Reciprocal translocation is a chromosomal structural abnormal- ity that arises when two non-homologous chromosomes rearrange and attach with each other, an incidence that occurs in about 1/500 to 1/625 newborns （Mack...Reciprocal translocation is a chromosomal structural abnormal- ity that arises when two non-homologous chromosomes rearrange and attach with each other, an incidence that occurs in about 1/500 to 1/625 newborns （Mackie and Scriven, 2002）. This event typically does not lead to any significant loss of genetic material, thus recip- rocal translocation carriers do not exhibit any severe abnormal phenotypes （Scriven et al., 1998; Zhang et al., 2016）.展开更多
Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to charact...Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated withsalt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1to 9 score at EC = 10 dSm^-1 under controlled environmental conditions. Seven new breeding linesincluding three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 andcan be good sources of new genes/alleles for salt tolerance. Simple sequence repeat （SSR） markerRM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information contentvalue varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54lines were clearly separated into two major clusters. Fourteen haplotypes were identified based onSaltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminatebetween the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assistedselection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 onchromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.展开更多
Paeonia suffruticosa Andr.is an endemic shrub flower in China with 2n=10.This study used 228 cultivars from four populations,i.e.,Jiangnan,Japan,Northwest,and Zhongyuan,as materials to explore the genetic diversity le...Paeonia suffruticosa Andr.is an endemic shrub flower in China with 2n=10.This study used 228 cultivars from four populations,i.e.,Jiangnan,Japan,Northwest,and Zhongyuan,as materials to explore the genetic diversity levels among different populations of tree peony varieties.The results showed that 34 bands were amplified using five pairs of cp SSR primers,with an average of 6.8 bands per primer pair.The average number of different alleles(N_(a)),effective alleles(N_(e)),Shannon's information index(I),diversity(H),and polymorphic information content(PIC)were 3.600,2.053,0.708,0.433,and 0.388,respectively.The PIC value was between 0.250 and 0.500,indicating a moderate level of polymorphism for the five cp SSR primer pairs.The genetic diversity levels of peony cultivars varied among different populations,with the Northwest population showing relatively lower levels(I=0.590,H=0.289,and PIC=0.263).A total of 52 haplotypes were identified in the four examined populations,and the number of haplotypes per population ranged from 11 to 22.Forty-four private haplotypes were detected across populations,and the Northwest population exhibiting the highest count of private haplotypes with 17.The mean number of effective number of haplotypes(N_(eh)),haplotypic richness(R_(h)),and diversity(H)were 8.351,6.824,and 0.893,respectively.Analysis of molecular variance indicated that genetic variation within tree peony germplasm was greater than that between germplasm resources,and the main variation was found within individuals of peony germplasm.Cluster analysis,principal coordinate analysis,and genetic structure analysis classified tree peonies from different origins into two groups,indicating a certain degree of genetic differentiation among these four tree peony cultivation groups.This study provides a theoretical basis for the exploration,utilization,and conservation of peony germplasm resources,as well as for research on the breeding of excellent varieties.展开更多
Spike length(SL)is an important factor affecting yield in wheat(Triticum aestivum L.).Here,a recombinant inbred line(RIL)population derived from a cross between Shannong 4155(SN4155)and Shimai 12(SM12)was used to map ...Spike length(SL)is an important factor affecting yield in wheat(Triticum aestivum L.).Here,a recombinant inbred line(RIL)population derived from a cross between Shannong 4155(SN4155)and Shimai 12(SM12)was used to map quantitative trait loci(QTL)controlling SL.A QTL,q SL2B,on chromosome 2B was identified in all experiments and explained 9.92%–12.71%of the phenotypic variation.Through transcriptome and gene expression analysis,we identified a gene encoding Elongation Factor 1-alpha(Tae EF1A)as the candidate gene for q SL2B.Genome editing of Tae EF1A demonstrated that Tae EF1A positively regulates SL,spikelet number per spike(SNS),and grain number per spike(GN).Transcriptome analysis showed that Tae EF1A may affect the protein translation process and photosynthesis to regulate spike development.We used haplotype analysis of wheat germplasm to identify seven types of genetic variations in Tae EF1A,with TypeⅠ,TypeⅡ,and TypeⅢbeing the major haplotypes.Screening of 428 cultivars and breeding lines identified 225 and 203 accessions as TypeⅠand TypeⅡhaplotypes,respectively,with TypeⅢnot detected.Comparison of SL,SNS,and GN between the TypeⅠand TypeⅡhaplotypes revealed that the TypeⅠallele can increase SL,SNS,and GN simultaneously,and is thus preferred for use in wheat molecular breeding efforts to increase SL,SNS,and GN.展开更多
Coat color polymorphism in domestic animals provides a robust framework for elucidating mechanisms of species adaptation,domestication,and genomic diversity.Leiqiong cattle,a representative indicine breed from souther...Coat color polymorphism in domestic animals provides a robust framework for elucidating mechanisms of species adaptation,domestication,and genomic diversity.Leiqiong cattle,a representative indicine breed from southern China,are predominantly yellow-coated,although a subset exhibits a solid black phenotype.To determine the genetic basis of this variation,a genome-wide association study(GWAS)was performed in 212 Leiqiong bulls.A pronounced association signal was detected on chromosome 6 within the fifth intron of the CORIN gene,providing the first evidence of the potential influence of CORIN on bovine coat color variation.Integration of these results with publicly available genomic datasets and haplotype analyses indicated that the yellow coat phenotype is derived from Indian indicine ancestry,whereas the black coat phenotype emerged through introgression from wild bovine lineages and artificial hybridization with Wagyu cattle.Comparative analysis of Indian indicine cattle with divergent coat colors revealed distinct LEF1 haplotypes within a shared CORIN background,suggesting an ancient and complex domestication history underlying coat color variation.These findings provide direct evidence that introgression has shaped phenotypic variation in East Asian cattle and offer novel insights into the genetic architecture of pigmentation,with implications for future breeding strategies.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
Sagittaria trifolia L.is a perennial aquatic herb that primarily reproduces clonally and through generative propagation.In recent years,S.trifolia has evolved a drastic resistance to acetohydroxy acid synthase(AHAS)-i...Sagittaria trifolia L.is a perennial aquatic herb that primarily reproduces clonally and through generative propagation.In recent years,S.trifolia has evolved a drastic resistance to acetohydroxy acid synthase(AHAS)-inhibiting herbicides in Northeast China.The phylogeographic patterns of S.trifolia with 31 purified resistance genotypes and five sensitive genotypes using chloroplast DNA(cpDNA)atpB-rbcL intergenic spacers were studied.Five haplotypes were characterized,and two of them were widely distributed in 36 genotypes.The dose response to bensulfuron-methyl showed that the GR50 ranged from 2.07 g a.i.·hm^(-2) to 220.15 g a.i.·hm^(-2).Sequencing of the AHAS gene indicated that 17 genotypes with the Pro197 mutation were distributed in haplotype 1,six genotypes with the Trp574 mutation were distributed in haplotype 3,and 13 genotypes with the wild AHAS gene were distributed in haplotypes 2,4 and 5.In the minimum-spanning network,the ancestral haplotypes 1 and 2 were widely distributed.Two primary clades were separated in the Bayes tree,and the result was consistent with the maximum likelihood tree.展开更多
Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma metabolite.To enhance high-aromatic coconut breeding efforts,it is essential t...Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma metabolite.To enhance high-aromatic coconut breeding efforts,it is essential to deeply understand the hereditary factors governing the production of 2AP.In this study,a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism(SNP)variations from 168 aromatic coconut germplasm resources.Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism.Proteins encoded by these genes are involved in amino acid metabolism,glycolysis,and secondary metabolism.Among these,Asparagine synthetase coding gene ASN1,Gamma-glutamylcysteine synthetase coding gene GSH1,and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504.In particular,the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein,potentially resulting in differences in 2AP content among haplotype populations.Identifying variations in related candidate genes,particularly the gene CnASN1,provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.展开更多
FLOWERING LOCUS T (FT),a key regulator of photoperiod pathway,plays a pivotal role in modulating flowering time and growth period-related traits in plants.In this study,we identified 10 FT family genes in soybean and ...FLOWERING LOCUS T (FT),a key regulator of photoperiod pathway,plays a pivotal role in modulating flowering time and growth period-related traits in plants.In this study,we identified 10 FT family genes in soybean and examined their functional divergences through sequence alignment analysis.Phylogenetic and amino acid sequence analysis revealed that the 92nd residue and the Segment B domain (sites 129,131,134,135) are the critical determinants of potential functional divergence and activity variation among Gm FT.Using the Soy Omics website,we detected natural variations in the genomic and promoter regions of Gm FTs,along with numerous haplotypes.By correlating these haplotypes with flowering time,we identified 7 potential KASP markers associated with soybean growth period:Gm FT1a-60297360,Gm FT1b-60311669,Gm FT2a-31695562,Gm FT2b-31739433,Gm FT3a-4106476,Gm FT5a-4078626,and Gm FT5b-37490962.All KASP markers exhibited high selection efficiency (97.56%–100.00%) and reliable genotyping accuracy when validated across 82 soybean varieties spanning multiple maturity groups (MGs).This study systematically elucidates the functional divergence of Gm FTs and develops efficient KASP markers,providing essential technological support for photoperiodadaptive breeding and germplasm innovation.展开更多
Elucidating crops'physiological and molecular mechanisms to adapt to low nitrogen environment and promoting nitrogen transfer from senescent leaves to new leaves is crucial in improving Brassica's nitrogen use...Elucidating crops'physiological and molecular mechanisms to adapt to low nitrogen environment and promoting nitrogen transfer from senescent leaves to new leaves is crucial in improving Brassica's nitrogen use efficiency(NUE).Glutamine synthetase gene(GS)plays a vital role in helping plants reassimilate ammonium released from protein degradation in leaves,and it was the focus of our research on this topic.In this study,we identified high(H141)and low(L65)NUE genotypes of Brassica juncea with different responses to low-nitrogen stress.We found that H141 has a lower nitrate content but higher ammonium and free amino acid contents as well as higher nitrate reductase and GS activities in the shoots.These physiological indicators are responsible for the high NUE of H141.Wholegenome resequencing data revealed that 5,880 genes associated with NUE are polymorphic between H141 and L65.These genes participate in various amino acid,carbohydrate,and energy metabolic pathways.Haplotype analysis revealed two haplotypes for BjuB05.GS1.4,Hap1 and Hap2,which have multiple single nucleotide polymorphisms or insertions/deletions in the regulatory regions of the 5′and 3′untranslated regions and introns.Furthermore,the shoot NUE of Hap1 is significantly lower than that of Hap2.These two haplotypes of BjuB05.GS1.4 lead to differences in the shoot NUEs of different genetic populations of mustard and are associated with the local soil nitrogen content,suggesting that they might help mustard to adapt to different geographic localities.In conclusion,the results of our study shed light on the physiological and molecular mechanisms underlying different mustard NUE genotypes and demonstrate the enormous potential of NUE breeding in B.juncea.展开更多
Understanding the genetic diversity–area relationship(GAR)is essential for comprehending how species adapt to environmental changes,as genetic diversity is an indicator of a species’adaptive potential.Variation in e...Understanding the genetic diversity–area relationship(GAR)is essential for comprehending how species adapt to environmental changes,as genetic diversity is an indicator of a species’adaptive potential.Variation in environmental adaptation capacity exists among species and animal taxa with different distribution areas,highlighting the importance of understanding the GAR.To obtain a more comprehensive understanding of the GAR in terrestrial vertebrates,we assessed both haplotype diversity–area and nucleotide diversity–area relationships using 25,453 cytochrome c oxidase subunit I(COI)sequences from 142 amphibian species,574 bird species,and 342 mammal species.We found that both measures of genetic diversity increased with species range size across major animal groups.Nevertheless,the GAR did not differ among animal groups,while haplotype diversity performed better than nucleotide diversity in profiling the GAR,as indicated by higher R2 values.The difference in the modeling fit may stem from the distinct biological and mathematical significance of nucleotide diversity and haplotype diversity.These results suggest that the GAR follows similar rules among different animal taxa.Furthermore,haplotype diversity may serve as a more reliable indicator for assessing the potential effects of area size changes on animal populations and provide better guidance for conserving genetic diversity.展开更多
The investigation of genetic differences among humans has given evidence thatmutations in DNA sequences are responsible for some genetic diseases. The most common mutation isthe one that involves only a single nucleot...The investigation of genetic differences among humans has given evidence thatmutations in DNA sequences are responsible for some genetic diseases. The most common mutation isthe one that involves only a single nucleotide of the DNA sequence, which is called a singlenucleotide polymorphism (SNP). As a consequence, computing a complete map of all SNPs occurring inthe human populations is one of the primary goals of recent studies in human genomics. Theconstruction of such a map requires to determine the DNA sequences that from all chromosomes. Indiploid organisms like humans, each chromosome consists of two sequences called haplotypes.Distinguishing the information contained in both haplotypes when analyzing chromosome sequencesposes several new computational issues which collectively form a new emerging topic of ComputationalBiology known as Haplotyping. This paper is a comprehensive study of some new combinatorialapproaches proposed in this research area and it mainly focuses on the formulations and algorithmicsolutions of some basic biological problems. Three statistical approaches are briefly discussed atthe end of the paper.展开更多
Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(...Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.展开更多
Background Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry.Multi-omics approaches enable the comprehensive investigation of the complex interactions between ...Background Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry.Multi-omics approaches enable the comprehensive investigation of the complex interactions between mul-tiple layers of information to provide a more holistic view of disease pathogenesis.Therefore,this study investigated the genomic and epigenomic signatures and the possible regulatory mechanisms underlying subclinical mastitis by integrating RNA sequencing data(mRNA and lncRNA),small RNA sequencing data(miRNA)and DNA methylation sequencing data of milk somatic cells from 10 healthy cows and 20 cows with naturally occurring subclinical mastitis caused by Staphylococcus aureus or Staphylococcus chromogenes.Results Functional investigation of the data sets through gene set analysis uncovered 3458 biological process GO terms and 170 KEGG pathways with altered activities during subclinical mastitis,provided further insights into subclin-ical mastitis and revealed the involvement of multi-omics signatures in the altered immune responses and impaired mammary gland productivity during subclinical mastitis.The abundant genomic and epigenomic signatures with sig-nificant alterations related to subclinical mastitis were observed,including 30,846,2552,1276 and 57 differential methylation haplotype blocks(dMHBs),differentially expressed genes(DEGs),lncRNAs(DELs)and miRNAs(DEMs),respectively.Next,5 factors presenting the principal variation of differential multi-omics signatures were identified.The important roles of Factor 1(DEG,DEM and DEL)and Factor 2(dMHB and DEM),in the regulation of immune defense and impaired mammary gland functions during subclinical mastitis were revealed.Each of the omics within Factors 1 and 2 explained about 20%of the source of variation in subclinical mastitis.Also,networks of impor-tant functional gene sets with the involvement of multi-omics signatures were demonstrated,which contributed to a comprehensive view of the possible regulatory mechanisms underlying subclinical mastitis.Furthermore,multi-omics integration enabled the association of the epigenomic regulatory factors(dMHBs,DELs and DEMs)of altered genes in important pathways,such as‘Staphylococcus aureus infection pathway’and‘natural killer cell mediated cyto-toxicity pathway’,etc.,which provides further insights into mastitis regulatory mechanisms.Moreover,few multi-omics signatures(14 dMHBs,25 DEGs,18 DELs and 5 DEMs)were identified as candidate discriminant signatures with capac-ity of distinguishing subclinical mastitis cows from healthy cows.Conclusion The integration of genomic and epigenomic data by multi-omics approaches in this study provided a better understanding of the molecular mechanisms underlying subclinical mastitis and identified multi-omics candidate discriminant signatures for subclinical mastitis,which may ultimately lead to the development of more effective mastitis control and management strategies.展开更多
Pre-harvest sprouting(PHS)poses a significant global challenge to cereal production,impacting both yield and quality.In this study,we employed genome-wide association studies(GWAS)on diverse rice accessions to identif...Pre-harvest sprouting(PHS)poses a significant global challenge to cereal production,impacting both yield and quality.In this study,we employed genome-wide association studies(GWAS)on diverse rice accessions to identify novel PHS-associated haplotypes.An assessment of 127 cultivated accessions for panicle germination(PHS)and detached grain germination(germination rate of detached grains at the 14th day(D14))revealed considerable phenotypic variation among rice ecotypes.GWAS analysis identified 91 significant signals at–log10(P-value)>5,including 15SNPs for PHS and 76 SNPs for D14.A subsequent linkage disequilibrium(LD)block-based GWAS analysis detected 227 significant SNPs for both traits,consisting of 18 nonsynonymous substitutions located on the coding regions of nine genes.Further haplotype analysis identified 32 haplotypes,with 10 specific to cultivated accessions,19 specific to the wild type,and three shared between them.A phenotypic assessment of major haplotypes revealed significant differences between resistant(Hap1 and Hap2)and susceptible haplotypes(Hap5,Hap27,and Hap28),distinguished by a G/A SNP within a novel gene,Os04g0545200.The identified haplotypes offer promising prospects for haplotypebased breeding aimed at enhancing PHS resistance in rice.展开更多
Bread wheat(Triticum aestivum)is a staple food crop worldwide.The genetic dissection of important nutrient traits is essential for the biofortification of wheat to meet the nutritional needs of the world's growing...Bread wheat(Triticum aestivum)is a staple food crop worldwide.The genetic dissection of important nutrient traits is essential for the biofortification of wheat to meet the nutritional needs of the world's growing population.Here,45,298 single-nucleotide polymorphisms(SNPs)from 55K chip arrays were used to genotype a panel of 768 wheat cultivars,and a total of 154 quantitative trait loci(QTLs)were detected for eight traits under three environments by genome-wide association study(GWAS).Three QTLs(qMn-3B.1,qFe-3B.4,and qSe-3B.1/qFe-3B.6)detected repeatedly under different environments or traits were subjected to subsequent analyses based on linkage disequilibrium decay and the P-values of significant SNPs.Significant SNPs in the three QTL regions formed six haplotypes for qMn-3B.1,three haplotypes for qFe-3B.4,and three haplotypes for qSe-3B.1/qFe-3B.6.Phenotypic analysis revealed significant differences among haplotypes.These results indicated that the concentrations of several nutrient elements have been modified during the domestication of landraces to modern wheat.Based on the QTL regions,we identified 15 high-confidence genes,eight of which were stably expressed in different tissues and/or developmental stages.TraesCS3B02G046100 in qMn-3B.1 and TraesCS3B02G199500 in qSe-3B.1/qFe-3B.6 were both inferred to interact with metal ions according to the Gene Ontology(GO)analysis.TraesCS3B02G199000,which belongs to qSe-3B.1/qFe-3B.6,was determined to be a member of the WRKY gene family.Overall,this study provides several reliable QTLs that may significantly affect the concentrations of nutrient elements in wheat grain,and this information will facilitate the breeding of wheat cultivars with improved grain properties.展开更多
Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and ...Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic traits.Constructing a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.Results To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples.By constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose genomes.Furthermore,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among geese.Genome-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition traits.For instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length.Notably,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild counterparts.Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.Conclusion This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits,thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese.Moreover,assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome,establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.展开更多
Objective To examine the clinical phenotype and genetic deficiencies present in Chinese aniridia families with PAX6 haplotype deficiency.Methods A comprehensive questionnaire and ophthalmological assessments were admi...Objective To examine the clinical phenotype and genetic deficiencies present in Chinese aniridia families with PAX6 haplotype deficiency.Methods A comprehensive questionnaire and ophthalmological assessments were administered to both affected patients and unaffected relatives.The clinical feature analysis included the evaluation of visual acuity,intraocular pressure,slit-lamp anterior segment examination,fundus photography,and spectral domain optical coherence tomography.To identify the mutation responsible for aniridia,targeted next-generation sequencing was used as a beneficial technique.Results A total of 4 mutations were identified,consisting of two novel frameshift mutations(c.314delA,p.K105Sfs*33 and c.838_845dup AACACACC,p.S283Tfs*85),along with two recurring nonsense mutations(c.307C>T,p.R103X and c.619A>T,p.K207*).Complete iris absence,macular foveal hypoplasia,and nystagmus were consistent in these PAX6 haplotype-deficient Chinese aniridia families,while corneal lesions,cataracts,and glaucoma exhibited heterogeneity both among the families and within the same family.Conclusion In our study,two novel PAX6 mutations associated with aniridia were identified in Chinese families,which expanded the phenotypic and genotypic spectrum of PAX6 mutations.We also analyzed the clinical characteristics of PAX6 haplotype deficiency in Chinese aniridia families.展开更多
The grain protein content(GPC)is the key parameter for wheat grain nutritional quality.This study conducted a resampling GWAS analysis using 406 wheat accessions across eight environments,and identified four previousl...The grain protein content(GPC)is the key parameter for wheat grain nutritional quality.This study conducted a resampling GWAS analysis using 406 wheat accessions across eight environments,and identified four previously reported GPC QTLs.An analysis of 87 landraces and 259 modern cultivars revealed the loss of superior GPC haplotypes,especially in Chinese cultivars.These haplotypes were preferentially adopted in different agroecological zones and had broad effects on wheat yield and agronomic traits.Most GPC QTLs did not significantly reduce yield,suggesting that high GPC can be achieved without a yield penalty.The results of this study provide a reference for future GPC breeding in wheat using the four identified QTLs.展开更多
The leopard coral grouper(Plectropomus leopardus)is a species of significant economic importance.Although artificial cultivation of P.leopardus has thrived in recent decades,the advancement of selective breeding has b...The leopard coral grouper(Plectropomus leopardus)is a species of significant economic importance.Although artificial cultivation of P.leopardus has thrived in recent decades,the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data.In this study,we identified over 8.73 million single nucleotide polymorphisms(SNPs)through whole-genome resequencing of 326 individuals spanning six distinct groups.Furthermore,we categorized 226 individuals with high-coverage sequencing depth(≥14×)into eight clusters based on their genetic profiles and phylogenetic relationships.Notably,four of these clusters exhibited pronounced genetic differentiation compared with the other populations.To identify potentially advantageous loci for P.leopardus,we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity(θπ)and fixation index(FST)in these four clusters.Using these high-coverage resequencing data,we successfully constructed the first haplotype reference panel specific to P.leopardus.This achievement holds promise for enabling high-quality,cost-effectiveimputationmethods.Additionally,we combined low-coverage sequencing data with imputation techniques for a genome-wide association study,aiming to identify candidate SNP loci and genes associated with growth traits.A significant concentration of these genes was observed on chromosome 17,which is primarily involved in skeletal muscle and embryonic development and cell proliferation.Notably,our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs,showing potential for genetic selective breeding efforts.These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P.leopardus.展开更多
基金supported by the National Natural Science Foundation of China (No. 31522034)Ministry of Science and Technology of China (2016YFC0900103)the National High Technology Research and Development Program Grant (2015AA020407)
文摘Reciprocal translocation is a chromosomal structural abnormal- ity that arises when two non-homologous chromosomes rearrange and attach with each other, an incidence that occurs in about 1/500 to 1/625 newborns （Mackie and Scriven, 2002）. This event typically does not lead to any significant loss of genetic material, thus recip- rocal translocation carriers do not exhibit any severe abnormal phenotypes （Scriven et al., 1998; Zhang et al., 2016）.
基金Financial support of Department of Biotechnology,Government of India[Grant Nos.BT/AB/FG-2(PH-II)2009 and BT/PR13357/AGR/02/695/2009]
文摘Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated withsalt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1to 9 score at EC = 10 dSm^-1 under controlled environmental conditions. Seven new breeding linesincluding three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 andcan be good sources of new genes/alleles for salt tolerance. Simple sequence repeat （SSR） markerRM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information contentvalue varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54lines were clearly separated into two major clusters. Fourteen haplotypes were identified based onSaltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminatebetween the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assistedselection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 onchromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.
基金supported by Innovation Scientists and Technicians Troop Construction Projects of Henan Province(Grant No.212101510003)the Central Plains Scholar Workstation Project(Grant No.224400510002)+1 种基金the Youth Science Foundation of Henan Province(Grant No.202300410136)the Experimental Development Foundation of Henan University of Science and Technology(Grant No.SY2324004)。
文摘Paeonia suffruticosa Andr.is an endemic shrub flower in China with 2n=10.This study used 228 cultivars from four populations,i.e.,Jiangnan,Japan,Northwest,and Zhongyuan,as materials to explore the genetic diversity levels among different populations of tree peony varieties.The results showed that 34 bands were amplified using five pairs of cp SSR primers,with an average of 6.8 bands per primer pair.The average number of different alleles(N_(a)),effective alleles(N_(e)),Shannon's information index(I),diversity(H),and polymorphic information content(PIC)were 3.600,2.053,0.708,0.433,and 0.388,respectively.The PIC value was between 0.250 and 0.500,indicating a moderate level of polymorphism for the five cp SSR primer pairs.The genetic diversity levels of peony cultivars varied among different populations,with the Northwest population showing relatively lower levels(I=0.590,H=0.289,and PIC=0.263).A total of 52 haplotypes were identified in the four examined populations,and the number of haplotypes per population ranged from 11 to 22.Forty-four private haplotypes were detected across populations,and the Northwest population exhibiting the highest count of private haplotypes with 17.The mean number of effective number of haplotypes(N_(eh)),haplotypic richness(R_(h)),and diversity(H)were 8.351,6.824,and 0.893,respectively.Analysis of molecular variance indicated that genetic variation within tree peony germplasm was greater than that between germplasm resources,and the main variation was found within individuals of peony germplasm.Cluster analysis,principal coordinate analysis,and genetic structure analysis classified tree peonies from different origins into two groups,indicating a certain degree of genetic differentiation among these four tree peony cultivation groups.This study provides a theoretical basis for the exploration,utilization,and conservation of peony germplasm resources,as well as for research on the breeding of excellent varieties.
基金supported by the Key R&D Program of Shandong province(2022LZGC001,2024CXPT072)the National Natural Science Foundation of China(32201863)the Tai’shan Scholars Program。
文摘Spike length(SL)is an important factor affecting yield in wheat(Triticum aestivum L.).Here,a recombinant inbred line(RIL)population derived from a cross between Shannong 4155(SN4155)and Shimai 12(SM12)was used to map quantitative trait loci(QTL)controlling SL.A QTL,q SL2B,on chromosome 2B was identified in all experiments and explained 9.92%–12.71%of the phenotypic variation.Through transcriptome and gene expression analysis,we identified a gene encoding Elongation Factor 1-alpha(Tae EF1A)as the candidate gene for q SL2B.Genome editing of Tae EF1A demonstrated that Tae EF1A positively regulates SL,spikelet number per spike(SNS),and grain number per spike(GN).Transcriptome analysis showed that Tae EF1A may affect the protein translation process and photosynthesis to regulate spike development.We used haplotype analysis of wheat germplasm to identify seven types of genetic variations in Tae EF1A,with TypeⅠ,TypeⅡ,and TypeⅢbeing the major haplotypes.Screening of 428 cultivars and breeding lines identified 225 and 203 accessions as TypeⅠand TypeⅡhaplotypes,respectively,with TypeⅢnot detected.Comparison of SL,SNS,and GN between the TypeⅠand TypeⅡhaplotypes revealed that the TypeⅠallele can increase SL,SNS,and GN simultaneously,and is thus preferred for use in wheat molecular breeding efforts to increase SL,SNS,and GN.
基金supported by the National Key R&D Program of China(2022YFF1000100)Shaanxi Innovation Team Project(2022TD-10)+1 种基金Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project(2022GD-TSLD-46-0401)Postdoctoral Research Funding of Hainan Province。
文摘Coat color polymorphism in domestic animals provides a robust framework for elucidating mechanisms of species adaptation,domestication,and genomic diversity.Leiqiong cattle,a representative indicine breed from southern China,are predominantly yellow-coated,although a subset exhibits a solid black phenotype.To determine the genetic basis of this variation,a genome-wide association study(GWAS)was performed in 212 Leiqiong bulls.A pronounced association signal was detected on chromosome 6 within the fifth intron of the CORIN gene,providing the first evidence of the potential influence of CORIN on bovine coat color variation.Integration of these results with publicly available genomic datasets and haplotype analyses indicated that the yellow coat phenotype is derived from Indian indicine ancestry,whereas the black coat phenotype emerged through introgression from wild bovine lineages and artificial hybridization with Wagyu cattle.Comparative analysis of Indian indicine cattle with divergent coat colors revealed distinct LEF1 haplotypes within a shared CORIN background,suggesting an ancient and complex domestication history underlying coat color variation.These findings provide direct evidence that introgression has shaped phenotypic variation in East Asian cattle and offer novel insights into the genetic architecture of pigmentation,with implications for future breeding strategies.
基金supported by the Shenzhen Science and Technology Program,China(Grant No.KCXFZ20211020163808012)the Nanfan Special Project,Chinese Academy of Agricultural Sciences,China(Grant No.YBXM2426).
文摘Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.
基金Supported by the"Young Talents"Project of Northeast Agricultural University(22QC04)the Domestic Post Training Excellent Program of Northeast Agricultural University(23ZYZZ0706)。
文摘Sagittaria trifolia L.is a perennial aquatic herb that primarily reproduces clonally and through generative propagation.In recent years,S.trifolia has evolved a drastic resistance to acetohydroxy acid synthase(AHAS)-inhibiting herbicides in Northeast China.The phylogeographic patterns of S.trifolia with 31 purified resistance genotypes and five sensitive genotypes using chloroplast DNA(cpDNA)atpB-rbcL intergenic spacers were studied.Five haplotypes were characterized,and two of them were widely distributed in 36 genotypes.The dose response to bensulfuron-methyl showed that the GR50 ranged from 2.07 g a.i.·hm^(-2) to 220.15 g a.i.·hm^(-2).Sequencing of the AHAS gene indicated that 17 genotypes with the Pro197 mutation were distributed in haplotype 1,six genotypes with the Trp574 mutation were distributed in haplotype 3,and 13 genotypes with the wild AHAS gene were distributed in haplotypes 2,4 and 5.In the minimum-spanning network,the ancestral haplotypes 1 and 2 were widely distributed.Two primary clades were separated in the Bayes tree,and the result was consistent with the maximum likelihood tree.
基金supported by the Major Science and Technology Project of Hainan Province(ZDKJ2021012)National Natural Science Foundation of China(32071805)the National Key Research and Development Program of China(2023YFD2200700)。
文摘Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma metabolite.To enhance high-aromatic coconut breeding efforts,it is essential to deeply understand the hereditary factors governing the production of 2AP.In this study,a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism(SNP)variations from 168 aromatic coconut germplasm resources.Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism.Proteins encoded by these genes are involved in amino acid metabolism,glycolysis,and secondary metabolism.Among these,Asparagine synthetase coding gene ASN1,Gamma-glutamylcysteine synthetase coding gene GSH1,and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504.In particular,the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein,potentially resulting in differences in 2AP content among haplotype populations.Identifying variations in related candidate genes,particularly the gene CnASN1,provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.
基金supported by the National Key R&D Program of China (2023YFD1201300)the Nanfan Special Project of Chinese Academy of Agricultural Sciences (YBXM2428)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences。
文摘FLOWERING LOCUS T (FT),a key regulator of photoperiod pathway,plays a pivotal role in modulating flowering time and growth period-related traits in plants.In this study,we identified 10 FT family genes in soybean and examined their functional divergences through sequence alignment analysis.Phylogenetic and amino acid sequence analysis revealed that the 92nd residue and the Segment B domain (sites 129,131,134,135) are the critical determinants of potential functional divergence and activity variation among Gm FT.Using the Soy Omics website,we detected natural variations in the genomic and promoter regions of Gm FTs,along with numerous haplotypes.By correlating these haplotypes with flowering time,we identified 7 potential KASP markers associated with soybean growth period:Gm FT1a-60297360,Gm FT1b-60311669,Gm FT2a-31695562,Gm FT2b-31739433,Gm FT3a-4106476,Gm FT5a-4078626,and Gm FT5b-37490962.All KASP markers exhibited high selection efficiency (97.56%–100.00%) and reliable genotyping accuracy when validated across 82 soybean varieties spanning multiple maturity groups (MGs).This study systematically elucidates the functional divergence of Gm FTs and develops efficient KASP markers,providing essential technological support for photoperiodadaptive breeding and germplasm innovation.
基金supported by the National Natural Science Foundation of China(U21A20236,32072664)the Natural Science Foundation of Hunan Province,China(2022RC3053,2021JC0001,2021RC3086,2022NK2009)+1 种基金the China Agriculture Research System(CARS-01-30)the Innovation Foundation for Graduate of Hunan Agricultural University,China(2023XC116)。
文摘Elucidating crops'physiological and molecular mechanisms to adapt to low nitrogen environment and promoting nitrogen transfer from senescent leaves to new leaves is crucial in improving Brassica's nitrogen use efficiency(NUE).Glutamine synthetase gene(GS)plays a vital role in helping plants reassimilate ammonium released from protein degradation in leaves,and it was the focus of our research on this topic.In this study,we identified high(H141)and low(L65)NUE genotypes of Brassica juncea with different responses to low-nitrogen stress.We found that H141 has a lower nitrate content but higher ammonium and free amino acid contents as well as higher nitrate reductase and GS activities in the shoots.These physiological indicators are responsible for the high NUE of H141.Wholegenome resequencing data revealed that 5,880 genes associated with NUE are polymorphic between H141 and L65.These genes participate in various amino acid,carbohydrate,and energy metabolic pathways.Haplotype analysis revealed two haplotypes for BjuB05.GS1.4,Hap1 and Hap2,which have multiple single nucleotide polymorphisms or insertions/deletions in the regulatory regions of the 5′and 3′untranslated regions and introns.Furthermore,the shoot NUE of Hap1 is significantly lower than that of Hap2.These two haplotypes of BjuB05.GS1.4 lead to differences in the shoot NUEs of different genetic populations of mustard and are associated with the local soil nitrogen content,suggesting that they might help mustard to adapt to different geographic localities.In conclusion,the results of our study shed light on the physiological and molecular mechanisms underlying different mustard NUE genotypes and demonstrate the enormous potential of NUE breeding in B.juncea.
基金supported by the National Natural Science Foundation of China(32130013,32070434)the National Key Research and Development Program of China(2022YFC2601601)+1 种基金the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK05010112,2019QZKK0304-02)Hainan Tropical Rainforest Conservation Research Project,ZDYF2023RDYL01(supported by the Hainan Institute of National Park,HINP,KY-24ZK02).
文摘Understanding the genetic diversity–area relationship(GAR)is essential for comprehending how species adapt to environmental changes,as genetic diversity is an indicator of a species’adaptive potential.Variation in environmental adaptation capacity exists among species and animal taxa with different distribution areas,highlighting the importance of understanding the GAR.To obtain a more comprehensive understanding of the GAR in terrestrial vertebrates,we assessed both haplotype diversity–area and nucleotide diversity–area relationships using 25,453 cytochrome c oxidase subunit I(COI)sequences from 142 amphibian species,574 bird species,and 342 mammal species.We found that both measures of genetic diversity increased with species range size across major animal groups.Nevertheless,the GAR did not differ among animal groups,while haplotype diversity performed better than nucleotide diversity in profiling the GAR,as indicated by higher R2 values.The difference in the modeling fit may stem from the distinct biological and mathematical significance of nucleotide diversity and haplotype diversity.These results suggest that the GAR follows similar rules among different animal taxa.Furthermore,haplotype diversity may serve as a more reliable indicator for assessing the potential effects of area size changes on animal populations and provide better guidance for conserving genetic diversity.
文摘The investigation of genetic differences among humans has given evidence thatmutations in DNA sequences are responsible for some genetic diseases. The most common mutation isthe one that involves only a single nucleotide of the DNA sequence, which is called a singlenucleotide polymorphism (SNP). As a consequence, computing a complete map of all SNPs occurring inthe human populations is one of the primary goals of recent studies in human genomics. Theconstruction of such a map requires to determine the DNA sequences that from all chromosomes. Indiploid organisms like humans, each chromosome consists of two sequences called haplotypes.Distinguishing the information contained in both haplotypes when analyzing chromosome sequencesposes several new computational issues which collectively form a new emerging topic of ComputationalBiology known as Haplotyping. This paper is a comprehensive study of some new combinatorialapproaches proposed in this research area and it mainly focuses on the formulations and algorithmicsolutions of some basic biological problems. Three statistical approaches are briefly discussed atthe end of the paper.
基金supported by the Major Program of National Agricultural Science and Technology of China(NK20220607)the West Light Foundation of the Chinese Academy of Sciences(2022XBZG_XBQNXZ_A_001)the Sichuan Science and Technology Program,China(2022ZDZX0014)。
文摘Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.
基金The help and support of owners of the dairy farms enrolled in this study is gratefully acknowledged.The financial support from the program of China Scholarship Council during the PhD study of Mengqi Wang in Canada is acknowledged(No.202008880009).
文摘Background Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry.Multi-omics approaches enable the comprehensive investigation of the complex interactions between mul-tiple layers of information to provide a more holistic view of disease pathogenesis.Therefore,this study investigated the genomic and epigenomic signatures and the possible regulatory mechanisms underlying subclinical mastitis by integrating RNA sequencing data(mRNA and lncRNA),small RNA sequencing data(miRNA)and DNA methylation sequencing data of milk somatic cells from 10 healthy cows and 20 cows with naturally occurring subclinical mastitis caused by Staphylococcus aureus or Staphylococcus chromogenes.Results Functional investigation of the data sets through gene set analysis uncovered 3458 biological process GO terms and 170 KEGG pathways with altered activities during subclinical mastitis,provided further insights into subclin-ical mastitis and revealed the involvement of multi-omics signatures in the altered immune responses and impaired mammary gland productivity during subclinical mastitis.The abundant genomic and epigenomic signatures with sig-nificant alterations related to subclinical mastitis were observed,including 30,846,2552,1276 and 57 differential methylation haplotype blocks(dMHBs),differentially expressed genes(DEGs),lncRNAs(DELs)and miRNAs(DEMs),respectively.Next,5 factors presenting the principal variation of differential multi-omics signatures were identified.The important roles of Factor 1(DEG,DEM and DEL)and Factor 2(dMHB and DEM),in the regulation of immune defense and impaired mammary gland functions during subclinical mastitis were revealed.Each of the omics within Factors 1 and 2 explained about 20%of the source of variation in subclinical mastitis.Also,networks of impor-tant functional gene sets with the involvement of multi-omics signatures were demonstrated,which contributed to a comprehensive view of the possible regulatory mechanisms underlying subclinical mastitis.Furthermore,multi-omics integration enabled the association of the epigenomic regulatory factors(dMHBs,DELs and DEMs)of altered genes in important pathways,such as‘Staphylococcus aureus infection pathway’and‘natural killer cell mediated cyto-toxicity pathway’,etc.,which provides further insights into mastitis regulatory mechanisms.Moreover,few multi-omics signatures(14 dMHBs,25 DEGs,18 DELs and 5 DEMs)were identified as candidate discriminant signatures with capac-ity of distinguishing subclinical mastitis cows from healthy cows.Conclusion The integration of genomic and epigenomic data by multi-omics approaches in this study provided a better understanding of the molecular mechanisms underlying subclinical mastitis and identified multi-omics candidate discriminant signatures for subclinical mastitis,which may ultimately lead to the development of more effective mastitis control and management strategies.
基金supported by the National Research Foundation of Korea(NRF)grants funded by the Ministry of Science and Information and Communication Technology(MSIT),Republic of Korea(NRF2022R1A4A1030348 and 2023R1A2C1004432)the Korea Institute of Planning and Evaluation for Technology in Food,Agriculture and Forestry(IPET)through the Digital Breeding Transformation Technology Development Program,funded by the Ministry of Agriculture,Food and Rural Affairs(MAFRA),Republic of Korea(322060031HD020)the Cooperative Research Program for Agriculture Science and Technology Development,Rural Development Administration,Republic of Korea(RS-2023-00222739)。
文摘Pre-harvest sprouting(PHS)poses a significant global challenge to cereal production,impacting both yield and quality.In this study,we employed genome-wide association studies(GWAS)on diverse rice accessions to identify novel PHS-associated haplotypes.An assessment of 127 cultivated accessions for panicle germination(PHS)and detached grain germination(germination rate of detached grains at the 14th day(D14))revealed considerable phenotypic variation among rice ecotypes.GWAS analysis identified 91 significant signals at–log10(P-value)>5,including 15SNPs for PHS and 76 SNPs for D14.A subsequent linkage disequilibrium(LD)block-based GWAS analysis detected 227 significant SNPs for both traits,consisting of 18 nonsynonymous substitutions located on the coding regions of nine genes.Further haplotype analysis identified 32 haplotypes,with 10 specific to cultivated accessions,19 specific to the wild type,and three shared between them.A phenotypic assessment of major haplotypes revealed significant differences between resistant(Hap1 and Hap2)and susceptible haplotypes(Hap5,Hap27,and Hap28),distinguished by a G/A SNP within a novel gene,Os04g0545200.The identified haplotypes offer promising prospects for haplotypebased breeding aimed at enhancing PHS resistance in rice.
基金This work was supported by grants from the Natural Science Foundation of Shandong Province,China(ZR2020MC096,ZR2021ZD31,and ZR2020MC151)the Agricultural Variety Improvement Project of Shandong Province,China(2021LZGC013 and 2022LZGC002).
文摘Bread wheat(Triticum aestivum)is a staple food crop worldwide.The genetic dissection of important nutrient traits is essential for the biofortification of wheat to meet the nutritional needs of the world's growing population.Here,45,298 single-nucleotide polymorphisms(SNPs)from 55K chip arrays were used to genotype a panel of 768 wheat cultivars,and a total of 154 quantitative trait loci(QTLs)were detected for eight traits under three environments by genome-wide association study(GWAS).Three QTLs(qMn-3B.1,qFe-3B.4,and qSe-3B.1/qFe-3B.6)detected repeatedly under different environments or traits were subjected to subsequent analyses based on linkage disequilibrium decay and the P-values of significant SNPs.Significant SNPs in the three QTL regions formed six haplotypes for qMn-3B.1,three haplotypes for qFe-3B.4,and three haplotypes for qSe-3B.1/qFe-3B.6.Phenotypic analysis revealed significant differences among haplotypes.These results indicated that the concentrations of several nutrient elements have been modified during the domestication of landraces to modern wheat.Based on the QTL regions,we identified 15 high-confidence genes,eight of which were stably expressed in different tissues and/or developmental stages.TraesCS3B02G046100 in qMn-3B.1 and TraesCS3B02G199500 in qSe-3B.1/qFe-3B.6 were both inferred to interact with metal ions according to the Gene Ontology(GO)analysis.TraesCS3B02G199000,which belongs to qSe-3B.1/qFe-3B.6,was determined to be a member of the WRKY gene family.Overall,this study provides several reliable QTLs that may significantly affect the concentrations of nutrient elements in wheat grain,and this information will facilitate the breeding of wheat cultivars with improved grain properties.
基金funding from several sources,including the Chongqing Scientific Research Institution Performance Incentive Project(grant number cstc2022jxjl80007)the Earmarked Fund for China Agriculture Research System(grant number CARS-42-51)+5 种基金the Chongqing Scientific Research Institution Performance Incentive Project(grant number 22527 J)the Key R&D Project in Agriculture and Animal Husbandry of Rongchang(grant number No.22534C-22)Natural Science Foundation of Chongqing Project,grant number CSTB2022NSCQ-MSX0434Natural Science Foundation of Sichuan Project,grant number 2022NSFSC0605Natural Science Foundation of Sichuan Project,grant number 2021YFS0379the Chongqing Technology Innovation and Application Development Project(grant number No.cstc2021ycjh-bgzxm0248)。
文摘Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic traits.Constructing a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.Results To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples.By constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose genomes.Furthermore,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among geese.Genome-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition traits.For instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length.Notably,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild counterparts.Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.Conclusion This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits,thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese.Moreover,assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome,establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.
文摘Objective To examine the clinical phenotype and genetic deficiencies present in Chinese aniridia families with PAX6 haplotype deficiency.Methods A comprehensive questionnaire and ophthalmological assessments were administered to both affected patients and unaffected relatives.The clinical feature analysis included the evaluation of visual acuity,intraocular pressure,slit-lamp anterior segment examination,fundus photography,and spectral domain optical coherence tomography.To identify the mutation responsible for aniridia,targeted next-generation sequencing was used as a beneficial technique.Results A total of 4 mutations were identified,consisting of two novel frameshift mutations(c.314delA,p.K105Sfs*33 and c.838_845dup AACACACC,p.S283Tfs*85),along with two recurring nonsense mutations(c.307C>T,p.R103X and c.619A>T,p.K207*).Complete iris absence,macular foveal hypoplasia,and nystagmus were consistent in these PAX6 haplotype-deficient Chinese aniridia families,while corneal lesions,cataracts,and glaucoma exhibited heterogeneity both among the families and within the same family.Conclusion In our study,two novel PAX6 mutations associated with aniridia were identified in Chinese families,which expanded the phenotypic and genotypic spectrum of PAX6 mutations.We also analyzed the clinical characteristics of PAX6 haplotype deficiency in Chinese aniridia families.
基金supported by the“Integration of Two Chains”Key Research and Development Projects of Shaanxi Province“Wheat Seed Industry Innovation Project”,Chinathe Key R&D of Yangling Seed Industry Innovation Center,China(Ylzy-xm-01)。
文摘The grain protein content(GPC)is the key parameter for wheat grain nutritional quality.This study conducted a resampling GWAS analysis using 406 wheat accessions across eight environments,and identified four previously reported GPC QTLs.An analysis of 87 landraces and 259 modern cultivars revealed the loss of superior GPC haplotypes,especially in Chinese cultivars.These haplotypes were preferentially adopted in different agroecological zones and had broad effects on wheat yield and agronomic traits.Most GPC QTLs did not significantly reduce yield,suggesting that high GPC can be achieved without a yield penalty.The results of this study provide a reference for future GPC breeding in wheat using the four identified QTLs.
基金supported by the National Key Research and Development Program of China (2022YFD2400501)Key R&D Project of Hainan Province (ZDYF2021XDNY133)+2 种基金Project of Sanya Yazhouwan Science and Technology City Management Foundation (SKJC-2020-02-009)PhD Scientific Research and Innovation Foundation of Sanya Yazhou Bay Science and Technology City (HSPHDSRF-2022-02-007)Young Elite Scientists Sponsorship Program by CAST (2023QNRC001)。
文摘The leopard coral grouper(Plectropomus leopardus)is a species of significant economic importance.Although artificial cultivation of P.leopardus has thrived in recent decades,the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data.In this study,we identified over 8.73 million single nucleotide polymorphisms(SNPs)through whole-genome resequencing of 326 individuals spanning six distinct groups.Furthermore,we categorized 226 individuals with high-coverage sequencing depth(≥14×)into eight clusters based on their genetic profiles and phylogenetic relationships.Notably,four of these clusters exhibited pronounced genetic differentiation compared with the other populations.To identify potentially advantageous loci for P.leopardus,we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity(θπ)and fixation index(FST)in these four clusters.Using these high-coverage resequencing data,we successfully constructed the first haplotype reference panel specific to P.leopardus.This achievement holds promise for enabling high-quality,cost-effectiveimputationmethods.Additionally,we combined low-coverage sequencing data with imputation techniques for a genome-wide association study,aiming to identify candidate SNP loci and genes associated with growth traits.A significant concentration of these genes was observed on chromosome 17,which is primarily involved in skeletal muscle and embryonic development and cell proliferation.Notably,our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs,showing potential for genetic selective breeding efforts.These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P.leopardus.
