Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is...Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(p<0.001),this suggested that the genetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T.cuspidata species.These developed SNP markers can provide a molecular foundation for T.cuspidata breeding,construction of genetic maps,variety identification,and association analysis of agronomic traits.展开更多
The purpose of the present paper is to study and develop indicators and procedures for the evaluation of genetic structure changes in germplasm conservation due to social and natural environment reasons. Some basic ...The purpose of the present paper is to study and develop indicators and procedures for the evaluation of genetic structure changes in germplasm conservation due to social and natural environment reasons. Some basic concepts in germplasm study were introduced at first. Then, six kinds of indicators for genetic diversity as a measure of genetic potential of a germplasm collection were presented, i.e., numbers of different entities at certain level, evenness of the entity distribution, genetic similarity and genetic distance, genetic variance and genetic coefficient of variation, multivariate genetic variation indices, and coefficient of parentage. It was pointed out that genetic dispersion did not provide a complete concept of genetic diversity if without any information from genetic richness. Based on the above, the indicators for genetic erosion as the genetic structure changes of germplasm conservation due to social reasons, the indicators of genetic vulnerability as the genetic structure changes of germplasm conservation due to environmental stresses, the measurement of genetic drift and genetic shift as the genetic structure changes of germplasm collection during reproduction or seed increase were reviewed and developed. Furthermore, the estimation procedures of the indicators by using molecular markers were suggested. Finally, the case studies on suitable conservation sample size of self-pollinated and open-pollinated populations were given for reference.展开更多
Pinus yunnanensis Franch. is an particular conifer tree species in Yunnan-Guizhou plateau in south- west China. The morphological and anatomical traits of needles are important to evaluate geographic variation and pop...Pinus yunnanensis Franch. is an particular conifer tree species in Yunnan-Guizhou plateau in south- west China. The morphological and anatomical traits of needles are important to evaluate geographic variation and population dynamics of conifer species. Seedlings from seven populations of P. yunnanensis were analyzed, look- ing at 22 morphological and anatomical needle traits. The results showed that variations among and within popula- tions were significantly different for all traits and the variance components within populations were generally higher than that among populations in the most tested needle traits. The proportions of three-needle fascicle were significantly different among populations. The traits related to needle size in both morphology and anatomy were positive with latitude and negative with annual temperature and precipitation. Ratio indices, including mesophyllarea/vascular bundle area, mesophyll area/resin canals area, vascular bundle area/resin canals area and mesophyU area/(resin canals area and vascular bundle area), were negatively correlated with elevation and positively corre- lated with the annual mean temperature, showing some fitness feature for the populations. Needle traits were more significantly correlated with longitude than with other four environmental factors. Needle length was significantly correlated with almost all environmental factors. First four principal components accounted for 81.596 % of the variation with eigenvalues 〉1; the differences among populations were mainly dependent on needle width, stomatal density, section areas of vascular bundle, total resin canals, and mesophyll, as well as area ratio traits. Seven populations were divided into three categories by Euclidean distance. Variations in needle traits among the populations have shown systematic microevolution in terms of geographic impact on P. yunnanensis. This study would provide empirical data to characterize adaptation and genetic variation of P. yunnanensis, which would be helpful for management of genetic resources and reason- able utilization of them in future.展开更多
Bemisia tabaci (Gennadius) biotypes B and Q are two invasive biotypes in the species complex. The comparison of the population genetic structure of the two biotypes is of significance to show their invasive mechanis...Bemisia tabaci (Gennadius) biotypes B and Q are two invasive biotypes in the species complex. The comparison of the population genetic structure of the two biotypes is of significance to show their invasive mechanism and to their control. The intersimple sequence repeats (ISSR) marker was used to analyze the 16 B-biotype populations and 4 Q-biotype populations worldwide with a Trialeurodes vaporariorum population in Shanxi Province, China, and a B. tabaci non-B/Qbiotype population in Zhejiang Province, China, was used as control populations. The analysis of genetic diversity showed that the diversity indexes of biotype Q including Nei's gene diversity index, Shannon informative index, and the percentage of polymorphic loci were higher than those of biotype B. The high genetic diversity of biotype Q might provide the genetic basis for the excellent ecological adaptation. Cluster analysis suggested that the ISSR could not be used in the phylogenetic analysis though it could easily distinguish the biotypes of B. tabaci. The difference of the population genetic structure between the biotype B and the biotype Q exists based on the ISSR marker. Meanwhile, the results suggested that the molecular marker has its limitation in the phylogenetic analysis among the biotypes of B. tabaci.展开更多
Compared with other terrestrial environments,the stream environment generally presents a linear spatial structure and relatively simple environment.In a stream landscape,the dispersal direction of stream-type organism...Compared with other terrestrial environments,the stream environment generally presents a linear spatial structure and relatively simple environment.In a stream landscape,the dispersal direction of stream-type organisms usually presents a linear structure along the stream,which results in the limited dispersal and the genetic differentiation of stream-type organisms across different stream sections.The Shangcheng Stout Salamander(Pachyhynobius shangchengensis)is a narrowly distributed stream salamander in Dabie Mountains of East China.In the present study,we tested for the impact of stream landscape(i.e.waterfalls and underground river)on genetic structure and dispersal pattern in P.shangchengensis based on 12 nuclear microsatellite loci from 195 individuals in 3 populations(A,B and C)from three closely connected sections within one stream.Genetic diversity results suggested that Population B contains relatively high genetic diversity for P.shangchengensis when compared to the other populations(A and C).Detectable genetic differentiation was found(FST=0.008,P=0.007)among three populations,which was also supported by the Structure,FCA analysis and relatedness estimates of each pair of individuals among populations.The assignment test suggested that P.shangchengensis has philopatric males and female-biased dispersal(mean female Alc=.0.031,SE=0.225;mean male Alc=0.026,SE=0.198).Female-biased dispersal was also supported by analyses for each sex(i.e.Spatial autocorrelation,Genetic distance,Relatedness analysis).Our study indicated that small and isolated populations(A and C)had relatively low genetic diversity due to the limited population size.For stream salamanders,landscape features(i.e.waterfalls and underground river)can influence the ability of an individual to disperse through the landscape,and consequently influence the formation of strong genetic differentiation of P.shangchengensis.展开更多
Background:The Rufous-backed Bunting,Emberiza jankowskii,is an endangered species that is primarily distributed in Inner Mongolia,China.The main threats to the continued persistence of this species are habitat loss an...Background:The Rufous-backed Bunting,Emberiza jankowskii,is an endangered species that is primarily distributed in Inner Mongolia,China.The main threats to the continued persistence of this species are habitat loss and degradation.However,the impact of population loss on genetic diversity remains unclear.To support future conservation and management efforts,we assessed the genetic diversity and population structure of E.jankowskii using mitochondrial DNA and microsatellites.Methods:Blood samples were collected from 7-8-day-old nestlings in Inner Mongolia,China between May and August of 2012 and 2013.Mitochondrial DNA sequences and microsatellite markers were used to assess the genetic diversity,genetic structure and inbreeding of E.jankowskii.The results of genetic diversity and inbreeding were compared to other avian species.Results:We found an unexpectedly high level of genetic diversity in terms of mitochondrial DNA and microsatellite compared to other avian species.However,there were high levels of gene flow and minimal genetic structuring,among the fragmented breeding populations of E.jankowskii in Inner Mongolia.These findings suggest that E.jankowskii in Inner Mongolia is a metapopulation.Despite the high genetic diversity of E.jankowskii,local populations in each small patch remain at risk of extinction due to habitat loss.In addition,the E.jankowskii population has a high risk of inbreeding.Conclusions:To minimize further loss of genetic diversity of this endangered species,we suggest that the E.jankowskii in Inner Mongolia should be considered as a protected species for management purposes.Conservation efforts should concentrate on E.jankowskii habitat management.This may be most effectively achieved by protecting the current breeding habitats and prohibiting over-grazing.展开更多
[Objectives]The genetic diversity and population genetic structure of 107 inbred lines of maize in Yunnan were analyzed,in order to provide technical support for maize germplasm innovation,genetic improvement of germp...[Objectives]The genetic diversity and population genetic structure of 107 inbred lines of maize in Yunnan were analyzed,in order to provide technical support for maize germplasm innovation,genetic improvement of germplasm resources,variety management,and lay a solid foundation for exploring genes related to fine traits in the future.[Methods]The 107 maize inbred lines generalized in Yunnan were selected,and 45 backbone inbred lines commonly used in China were used as reference for heterotic group classification.On Axiom Maize 56K SNP Array platform,maize SNP chips(56K)were used to scan the whole maize genome,and the NJ-tree model of Treebest was used to construct a phylogenetic tree.Principal component analysis(PCA)was conducted by GCTA(genome-wide complex trait analysis)to reveal the genetic diversity and population genetic structure.[Results]In the 107 Yunnan local inbred lines,5533 uniformly distributed high-quality SNP marker sites were finally detected.Based on the analysis of these SNP marker sites,Nei s gene diversity index(H)of 107 maize germplasm genes was 0.2981-0.5000 with an average value being 0.4832,and polymorphism information content(PIC)values were 0.2536-0.3750 with an average value being 0.3662.The minimum allele frequency value was 0.5000-0.8178 with an average value being 0.5744.The analysis of population genetic structure showed that when K=6,the maximum value of△K was the maximum,which meant that the inbred lines used in this study could be divided into six groups.They were Tangsi Pingtou blood relationship group,PB blood relationship group,335 female blood relationship group,Zi 330 and the Lüda Honggu blood relationship group,unknown group 1 and unknown group 2.No inbred lines were divided into other heterotic groups.Among them,37 inbred lines from the 2 unknown groups could not be classified into the same group as the 10 known heterotic groups in China.The results of principal component analysis showed that the 107 maize inbred lines generalized in Yunnan could be clearly distinguished from the backbone maize inbred lines commonly used in China.Most of the maize inbred lines in Yunnan were concentrated near the reference backbone inbred lines.But some Yunnan inbred lines were far away from the reference inbred lines commonly used in China.[Conclusions]The maize germplasm resources in Yunnan area were rich in genetic diversity,including multiple heterotic groups,and there was a rich genetic basis of breeding parents.They could be clearly distinguished from the backbone inbred lines commonly used in China,and some of them had a long genetic distance from the backbone inbred lines.The resources which have good application potential can be used to create new heterotic groups.展开更多
To explore the spatial genetic structure of two HIV-Ⅰ-resistant polymorphisms (CCR2-64 Ⅰ and SDF1-3'A) alleles in the population of Shandong Province, China. Methods Using the techniques of spatial stratified sam...To explore the spatial genetic structure of two HIV-Ⅰ-resistant polymorphisms (CCR2-64 Ⅰ and SDF1-3'A) alleles in the population of Shandong Province, China. Methods Using the techniques of spatial stratified sampling and spatial statistics, the spatial genetic structure of the locus (CCR2-64 Ⅰ and SDF1-3'A), which was shown to be important co-receptor for HIV infection, was quantified from the populations of 36 sampled counties of Shandong Province, and a total of 3147 and 3172 samples were taken for testing CCR2-64Ⅰ and SDF1-3'A respectively from individuals without known history of HIV-Ⅰ infection and AIDS symptoms. Results There were significantly spatial genetic structures of the two alleles at different spatial distance classes on the scale of populations, but on the scale of individuals, no spatial structure was found in either the whole area of Shandong Province or the area of each sampled county. Although the change of frequencies of the two alleles with geographic locations in Shandong Province both showed gradual increase trends, their changing directions were inverse. The frequency of CCR2-64Ⅰallele gradually increased from the southwest to the northeast, while the frequency of SDF1-3'A allele gradually increased from the northeast to the southwest. However the RH to AIDS of combined types of their different genotypes did not represent obvious geographic diversity on the whole area of the Province. Conclusion The frequency of allele usually has some spatial genetic structures or spatial autocorrelation with different spatial distance classes, but the genotypes of individuals have random distribution in the same geographic area. Evaluating spatial distribution of the genetic susceptibility of HIV (AIDS) to CCR2-64Ⅰand SDF1-3'A alleles, should focus on the frequencies of combined genotypes of CCR2 and SDFI based on the two-locus genotypes of each individual rather than the frequencies of CCR2-641 and SDF1-3'A alleles.展开更多
Variations of structural loci among 4 sheep populations in China were examined by the method of multiloci electrophoresis, and similar data from 11 sheep populations were taken as basic references to analyze the genet...Variations of structural loci among 4 sheep populations in China were examined by the method of multiloci electrophoresis, and similar data from 11 sheep populations were taken as basic references to analyze the genetic structure of the native sheep populations in East and South Asia. The results showed that the average heterozygosity and effective number of alleles among 15 populations were 0.2746 and 1.559, respectively. Mongolian sheep possessed the largest average heterozygosity and effective number of alleles. Genetic diversity of sheep populations in Mongolia, China, Vietnam, Bangladesh and Nepal was reduced in this order. The coefficients of genetic differentiation were between 0.0126 and 0.3083, with the average of 0.148, demonstrating that genetic variations lay mainly in populations with 85.2% of the total variations. There exists no correlation between geographical distances and genetic distances. Gene flow was smooth among most populations, which led to inconsistency between geographical distances and genetic distances. The 15 native sheep populations in East and South Asia could be divided into two groups: One group included part populations of China and Mongolia, and the other included Yunnan populations of China, and part populations of Nepal and Bangladesh. Other populations did not cluster together and divide into the above-mentioned two groups. Tills study indicated genetic differentiation of the 15 native sheep populations in East and South Asia was relatively low, geographical isolation was not the main reason affecting genetic differentiation, and the fifteen sheep populations could be divided into two groups according to phylogenetic relationships.展开更多
We used 39 SSR markers to analyze the genetic structure of 304 major Chinese inbred rice varieties, and to compare changes in the indica or japonica components in these varieties that have been widely cultivated from ...We used 39 SSR markers to analyze the genetic structure of 304 major Chinese inbred rice varieties, and to compare changes in the indica or japonica components in these varieties that have been widely cultivated from the 1950s to the 1990s in China. The genetic structure analysis showed that these rice varieties were distinctly divided into two populations,' indica and japonica. The sub-structure of indica varieties was more complex than that of japonica ones. Among the various lines, late-season indica and early season japonica varieties had simpler genetic backgrounds. The seasonal ecotypes were not quite consistent with the subtypes of genetic structure. Twelve SSR loci with specific differentiation between indica and japonica were used to calculate the indica/japonica components. The differences in indica/japonica components among the five decades were not significant, except for late-season indica varieties in the 1990s, which had a significantly higher japonica component. These results will help to understand the genetic structure of the major Chinese inbred rice varieties and will be useful for indica-japonica hybrid breeding in China.展开更多
[ Objective] To analyze the genetic structure and genetic differentiation of Tibetan Mastiff populations and provide a theoretical basis for the protection and rational development and utilization of the Tibetan Masti...[ Objective] To analyze the genetic structure and genetic differentiation of Tibetan Mastiff populations and provide a theoretical basis for the protection and rational development and utilization of the Tibetan Mastiff breed resources. [ Method] A total of 86 blood samples were collected from two populations of Hequ Tibetan Mastiff (HTM) and Qinghai Tibetan Mastiff (QTM). The genetic structure and genetic differentiation of nine blood protein loci of "If, Po, Es-1, Es-2, S(alpha)2, Hb, AIb, Pr and Amy between these two populations were examined by vertical polyacrylam- ide gel electrophoresis with discontinuous buffer system. [ Result] The effective number of alleles (Ne), Shannon genetic diversity index (I) and Nei average expected gene heterozygosity (H) of the HTM were respectively 1.690 7, 0.485 5 and 0.295 9, and these were higher than those of QTM. The Nei's standard genetic distance (D) between HTM and QTM was 0.012 3, and the degree of genetic similarity was 0.987 8. The gene flow (Nm) of these two Tibetan Mastiff populations was 14.543 7. [ Conclusion] The genetic variability of intra-population of HTM was higher than that of QTM, and the genetic differentiation of inter-population was very low ( GsT = 0.018 7). Thereby, the great gene flow ( Nm = 14.543 7) is the main factor leading to the low genetic differentiation of the inter-population in different geographical groups.展开更多
We analyzed the fine-scale spatial genetic structure of the individuals of Zelkova schneideriana , which were classified by age using the spatial autocorrelation method, to quantify spatial patterns of genetic variati...We analyzed the fine-scale spatial genetic structure of the individuals of Zelkova schneideriana , which were classified by age using the spatial autocorrelation method, to quantify spatial patterns of genetic variation within the population and to explore potential mechanisms that determine genetic variation in population. The spatial autocorrelation coefficient ( r ) at 13 distance classes was determined on the basis of both geographical distance and genetic distance matrix which was derived from co-dominant SSR data using GenAlEx software. The results showed that all the individuals of Z. schneideriana exhibited significantly positive spatial genetic structure at distance less than 40 m (the X -intercept was 53.568), indicating that the average length of the smallest genetic patch for the same genotype clustering of the Z. schneideriana Mailing population was about 50 m. Limited seed dispersal is the main factor that leads to the spatial genetic variation within populations. The individuals in age Class II showed significantly positive spatial genetic structure at distance less than 30 m (the X -intercept was 47.882), while the individuals in age Class I and age Class III showed no significant spatial genetic structure in any of the spatial distance classes. Z. schneideriana is a long-lived perennial plant; the self-thinning resulted from the cohort competition between individuals in the growing process may lead to this certain spatial structure in age Class III of Z. schneideriana population.展开更多
To estimate the impact of crop rotation on the pathotype and genetic structure of Phythophthora sojae in fields, 372 isolates of P. sojae were obtained from long-term localisation experimental fields in Heilongjiang P...To estimate the impact of crop rotation on the pathotype and genetic structure of Phythophthora sojae in fields, 372 isolates of P. sojae were obtained from long-term localisation experimental fields in Heilongjiang Province of China. The hypocotyl inoculation method was used to characterize the virulence of P. sojae on 13 differential cultivars, and the amplified fragment length polymorphism(AFLP) technique was used to analyze difference in the genetic structure of P. sojae. The results indicated that an abundant diversity of genetic structures and pathotypes of P. sojae, a more uniform distribution of pathotypes and less dominance of pathotypes occurred in corn-soybean and wheat-soybean rotation fields than in a continuous soybean mono-cropping field. These findings suggested that P. sojae did not easily become the dominant race in rotation fields, which maintain disease resistance in soybean varieties. Therefore, the results of this study suggested that Phytophthora stem and root rot of soybeans could be effectively controlled by rotating soybeans with non-host crops of corn and wheat.展开更多
Massive actions have been and are being taken into protecting the world’s primates from extinction,while the study of the properties of genetic diversity,demographic history,and ecological relationships will benefit t...Massive actions have been and are being taken into protecting the world’s primates from extinction,while the study of the properties of genetic diversity,demographic history,and ecological relationships will benefit the understand-ing of the long-term survival of a species.The Taihangshan macaque(Macaca mulatta tcheliensis),a subspecies of rhesus macaque(Macaca mulatta),is endemic to China and currently restricted to southern Mt.Taihangshan area.Herein,we evaluated the genetic diversity,population structure,and demographic history of this subspecies using mitochondrial(Cytb and high variable region I:HVR I)and nuclear markers(microsatellite loci)of 131 in-dividuals collected from 9 localities covering the distribution range of this subspecies.Both phylogenetic analyses and genetic assignment revealed that the wild populations of Taihangshan macaques could be divided into 2 major highly divergent clades,THS-east and THS-west.Low genetic diversity(π:0.00266±0.00016)but high haplotype diversity(Hd:0.80352±0.015)were detected in the Taihangshan macaques,particularly in THS-east.Analyses of demographic history suggested that the Taihangshan macaques experiencedfirst a stable historical population size from Holocene to early 19th century but a subtle decline and then slight growth in the recent 200 years.We suggest that bridging the neighbor populations(i.e.setting corridors)would facilitate the male-mediated geneflow and subsequently increase the genetic diversity of the Taihangshan macaque populations.展开更多
The genetic diversity and genetic structure of a population of isolates of Sclerotinia sclerotiorum (Lib.) de Bary from different regions and host plants were investigated using the random amplified polymorphic DNA (R...The genetic diversity and genetic structure of a population of isolates of Sclerotinia sclerotiorum (Lib.) de Bary from different regions and host plants were investigated using the random amplified polymorphic DNA (RAPD) method with 20 random decamer primer pairs in order to provide some information on the phylogenetic taxa and breeding for resistance to sclerotinia stem rot. A minimum of three and a maximum of 15 unambiguously amplified bands were generated, furnishing a total of 170 bands ranging in size from 100 to 3 200 bp, corresponding to an average of 8.5 bands per primer pair. One hundred and four of these 170 bands (61.2%) were polymorphic, the percentage of polymorphic bands for each primer pair ranging from 0.0% to 86.7%. The genetic relationships among the isolates, based on the results of RAPD analysis, were examined. The genetic similarity of all selected isolates was quite high. At the species level, the genetic diversity estimated by Nei's gene diversity (h) was 0.197 and Shannon's index of diversity (I) was 0.300. The unweighted pair-group mean analysis (UPGMA) cluster analysis showed that most isolates from the same regions were grouped in the same cluster or a close cluster. The population of isolates from Hefei (Anhui Province, China) was more uniform and relatively distant to other populations. The Canadian population collected from carrot (Daucus carota var. sativa DC.) was relatively close to the Polish population collected from oilseed rape (Brassica napus L.) plants. There was no relationship between isolates from the same host plants. An analysis of molecular variance (AMOVA) revealed that the percentage of variance attributable to variation among and within populations was 50.62% and 49.38%, respectively. When accessions from China, Europe, and Canada were treated as three separate groups, the variance components among groups, among populations within groups, and within populations were ?0.96%, 51.48%, and 49.47%, respectively. The genetic differentiations among and within populations were highly significant (P < 0.001). Similarly, the coefficient of gene differentiation (Gst) in total populations calculated by population genetic analysis was 0.229 4, which indicated that the genetic variation among populations was 22.94%. The gene flow (Nm) was 1.68, which indicated that the gene permutation and interaction among populations was relatively high.展开更多
China is a center of diversity for Malus Mill,with 27 native species including 21 wild species and six domesticated species.We applied a set of 19 simple sequence repeat markers to genotype 798 accessions of 17 specie...China is a center of diversity for Malus Mill,with 27 native species including 21 wild species and six domesticated species.We applied a set of 19 simple sequence repeat markers to genotype 798 accessions of 17 species(12 wild species and five cultivated species)of Malus originating from 14 provinces in China.A total of 500 alleles were detected.Diversity statistics indicated a high level of genetic variation as quantified by the average values of the effective allele number(N_(e)).expected heterozygosity(H_(e)),and Shannon's Information Index(I)(10.309,0.886,and 2.545,respectively).Malus sieversii(MSR;H_(e)=0.814,I=2.041,N_(e)=6.054),M.baccata(MBB;H_(e)=0.848,/=2.350,N_(e)=8.652),M.toringoides(MTH;He=0.663,I=1.355,N_(e)=3.332),and M.hupehensis(MHR;H_(e)=0.539,I=0.912,N_(e)=0.579)showed a higher level of genetic diversity in this study than the previous studies.MSR and MBB contributed to the origin and evolution of some accessions of M.domestica subsp.chinensis(MDC).However,other accessions of MDC showed a closer genetic distance with MBB and cultivated species,especially M.robusta(MRB),M.asiatica(MAN),and M.prunifolia(MPB).Not all accessions of MDC were descended from MSR in Xinjiang Uygur Autonomous Region of China.This research provides novel insights into the genetic relationships of Malus native to China,which will be useful for genetic association studies,germplasm conservation,and breeding programs.展开更多
The traditional medicinal plant,and endangered species Aristolochia delavayi(Aristolochiaceae)is an endemic species in China and occurs in the warm and dry areas along the Jinsha river.It is also a specific host of th...The traditional medicinal plant,and endangered species Aristolochia delavayi(Aristolochiaceae)is an endemic species in China and occurs in the warm and dry areas along the Jinsha river.It is also a specific host of the larvae of Byasa daemonius,a vulnerable butterfly.In this study,15 pairs of polymorphic microsatellite primers of A.delavayi were designed and screened based on the Simple Sequence Repeats(SSR)loci found by using the results of genome skimming.Based on these 15 SSR markers,the genetic diversity and structure of 193 individuals from ten natural populations were analyzed in detail.In comparison to other endemic and endangered plants in the region,the population of A.delavayi possess a relatively high genetic diversity(He=0.550,I=1.112).AMOVA analysis showed that 68.4%of the total genetic diversity was within populations and 31.6%of the variation occurred among populations.There was a significant genetic differentiation among natural populations of A.delavayi detectable,with low gene flow(Nm=0.591).This might be attributed to geographical barriers and limited seed dispersal.To test the isolation by distance(IBD),we performed Mantel test,which showed a significant correlation between the geographic and genetic distances.In order to cope with the possible biases caused by IBD,we additionally performed Bayesian genetic cluster analyses and principal coordinate analysis(PCoA).The final cluster analysis revealed three groups with distinct geographical distribution.Habitat fragmentation and limited gene flow between these populations may be the main reasons for the current genetic structure.For conservation of this species,we suggest to divide its populations into three protection management units,with subsequent focus on the Yongsheng and Luquan populations which experienced a genetic bottleneck event in the past.展开更多
Aims The dispersal of pollen and seeds is spatially restricted and may vary among plant populations because of varying biotic interactions,population histories or abiotic conditions.Because gene dispersal is spatially...Aims The dispersal of pollen and seeds is spatially restricted and may vary among plant populations because of varying biotic interactions,population histories or abiotic conditions.Because gene dispersal is spatially restricted,it will eventually result in the development of spatial genetic structure(SGS),which in turn can allow insights into gene dispersal processes.Here,we assessed the effect of habitat characteristics like population density and community structure on small-scale SGS and estimate historical gene dispersal at different spatial scales.Methods In a set of 12 populations of the subtropical understory shrub Ardisia crenata,we assessed genetic variation at 7 microsatellite loci within and among populations.We investigated small-scale genetic structure with spatial genetic autocorrelation statistics and heterogeneity tests and estimated gene dispersal distances based on population differentiation and on within-population SGS.SGS was related to habitat characteristics by multiple regression.Important Findings The populations showed high genetic diversity(He=0.64)within populations and rather strong genetic differentiation(F#ST=0.208)among populations,following an isolation-by-distance pattern,which suggests that populations are in gene flow–drift equilibrium.Significant SGS was present within populations(mean Sp=0.027).Population density and species diversity had a joint effect on SGS with low population density and high species diversity leading to stronger small-scale SGS.Estimates of historical gene dispersal from between-population differentiation and from within-population SGS resulted in similar values between 4.8 and 22.9 m.The results indicate that local-ranged pollen dispersal and inefficient long-distance seed dispersal,both affected by population density and species diversity,contributed to the genetic population structure of the species.We suggest that SGS in shrubs is more similar to that of herbs than to trees and that in communities with high species diversity gene flow is more restricted than at low species diversity.This may represent a process that retards the development of a positive species diversity–genetic diversity relationship.展开更多
Camellia huana is an endangered species with a narrow distribution in limestone hills of northern Guangxi and southern Guizhou provinces,China.We used one chloroplast DNA(cpDNA)fragment and 12 pairs of microsatellite(...Camellia huana is an endangered species with a narrow distribution in limestone hills of northern Guangxi and southern Guizhou provinces,China.We used one chloroplast DNA(cpDNA)fragment and 12 pairs of microsatellite(simple sequence repeat;SSR)markers to assess the genetic diversity and structure of 12 C.huana populations.A total of 99 alleles were detected for 12 polymorphic loci,and eight haplotypes and nine polymorphic sites were detected within 5200 bp of cpDNA.C.huana populations showed a low level of genetic diversity(n=8,Hd=0.759,Pi=0.00042 for cpDNA,NA=3.931,HE=0.466 for SSRs),but high genetic differentiation between populations(FST=0.2159 for SSRs,FST=0.9318 for cpDNA).This can be attributed to the narrow distribution and limestone habitat of C.huana.STRUCTURE analysis divided natural C.huana populations into two groups,consistent with their geographical distribution.Thus,we suggest that five natural C.huana populations should be split into two units to be managed effectively.展开更多
Compared with traditional genetic markers,genomic approaches have proved valuable to the conservation of endangered species.Paeonia ludlowii having rarely and pure yellow flowers,is one of the world’s most famous tre...Compared with traditional genetic markers,genomic approaches have proved valuable to the conservation of endangered species.Paeonia ludlowii having rarely and pure yellow flowers,is one of the world’s most famous tree peonies.However,only several wild populations remain in the Yarlung Zangbo Valley(Nyingchi and Shannan regions,Xizang)in China due to increasing anthropogenic impact on the natural habitats.We used genome-wide single nucleotide polymorphisms to elucidate the spatial pattern of genetic variation,population structure and demographic history of P.ludlowii from the fragmented region comprising the entire range of this species,aiming to provide a basis for conserving the genetic resources of this species.Unlike genetic uniformity among populations revealed in previous studies,we found low but varied levels of intra-population genetic diversity,in which lower genetic diversity was detected in the population in Shannan region compared to those in Nyingzhi region.These spatial patterns may be likely associated with different population sizes caused by micro-environment differences in these two regions.Additionally,low genetic differentiation among populations(Fst=0.0037)were detected at the species level.This line of evidence,combined with the result of significant genetic differentiation between the two closest populations and lack of isolation by distance,suggested that shared ancestry among now remnant populations rather than contemporary genetic connectivity resulted in subtle population structure.Demographic inference suggested that P.ludlowii probably experienced a temporal history of sharp population decline during the period of Last Glacial Maximum,and a subsequent bottleneck event resulting from prehistoric human activities on the Qinghai-Tibet Plateau.All these events,together with current habitat fragment and excavation might contribute to the endangered status of P.ludlowii.Our study improved the genetic characterization of the endangered tree peony(P.ludlowii)in China,and these genetic inferences should be considered when making different in situ and ex situ conservation actions for P.ludlowii in this evolutionary hotspot region.展开更多
基金This work was supported by Grants from the National Science Foundation of China to Yanwen Zhang(32272757,31972363)Grants from the Liaoning Provincial Department of Education Project to Dandan Wang(JYTMS20230698)Grants from the Liaoning Provincial Science and Technology Fund Project:Comparative Multi-Omics Study of Wild and Cultivated Species of Taxus chinensis.
文摘Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(p<0.001),this suggested that the genetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T.cuspidata species.These developed SNP markers can provide a molecular foundation for T.cuspidata breeding,construction of genetic maps,variety identification,and association analysis of agronomic traits.
基金supported by the National Natural Science Foundation of China(30270805 and 30490250)Doctorate Foundation of Higher Education(20020307028).
文摘The purpose of the present paper is to study and develop indicators and procedures for the evaluation of genetic structure changes in germplasm conservation due to social and natural environment reasons. Some basic concepts in germplasm study were introduced at first. Then, six kinds of indicators for genetic diversity as a measure of genetic potential of a germplasm collection were presented, i.e., numbers of different entities at certain level, evenness of the entity distribution, genetic similarity and genetic distance, genetic variance and genetic coefficient of variation, multivariate genetic variation indices, and coefficient of parentage. It was pointed out that genetic dispersion did not provide a complete concept of genetic diversity if without any information from genetic richness. Based on the above, the indicators for genetic erosion as the genetic structure changes of germplasm conservation due to social reasons, the indicators of genetic vulnerability as the genetic structure changes of germplasm conservation due to environmental stresses, the measurement of genetic drift and genetic shift as the genetic structure changes of germplasm collection during reproduction or seed increase were reviewed and developed. Furthermore, the estimation procedures of the indicators by using molecular markers were suggested. Finally, the case studies on suitable conservation sample size of self-pollinated and open-pollinated populations were given for reference.
基金finically supported by the Natural Science Foundation of China(31070591)Special National Forestry Public Welfare Industry Research(201104022)the support of Southwest Forestry University
文摘Pinus yunnanensis Franch. is an particular conifer tree species in Yunnan-Guizhou plateau in south- west China. The morphological and anatomical traits of needles are important to evaluate geographic variation and population dynamics of conifer species. Seedlings from seven populations of P. yunnanensis were analyzed, look- ing at 22 morphological and anatomical needle traits. The results showed that variations among and within popula- tions were significantly different for all traits and the variance components within populations were generally higher than that among populations in the most tested needle traits. The proportions of three-needle fascicle were significantly different among populations. The traits related to needle size in both morphology and anatomy were positive with latitude and negative with annual temperature and precipitation. Ratio indices, including mesophyllarea/vascular bundle area, mesophyll area/resin canals area, vascular bundle area/resin canals area and mesophyU area/(resin canals area and vascular bundle area), were negatively correlated with elevation and positively corre- lated with the annual mean temperature, showing some fitness feature for the populations. Needle traits were more significantly correlated with longitude than with other four environmental factors. Needle length was significantly correlated with almost all environmental factors. First four principal components accounted for 81.596 % of the variation with eigenvalues 〉1; the differences among populations were mainly dependent on needle width, stomatal density, section areas of vascular bundle, total resin canals, and mesophyll, as well as area ratio traits. Seven populations were divided into three categories by Euclidean distance. Variations in needle traits among the populations have shown systematic microevolution in terms of geographic impact on P. yunnanensis. This study would provide empirical data to characterize adaptation and genetic variation of P. yunnanensis, which would be helpful for management of genetic resources and reason- able utilization of them in future.
基金funded by the National Program on Basic Research Projects of China (973 Program,2002CB111400)National Natural Science Foundation of China (30500331,30771410)+4 种基金the Natural Science Foundation of Beijing Municipal (6062024)Excellent Young Scientist Foundation of Shandong Province(2007BS06013)Innovation Foundation of Shandong Academy of Agricultural Sciences (Q2006B052007YCX030)the National Key Technologies R&D Program of China during the 11th Five-Year Plan period (2006BAD08A18)
文摘Bemisia tabaci (Gennadius) biotypes B and Q are two invasive biotypes in the species complex. The comparison of the population genetic structure of the two biotypes is of significance to show their invasive mechanism and to their control. The intersimple sequence repeats (ISSR) marker was used to analyze the 16 B-biotype populations and 4 Q-biotype populations worldwide with a Trialeurodes vaporariorum population in Shanxi Province, China, and a B. tabaci non-B/Qbiotype population in Zhejiang Province, China, was used as control populations. The analysis of genetic diversity showed that the diversity indexes of biotype Q including Nei's gene diversity index, Shannon informative index, and the percentage of polymorphic loci were higher than those of biotype B. The high genetic diversity of biotype Q might provide the genetic basis for the excellent ecological adaptation. Cluster analysis suggested that the ISSR could not be used in the phylogenetic analysis though it could easily distinguish the biotypes of B. tabaci. The difference of the population genetic structure between the biotype B and the biotype Q exists based on the ISSR marker. Meanwhile, the results suggested that the molecular marker has its limitation in the phylogenetic analysis among the biotypes of B. tabaci.
基金supported by the National Na tural Science Founda tion of China(Grant No.31272332)Biodiversity Survey,Monitoring and Assessment Project of Ministry of Ecology and Environment China(2019HB2096001006)+6 种基金National Key Research and Development Program(2016YFC1200705)Anhui Province Higher Education Revitalization Plan2014 Colleges and Universities Outstanding Youth Talent Support Program2017 Anhui Province academic and technical leaders candidates(2017H130)Anhui Natural Science Foundation(Youth,1908085QC127)Research start-up funds of Anhui Normal University(No.751865)The Natural Science Foundation of the Jiangsu Higher Education Institutions of China(15KJB180003)。
文摘Compared with other terrestrial environments,the stream environment generally presents a linear spatial structure and relatively simple environment.In a stream landscape,the dispersal direction of stream-type organisms usually presents a linear structure along the stream,which results in the limited dispersal and the genetic differentiation of stream-type organisms across different stream sections.The Shangcheng Stout Salamander(Pachyhynobius shangchengensis)is a narrowly distributed stream salamander in Dabie Mountains of East China.In the present study,we tested for the impact of stream landscape(i.e.waterfalls and underground river)on genetic structure and dispersal pattern in P.shangchengensis based on 12 nuclear microsatellite loci from 195 individuals in 3 populations(A,B and C)from three closely connected sections within one stream.Genetic diversity results suggested that Population B contains relatively high genetic diversity for P.shangchengensis when compared to the other populations(A and C).Detectable genetic differentiation was found(FST=0.008,P=0.007)among three populations,which was also supported by the Structure,FCA analysis and relatedness estimates of each pair of individuals among populations.The assignment test suggested that P.shangchengensis has philopatric males and female-biased dispersal(mean female Alc=.0.031,SE=0.225;mean male Alc=0.026,SE=0.198).Female-biased dispersal was also supported by analyses for each sex(i.e.Spatial autocorrelation,Genetic distance,Relatedness analysis).Our study indicated that small and isolated populations(A and C)had relatively low genetic diversity due to the limited population size.For stream salamanders,landscape features(i.e.waterfalls and underground river)can influence the ability of an individual to disperse through the landscape,and consequently influence the formation of strong genetic differentiation of P.shangchengensis.
基金financed by the National Natural Science Foundation of China(Grant Nos.31601856 and 31670398)。
文摘Background:The Rufous-backed Bunting,Emberiza jankowskii,is an endangered species that is primarily distributed in Inner Mongolia,China.The main threats to the continued persistence of this species are habitat loss and degradation.However,the impact of population loss on genetic diversity remains unclear.To support future conservation and management efforts,we assessed the genetic diversity and population structure of E.jankowskii using mitochondrial DNA and microsatellites.Methods:Blood samples were collected from 7-8-day-old nestlings in Inner Mongolia,China between May and August of 2012 and 2013.Mitochondrial DNA sequences and microsatellite markers were used to assess the genetic diversity,genetic structure and inbreeding of E.jankowskii.The results of genetic diversity and inbreeding were compared to other avian species.Results:We found an unexpectedly high level of genetic diversity in terms of mitochondrial DNA and microsatellite compared to other avian species.However,there were high levels of gene flow and minimal genetic structuring,among the fragmented breeding populations of E.jankowskii in Inner Mongolia.These findings suggest that E.jankowskii in Inner Mongolia is a metapopulation.Despite the high genetic diversity of E.jankowskii,local populations in each small patch remain at risk of extinction due to habitat loss.In addition,the E.jankowskii population has a high risk of inbreeding.Conclusions:To minimize further loss of genetic diversity of this endangered species,we suggest that the E.jankowskii in Inner Mongolia should be considered as a protected species for management purposes.Conservation efforts should concentrate on E.jankowskii habitat management.This may be most effectively achieved by protecting the current breeding habitats and prohibiting over-grazing.
基金Study on Maize Variety Management Based on DUS Test and SNP Molecular Fingerprint.
文摘[Objectives]The genetic diversity and population genetic structure of 107 inbred lines of maize in Yunnan were analyzed,in order to provide technical support for maize germplasm innovation,genetic improvement of germplasm resources,variety management,and lay a solid foundation for exploring genes related to fine traits in the future.[Methods]The 107 maize inbred lines generalized in Yunnan were selected,and 45 backbone inbred lines commonly used in China were used as reference for heterotic group classification.On Axiom Maize 56K SNP Array platform,maize SNP chips(56K)were used to scan the whole maize genome,and the NJ-tree model of Treebest was used to construct a phylogenetic tree.Principal component analysis(PCA)was conducted by GCTA(genome-wide complex trait analysis)to reveal the genetic diversity and population genetic structure.[Results]In the 107 Yunnan local inbred lines,5533 uniformly distributed high-quality SNP marker sites were finally detected.Based on the analysis of these SNP marker sites,Nei s gene diversity index(H)of 107 maize germplasm genes was 0.2981-0.5000 with an average value being 0.4832,and polymorphism information content(PIC)values were 0.2536-0.3750 with an average value being 0.3662.The minimum allele frequency value was 0.5000-0.8178 with an average value being 0.5744.The analysis of population genetic structure showed that when K=6,the maximum value of△K was the maximum,which meant that the inbred lines used in this study could be divided into six groups.They were Tangsi Pingtou blood relationship group,PB blood relationship group,335 female blood relationship group,Zi 330 and the Lüda Honggu blood relationship group,unknown group 1 and unknown group 2.No inbred lines were divided into other heterotic groups.Among them,37 inbred lines from the 2 unknown groups could not be classified into the same group as the 10 known heterotic groups in China.The results of principal component analysis showed that the 107 maize inbred lines generalized in Yunnan could be clearly distinguished from the backbone maize inbred lines commonly used in China.Most of the maize inbred lines in Yunnan were concentrated near the reference backbone inbred lines.But some Yunnan inbred lines were far away from the reference inbred lines commonly used in China.[Conclusions]The maize germplasm resources in Yunnan area were rich in genetic diversity,including multiple heterotic groups,and there was a rich genetic basis of breeding parents.They could be clearly distinguished from the backbone inbred lines commonly used in China,and some of them had a long genetic distance from the backbone inbred lines.The resources which have good application potential can be used to create new heterotic groups.
文摘To explore the spatial genetic structure of two HIV-Ⅰ-resistant polymorphisms (CCR2-64 Ⅰ and SDF1-3'A) alleles in the population of Shandong Province, China. Methods Using the techniques of spatial stratified sampling and spatial statistics, the spatial genetic structure of the locus (CCR2-64 Ⅰ and SDF1-3'A), which was shown to be important co-receptor for HIV infection, was quantified from the populations of 36 sampled counties of Shandong Province, and a total of 3147 and 3172 samples were taken for testing CCR2-64Ⅰ and SDF1-3'A respectively from individuals without known history of HIV-Ⅰ infection and AIDS symptoms. Results There were significantly spatial genetic structures of the two alleles at different spatial distance classes on the scale of populations, but on the scale of individuals, no spatial structure was found in either the whole area of Shandong Province or the area of each sampled county. Although the change of frequencies of the two alleles with geographic locations in Shandong Province both showed gradual increase trends, their changing directions were inverse. The frequency of CCR2-64Ⅰallele gradually increased from the southwest to the northeast, while the frequency of SDF1-3'A allele gradually increased from the northeast to the southwest. However the RH to AIDS of combined types of their different genotypes did not represent obvious geographic diversity on the whole area of the Province. Conclusion The frequency of allele usually has some spatial genetic structures or spatial autocorrelation with different spatial distance classes, but the genotypes of individuals have random distribution in the same geographic area. Evaluating spatial distribution of the genetic susceptibility of HIV (AIDS) to CCR2-64Ⅰand SDF1-3'A alleles, should focus on the frequencies of combined genotypes of CCR2 and SDFI based on the two-locus genotypes of each individual rather than the frequencies of CCR2-641 and SDF1-3'A alleles.
基金This study was supported by Basic Natural Science Foundation for Colleges and Universities of Jiangsu Province, China (06KJD230203)International Cooperation Project of the National Natural Science Foundation, China (30213001, 30210103007,3041013150).
文摘Variations of structural loci among 4 sheep populations in China were examined by the method of multiloci electrophoresis, and similar data from 11 sheep populations were taken as basic references to analyze the genetic structure of the native sheep populations in East and South Asia. The results showed that the average heterozygosity and effective number of alleles among 15 populations were 0.2746 and 1.559, respectively. Mongolian sheep possessed the largest average heterozygosity and effective number of alleles. Genetic diversity of sheep populations in Mongolia, China, Vietnam, Bangladesh and Nepal was reduced in this order. The coefficients of genetic differentiation were between 0.0126 and 0.3083, with the average of 0.148, demonstrating that genetic variations lay mainly in populations with 85.2% of the total variations. There exists no correlation between geographical distances and genetic distances. Gene flow was smooth among most populations, which led to inconsistency between geographical distances and genetic distances. The 15 native sheep populations in East and South Asia could be divided into two groups: One group included part populations of China and Mongolia, and the other included Yunnan populations of China, and part populations of Nepal and Bangladesh. Other populations did not cluster together and divide into the above-mentioned two groups. Tills study indicated genetic differentiation of the 15 native sheep populations in East and South Asia was relatively low, geographical isolation was not the main reason affecting genetic differentiation, and the fifteen sheep populations could be divided into two groups according to phylogenetic relationships.
基金supported by the Special Fund for Agro-scientific Research in the Public Interest(Grant No. 200903008-05)the Basic Research Budget of China National Rice Research Institute (Grant No. 2009RG001-3)the Crop Genetic Resource Protection Program of Ministry of Agriculture,China (Grant No. NB2130135)
文摘We used 39 SSR markers to analyze the genetic structure of 304 major Chinese inbred rice varieties, and to compare changes in the indica or japonica components in these varieties that have been widely cultivated from the 1950s to the 1990s in China. The genetic structure analysis showed that these rice varieties were distinctly divided into two populations,' indica and japonica. The sub-structure of indica varieties was more complex than that of japonica ones. Among the various lines, late-season indica and early season japonica varieties had simpler genetic backgrounds. The seasonal ecotypes were not quite consistent with the subtypes of genetic structure. Twelve SSR loci with specific differentiation between indica and japonica were used to calculate the indica/japonica components. The differences in indica/japonica components among the five decades were not significant, except for late-season indica varieties in the 1990s, which had a significantly higher japonica component. These results will help to understand the genetic structure of the major Chinese inbred rice varieties and will be useful for indica-japonica hybrid breeding in China.
基金supported by the Project of Gansu Province Scientific Department(GKC-97-27-5)Young Teacher Project of Tianshui Normal University
文摘[ Objective] To analyze the genetic structure and genetic differentiation of Tibetan Mastiff populations and provide a theoretical basis for the protection and rational development and utilization of the Tibetan Mastiff breed resources. [ Method] A total of 86 blood samples were collected from two populations of Hequ Tibetan Mastiff (HTM) and Qinghai Tibetan Mastiff (QTM). The genetic structure and genetic differentiation of nine blood protein loci of "If, Po, Es-1, Es-2, S(alpha)2, Hb, AIb, Pr and Amy between these two populations were examined by vertical polyacrylam- ide gel electrophoresis with discontinuous buffer system. [ Result] The effective number of alleles (Ne), Shannon genetic diversity index (I) and Nei average expected gene heterozygosity (H) of the HTM were respectively 1.690 7, 0.485 5 and 0.295 9, and these were higher than those of QTM. The Nei's standard genetic distance (D) between HTM and QTM was 0.012 3, and the degree of genetic similarity was 0.987 8. The gene flow (Nm) of these two Tibetan Mastiff populations was 14.543 7. [ Conclusion] The genetic variability of intra-population of HTM was higher than that of QTM, and the genetic differentiation of inter-population was very low ( GsT = 0.018 7). Thereby, the great gene flow ( Nm = 14.543 7) is the main factor leading to the low genetic differentiation of the inter-population in different geographical groups.
基金Supported by the Scientific Research and Technological Development Project of Guangxi(1598025-42)the Guangxi Youth Fund Project(2013GXNSFBA019093)+1 种基金the National Forestry Public Welfare Industry Research Project(200904011)the Open Project for Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation(15-B-03-01)
文摘We analyzed the fine-scale spatial genetic structure of the individuals of Zelkova schneideriana , which were classified by age using the spatial autocorrelation method, to quantify spatial patterns of genetic variation within the population and to explore potential mechanisms that determine genetic variation in population. The spatial autocorrelation coefficient ( r ) at 13 distance classes was determined on the basis of both geographical distance and genetic distance matrix which was derived from co-dominant SSR data using GenAlEx software. The results showed that all the individuals of Z. schneideriana exhibited significantly positive spatial genetic structure at distance less than 40 m (the X -intercept was 53.568), indicating that the average length of the smallest genetic patch for the same genotype clustering of the Z. schneideriana Mailing population was about 50 m. Limited seed dispersal is the main factor that leads to the spatial genetic variation within populations. The individuals in age Class II showed significantly positive spatial genetic structure at distance less than 30 m (the X -intercept was 47.882), while the individuals in age Class I and age Class III showed no significant spatial genetic structure in any of the spatial distance classes. Z. schneideriana is a long-lived perennial plant; the self-thinning resulted from the cohort competition between individuals in the growing process may lead to this certain spatial structure in age Class III of Z. schneideriana population.
基金Supported by the Special Fund for Agro-scientific Research in the Public Interest(201303018)the National Natural Science Foundation of China(31370449)
文摘To estimate the impact of crop rotation on the pathotype and genetic structure of Phythophthora sojae in fields, 372 isolates of P. sojae were obtained from long-term localisation experimental fields in Heilongjiang Province of China. The hypocotyl inoculation method was used to characterize the virulence of P. sojae on 13 differential cultivars, and the amplified fragment length polymorphism(AFLP) technique was used to analyze difference in the genetic structure of P. sojae. The results indicated that an abundant diversity of genetic structures and pathotypes of P. sojae, a more uniform distribution of pathotypes and less dominance of pathotypes occurred in corn-soybean and wheat-soybean rotation fields than in a continuous soybean mono-cropping field. These findings suggested that P. sojae did not easily become the dominant race in rotation fields, which maintain disease resistance in soybean varieties. Therefore, the results of this study suggested that Phytophthora stem and root rot of soybeans could be effectively controlled by rotating soybeans with non-host crops of corn and wheat.
基金financially supported by the Cultivation Fund for Young Teachers in Natural Science Basic Research of Zhengzhou University(JC2020043029)the National Natural Science Foundation of China(Nos.31672302 and 32070446).
文摘Massive actions have been and are being taken into protecting the world’s primates from extinction,while the study of the properties of genetic diversity,demographic history,and ecological relationships will benefit the understand-ing of the long-term survival of a species.The Taihangshan macaque(Macaca mulatta tcheliensis),a subspecies of rhesus macaque(Macaca mulatta),is endemic to China and currently restricted to southern Mt.Taihangshan area.Herein,we evaluated the genetic diversity,population structure,and demographic history of this subspecies using mitochondrial(Cytb and high variable region I:HVR I)and nuclear markers(microsatellite loci)of 131 in-dividuals collected from 9 localities covering the distribution range of this subspecies.Both phylogenetic analyses and genetic assignment revealed that the wild populations of Taihangshan macaques could be divided into 2 major highly divergent clades,THS-east and THS-west.Low genetic diversity(π:0.00266±0.00016)but high haplotype diversity(Hd:0.80352±0.015)were detected in the Taihangshan macaques,particularly in THS-east.Analyses of demographic history suggested that the Taihangshan macaques experiencedfirst a stable historical population size from Holocene to early 19th century but a subtle decline and then slight growth in the recent 200 years.We suggest that bridging the neighbor populations(i.e.setting corridors)would facilitate the male-mediated geneflow and subsequently increase the genetic diversity of the Taihangshan macaque populations.
基金Basic Research and Development Plan of China,国家科技攻关项目,the Sino-Polish Scientific and Technological Cooperation Project for 2004-2006,中国科学院资助项目
文摘The genetic diversity and genetic structure of a population of isolates of Sclerotinia sclerotiorum (Lib.) de Bary from different regions and host plants were investigated using the random amplified polymorphic DNA (RAPD) method with 20 random decamer primer pairs in order to provide some information on the phylogenetic taxa and breeding for resistance to sclerotinia stem rot. A minimum of three and a maximum of 15 unambiguously amplified bands were generated, furnishing a total of 170 bands ranging in size from 100 to 3 200 bp, corresponding to an average of 8.5 bands per primer pair. One hundred and four of these 170 bands (61.2%) were polymorphic, the percentage of polymorphic bands for each primer pair ranging from 0.0% to 86.7%. The genetic relationships among the isolates, based on the results of RAPD analysis, were examined. The genetic similarity of all selected isolates was quite high. At the species level, the genetic diversity estimated by Nei's gene diversity (h) was 0.197 and Shannon's index of diversity (I) was 0.300. The unweighted pair-group mean analysis (UPGMA) cluster analysis showed that most isolates from the same regions were grouped in the same cluster or a close cluster. The population of isolates from Hefei (Anhui Province, China) was more uniform and relatively distant to other populations. The Canadian population collected from carrot (Daucus carota var. sativa DC.) was relatively close to the Polish population collected from oilseed rape (Brassica napus L.) plants. There was no relationship between isolates from the same host plants. An analysis of molecular variance (AMOVA) revealed that the percentage of variance attributable to variation among and within populations was 50.62% and 49.38%, respectively. When accessions from China, Europe, and Canada were treated as three separate groups, the variance components among groups, among populations within groups, and within populations were ?0.96%, 51.48%, and 49.47%, respectively. The genetic differentiations among and within populations were highly significant (P < 0.001). Similarly, the coefficient of gene differentiation (Gst) in total populations calculated by population genetic analysis was 0.229 4, which indicated that the genetic variation among populations was 22.94%. The gene flow (Nm) was 1.68, which indicated that the gene permutation and interaction among populations was relatively high.
基金the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ASTIP).
文摘China is a center of diversity for Malus Mill,with 27 native species including 21 wild species and six domesticated species.We applied a set of 19 simple sequence repeat markers to genotype 798 accessions of 17 species(12 wild species and five cultivated species)of Malus originating from 14 provinces in China.A total of 500 alleles were detected.Diversity statistics indicated a high level of genetic variation as quantified by the average values of the effective allele number(N_(e)).expected heterozygosity(H_(e)),and Shannon's Information Index(I)(10.309,0.886,and 2.545,respectively).Malus sieversii(MSR;H_(e)=0.814,I=2.041,N_(e)=6.054),M.baccata(MBB;H_(e)=0.848,/=2.350,N_(e)=8.652),M.toringoides(MTH;He=0.663,I=1.355,N_(e)=3.332),and M.hupehensis(MHR;H_(e)=0.539,I=0.912,N_(e)=0.579)showed a higher level of genetic diversity in this study than the previous studies.MSR and MBB contributed to the origin and evolution of some accessions of M.domestica subsp.chinensis(MDC).However,other accessions of MDC showed a closer genetic distance with MBB and cultivated species,especially M.robusta(MRB),M.asiatica(MAN),and M.prunifolia(MPB).Not all accessions of MDC were descended from MSR in Xinjiang Uygur Autonomous Region of China.This research provides novel insights into the genetic relationships of Malus native to China,which will be useful for genetic association studies,germplasm conservation,and breeding programs.
基金Support for this study was provided by grants from the NSFC(National Natural Science Foundation of China)-Yunnan Joint fund to support key projects(No.U1602264)Yunnan Ten Thousand Talents Plan Young&Elite Talent Project to G.Chen(YNWR-QNBJ-2018-017)+2 种基金NSFC(National Natural Science Foundation of China)(No.31660057)Y.P.GengScience&Technology Basic Resources Investigation Program of China for Survey and Germplasm Conservation of PSESP in Southwest China(2017FY100100)to W.B.Sun.
文摘The traditional medicinal plant,and endangered species Aristolochia delavayi(Aristolochiaceae)is an endemic species in China and occurs in the warm and dry areas along the Jinsha river.It is also a specific host of the larvae of Byasa daemonius,a vulnerable butterfly.In this study,15 pairs of polymorphic microsatellite primers of A.delavayi were designed and screened based on the Simple Sequence Repeats(SSR)loci found by using the results of genome skimming.Based on these 15 SSR markers,the genetic diversity and structure of 193 individuals from ten natural populations were analyzed in detail.In comparison to other endemic and endangered plants in the region,the population of A.delavayi possess a relatively high genetic diversity(He=0.550,I=1.112).AMOVA analysis showed that 68.4%of the total genetic diversity was within populations and 31.6%of the variation occurred among populations.There was a significant genetic differentiation among natural populations of A.delavayi detectable,with low gene flow(Nm=0.591).This might be attributed to geographical barriers and limited seed dispersal.To test the isolation by distance(IBD),we performed Mantel test,which showed a significant correlation between the geographic and genetic distances.In order to cope with the possible biases caused by IBD,we additionally performed Bayesian genetic cluster analyses and principal coordinate analysis(PCoA).The final cluster analysis revealed three groups with distinct geographical distribution.Habitat fragmentation and limited gene flow between these populations may be the main reasons for the current genetic structure.For conservation of this species,we suggest to divide its populations into three protection management units,with subsequent focus on the Yongsheng and Luquan populations which experienced a genetic bottleneck event in the past.
基金German Science Foundation(DFG FOR 891/1Du 404/3 to W.D.)is highly acknowledged.
文摘Aims The dispersal of pollen and seeds is spatially restricted and may vary among plant populations because of varying biotic interactions,population histories or abiotic conditions.Because gene dispersal is spatially restricted,it will eventually result in the development of spatial genetic structure(SGS),which in turn can allow insights into gene dispersal processes.Here,we assessed the effect of habitat characteristics like population density and community structure on small-scale SGS and estimate historical gene dispersal at different spatial scales.Methods In a set of 12 populations of the subtropical understory shrub Ardisia crenata,we assessed genetic variation at 7 microsatellite loci within and among populations.We investigated small-scale genetic structure with spatial genetic autocorrelation statistics and heterogeneity tests and estimated gene dispersal distances based on population differentiation and on within-population SGS.SGS was related to habitat characteristics by multiple regression.Important Findings The populations showed high genetic diversity(He=0.64)within populations and rather strong genetic differentiation(F#ST=0.208)among populations,following an isolation-by-distance pattern,which suggests that populations are in gene flow–drift equilibrium.Significant SGS was present within populations(mean Sp=0.027).Population density and species diversity had a joint effect on SGS with low population density and high species diversity leading to stronger small-scale SGS.Estimates of historical gene dispersal from between-population differentiation and from within-population SGS resulted in similar values between 4.8 and 22.9 m.The results indicate that local-ranged pollen dispersal and inefficient long-distance seed dispersal,both affected by population density and species diversity,contributed to the genetic population structure of the species.We suggest that SGS in shrubs is more similar to that of herbs than to trees and that in communities with high species diversity gene flow is more restricted than at low species diversity.This may represent a process that retards the development of a positive species diversity–genetic diversity relationship.
基金This study was supported by the National Natural Science Foundation of China(grant number 31760088)Biodiversity Survey,Observation and Assessment Program of the Ministry of Ecology and Environment of China(grant number 837208).
文摘Camellia huana is an endangered species with a narrow distribution in limestone hills of northern Guangxi and southern Guizhou provinces,China.We used one chloroplast DNA(cpDNA)fragment and 12 pairs of microsatellite(simple sequence repeat;SSR)markers to assess the genetic diversity and structure of 12 C.huana populations.A total of 99 alleles were detected for 12 polymorphic loci,and eight haplotypes and nine polymorphic sites were detected within 5200 bp of cpDNA.C.huana populations showed a low level of genetic diversity(n=8,Hd=0.759,Pi=0.00042 for cpDNA,NA=3.931,HE=0.466 for SSRs),but high genetic differentiation between populations(FST=0.2159 for SSRs,FST=0.9318 for cpDNA).This can be attributed to the narrow distribution and limestone habitat of C.huana.STRUCTURE analysis divided natural C.huana populations into two groups,consistent with their geographical distribution.Thus,we suggest that five natural C.huana populations should be split into two units to be managed effectively.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(2019QZKK0502)the National Natural Science Foundation of China(NSFC,31400324)+1 种基金Independent research project of Yunnan Provincial Key Laboratory of Wild Resources Plant Research(E03K581261)National Key Research Development Program of China(2022YFC2601200)。
文摘Compared with traditional genetic markers,genomic approaches have proved valuable to the conservation of endangered species.Paeonia ludlowii having rarely and pure yellow flowers,is one of the world’s most famous tree peonies.However,only several wild populations remain in the Yarlung Zangbo Valley(Nyingchi and Shannan regions,Xizang)in China due to increasing anthropogenic impact on the natural habitats.We used genome-wide single nucleotide polymorphisms to elucidate the spatial pattern of genetic variation,population structure and demographic history of P.ludlowii from the fragmented region comprising the entire range of this species,aiming to provide a basis for conserving the genetic resources of this species.Unlike genetic uniformity among populations revealed in previous studies,we found low but varied levels of intra-population genetic diversity,in which lower genetic diversity was detected in the population in Shannan region compared to those in Nyingzhi region.These spatial patterns may be likely associated with different population sizes caused by micro-environment differences in these two regions.Additionally,low genetic differentiation among populations(Fst=0.0037)were detected at the species level.This line of evidence,combined with the result of significant genetic differentiation between the two closest populations and lack of isolation by distance,suggested that shared ancestry among now remnant populations rather than contemporary genetic connectivity resulted in subtle population structure.Demographic inference suggested that P.ludlowii probably experienced a temporal history of sharp population decline during the period of Last Glacial Maximum,and a subsequent bottleneck event resulting from prehistoric human activities on the Qinghai-Tibet Plateau.All these events,together with current habitat fragment and excavation might contribute to the endangered status of P.ludlowii.Our study improved the genetic characterization of the endangered tree peony(P.ludlowii)in China,and these genetic inferences should be considered when making different in situ and ex situ conservation actions for P.ludlowii in this evolutionary hotspot region.