Genetic Structure of Malus sieversii Population from Xinjiang,China,Revealed by SSR Markers

One hundred and nine Malus sieversii accessions from four geographical populations located at Kuerdening in Mohe town, Gongliu County, Jiaowutuohai, in Xinyuan County, Daxigou in Houcheng County of Ily State, and Baerluke Mountain in Yumin County of Tacheng State, Xinjiang Uygur Autonomous Region of China were studied by SSR markers. The purpose of the study was to determine the genetic structure and diversity in these eco-geographical populations with eight pair SSR primers of apple. The results indicated that： an average of 16 bands was detected in the four populations. The percentage of polymorphic bands in Gongliu population （89.06%） was the highest in the four populations. The average Nei＇s gene diversity index was 0.257 for all the loci. Totally, 128 polymorphic loci were detected and the percentage of polymorphic loci （P） was 100%, 88.28%, 84.83%, 87.50%, and 87.12%, respectively, at the species level and Gongliu, Xinyuan, Huocheng, and Yumin population levels. The Nei＇s gene diversity index （H = 0.2619） and Shannon＇s information index （1 = 0.4082） in the species level were higher than in the population level. The Nei＇s gene diversity index and Shannon＇s information index in the four populations were Gongliu 〉 Huocheng 〉 Xinyuan 〉 Yumin. Gongliu population and Xinyuan population were the highest in genetic identity and the closest in genetic distance. Gene flow between the populations was 7.265 based on genetic differentiation coefficient （GST = 0.064）. The UPGMA cluster analysis indicated that the genetic relationships between the Gongliu and Xinyuan population were the closest, and the Yumin population were the farthest with the other three populations. The UPGMA cluster analysis indicated that the four geographical populations located in Gongliu, Xinyuan, Huocheng, and Yumin were relatively independent populations. Concurrently, there was also mild gene exchange between the populations. On the basis of the study of population genetic structure and the highest genetic diversity, Gongliu population should be given a high priority consideration in Malus sieversii population＇s in situ germplasm conservation.

Population Genetic Diversity in Chinese Pomegranate (Punica granatum L.) Cultivars Revealed by Fluorescent-AFLP Markers

Eighty-five pomegranate （Punica granatum L.） cultivars from six geographical populations located at Shandong, Anhui, Shaanxi, Henan, Yunnan, and Xinjiang Provinces were studied for its population genetic diversity by means of fluorescent-AFLP markers. The results indicated that 135-185 polymorphic loci were amplified by eight pairs of primers at species level. An average of 158.25 polymorphic loci was amplified for each primer combination. The polymorphism percentage ranged from 62.5% to 86.11%, and the average polymorphism percentage was 73.26%. This indicated that there was plentiful genetic diversity in pomegranate cultivars. The genetic diversity at the species level was higher than that at the population level. The order of the genetic diversity was Henan population 〉 Xinjiang population 〉 Shaanxi population 〉 Anhui population 〉 Shandong population 〉 Yunnan population. Variance analysis showed that there was significant difference between populations in genetic diversity. The genetic differentiation coefficient between populations （Gsr） was 0.2018, which indicated that gene differentiation was mainly within the population, and between populations, it accounted for 20.18% of the total variation. Gene flow （Nm） between the populations measured was 1.9027 based on the genetic differentiation coefficient between populations, indicating that there was mild gene flow between populations. The UPGMA cluster analysis showed that most accessions from the same population were clustered together, but there was partly gene exchange. All genetic parameters indicated that there was plentiful genetic diversity in pomegranate cultivars in China, of which Henan population was significantly higher than the other populations, and it had wide application foreground in pomegranate breeding in China.

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

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

Genetic Diversity and Population Structure in Landraces and Improved Rice Varieties from India

A set of 50 rice genotypes comprising landraces, local selections, and improved varieties were characterized using simple sequence repeat（SSR） and inter simple sequence repeat（ISSR） markers to study genetic diversity and population structure. Following unweighted pair group method with arithmetic mean based clustering using binary data of polymorphic markers, the genotypes were grouped into 5 clusters and 11 sub-clusters, whereas population structure analysis separated 50 rice genotypes into 5 sub-populations. Grouping of rice genotypes showed better resemblance with the pedigree information of the genotypes. Both genetic diversity and population structure analysis separated majority of the improved varieties from landraces and local selections. Some of the SSR markers amplified unique alleles which were specific to a particular genotype and could distinguish them from the rest. The results indicate that these rice genotypes exhibit a higher genetic diversity and can be very useful in rice improvement program.

Molecular phylogenetics and population demographic history of Amphioctopus fangsiao,inferred from mitochondrial and microsatellite DNA markers

Amphioctopus fangsiao(Cephalopoda:Octopodidae)is an important commercial species in the coastal waters of China.In recent years,however,the resource of A.fangsiao have declined because of habitat destruction and overfishing.To analyze the genetic variations of A.fangsiao caused by the fluctuation of resources,the population genetic structure of nine sampling locations collected from the Bohai Sea to the South China Sea were investigated,using mtDNA COI fragments and microsatellite DNA.The results of F-statistics,AMOVA,STRUCTURE and PCA analyses showed three phylogeographic clades(Clades A,B and C),revealing limited genetic exchange between north and south populations.These clades diverged in 2.23(Clades A and B)and 3.67(Clades A,B and C)million years ago,during the dramatic environmental fluctuations,such as sea level and temperature changes,have exerted great influence on the survival distribution pattern of global organisms.Our results for low genetic connectivity among A.fangsiao populations provide insights into the development of management strategies,that is,to manage this species as separate management unit.

Exploring genetic diversity in Northeastern Sika deer population （Cervus nippon hortulorum） by AFLP molecular markers

The genetic diversity of 27 different Cervus nippon hortulorum was studied to provide theoretical evidence for their identification and utilization. The genomie DNA of 27 different Cereus nippon hortulorum were analyzed by amplified fragment length polymorphism （AFLP）. 11,443 bands associated with genetic polymorphism among total 15,169 bands were obtained with 9 kinds of primer pairs and restriction endonuclease EcoRI/Msel, percentage of polymorphie band was 78.43%, 1,271 polymorphic locus were shown per primer pair. The AFLP data showed that average genetic similarity was 0.7841 （0.6809-0.8648）. 27 samples were classified into Group I and Group II with cluster analysis, and Group II was divided into five subgroups. The result of AFLP and cluster analysis concluded that there was high genetic variation, which associated with orientated artificial breed selection and breeding in the population. Genetic similarity of Group II-4 was the highest, more than 0.82, while genetic distance in this group was the shortest, from 0.1354 to 0.1563, which was coordinated with breeding record. All these showed that there was great genetic polymorphism among the deer population. The results laid the foundation for main quantitative trait locus （QTLs） of Cervus nippon hortulorum.

High regional genetic differentiation of an endangered relict plant Craigia yunnanensis and implications for its conservation

Of the genus Craigia,widespread in the Tertiary,only two relict species survived to modern times.One species is now possibly extinct and the other one,Craigia yunnanensis,is severely endangered.Extensive surveys have located six C.yunnanensis populations in Yunnan province,southwest China.Using fluorescent amplified fragment length polymorphism(AFLP),the genetic diversity and population structure of these populations were examined.It was found that genetic diversity of C.yunnanensis was moderate at the species level,but low at regional and population levels.Analysis of population structure showed significant genetic differentiation between Wenshan and Dehong regions,apparently representing two geographically isolated for long time refuges.There are also clear indications of isolation between populations,which,together with anthropogenically caused decline of population size,will lead to general loss of the species genetic variation with subsequent loss of adaptive potential.To conserve the genetic integrity of C.yunnanensis,we recommend that ex-situ conservation should include representative samples from every population of the two differentiated regions(e.g.Wenshan and Dehong).The crosses between individuals originated from different regions should be avoided because of a high risk of outbreeding depression.As all the extant populations of C.yunnanensis are in unprotected areas with strong anthropogenic impact,there is no alternative to reintroduction of C.yunnanensis into suitable protected locations.

Genetic diversity of pepper(Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution

Pepper（Capsicum spp.） is an important vegetable crop in the world. Now the pepper in China contributes one-third of the world＇s peppers production. Genetic diversity of the pepper germplasm of China is expected interesting to know. To explore the structure of genetic diversity in Chinese pepper germplasm resources and possible relationship with cultivar types or geographic origin, we sampled and compared 372 Gen Bank pepper accessions（local cultivars and landraces） from 31 provinces, autonomous regions and municipalities of China and 31 additional accessions from other countries. These accessions were genotyped using 28 simple sequence repeat（SSR） markers spanning the entire pepper genome. We then investigated the genetic structure of the sampled collection using model-based analysis in STRUCTURE v2.3.4 and examined genetic relationships by the unweighted pair-group method of mathematical averages（UPGMA） in MEGA. In addition to geographic origin, we evaluated eight plant and fruit traits. In total, 363 alleles were amplified using the 28 SSR primers. Gene diversity, polymorphism information content and heterozygosity of the 28 SSR loci were estimated as 0.09–0.92, 0.08–0.92 and 0.01–0.34, respectively. The UPGMA cluster analysis clearly distinguished Capsicum annuum L. from other cultivated pepper species. Population structure analysis of the 368 C. annuum accessions uncovered three genetic groups which also corresponded to distinct cultivar types with respect to the plant and fruit descriptors. The genetic structure was also related to the geographic origin of the landraces. Overall results indicate that genetic diversity of Chinese pepper landraces were structured by migration of genotypes followed by human selection for cultivar types in agreement with consumption modes and adaptation to the highly diversified agro-climatic conditions.

Informative ISSR Markers Help Identify Genetically Distinct Accessions of Oryza rufipogon in Yield Improvement

Inter simple sequence repeat（ISSR） polymorphism was used to determine genetic diversity and phylogenetic relationships in 90 genotypes of wild and cultivated species of Oryza from different geographical regions of the world. In all the 17 primers used in ISSR-PCR, a total of 11 464 bands were amplified at 253 band positions/loci. The primer UBC-809 amplified the maximum bands（1 059） at 21 band positions. UBC-810 and UBC-835 amplified the minimum of 391 bands each at 7 and 14 band positions, respectively. The mean polymorphism information content ranged from 0.44 to 0.84 and resolving power ranged from 8.69 to 23.53. Un-weighted pair group method with arithmetic mean dendrogram and population structure based on the 17 primers separated all genotypes into 4 major clusters with a genetic similarity of 53%–100%. The first two clusters consisted of 30 O. rufipogon accessions each. In the third cluster, O. nivara and O. longistaminata grouped as one sub-cluster and all other O. nivara accessions and cultivars grouped as another sub-cluster. The fourth cluster had only five O. rufipogon accessions which can be a source of new genes. Four sub-populations were identified within O. rufipogon and two sub-populations within O. nivara at K = 7. A subset of six primers with high resolving power values were the most informative and grouped all genotypes almost similarly as the 17 primers did. Use of these six highly informative primers in ISSR-PCR is a cost effective and robust method for assessing genetic diversity in large germplasm collections of wild rice species.

Genetic structure of the oriental white stork (Ciconia boyciana): implications for a breeding colony in a non-breeding area

The oriental white stork (Ciconia boyciana) is a threatened species, and their numbers are still in decline due tohabitat loss and poaching. China is a breeding and main wintering area for this animal and in recent years someindividuals have been found breeding in wintering areas and at some stopover sites. These new breeding coloniesare an exciting sign, however, little is understood of the genetic structure of this species. Based on the analysis ofa 463-bp mitochondrial DNA (mtDNA) control region, we investigated the genetic structure and genetic diversity of66 wild oriental white storks from a Chinese population. We analyzed the sequences of 66 storks obtained in thisstudy and the data of 17 storks from a Japanese population. Thirty-seven different haplotypes were detected amongthe 83 samples. An analysis of molecular variance showed a significant population subdivision between the twopopulations (FST = 0.316, P < 0.05). However, the phylogenetic analysis revealed that the samples from the differentpopulations did not form separate clusters and that there were genetic exchanges between the two populations.Compared with the Japanese population, the Chinese population had a relatively higher genetic diversity with ahaplotype diversity (h ± SD) of 0.953 ± 0.013 and a nucleotide diversity (π ± SD) of 0.013 ± 0.007. The high haplotypediversity and low nucleotide diversity indicate that this population might be in a rapidly increasing period from asmall effective population. A neighbor-joining tree analysis indicated that genetic exchange had occurred betweenthe newly arisen southern breeding colony and the northern breeding colony wintering in the middle and lowerYangtze River floodplain. These results have important implications for the conservation of the oriental white storkpopulation in China.

Genetic boundary and gene flow between 2 parapatric subspecies of brown rats

Two parapatric Rattus norvegicus subspecies,R.n.humiliatus(RNH)and R.n.caraco(RNC),are classified accordi ng to morphological diverge nee and are mainly distributed in North and Northeast China.Here,we aimed to explore the population genetic structure,genetic boundary,and gene flow in these rats using 16 microsatellite loci.Structure analysis and principal component an alysis revealed 3 ancestral clusters.We found that the in termediate cluster exhibited higher genetic diversity and a lower in breeding coefficie nt tha n the other 2 clusters.The genetic differentiation between the 3 clusters was significant but weak,with a higher FST value being observed betwee n the clusters on both sides.The subspecies bou ndary inf erred from microsatellite markers may indicate the existence of an admixture or hybridization area covering Liaoning,Inner Mongolia,and Jilin Provinces,rather than corresponding to the administrative provincial boundaries between Liaoning and Jilin.The RNH and RNC subspecies presented moderate gene exchange and an asymmetric bidirectional gene flow pattern,with higher gene flow from the RNH subspecies to the RNC subspecies,constraining speciation.Such genetic characteristics might be explained by biological processes such as dispersal ability,mate choice,and dynamic lineage boundaries.

Patterns of geographic variation between mitochondrial and nuclear markers in Heaviside’s(Benguela)dolphins(Cephalorhynchus heavisidii)

The Heaviside’s(or Benguela)dolphin(Cephalorhynchus heavisidii)is endemic to the west coast of southern Africa.The present study investigated the population genetic structure across a large portion of the species dis­tribution using mitochondrial control region and nuclear(microsatellite)markers.A total of 395 biopsy skin samples were analyzed;they were collected from free-ranging Heaviside’s dolphins in 7 locations along 1650 km of coast between Table Bay,South Africa and Walvis Bay,Namibia.Both genetic markers rejected the hy­pothesis of 1 homogenous population but revealed contrasting results in the genetic structuring of putative pop­ulations.Mitochondrial DNA suggested either 2 populations or a fine-scale division with 6(sub)populations,while microsatellite markers were indicative of 2 widespread populations with measurable gene flow between them.Neutrality tests and mismatch distribution of the mitochondrial sequences indicated a departure from mu­tation-drift equilibrium due to a population expansion at the 2 extremes of the geographic range,but not to­wards the middle of the distribution.These results highlight the importance of evaluating multiple genetic mark­ers to gain reliable insights into population processes and structure.

Resolving the taxonomy of emerging zoonotic pathogens in the Trichophyton benhamiae complex

Species of the Trichophyton benhamiae complex are predominantly zoophilic pathogens with a worldwide distribution.These pathogens have recently become important due to their epidemic spread in pets and pet owners.Considerable genetic and phenotypic variability has been revealed in these emerging pathogens,but the species limits and host spectra have not been clearly elucidated.In this study,we used an approach combining phylogenetic analysis based on four loci,population-genetic data,phenotypic and physiological analysis,mating type gene characterization and ecological data to resolve the taxonomy of these pathogens.This approach supported the inclusion of nine taxa in the complex,including three new species and one new variety.Trichophyton benhamiae var.luteum var.nov.(“yellow phenotype”strains)is currently a major cause of zoonotic tinea corporis and capitis in Europe(mostly transmitted from guinea pigs).The isolates of the“white phenotype”do not form a monophyletic group and are segregated into three taxa,T.benhamiae var.benhamiae(mostly North America;dogs),T.europaeum sp.nov.(mostly Europe;guinea pigs),and T.japonicum sp.nov.(predominant in East Asia but also found in Europe;rabbits and guinea pigs).The new species T.africanum sp.nov.is proposed for the“African”race of T.benhamiae.The introduction to new geographic areas and host jump followed by extinction of one mating type gene have played important roles in the evolution of these pathogens.Due to considerable phenotypic similarity of many dermatophytes and phenomena such as incomplete lineage sorting or occasional hybridization and introgression,we demonstrate the need to follow polyphasic approach in species delimitation.Neutrally evolving and noncoding DNA regions showed significantly higher discriminatory power compared to conventional protein-coding loci.Diagnostic options for species identification in practice based on molecular markers,phenotype and MALDI-TOF spectra are presented.A microsatellite typing scheme developed in this study is a powerful tool for the epidemiological surveillance of these emerging pathogens.