Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing

The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independently reported in two Asian primate research centers.Nevertheless,the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated.Here,we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing.We identified 14558184 single nucleotide polymorphisms(SNPs)from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples.Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers.In addition,SNP and copy number variation(CNV)analyses suggested that the WW domain-containing oxidoreductase(WWOX)and Tyrosine-protein phosphatase nonreceptor type 21(PTPN21)genes may be associated with epilepsy in marmosets.Notably,KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets.This study provides valuable population genomic resources for marmosets in two Asian primate centers.Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers,while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.

Population genetics of Sargassum horneri (Fucales, Phaeophyta) in China revealed by ISSR and SRAP markers

Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR (inter simple sequence repeat) and SRAP (sequence related amplified polymorphism) markers were used to analyze the population genetics among nine natural populations of S. horneri. The nine studied populations were distributed over 2 000 km from northeast to south China. The percentage of polymorphic loci P% (ISSR, 99.44%; SRAP, 100.00%), Nei's genetic diversity H (ISSR, 0.107-0.199; SRAP, 0.100-0.153), and Shannon's information index I (ISSR, 0.157-0.291; SRAP, 0.148-0.219) indicated a fair amount of genetic variability among the nine populations. Moreover, the high degree of gene differentiation G st (ISSR, 0.654; SRAP, 0.718) and low gene flow N m (ISSR, 0.265; SRAP, 0.196) implied that there was significant among-population differentiation, possibly as a result of habitat fragmentation. The matrices of genetic distances and fixation indices (F st ) among the populations correlated well with their geographical distribution (Mantel test R=0.541 5, 0.541 8; P=0.005 0, 0.002 0 and R=0.728 6, 0.641 2; P=0.001 0, 0.001 0, respectively); the Rongcheng population in the Shandong peninsula was the only exception. Overall, the genetic differentiation agreed with the geographic isolation. The fair amount of genetic diversity that was revealed in the S. horneri populations in China indicated that the seaweed resources had not been seriously affected by external factors.

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.

Molecular Population Genetics of Rice Domestication

Domestication is a selection process that genetically modifies species to meet human needs. A most intriguing feature of domestication is the extreme phenotypic diversification among breeds. What could be the ultimate source of such genetic variations？ Another notable outcome of artificial selection is the reduction In the fitness of domesticated species when they live In the wild without human assistance. The complete sequences of the two subspecies of rice cultlvars provide an opportunity to address these questions. Between the two subspecies, we found much higher rates of non-synonymous （N） than synonymous （S） substitutions and the N/S ratios are higher between cultivars than between wild species. Most interestingly, substitutions of highly dissimilar amino acids that are deleterious and uncommon between natural species are disproportionately common between the two subspecies of rice. We suggest strong selection in the absence of effective recombination may be the driving force, which we called the domestication-associated Hill-Robertson effect. These hitchhiking mutations may contribute to some fitness reduction in cultivars. Comparisons of the two genomes also reveal the existence of highly divergent regions in the genomes. Haplotypes in these regions often form highly polymorphic linkage blocks that are much older than speciation between wild species. Genes from such regions could contribute to the differences between indica and japonica and are likely to be involved in the diversifying selection under domestication. Their existence suggests that the amount of genetic variation within the single progenitor species Oryza rufipogon may be insufficient to account for the variation among rice cultivars, which may come from a more inclusive gene pool comprising most of the A-genome wild species. Genes from the highly polymorphic regions also provide strong support for the Independent domestication of the two subspecies. The genomic variation in rice has revealing implications for studying the genetic basis of indica-japonica differentiation under rice domestication and subsequent improvement.

Population genetics and forensic efficiency of 30 InDel markers in four Chinese ethnic groups residing in Sichuan

Sichuan Province is located at the transitional junction regions of the Qinghai-Tibet Plateau and the low-altitude plains.It also serves as the corridor of Sino Tibetan-speaking population migration and expansion since neolithic expansion of Proto-Tibeto-Burman populations from Middle/Upper Yellow River during Majiayao period(3300-2000 BC).However,the population structure and the corresponding genetic diversity of forensic-related markers in this region remain unclear.Thus,we genotyped 30 insertion-deletion(InDel)markers in 444 samples from four ethnic groups(Han,Tibetan,Hui and Yi)from Sichuan Province using the Investigator■ DIPplex kit to explore the characteristics of population genetics and forensic genetic focuses.All the loci were found to be in Hardy-Weinberg Equlibrium(HWE)after applying a Bonferroni correction and no pairwise loci showed prominent linkage disequilibrium.The combined matching probability(CMP)and the combined power of discrimination(CPD)are larger than 1.8089×10^(11)and 0.9999999995,respectively.Principal component analysis,multi-dimen-sional scaling plots and Neighbour-Joining tree among 65 worldwide populations indicated that Sichuan Hui and Han are genetically close to Hmong-Mien and Tai-Kadai-speaking popula-tions,and Sichuan Tibetan and Yi bear a strong genetic affinity with Tibeto-Burman-speaking populations.The model-based genetic structure further supports the genetic affinity between the studied populations and linguistically close populations.

The Hardy-Weinberg principle and its applications in modern population genetics

The discovery of the Hardy-Weinberg principle marked the beginning of the field of population genetics.Over the past hundred years,it has provided a starting point for many population genetic investigations.In this review,the Hardy-Weinberg principle,its statistical testing,and several of its applications in various modern population genetic research areas,including allelic variability and selection in the human leukocyte antigen region,microsatellite genotyping error detection,and accuracy of haplotype estimation,are discussed.

DISTRIBUTION OF ALPHA-1-ANTITRYPSIN VARIANT ETOKYO AND ITS IMPLICATION IN HUMAN POPULATION GENETICS

Ⅰ. INTRODUCTION Alpha-1-antitrypsin (A1AT; locus symbol, PI) is one of the main protease inhibitors in serum. Up to now there are at least 50 A1AT variants that have been found in human populations (Cox, D. W., private communication). The distribution of A1AT variants appears highly racial specificity and geographical variability. This

Haplotype and Genetic Analysis of 41 Y-STR Loci in the Wuwei Han Population from Gansu Province,China

Objective Y-Chromosomal short tandem repeat polymorphism(Y-STR)analysis plays an indispensable role in the identification of male individuals,population genetics,and biogeographic research.While profiles of many populations based on Y-STR markers in human genomes are ample,haplotype data for the Wuwei Han are still scarce.Methods In this study,2180 unrelated Wuwei Han male individuals residing in Gansu Province,China were collected and genotyped using the novel Microreader™40Y Plus ID system.Phylogenetic relationship reconstructions,multidimensional scaling(MDS),and heatmap analysis were performed based on the genetic distance(Rst)values between our studied population and other populations of the Ymax module in the Y-STR Haplotype Reference Database(YHRD).Results A total of 2129 unique haplotypes were obtained,and the haplotype diversity(HD)and discrimination capacity(DC)for the Wuwei Han were 0.9999 and 0.9931,respectively.Conclusion Our results demonstrate that the Wuwei Han population had intimate genetic relationships with East Asians,especially the geographically close Han populations.Overall,this Y-Chromosomal assay gives valuable information about paternal lineages in male individual tracking and genealogical database construction.

Genetic Structure of Three Populations of Oxya chinensis in Shanxi,China

Starch gel electrophoresis was used to analyze genetic structure of three populations of Oxya chinensis from Shanxi Province,China.Four allozyme polymorphic loci (MDH-1,MDH-2,LDH,ME) were found.The data suggest that two populations of O.chinensis about 41 kilometers apart are genetically similar,but differentiated from the third population with a geographic distance of 357 kilometers.However,the heterozygosity levels of those two genetically similar populations were much different.The Nei's genetic distance between two geographically close populations is 0.068,which is much smaller than those of geographically distant populations (0.23 in average).The observed overlap of geographical distance and genetic distance implies that for O.chinensis population divergence may correlate with geographic isolation.

Population genetic diversity and regional differentiation of Chinese forest frog s (Rana chensinensis) in Heilongjiang Province

The Random Amplified Polymorphism DNA (RAPD) markers were used to stu dy the intra-specific diversity and regional differentiation of the Chinese fore st frogs (Rana chensinensis), which were sampled from the fields of 8 regions in Heilongjiang Province. Totally 78 polymorphic DNA loci were amplified by 10 RAP D primers. By genetic distance analysis and phylogenetic tree reconstruction wit h the Neighbor-Joining (NJ) method the results showed that the populations of Ch inese forest frogs distributed in 8 regions existed great differentiation (Avera ge Fst=0.347, SD=0.235) while there was the paradox between geographic distances and genetic distances. Based on geographic and geological data, a hypothesis wa s posed that it is very possible that the hilly lands in the downstream of the S onghua River and the Heilong River were the center of the origin of the Chinese forest frogs in Heilongjiang Province. And mainly through the Songhua River syst em, the Chinese forest frogs dispersed into the Songneng Plain from the Sanjiang Plain whereas the Fangzheng region became a sub-center for the western dispersi on.

Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs

Background Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones.Nevertheless,the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear.Results Here,we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical,high-altitude,and frigid regions.Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds.Analysis of selection signals revealed regions under selection for adaptation in tropical(55.5 Mb),high-altitude(43.6 Mb),and frigid(17.72 Mb)regions.The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments,including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments.Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation.These pathways included blood circulation,protein degradation,and inflammation for adaptation to tropical environments;heart and lung development,hypoxia response,and DNA damage repair for high-altitude adaptation;and thermogenesis,cold-induced vasodilation(CIVD),and the cell cycle for adaptation to frigid environments.By examining the chromatin state of the selection signatures,we identified the lung and ileum as two candidate functional tissues for environmental adaptation.Finally,we identified a mutation(chr1:G246,175,129A)in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments.Conclusions In this study,we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical,high-altitude,and frigid environments.Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.

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

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

Relatedness of Helicobacter pylori populations to gastric carcinogenesis

Helicobacter pylori （H. pylorl） is a Gram-negative bac- terium that infects half of the human population. The infection is associated with chronic inflammation of the gastric mucosa and peptic ulcers. It is also a major risk factor for gastric cancer. Phylogenetic analysis of global strains reveals there are seven populations of H. pylori, including hpAfrical, hpAfrica2, hpEastAsia, hpEurope, hpNEAfrica, hpAsia2 and hpSahul. These populations are consistent with their geographical origins, and pos- sibly result from geographical separation of the bac- terium leading to reduced bacterial recombination in some populations. For each population, H. pylori has evolved to possess genomic contents distinguishable from others. The hpEurope population is distinct in that it has the largest genome of 1.65 mbp on average, and the highest number of coding sequences. This confers its competitive advantage over other populations but at the cost of a lower infection rate. The large genomic size could be a cause of the frequent occurrence of the deletion of the cag pathogenicity island in H. pylori strains from hpEurope. The incidence of gastric cancer varies among different geographical regions. This can be attributed in part to different rates of infection of H. pylori. Recent studies found that different popula- tions of H, pylori vary in their carcinogenic potential and contribute to the variation in incidence of gastric cancer among geographical regions. This could be related to the ancestral origin of H, pylori. Further studies are indi- cated to investigate the bacterial factors contributing to differential virulence and their influence on the clinical features in infected individuals.

Population Genetic Structure and Genetic Differentiation of the Pufferfish Takifugu Rubripes and Takifugu Pseudommus Revealed by RAPD Analysis

RAPD analysis is used to assay the population genetic structure and genetic differentiation of pufferfish T. rubripes and T. pseudammus. One hundred and twenty fragments are amplified with 21 random sequence 10-mer primers. The proportion of polymorphic fragments of T. rubripes populations from the coast of China (TRC), the coast of Japan (TRJ), general population of T. rubripes both from China and Japan (TRCJ), and the population of T. pseudommus are 31.7%, 33.3%, 35.0% and 39.2 % respectively. The mean expected heterozygositiee of the four populations are 0. 116, 0. 125, 0. 126, and 0. 144, respectively. Low genetic distances (ranging from 0.0118 to 0.0309) and Fst estimates (0.020 to 0.024) among the populations in-dicated that there is no significant differentiation between T. rubripes and T. pseudommus and suggested that only one species is involved.

Mitochondrial DNA control region diversity and population structure of Pacific herring(Clupea pallasii)in the Yellow Sea and the Sea of Japan

To investigate the genetic variation and population structure of Pacific herring in the Yellow Sea and the genetic differentiation between the Yellow Sea and the Sea of Japan, fragments of 479-bp mitochondrial DNA control region were sequenced for 110 individuals collected from three different periods in the Yellow Sea and one locality in the Sea of Japan. High haplotype diversity and moderate nucleotide diversity were observed in Pacific herring. AMOVA and exact test of population differentiation showed no significant genetic differentiations among the three populations of the Yellow Sea and suggested the populations can be treated as a single panmictic stock in the Yellow Sea. However, a large and significant genetic differentiation （ФST=0.11; P=0.00） was detected between the populations in the Yellow Sea and the Sea of Japan. The high sea water temperature in the Tsushima Strait was thought a barrier to block the gene exchange between populations of the two sea areas. The neutrality tests and mismatch distribution indicated recent population expansion in Pacific herring.

Population structure of the blacklegged tick Ixodes scapularis revealed by SSCP data using the mitochondrial Cyt b and the nuclear ITS1 markers

The population genetic structure of the blacklegged tick Ixodes scapularis was analyzed using 853 individual ticks collected from 12 sites along the eastern seaboard of the United States. PCR-based DNA single strand conformation polymorphism(SSCP) was used for analysis of one haploid locus, the mitochondrial cytochrome b(Cyt b), and one diploid locus, the internal transcribed spacer 1(ITS1) of nuclear ribosomal RNA. Seven haplotypes in the Cyt b locus and 13 genotypes in the ITS1 locus were identified. Population differentiation and isolation by distance were found. Distribution of haplotype and genotype frequencies across geographic regions suggests that two distinct populations exist along the Eastern Coast of the US. However, genetic variation among individuals within regions was large. This degree of variation suggests frequent gene flow between regions. Moreover, overall genetic diversity among individuals was much higher in ticks from the southern population.

Mitogenomic Conservation Genetics of the Critically Endangered Liaoning Clawed Salamander

The Liaoning clawed salamander(Onychodactylus zhaoermii)is an endemic and critically endangered amphibian species of China.To study the population genetics of natural populations of this species,32 samples were collected from six different locations,and the mitochondrial genome was sequenced.Population genetic analyses showed that the Liaoning clawed salamander is composed of only one radialized cluster with ultralow nucleotide diversity.Late Pleistocene climate cooling(-100 to-30 kya)may have reduced the effective population size of the Liaoning clawed salamander,and the subsequent temperature increase(~25 kya to present)provided the opportunity for population expansion.Because of heat sensitivity,the maximum temperature of the prebreeding period,especially from March to May,is very important for the surface environment living in the Liaoning clawed salamander.Three suitable regions were predicted by the MaxEnt model,and the largest suitable region(approximately 899 km2)was at the four-county boundary area and was larger than the present’Natural Conservation Community of the Liaoning Clawed Salamander’.To ensure more effective protection of all Liaoning clawed salamanders,we suggest extending the current’Natural Conservation Community of the Liaoning Clawed Salamander’to include the four-county boundary area.

A harmonisation approach to traditional Chinese medicine registration in Asian countries

The traditional Chinese medicine(TCM)industry is critical to not only for public health but also for economic growth.According to the European Union(EU)directives,under the EU framework for(traditional)herbal medicinal products,herbal medicines with long history of use can be registered in EU.However,there is a condition in this directive in which only those that have at least 10e15 years in the EU market are accepted for registration and/or marketing authorization.In author opinion,the condition of 10-15 years of use in EU countries set within the EU regulatory framework is with consideration of the genetic differences which can result in variation in adverse drug responses among different world populations.With this concept in mind,it is reasonable to project the principal of the EU directive to the Asian countries where TCM is originated.Countries like China,Singapore,Japan and South Korea that have well established drug registration framework are in best position in executing the best practice and facilitate harmonization of registration for TCM within the region.Furthermore,the registration process itself allows more safety and efficacy data to be collected systemically before and after product registration/marketing authorization.These are valuable information for future drug development.The therapeutic value of TCM is limitless,it has been left out in the EU regulatory framework,and the opportunity for it to be expanded and carried forward in modern medicines is shadowed by the limited number of TCM that are qualified to be registered under the EU regulatory framework.An early establishment of a harmonized risk-based registration process for TCM in Asian countries is important.This will strengthen the database to substantiate the history of safe use and further preserving and expanding the therapeutic values of TCM within and beyond the Asian region.