Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

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.

Genome-wide association studies reveal the genetic basis of amino acid content variation in tea plants

Tea is one of the most popular non-alcoholic beverages in the world,and free amino acids,especially theanine,make a major contribution to the umami taste of tea.However,the genetic basis of the variation in amino acid content in tea plants remains largely unknown.Here,we measured the free amino acid content in fresh leaves of 174 tea accessions over two years using a targeted metabolomics approach and obtained genotype data via RNA sequencing.Genome-wide association studies were conducted to investigate loci affecting the content of free amino acids.A total of 69 quantitative trait loci(–log10(P-value)>5)were identified.Functional annotation revealed that branched-chain amino acid aminotransferase,glutamine synthetase,nitrate transporter,and glutamate decarboxylase might be important for amino acid metabolism.Two significant loci,glutamine synthetase(Glu1,P=3.71×10^(−4);Arg1,P=4.61×10^(−5))and branched-chain amino acid aminotransferase(Val1,P=4.67×10^(−5);I_Leu1,P=3.56×10^(−6)),were identified,respectively.Based on the genotyping result,two alleles of CsGS(CsGS-L and CsGS-H)and CsBCAT(CsBCAT-L and CsBCAT-H)were selected to perform function verification.Overexpression of CsGS-L and CsGS-H enhanced the contents of glutamate and arginine in transgenic plants,and overexpression of CsBCAT-L and CsBCAT-H promoted the accumulation of valine,isoleucine and leucine.Enzyme activity assay uncovered that SNP1054 is important for CsGS catalyzing glutamate into glutamine.Furthermore,CsGS-L and CsGS-H differentially regulated the accumulation of glutamine,and CsBCAT-L and CsBCAT-H differentially regulated the accumulation of branched-chain amino acids.In summary,the findings in our study would provide new insights into the genetic basis of amino acids contents variation in tea plants and facilitate the identification of elite genes to enhance amino acids content.

Population genetic variation and historical dynamics of the natural enemy insect Propylea japonica(Coleoptera: Coccinellidae) in China

Propylea japonica(Coleoptera:Coccinellidae)is a natural enemy insect with a wide range of predation in Chinese mainland and is commonly used in pest management.However,its genetic pattern(i.e.,genetic variation,genetic structure,and historical population dynamics)is still unclear,impeding the development of biological control of insect pests.Population genetic research has the potential to optimize strategies at different stages of the biological control processes.This study used 23 nuclear microsatellite sites and mitochondrial COI genes to investigate the population genetics of Propylea japonica based on 462 specimens collected from 30 sampling sites in China.The microsatellite dataset showed a moderate level of genetic diversity,but the mitochondrial genes showed a high level of genetic diversity.Populations from the Yellow River basin were more genetically diverse than those in the Yangtze River basin.Propylea japonica has not yet formed a significant genealogical structure in China,but there was a population structure signal to some extent,which may be caused by frequent gene flow between populations.The species has experienced population expansion after a bottleneck,potentially thanks to the tri-trophic plant–insect–natural enemy relationship.Knowledge of population genetics is of importance in using predators to control pests.Our study complements existing knowledge of an important natural predator in agroecosystems through estimating its genetic diversity and population differentiation and speculating about historical dynamics.

Discordant patterns of genetic variation between mitochondrial and microsatellite markers in Acanthogobius ommaturus across the coastal areas of China

Acanthogobius ommaturus, which belongs to the family Gobiidae, is a euryhaline and demersal fish that is widely distributed in the coastal areas, harbors, and estuaries of China, D. P. R. Korea and Japan. In this study, the genetic diversity and genetic structure of five geographical populations of A. ommaturus was assessed using the mitochondrial hypervariable region gene and microsatellite markers. The results of the two genetic markers indicated that the A. ommaturus populations had a high level of genetic diversity. The mitochondrial marker detected weak genetic differentiation among populations, and the Neighbor-Joining tree showed that there was no obvious pedigree branches and geographic structure as well. However, population of Zhoushan showed significant genetic differentiation with other populations by microsatellite markers. The population of A.ommaturus has not experienced bottleneck effect recently. We speculated that the Pleistocene climate change and juvenile fish dispersal played an important role in the population differentiation of A. ommaturus.

Analysis of drought tolerance and genetic and epigenetic variations in a somatic hybrid between Ipomoea batatas (L.) Lam. and I. triloba L.

The somatic hybrid KT1 was previously obtained from protoplast fusion between sweetpotato （Ipomoea batatas （L.） Lam.） cv. Kokei No. 14 and its wild relative I. triloba L. However, its genetic and epigenetic variations have not been investigated. This study showed that KT1 exhibited significantly higher drought tolerance compared to the cultivated parent Kokei No. 14. The content of proline and activities of superoxide dismutase （SOD） and photosynthesis were significantly increased, while malonaldehyde （MDA） content was significantly decreased compared to Kokei No. 14 under drought stress. KT1 also showed higher expression level of well-known drought stress-responsive genes compared to Kokei No. 14 under drought stress. Amplified fragment length polymorphism （AFLP） and methylation-sensitive amplified polymorphism （MSAP） analyses indicated that KT1 had AFLP and MSAP band patterns consisting of both parent specific bands and changed bands. Fur- ther analysis demonstrated that in KT1. the proportions of Kokei No. 14 specific genome components and methylation sites were much greater than those of I. triloba. KT1 had the same chloroplast and mitochondrial genomes as Kokei No. 14. These results will aid in developing the useful genes ofI. triloba and understanding the evolution and phylogeny of the cultivated sweetpotato.

Genetic variation in ZmSO contributes to ABA response and drought tolerance in maize seedlings

Water scarcity impairs maize growth and yield.Identification and deployment of superior droughttolerance alleles is desirable for the genetic improvement of stress tolerance in maize.Our previous study revealed that maize sulfite oxidase(SO) catalyzes the oxidation of sulfite to sulfate and may be involved in drought response.But it was unclear whether the natural variation in Zm SO is directly associated with the drought resistance of maize.In the present study,we showed that Zm SO was associated with drought tolerance in maize seedlings,using gene association analysis and a transgene approach.A 14-bp insertion variation,containing two ABA-responsive elements,in the promoter region of Zm SO conferred ABAinducible expression,leading to increased drought tolerance.Genetic selection of this favorable allele increased drought tolerance.This study has identified elite alleles associated with sulfur metabolism for improving maize drought resistance.

Altitude shape genetic and phenotypic variations in growth curve parameters of Larix kaempferi

To study the effects of geoclimatic variables of provenances on growth phenotypes and selected plus provenances,over 3000 trees of 22-year-old Larix kaempferi were evaluated from trials established in two climate zones for provenance selection and to explore the influence of climate variables on provenance performance.The material was replicated plantings of 84 open pollinated families from six provenances distributed in the mountains of central Japan.Provenance variation was observed in most age groups and the heritability of growth traits showed large differences.The phenotypic maximum value of height and diameter were significantly positive with altitude,and mean annual precipitation being important factors.Diameter at breast height growth was significantly negative with altitude and spring rainfall.The Ina provenance of relatively high altitudes,was well adapted to a variety of climates.Altitude might be the driving force for phenotypic and genetic variations and local adaptation.

Genetic and Phenotypic Variation of Campylobacter jejuni NCTC11168 Caused by flhA Mutation during Laboratory Passage

Objective Campylobacter jejuni NCTC11168 is commonly used as a standard strain for flagellar biosynthesis research.In this report,two distinguished phenotypic isolates(CJ1Z,flhA mutant strain,lawn;CJ2S,flhA complemented strain,normal colony)appeared during laboratory passages for NCTC11168.Methods Phenotypic assessments,including motility plates,transmission electron microscopy,biofilm formation assay,autoagglutination assay,and genome re-sequencing for these two isolates(CJ1Z,flhA mutant strain;CJ2S,flhA complemented strain)were carried out in this study.Results Transmission electron microscopy revealed that the flagellum was lost in CJ1Z.Phenotypic assessments and genome sequencing of the two isolates were performed in this study.The capacity for biofilm formation,colony auto-agglutination,and isolate motility was reduced in the mutant CJ1Z.Comparative genomic analysis indicated a unique native nucleotide insertion in flhA(nt,2154)that caused the I719Y and I720Y mutations and early truncation in flhA.Conclusion FlhA has been found to influence the expression of flagella in C.jejuni.To the best of our knowledge,this is the first study to describe the function of the C-terminal of this protein.

Genetic variation of Laminaria japonica (Phaeophyta) populations in China as revealed by RAPD markers

For the population genetics analysis of the naturally grown brown seaweed Laminaria japonica （Laminariales,Phaeophyta） sampled from Dalian,Yantai,Weihai,Rongcheng and Qingdao in China,ten primers were employed to produce 88 bands as revealed by randomly amplified polymorphic DNA （RAPD） markers,and all these bands were polymorphic.According to these band patterns,there were 94 distinct phenotypes occurred in 100 samples indicating the high heterozygosity of this kelp.Dalian population samples showed the highest percentage of polymorphism （71.67%）,and also the higher diversity estimated on the basis of the Shannon’s index （8.498）,suggesting that this population could be chosen as the best resource for genetic breeding.The highest diversity of Yantai population possibly resulted from the introduction of L.longissima used for interspecific cross breeding with L.japonica cultivated in China.From Dalian southwards to Qingdao,the genetic variation of the five populations became less with a decrease in latitude,possibly due to the natural selection especially of high temperature.The genetic distance （Φ ST values） of the five populations was a little significantly correlated with the geographical distance （r=0.496） at P =0.05 by Mantel’s test.Weihai,Rongcheng and Yantai populations were closely grouped genetically together by Neighbor-joining cluster analysis probably in that the dispersal of the kelp by propagules more easily occurring in the range of relatively short distance.The analysis of molecular variance （AMOVA） also demonstrated that the relatively higher variation occurred among populations （71.49%） at an extremely significant level （P 0.000 1）.All these evidence showed that there was a relatively distinct genetic differentiation among the sampled kelp populations,and L.japonica grown in China was also rather heterozygous in heredity.

Genetic Variation in Triticum turgidum L. ssp. turgidum Landraces from China Assessed by EST-SSR Markers

It was helpful for the wheat improvement to evaluate the genetic resources of Triticum turgidum L. ssp. turgidum landraces. In this study, 68 turgidum landraces accessions, belonging to four geographic populations in China, were investigated by using EST-SSR markers. A total of 63 alleles were detected on 22 EST-SSR loci, and the number of alleles on each locus ranged from 1 to 5, with an average of 2.9. The results of the analysis of molecular variance （AMOVA） indicated that 92.5% of the total variations was attributed to the genetic variations within population, whereas only 7.5% variations among populations. Although the four populations had similar genetic diversity parameters, Sichuan population was yet distinguished from other populations when comparing the population samples in pairs. Significant correlations were detected by the statistic analysis among six genetic diversity parameters among each other. The selection difference between heterozygosty and homozygosty was also observed among different EST-SSR locus. The genetic similarity （GS） ranged from 0.18 to 0.98, with the mean of 0.72, and all accessions could be clustered into 7 groups. The dendrogram suggested that the genetic relationships among turgidum accessions evaluated by EST-SSR markers were unrelated to their geographic distributions. These results implied that turgidum landraces from China had the unique characters of genetic diversity.

AFLP analysis of genetic variation of Hyphantria cunea(Drury) populations in Beijing and a nearby site

Hyphantria cunea （Drury） is a severe invasive pest in Beijing. It is important to understand the reason for its successful invasion and outbreak. Accordingly, this study was tailored to assess molecular variation and genetic relationships among three H. cunea populations in Beijing and one population from Sanhe in Hebei Province as control （totally 100 individuals）. A silver-labeled amplified fragment length polymorphisms （AFLP） DNA profiling method was used to detect the genetic diversity and relationship among the populations. Five EcoRI and MseI primer combinations produced a total of 171 （91.2% polymorphic） informative fragments. The average Nei＇s genetic diversity in four H. cunea populations analyzed by Popgene3.2 software was 0.2287, and the level of genetic diversity ranked in the order BDR （reared population in Daxing, Beijing） 〉 BDN （natural population in Daxing, Beijing） 〉 HSN （natural population in Sanhe, Hebei Province） 〉 BFN （natural population in Fengtai, Beijing）. The value of genetic differentia- tion among populations was 0.3321, and the gene flow was 1.0057. The genetic distance between these populations ranged from 0.0735 to 0.3309, 0.0531 on average. The result of UPGMA （unweighed pair group method with arithmetic averages） clustering showed that populations BFN and HSN were closely related, while BFN and BDN had the largest genetic distance. These results indicate that H. cunea populations in Beijing might originate from several areas.

Genetic Variation in Tropical Tree Species and Plantations: A Review

The global efforts to restore tropical forests and their productive and ecological functions through plantation forestry largely depend on the available genetic variation in the tree species used to establish the plantations. However, there is limited information on the levels and trends of the genetic variation and variability of different plantation tree species in the tropics. Therefore, this study reviews several marker-based studies that have investigated genetic variation. Most of the top economic species like Eucalyptus tereticornis and Mansonia altissima are attributed to low levels of genetic diversity, while others like Pinus caribaea and Swietenia macrophylla still exhibit high expected heterozygosity across different populations. However, the levels of genetic diversity assessed may depend on the markers used. Microsatellites, i.e., simple sequence repeats (SSRs), mostly give higher estimates when compared to other polymerase chain reaction-based markers. Other factors that typically contribute to the directional pattern of genetic variation in tropical tree species and populations include their distribution, density, seed dispersal, succession, and reproduction. Also, anthropogenic impacts like logging and fragmentation have contributed to the vast genetic base reduction of many tropical species and populations. Having adequate genetic variation within the plantation populations is significant in improving their fitness, resilience, fecundity, productivity, and other ecological functions. It also provides a basis for tree improvement and breeding in plantation forests. Although clonal forestry is becoming widespread and considered highly productive, it is attributed to specific economic, technical, and ecological risks, such as the increased spread of pests and diseases. Therefore, further discussions and recommendations to maximise genetic diversity in tropical (clonal) plantations are provided.

Small RNAs and Transgenerational Epigenetic Variation

Small RNAs are found in eukaryotes and are responsible for regulation of chromatin structure, RNA processing and stability, translation and transcription. 24-nt small interfering RNA (siRNA) are known to mediate gene inactivation via the RNA-directed DNA methylation pathway (RdDM) and are important for natural heritable changes in plant species. DNA cytosine methylation can be maintained between generations and this may be important for accelerated adaption to stress conditions. Research is currently focused toward the epigenetic response to disease, the stability of DNA methylation over generations, the elucidation of newly discovered pathways for de novo DNA methylation, and the application of epigenetic variation to breeding programs. This review aims to give a brief but comprehensive examination on small RNAs and transgenerational epigenetic variation.

Genetic variation and selection of introduced provenances of Siberian Pine(Pinus sibirica) in frigid regions of the Greater Xing'an Range,Northeast China

Siberian Pine （Pinus sibirica） is an ecologically and eco-nomically important species in pristine forests throughout northern Rus-sia. Four provenances of P. sibirica were introduced from Mongolia and Russia to the Greater Xing’an Range （the Daxing’anling）, northeast China in 1993. The aim of this research was to study genetic variation and selection of the introduced four Pinus sibirica provenances. Heights （H）, basal diameters （BD）, survival rates （SR） and crown lengths （CL） of different families were measured as primary outcomes in different growth years. Results of data analyses demonstrated high coefficients of phenotypic variation （PCV） and heritability （H2） for H, BD and CL at 18 years after introduction. PCV and H2 increased with age. Correlations of＆amp;nbsp;growth traits between any two growth years were all significantly positive, but the correlation coefficient was smaller when the growth year interval was larger. Correlations between H and the original environment factors decreased gradually, indicating that with long-term subsistence in the new environment, the influence of the source environment declined. Colligation of multiple traits to estimate provenances showed that Novosibirsk, Tomsk, and Altai Mountains had higher survival rates and biomass, and proved more suitable for introduction and plantation in the Greater Xing’an Range in China.

Genetic variations in plant architecture traits in cotton(Gossypium hirsutum) revealed by a genomewide association study

Plant architecture traits influence crop yield. An understanding of the genetic basis of cotton plant architecture traits is beneficial for identifying favorable alleles and functional genes and breeding elite cultivars. We collected 121 cotton accessions including 100 brownfiber and 21 white-fiber accessions, genotyped them by whole-genome resequencing, and phenotyped them in multiple environments. This genome-wide association study(GWAS)identified 11 quantitative trait loci(QTL) for two plant architecture traits: plant height and fruit spur branch number. Negative-effect alleles were enriched in the elite cultivars. Based on these QTL, gene annotation information, and published QTL, candidate genes and natural genetic variations in four QTL were identified. Ghir_D02 G017510 and Ghir_D02 G017600 were identified as candidate genes for qD02-FSBN-1, and a premature start codon gain variation was found in Ghir_D02 G017510. Ghir_A12 G026570, the candidate gene of qA12-FSBN-2, belongs to the pectin lyase-like superfamily, and a significantly associated SNP, A12_105366045(T/C), in this gene represents an amino acid change. The QTL, candidate genes, and associated natural variations in this study are expected to lay a foundation for studying functional genes and developing breeding programs for desirable architecture in brown-fiber cotton.

Genetic variation in distant and inbred hybridization progenies from three sympodial bamboo parent species

To achieve germplasm innovation and study genetic variation of important traits of bamboo plants,we used Bambusa multiplex,B.chungii,and Dendrocalamus latiflorus as parent materials for distant and inbred hybridizations.Two hybrid populations and three inbred populations were obtained:two populations consisted of 57 hybrid progenies from B.multiplex 9 B.chungii,26 hybrid progenies from B.multiplex 9 D.latiflorus,and three inbred progenies were from B.multiplex,B.chungii,and D.latiflorus.Traits for growth,morphology,and fiber were examined from the five populations when plants were 3 years old.Two hybrid populations had significant growth advantages in terms of height,diameter at ground level and internodal length.In terms of variability in morphological traits,the two hybrid populations followed the same trend,namely,seven morphological traits showed phenotypes that were intermediate to those of their parents;three morphological traits showed strong maternal effects,and three other morphological traits showed strong paternal effects.Among the five populations,the two hybrid populations had high arithmetic average fiber length,lengthweighted average fiber length and mass-weighted average fiber length,moreover,extensive variations of these three traits were observed within these two hybrid populations.The establishment of distant hybrid populations from these three bamboo species increased the genetic diversity more than in the other species examined.This work provides excellent materials for breeding new varieties and lays the foundation for understanding the genetics of important traits by analyzing related functional genes.

Genetic variation and division of Pinus sylvestris provenances by ISSR markers

Inter Simple Sequence Repeat （ISSR） was used to detect genetic variation among nine provenances, including 135 individuals. A total of 108 loci were amplified using 10 random primers. The differentiation of the percentage of polymorphic bands （PPB） among different provenances was evident, ranging from 27% to 54%. of which Honghuaerji provenance had the highest PPB and Kalunshan provenance had the lowest PPB. Shannon＇s Information index （1） at species level was 0.1581 and Nei＇s gene diversity （h） was 0.2393. Coefficient of gene differentiation （Gsr） calculated by Popgene was 0.3965, these results indicated that majority of genetic variation （60.35%） was found within provenances. According to dendrogram among pinus sylvestriv provenances, nine provenances were divided into two provenance areas. namely Daxing＇an and Xiaoxing＇an Mountains provenance area and Hulunbeier provenance area.

Genetic Variation Analysis on the Whole Genomic Sequence of a H9N2 Subtype Avian Influenza Virus Isolate

A Objective3 This study was to understand the genetic variation characters of the H9N2 subtype avian influenza virus isolate （A/Chicken/ Hebei/WD/98, abbreviated as WD98） by comparing with other reference strains. I-Method3 Eight complete genes were amplified by RT-PCR and sequenced. The homology and genetic evolution relationship were analyzed between these sequences and that of the seven reference strains. [Result] The whole genomic sequence of WD98 strain was 91.1% -95.8% homologous to that of seven reference strains tested. This isolate shared the highest homology （95.8%） to D/HK/Y280/97 and the lowest homology （91.1% ） to C/Pak/2/99. The HA cleavage site of the WD98 strain was R-S-S-R G, and the 226th amino acid at receptor-binding site was Gin. [ Condmion] WD98 strain belongs to mildly pathogenic avian in- fluenza virus and may not infect human. The genetic relationship is the closest between A/Chicken/Hebei/wD/98 and A/duck/HongKong/Y280/ 97, both of which belong to the sub-line of A/Chicken/Beijing/1/94 in Eurasian line. And A/Chicken/Hebei/WD/98 and A/Chicken/Beijing/1/94 are genetically distant within the same sub-line.

Genetic variations in the SMAD4 gene and gastric cancer susceptibility

AIM:To explore the association between mothers against decapentaplegic homolog 4 (SMAD4) gene polymorphisms and gastric cancer risk.METHODS:Five tagging single nucleotide polymor-phisms (tSNPs) in the SMAD4 gene were selected and genotyped in 322 gastric cancer cases and 351 cancerfree controls in a Chinese population by using the polymerase chain reactionrestriction fragment length polymorphism method.Immunohistochemistry was used to examine SMAD4 protein expression in 10 normal gastric tissues adjacent to tumors.RESULTS:In the single-locus analysis,two significantly decreased risk polymorphisms for gastric cancer were observed:the SNP3 rs17663887 TC genotype (adjusted odds ratio=0.38,95% confidence interval:0.21-0.71),compared with the wild-type TT genotype and the SNP5 rs12456284 GG genotype (0.31,0.16-0.60),and with the wild-type AA genotype.In the combined analyses of these two tSNPs,the combined genotypes with 2-3 protective alleles (SNP3 C and SNP5 G allele) had a significantly decreased risk of gastric cancer (0.28,0.16-0.49) than those with 0-1 protective allele.Furthermore,individuals with 0-1 protective allele had significantly decreased SMAD4 protein expression levels in the norma tissues adjacent to tumors than those with 2-3 protective alleles (P=0.025).CONCLUSION:These results suggest that genetic variants in the SMAD4 gene play a protective role in gastric cancer in a Chinese population.

Genetic variation of Porphyra yezoensis by using AFLP1

Genetic variation of 11 lines of Porphyra yezoensis from the coastline of Kagoshima of Japan, Qingdao, Nantong, Putuo and Nanji Islands of China were studied by using amplified fragment length polymorphism (AFLP). 778 bands were obtained with AFLP analysis of 16 primer combinations, among which 15 were unique, about 98.07% were polymorphic. The AFLP data showed that the closest genetic distance was 0 - 180 between two Kagoshima samples, and the farthest one was 0.397 between Kagoshima No. 1 and Nantong No - 9 line. The genetic distance showed that the variation was within the inner species scope. Neighbor-joining cluster and UPGMA cluster indicated that samples from Kagoshima and Qingdao were with high similarity and either with the samples of Nantong, Putuo and Nanji Islands. P. yezoensis in China shared high genetic diversity, and the genetic distance showed positive correlation with the geographic distance.