seasonal variations in phytoplankton community structure were investigated for the Sanggou Bay （SGB） and the adjacent Ailian Bay （ALB） and Lidao Bay （LDB） in Shandong Peninsula,eastern China.The species composition and cell abundance of phytoplankton in the bay waters in spring （April 2011）,summer （August 2011）,autumn （October 2011）,and winter （January 2012） were examined using the Uterm6hl method.A total of 80 taxa of phytoplankton that belong to 39 genera of 3 phyla were identified.These included 64 species of 30 genera in the Phylum Bacillariophyta,13 species of 8 genera in the Phylum Dinophyta,and 3 species of 1 genus in the Phylum Chrysophyta.During the four seasons,the number of phytoplankton species （43） was the highest in spring,followed by summer and autumn （40）,and the lowest number ofphytoplankton species （35） was found in winter.Diatoms,especially Paralia sulcata （Ehrenberg） Cleve and Coscinodiscus oculus-iridis Ehrenberg,were predominant in the phytoplankton community throughout the study period,whereas the dominance of dinoflagellate appeared in summer only.The maximum cell abundance of phytoplankton was detected in summer （average 8.08 × 103 cells L-1） whereas their minimum abundance was found in autumn （average 2.60 x 103 cellsL-1）.The phytoplankton abundance was generally higher in the outer bay than in the inner bay in spring and autumn.In summer,the phytoplankton cells were mainly concentrated in the south of inner SGB,with peak abundance observed along the western coast.In winter,the distribution of phytoplankton cells showed 3 patches,with peak abundance along the western coast as well.On seasonal average,the Shannon-Wiener diversity indices of phytoplankton community ranged from 1.17 to 1.78 （autumn 〉 summer 〉 spring 〉 winter）,and the Pielou＇s evenness indices of phytoplankton ranged from 0.45 to 0.65 （autumn 〉 spring 〉 summer〉 winter）.According to the results of canonical correspondence analysis,phosphate level was the major factor that limited the occurrence of P.sulcata and C.oculus-iridis,whereas optimal temperature and low salinity were responsible for Prorocentrum blooms in summer.The detailed description of seasonal variations in phytoplankton community structure in the three bays provide reference data for future studies on marine ecosystems and mariculture in adjacent areas.

Temporal variations in internal tide multimodal structure on the continental shelf, South China Sea

Temporal variations in multimodal structures of diurnal( D_1) and semidiurnal( D_2) internal tides were investigated on the continental slope of the Dongsha Plateau, based on 2-month moored acoustic Doppler current profiler observations. Harmonic analysis indicated that the D_1 components( K_1 and O_1) dominated the internal tide field. The vertical structure of the K_1 constituent presented a first-mode structure while the M_2 constituent seemed to exhibit a high-mode structure. Amplitude spectra analysis of the current data revealed differences in baroclinic current amplitudes between different water depths. Temporal variations in modal structures ware analyzed, based on the D_1 and D_2 baroclinic tides extracted from the baroclinic velocity field with band-pass filters. Analysis showed that the magnitude of the D_1 internal tide current was much larger than the D_2 current, and temporal variations in the modal structure of the D_1 internal tide occurred on an approximately fortnightly cycle. The EOF analyses revealed temporal transformation of multimodal structures for D_1 and D_2 internal tides. The enhancement of the D_1 internal tide was mainly due to the superposition of K_1 and O_1, according to the temporal variation of coherent kinetic energy.

Genetic variation and population structure of the mushroom Pleurotus ferulae in China inferred from nuclear DNA analysis

To investigate the genetic diversity of an edible fungus Pleurotus ferulae, a total of 89 wild samples collected from six geographical locations in the Xinjiang Uygur Autonomous Region of China and two geographical locations in Italy, were analyzed using three DNA fragments including the translation elongation factor（EF1α）, the second largest subunit of t he RNA polymerase II（RPB2） and the largest subunit of the RNA polymerase II（RPB1）. The results indicated relatively abundant genetic variability in the wild resources of P. ferulae. The analysis of molecular variance（AMOVA） showed that the vast majority of the genetic variation was found within geographical populations. Both the Chinese populations and the Italian populations of P. ferulae displayed a limited genetic differentiation. The degree of differentiation between the Chinese populations and the Italian populations was obviously higher than that between the populations from the same region, and moreover the genetic differentiation among all the tested populations was correlated to the geographical distance. T he phylogeny analyses confirmed that samples from China and Italy belonged to another genetic group separated from Pleurotus eryngii. They were closely related to each other but were clustered according to their geographical origins, which implied the Chinese populations were highly differentiated from the Italian populations because of distance isolation, and the two populations from different regions might be still in the process of allopatric divergence.

A review of the pangenome:how it affects our understanding of genomic variation,selection and breeding in domestic animals?

As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.

Community structure and spatial-temporal variation of netzphytoplankton in the Bering Sea in summer

Marine biodiversity is changing in response to altered physical environment, subsequent ecological changes as well as anthropogenic disturbances. In this study, phytoplankton samples in situ collected in the Bering Sea in July of 1999 and 2010 were analyzed to obtain phytoplankton community structure and spatial-temporal variation between the beginning and end of this decade, and the correlation of phytoplankton community dynamics and environmental factors was investigated. A total of 5 divisions, 58 genera and 153 species of phytoplankton belonging to 3 ecological groups were identified. The vast majority of phytoplankton consisted of diatoms accounting for 66.7% of the total species and 95.2% of the total abundance. Considering differentiation in spatial extent and phytoplankton sample types, there were subtle changes in species composition, large altering in abundance and significant variation in spatial distribution between two surveys. The abundance peak area was located at the Bering Strait while sub peak was found at the Bering Sea Basin. The boreal-temperate diatom was the dominant flora, which was subsequently replaced by eurythermal and frigid-water diatom. Phytoplankton community in the Bering Sea was not a simplex uniform community but composed of deep-ocean assemblage and neritic assemblage. The deep-ocean assemblage was located in the northwestern Pacific Ocean and Bering Sea Basin, dominated by boreal-temperate species（Neodenticula seminae, Thalassiothrix longissima, Amphiprora hyperborean, Chaetoceros atlanticus, Thalassiosira trifulta, etc.） and eurychoric species（Thalassionema nitzschioides, Ch. compressus, Rhizosolenia styliformis, etc.）, and characterized by low abundance, even interspecies abundance allocations, diverse dominant species and high species diversity. The neritic assemblage was distributed on the continental shelf and slope of Bering Sea and was mainly composed of frigid-water species（Th.nordenski？ldii, Ch. furcellatus, Ch. socialis, Bacteriosira fragilis, etc.） and eurythermal and euryhaline species（L.danicus, Ch. curvisetus, Coscinodiscus curvatulus, etc.）, and it was characterized by high abundance, uneven interspecies allocations, prominent dominant species and low species diversity. Spatial-temporal variation of species composition and abundance of phytoplankton in the Bering Sea was directly controlled by surface circulation,nutrient supply and ice edge.

Deletion of a 1,049 bp sequence from the 5′UTR upstream of the SiHEC3 gene induces a seed non-shattering mutation in sesame

Sesame is a labor intensive crop with limited mechanized harvesting mainly due to the seed shattering(SS)trait.In this study,we performed a genetic analysis of the seed-shattering resistance(SR)trait with a SR sesame mutant 12M07.Unlike the SS type,the parenchyma cells in the abscission zone of the 12M07 mutant are arranged loosely but adhere to the seed coat.Inheritance analysis of six generations derived from 12M07(SR)×Xiangcheng Dazibai(SS)showed that the SR trait is recessive and controlled by a single gene pair.Association mapping of the F2population with 888,619 variants(single-nucleotide polymorphisms(SNPs)and insertion-deletion(InDels))and 31,884 structural variations(SVs)determined that only SV12002 in the 5′upstream region of gene Sindi0765000(named SiHEC3)in Chr.3 was significantly associated with the SR trait.SiHEC3 encodes the bHLH transcription factor.A 1,049 bp deletion occurred in the 5′UTR of Sihec3 in 12M07.SiHEC3 is mainly expressed in developing placental tissues,with the expression peaking in capsules at 45 days after pollination.A dual-luciferase reporter assay in tobacco confirmed that the promoter activity of Sihec3 was reduced because of the deletion of the 1,049 bp promoter sequence.Protein–protein interaction network analysis showed that HEC3 is co-expressed with nine key proteins,such as SHATTERPROOF1(SHP1)and SEEDSTICK(STK)which participate in the secondary wall biosynthesis of the abscission layer in plants.The findings of this study show the important function of Sihec3corresponding with the SR trait and supply the genetic information for breeding new varieties that are amenable to mechanized harvesting in sesame and other crops.

A telomere-to-telomere genome assembly of Zhonghuang 13,a widely-grown soybean variety from the original center of Glycine max

Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nevertheless,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into soybean.Here,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong reads.We employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly accuracy.The assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference genome.Our annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are novel.ZH13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier assemblies.Specifically,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic diversity.In summary,we deliver the first complete Chinese soybean cultivar T2T genome.The comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.

The identification of presence/absence variants associated with the apparent differences of growth period structures between cultivated and wild soybeans

The cultivated soybean（Glycine max（L.） Merr.） was distinguished from its wild progenitor Glycine soja Sieb.＆ Zucc.in growth period structure,by a shorter vegetative phase（V）,a prolonged reproductive phase（R） and hence a larger R/V ratio.However,the genetic basis of the domestication of soybean from wild materials is unclear.Here,a panel of 123 cultivated and 97 wild accessions were genotyped using a set of 24 presence/absence variants（PAVs） while at the same time the materials were phenotyped with respect to flowering and maturity times at two trial sites located at very different latitudes.The major result of this study showed that variation at PAVs is informative for assessing patterns of genetic diversity in Glycine spp.The genotyping was largely consistent with the taxonomic status,although a few accessions were intermediate between the two major clades identified.Allelic diversity was much higher in the wild germplasm than in the cultivated materials.A significant domestication signal was detected at 11 of the PAVs at 0.01 level.In particular,this study has provided information for revealing the genetic basis of photoperiodism which was a prominent feature for the domestication of soybean.A significant marker-trait association with R/V ratio was detected at 14 of the PAVs,but stripping out population structure reduced this to three.These results will provide markers information for further finding of R/V related genes that can help to understand the domestication process and introgress novel genes in wild soybean to broaden the genetic base of modern soybean cultivars.

Structural Variation Analysis of Mutated Nannochloropsis oceanica Caused by Zeocin Through Genome Re-Sequencing

Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such function of Zeocin, The results showed that Zeocin can mutate the N. oceanica genome and cause the structural variation. Zeocin either swept away or selected the alleles of genes functioning in ubiquitin-mediated proteolysis, alpha-linolenic acid metabolism, ascorbate and aldarate metabolism, ribosome biogenesis, and circadian rhythm, indicating that N. oceanica may have adjusted its metabolic performances for protein, carbohydrate, and lipid, and changed its ribosome biosynthesis and living rhythm to survive in Zeocin containing medium. In addition, Zeocin caused mutation may have influenced the expression of a set of tanscription factors. It was concluded that Zeocin effectively caused the structural variation of the genome of N. oceanica, and forced the microalgae to select out the alleles of a set of genes around these variations in order to adapt to Zeocin containing medium. Further studies on the genetic basis of the phenotypic adaptation of this haploid and asexual microalga and the application of Zeocin to its genetic improvement are very important.

Effect of CO_2 on the structural variation of Na_2WO_4/Mn/SiO_2 catalyst for oxidative coupling of methane to ethylene

In this work,the influence of CO2 on the structural variation and catalytic performance of Na2WO4/Mn/Si O2 for oxidative coupling of methane to ethylene was investigated. The catalyst was prepared by impregnation method and characterized by XRD,Raman and XPS techniques. Appropriate amount of CO2 in the reactant gases enhanced the formation of surface tetrahedral Na2WO4 species and promoted the migration of O in MOx,Na,W from the catalyst bulk to surface,which were favorable for oxidative coupling of methane. When the molar ratio of CH4/O2/CO2 was 3/1/2,enriched surface tetrahedral Na2WO4 species and high surface concentration of O in MOx,Na,W were detected,and then high CH4 conversion of 33.1% and high C2H4 selectivity of 56.2% were obtained. With further increase of CO2 in the reagent gases,the content of active surface tetrahedral Na2WO4 species and surface concentration of O in MOx,Na,W decreased,while that of inactive species（Mn WO4 and Mn2O3） increased dramatically,leading to low CH4 conversion and low C2H4 selectivity. It could be speculated that Na2WO4 crystal was transformed into Mn WO4 crystal with excessive CO2 added under the reaction conditions. Pretreatment of Na2WO4/Mn/Si O2 catalyst by moderate amount of CO2 before OCM also promoted the formation of Na2WO4 species.

我国公立医院财政拨款收入的结构变动特征分析

目的 分析公立医院财政拨款收入的结构变动特征。方法 基于2011—2020年将考察时间段调整为2010—2019年《中国卫生健康统计年鉴》的数据,应用结构变动度分析方法。结果 2010—2019年,全国公立医院的财政拨款收入规模呈现逐年上升的趋势。我国不同级别公立医院的财政拨款结构变动贡献率从大到小依次为三级医院(58.43%)、二级医院(39.26%)、基层医疗卫生机构(2.31%)。各类公立医院的贡献率从大到小依次为精神病医院(40.25%)、综合医院(17.13%)、传染病医院(14.64%)、中医(民族)医院(7.85%)、儿童医院(6.00%)、妇产医院/妇幼保健院(5.35%)、其他专科医院(4.90%)、职业病防治院(3.88%)。结论 需要政府落实职责,在财政拨款安排中重视各类型、各级别公立医院的合理平衡,科学规划财政投入标准及支持力度,进一步推动分级诊疗制度,保证不同类型、级别医院的平稳运行。

3D genome structural variations play important roles in regulating seed oil content of Brassica napus

Dissecting the complex regulatory mechanism of seed oil content(SOC)is one of the main research goals in Brassica napus.Increasing evidence suggests that genome architecture is linked to multiple biological functions.However,the effect of genome architecture on SOC regulation remains unclear.Here,we used high-throughput chromatin conformation capture to characterize differences in the three-dimen-sional(3D)landscape of genome architecture of seeds from two B.napus lines,N53-2(with high SOC)and Ken-C8(with low SOC).Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci(QTLs)/associated genomic regions(AGRs)for SOC.A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural varia-tions in QTLs/AGRs of B.napus.The candidate gene BnaA09g48250D,which showed structural variation in a QTL/AGR on chrA09,was identified byfine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8.Overexpression and knockout of BnaA09g48250D led to significant in-creases and decreases in SOC,respectively,in the transgenic lines.Taken together,our results reveal the 3D genome architecture of B.napus seeds and the roles of genome structural variations in SOC regulation,enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.

Genome assembly of KA105,a new resource for maize molecular breeding and genomic research

Superior inbred lines are central to maize breeding as sources of natural variation.Although many elite lines have been sequenced,less sequencing attention has been paid to newly developed lines.We constructed a genome assembly of the elite inbred line KA105,which has recently been developed by an arti-ficial breeding population named Shaan A and has shown desirable characteristics for breeding.Its pedigree showed genetic divergence from B73 and other lines in its pedigree.Comparison with the B73 reference genome revealed extensive structural variation,58 presence/absence variation(PAV)genes,and 1023 expanded gene families,some of which may be associated with disease resistance.A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes,of which eight were induced by at least one kind of stress,participating in gene modules responding to stress such as drought and southern leaf blight disease.More than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel development.The KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.

Genomic variation of 363 diverse tea accessions unveils the genetic diversity, domestication, and structural variations associated with tea adaptation

Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear.We here investigated the resequencing data of 363 diverse tea accessions collected extensively from almost all tea distributions and found that the population structure of tea plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The genetic diversity of tea plants in China decreased from southwest to east as latitude increased. Results also indicated that Camellia sinensis var. assamica(CSA) illustrated divergent selection signatures with Camellia sinensis var. sinensis(CSS). The domesticated genes of CSA were mainly involved in leaf development, flavonoid and alkaloid biosynthesis, while the domesticated genes in CSS mainly participated in amino acid metabolism, aroma compounds biosynthesis,and cold stress. Comparative population genomics further identified ~730 Mb novel sequences, generating 6,058 full-length protein-encoding genes,significantly expanding the gene pool of tea plants.We also discovered 217,376 large-scale structural variations and 56,583 presence and absence variations(PAVs) across diverse tea accessions, some of which were associated with tea quality and stress resistance. Functional experiments demonstrated that two PAV genes(CSS0049975 and CSS0006599)were likely to drive trait diversification in cold tolerance between CSA and CSS tea plants. The overall findings not only revealed the genetic diversity and domestication of tea plants, but also underscored the vital role of structural variations in the diversification of tea plant traits.

TWAS facilitates gene-scale trait genetic dissection through gene expression,structural variations,and alternative splicing in soybean

A genome-wide association study(GWAS)identifies trait-associated loci,but identifying the causal genes can be a bottleneck,due in part to slow decay of linkage disequilibrium(LD).A transcriptome-wide association study(TWAS)addresses this issue by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci with GWAS results.Here,we used self-pollinated soybean(Glycine max[L.]Merr.)as a model to evaluate the application of TWAS to the genetic dissection of traits in plant species with slow LD decay.We generated RNA sequencing data for a soybean diversity panel and identified the genetic expression regulation of 29286 soybean genes.Different TWAS solutions were less affected by LD and were robust to the source of expression,identifing known genes related to traits from different tissues and developmental stages.The novel pod-color gene L2 was identified via TWAS and functionally validated by genome editing.By introducing a new exon proportion feature,we significantly improved the detection of expression variations that resulted from structural variations and alternative splicing.As a result,the genes identified through our TWAS approach exhibited a diverse range of causal variations,including SNPs,insertions or deletions,gene fusion,copy number variations,and alternative splicing.Using this approach,we identified genes associated with flowering time,including both previously known genes and novel genes that had not previously been linked to this trait,providing insights complementary to those from GWAS.In summary,this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.