Analysis of genetic diversity and population structure in sweetpotato using SSR markers

Sweetpotato, Ipomoea batatas(L.) Lam., is an important food crop worldwide. Large scale evaluation of sweetpotato germplasm for genetic diversity is necessary to determine the genetic relationships between them and effectively use them in the genetic improvement. In this study, the genetic diversity of 617 sweetpotato accessions, including 376landraces and 162 bred varieties from China and 79 introduced varieties from 11 other countries, was assessed using 30 simple sequence repeat(SSR) primer pairs with high polymorphism. Based on the population structure analysis,these sweetpotato accessions were divided into three groups, Group 1, Group 2 and Group 3, which included 228, 136and 253 accessions, respectively. Consistent results were obtained by phylogenic analysis and principal coordinate analysis(PCoA). Of the three groups, Group 2 showed the highest level of genetic diversity and its accessions were mainly distributed in low-latitude regions. The accessions from South China exhibited the highest level of genetic diversity, which supports the hypothesis that Fujian and Guangdong were the first regions where sweetpotato was introduced to China. Analysis of molecular variance(AMOVA) indicated significant genetic differentiations between the different groups, but low levels of genetic differentiation existed between the different origins and accession types.These results provide valuable information for the better utilization of these accessions in sweetpotato breeding.

Genotypic Diversity Affects Age Structure of Tiller and Rhizome of Leymus chinensis Population,But Not Age Structure of Bud

The effect of genotypic diversity on the age structure and bud bank of the Leymus chinensis population has not yet been demonstrated.This experiment was designed to study the age structure of the tiller,rhizome,and bud of L.chinensis at genotypic diversity levels of 1,2,4,8,and 12.A total of 64 communities were established in this experiment,following the principle of randomized block experimental design.The results indicated that genotypic diversity had a significant or obviously significant effect on the cumulative length of rhizomes of 2a and 4a,dry matter accumulation of rhizomes of 1a and 2a,tiller number of 1a,tiller productivity of 3a,but had no significant effect age structure of buds.As the levels of genotypic diversity increased,the proportion of the cumulative length of rhizomes with 4a decreased and then increased,and dry matter accumulation of rhizomes with 1a and 2a gradually increased while the number of tillers with 1a gradually decreased,when the gradient of genotypic diversity increased.At the 1,2,4,8,and 12 genotype diversity levels,the number of tillers,the cumulative length of rhizomes,and dry matter accumulation in rhizomes and buds were all age structures of expanding type.However,tiller productivity was an expanding or stable age structure at levels of 1,2,4,8 genotypic diversity,while it was a declining age structure at the 12 genotype diversity gradient.An appropriate genotypic diversity is conducive to maintaining the growth and stability of the age structure of L.chinensis population,but too high a gradient of genotypic diversity can have a negative impact on the population age structure.This study provided that an appropriate number of genotypic diversity contributes to the stability of the population.

Genetic diversity and genetic differentiation of natural populations of Pinus kesiya var. langbinanensis

Genetic diversity and genetic differentiation of natural populations of Pinus kesiya var. langbinanensis were examined by means of electrophoresis technique. Analysis of 9 enzyme systems including 16 loci showed that all the three natural popu-lations of the pine were high in genetic diversity but low in inter-population genetic differentiation. The proportion of polymorphic loci is 0.667, with each locus holding 2.13 alleles, averagely. The average expected and observed heterozygosity was 0.288 and 0.197, respectively. The gene differentiation among populations was 0.052, but the mean genetic distance was only 0.015.

Genetic Diversity in Wild Populations of Poacynum hendersonii from Inland Arid Regions of Northwest China

[Objective] Study on the genetic diversity in wild populations of Poacynum hendersonii.[Method] Random amplified polymorphic DNA(RAPD)technique was employed to analyze the genetic diversity in five wild populations of P.hendersonii sampled from Xinjiang,Gansu and Qinghai provinces.[Result] Totally 165 clear and repeatable bands were generated in RAPD reaction by using 20 primers screened from 80 primers,of which 110 were polymorphic,accounting for 66.67%.At species level,Nei's gene diversity index(H),Shannon's information index(I)and genetic differentiation coefficient(Gst)were 0.220 5,0.304 7 and 0.908 2,respectively.P.hendersonii germplasm resources share a high level of genetic diversity,and genetic differentiation mainly exists among the populations.Results from genetic distances and cluster analysis showed that relationships among P.hendersonii populations were to some extent related with their geographical and climatic characters.[Conclusion] This study suggests that the conservation of P.hendersonii should focus on the protection of many populations,particularly the Qinghai population.

Allozyme Diversity and Population Genetic Structure of Three Medicinal Epimedium Species from Hubei

Three Epimedium species, E. pubescens Maxim., E. sagittatum （Sieb. ＆ Zucc.） Maxim., and E. wushanense T. S. Ying, which are sympatrically distributed in the western Hubei Province, have been used in traditional Chinese medicine （TCM） for about 2,000 years. Genetic variability and population genetic structure of 11 natural populations of these Epimedium species were investigated using isoelectric focusing in thin-layer polyacrylamide slab gels. Of the 22 enzyme systems prescreened, six coding for 13 loci and 45 alleles were resolved, which were used for analyzing genetic diversity and population structure at both intraspecific and interspecific levels. The results showed that： l） high levels of genetic diversity were observed in all three species （A = 2.6-3.2, P = 69.2%-84.6%, Ho= 0.274-0.377, HE= 0.282-0.369）, which were higher than that of other herbaceous and aulmal-pollinated species with similar life-history characteristics; 2） there was significant deviation from Hardy-Weinberg Equilibrium, with one half of the loci showing heterozygote excess and the other homozygote excess, in all populations, suggesting the complicated breeding system of Epimedium species; 3） the low level of intraspecific and interspecific genetic differentiation （GST= 0.0246-0.0409 and 0.0495-0.1213, respectively） indicated a high level of gene flow among populations and close genetic relationship among the three species; and 4） UPGMA cluster analysis further showed that E. pubescens was more closely related to E. sagittatum than to E. wushanense, which was in good agreement with the morphological characters and the recent phylogenetic analysis of these species. On the basis of these results, it was concluded that the mixed breeding system, long-lived perennial life form, ancient evolutionary history, and seed dispersal by ants in Epimedium are responsible for the genetic variation and population structure of these species.

AFLP analysis revealed differences in genetic diversity of four natural populations of Manila clam (Ruditapes philippinarum) in China

The amplified fragment length polymorphism （AFLP） technology was used to analyze the genetic diversities in four natural populations of Manila clam （ Ruditapes philippinarum）, distributed in four sea areas of China, i.e. , the Bohai Sea, the Huanghai Sea, the East China Sea and the South China Sea. Two hundred and sixty-four AFLP loci were analysed in 195 individuals and revealed high levels of genetic diversity. The percentage of polymorphic loci ranged from 92.13% to 96.06% and the Shannon＇ s information index was from 0.256 8 to 0. 275 6. By analyzing molecular variance （ AMOVA）, it was found that there were high levels of genetic differentiation between populations of Qingdao and the other three sea areas. Cluster analysis by Nei＇ s pairwise distances grouped specimens by geographical origin, except the population of Qingdao. A conclusion can be drawn that there are high genetic diversities in the four natural populations of Manila clam in China and some distinct differences existed among and between the four populations. The results also indicated that human cultivation activities will have great influence on the genetic structure of the population of Qingdao.

Assessing genetic diversity of wild populations of Japanese flounderusing AFLP markers

Amplified fragment length polymorphism （AFLP） analysis was used to evaluate the genetic diversity of four wild geographical populations of Japanese flounder （Paralichthys olivaceus）. A total of 775 loci （58.32% of which was polymorphic） in the range between 100 and 1 300 base pairs were detected from 110 individuals using seven primer combinations. The percentage of polymorphic loci detected by single primer combination for each population was calculated, ranging from 19.59% to 53.33%. Genetic similarities within and among the populations were calculated from the binary matrices of presence - absence. Phylogenetic tree of four populations was constructed by using the UPGMA method using PHYLIP Version 3.5. According to intrapopulation genetic similarities, CW population displayed the highest genetic diversity value and KY population had the lowest genetic diversity value. The distance between CW and CF populations was the farthest, which was possibly resulted from the farthest distance of Weihai of Shandong and Fujian of China compared with the geographical distance between other locations of populations. The subpopulation differentiation value （G.,） is 0. 356 5, showing a certain extent of differentiation among the four geographical populations. AFLP technology was confirmed to be an effective tool to assess within- and among-population genetic diversity of Japanese flounder. The present survey provided significant insights for research in the Japanese flounder breeding program.

Genetic diversity analysis of spawner and recaptured populations of Chinese shrimp(Fenneropenaeus chinensis)during stock enhancement in the Bohai Bay based on an SSR marker

Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles（N_a） were 8–63 and 6–60, respectively. The numbers of effective alleles（N_e） were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity（H_o） values（0.638–0.910 and 0.712–0.927） were lower than the expected heterozygosity（H_e） values（0.603–0.954 and 0.625–0.952）, which indicated that the two populations possessed a rich genetic diversity. In 16 tests（2 populations×8 loci）, 13 tests deviated from the HardyWeinberg equilibrium. F_（is） values were positive at seven loci and the inbreeding coefficients（F） of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_（st） values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes（3 060.2 and 3 842.8） were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.

Analysis of the diversity of population and convergence of genetic algorithms based on Negentropy

With its wide use in different fields, the problem of the convergence of simple genetic algorithms (GAs) has been concerned. In the past, the research on the convergence of GAs was based on Holland's model theorem. The diversity of the evolutionary population and the convergence of GAs are studied by using the concept of negentropy based on the discussion of the characteristic of GA. Some test functions are used to test the convergence of GAs, and good results have been obtained. It is shown that the global optimization may be obtained by selecting appropriate parameters of simple GAs if the evolution time is enough.

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.

Detection of Adaptive Genetic Diversity in Wild Potato Populations and Its Implications in Conservation of Potato Germplasm

A better understanding on how genetic diversity is structured at natural habitats can be helpful for exploration and acquisition of plant germplasm. Historically, studies have relied on DNA markers to elucidate potato genetic diversity. Current advances in genomics are broadening applications allowing the identification of markers linked to genomic regions under selection. Those markers, known as adaptive markers, unlock additional ways to value and organize germplasm diversity. For example, conservation priorities could be given to germplasm units containing markers associated to unique geographic identity, and/or linked to traits of tolerance to abiotic stresses. This study investigated if adaptive marker loci were possible to be identified in a large AFLP marker dataset of ninety-four populations of the wild potato species S. fendleri. These populations originated from six different mountain ranges in southern Arizona, USA. A total of 2094 polymorphic AFLP markers were used to conduct genetic diversity analyses of populations and mountain ranges. Adaptive markers were detected using Bayesian methods which distinguished marker loci departing significantly from frequencies expected under neutral models of genetic differentiation. This identified 16 AFLP loci that were considered to be adaptive. To contrast diversity parameters generated with each set of markers, analyses that included all the 2094 AFLP markers, and only the 16 adaptive markers were conducted. The results showed that both were efficient for establishing genetic associations among populations and mountain ranges. However, adaptive markers were better on revealing geographic patterns and identity which would suggest these markers were linked to selection at the natural sites. An additional test to determine if adaptive markers associated to climate variables found two loci associated to specific climate variables in populations from different regions but sharing similar environmental structure. The distribution of adaptive markers among populations revealed that only two were needed to build a core subset able to keep all the markers. This preliminary assessment shows that adaptive genetic diversity could offer an additional way to measure diversity in potato germplasm and to set up options for conservation and research.

Genetic Diversity Analysis of Cultured Populations of Jade Perch （Scortum bacoo） in China Using AFLP Markers

Genetic diversity of three cultured populations of jade perch （Scortum bacoo） are studied using amplified fragment length polymorphism （AFLP） markers, which is Guangzhou（GZ） population, Foshan （FS） population and Qingdao（QD） population. Nine primer combinations were used and 385 fragments were detected. Among the 385 fragments, 80 bands （20.78%） were polymorphic. And it can be speculated that the genetic diversity of the three cultured populations of jade perch was very poor according to the gene genetic diversity among populations （Ht）, the gene genetic diversity within populations （Hs） and Shannon-Weiner index （I）. From gene differentiation （Gst）, genetic distance （D）, genetic similarity （5）, and UPGMA analysis, it is found that the relationship among the three populations is very closed, and the difference in genetic diversity among the three populations is not significant. Further clustering relationships of the jade perch cultured populations also are correlated to historical-breeding observations and genetic relationships. The GZ population clustered together with the QD population first, then with FS population.

Structure of Allozymatic Diversity of Ten Temperate and Adapted Exotic Breeding Populations of Maize (Zea mays L.)

Ten temperate and adapted exotic breeding populations of maize were studied with electrophoretic techniques. Three isozyme systems coded by nine allozyme loci were used for evaluating the genetic variability within and among populations. The results revealed that 78.57% of allozyme loci were polymorphic. Low allelic variation with a mean number of 1.84 alleles per locus per population was detected. But, these populations still maintained higher level of heterozygosity; moreover, the exotic populations had greater gene diversity than the temperate populations. All the populations were non-panmictic with negative Wright＇s fixation indexes （-0.091— -0.424）. The tropical BS 16 was typified by maximum allelic richness, percent of polymorphic loci and heterozygosity. More than 93% of the gene diversity maintained within populations, and the genetic differentiation among populations was low （0.002—0.191）. Multivariate analysis demonstrated that the tropical BS29 diverged from other populations in the reverse direction. The temperate BS9 and tropical BS16 were divergent each other, and highly differentiated from other temperate and tropical populations, consequently, these two populations would be analogically postulated as potential germplasms to establish new heterotic groups for temperate maize breeding programs.

Structure and genetic diversity of natural populations of Guadua weberbaueri in the southwestern Amazon,Brazil

The Brazilian state of Acre has an extensive natural reserve of bamboo,making it one of the largest in loco gene banks.The aim of this study was to characterize the structure and genetic diversity of Guadua weberbaueri Pilg.in two populations,one native(FAPB)and the other anthropized(FAPBA),using ISSR markers.The results show that the FAPB population exhibited higher values for all estimates of population diversity.However,the FAPBA population also showed high heterozygosity,corroborated by estimated gene flow(Nm=3.9)between the populations.The study of the association between Nei’s genetic distances and the geographic distances between the populations were significantly correlated(r=0.45,p=0.01),corroborated by the dendrogram revealing two distinct groups corresponding to the collection sites,without mixing classes between populations in the same group.As for the coancestry coefficient,pairs of individuals in the first distance class were positive and significant,indicating that plants that are geographically closer share common alleles with a frequency greater than by chance,which means that there is a tendency that geographically closer individuals are related.Individuals presented similar genetic structure when the geographical distance between them was up to 56 m for FAPB and up to 156 m for FAPBA.It was concluded that anthropized environments exhibit less genetic diversity than native environments,inferring risks for species conservation if appropriate and planned management techniques are not adopted.

Tyrosine Aminotransferase Gene (SmTAT) Revealed Genetic Diversity and Phylogeny of Cultivated Danshen (Salvia miltiorrhiza) Populations

Chinese traditional medicine Danshen is the radix of the perennial herbs of Salvia miltiorrhiza Bunge, which has a variety of pharmacological effects and is traditionally and extensively applied clinically to treat cardiovascular disorders. In this research, the genomic genes for tyrosine aminotransferase (TAT) of 38 cultivated populations of Danshen in China were cloned and bioinformatic analyses were conducted to reveal its genetic diversity and phylogeny. The full-length SmTAT was 2296 - 2444 bp including 6 exons (encoding 411 amino acids) and 5 introns. Overall, the SmTAT genes in cultivated Danshen populations are highly conserved with a relative low level of genetic diversity. The spliced exons (1236 bp) had 23 SNP variations with a rate of 1.86%, of which 22 occurred in the white flower S. miltiorrhiza Bge.f.alba population (W-SCHY-W-1) and led to 5 amino acid variations. The entire 290 SNP variations with a rate of 24% in the 5 introns occurred exclusively in W-SCHY-W-1. Phylogenetic trees based on the full-length, combined introns, the spliced exons, and the deduced amino acid sequences of SmTAT all showed a two-clade basic structure with W-SCHY-W-1 uniquely standing alone. The SmTAT gene of the white flower population (W-SCHY-W-1) is unique and especially rich in variations. The first time clarified genomic SmTAT gene structure and genetic diversity in cultivated Danshen populations laid an excellent foundation for further studies on the biosynthesis of bioactives and the molecular breeding of Danshen as well as in plant tyrosine metabolism.

Microsatellite analysis of genetic diversity and population structure of Chinese mitten crab (Eriocheir sinensis)

Chinese mitten crab （Eriocheir sinensis） has higher commercial value as food source than any other species of Eriocheir in China. To evaluate the germplasm resources and characterize the genetic diversity and population structure of the crabs in different water systems, two stocks and two farming populations were assessed with 25 polymorphic microsallite loci available in public GenBank. Basic statistics showed that the average observed heterozygosity （Ho） amongst populations ranged from 0.5789 to 0.6824. However, a remarkable presence of inbreeding and heterozygote deficiencies were observed. To analyze population structure, pairwise FST coefficients explained only -10.3% variability from the subdivision of mitten crab populations, the remaining variability stems from the subdivision within subpopulations. Although the four populations had slight differentiation, different allelic frequencies resulted in distinct population structures. Two stocks and one farming population were clustered together to the phylogenetic branch of Yangtze crab, with an approximate membership of 95%. Whereas, another farming population was clustered singly to the phylogenetic branch of the Liaohe crab, with a membership of 97.1%. The tests for individual admixture showed that Yangtze crab had probably been contaminated with individuals from other water systems. Genetic relationships between populations also supported the conclusion that Yangtze crab and Liaohe crab had different gene pools in spite of the origins of the same species.

Analysis of genetic diversity and population structure of Chinese yak breeds (Bos grunniens) using microsatellite markers

Nine Chinese yak breeds （Maiwa, Tianzhu White, Qinghai Plateau, Sibu, Zhongdian, Pali, Tibetan High Mountain, Jiulong, and Xinjiang） and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations, genetic relationship between populations, and population structure for each breed. A total of 206 microsatellite alleles were observed. Mean F-statistics （0.056） for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds. The Neighbor-Joining phylogenetic tree was constructed based on Nei＇s standard genetic distances and two clusters were obtained. The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together. The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one cluster includes yaks from Tibet Autonomous Region and Qinghai Province, one cluster combines Zhongdian, Maiwa, and Tianzhu White, and Jiulong and Xinjiang come into the third cluster. Pali was mainly in the first cluster （90%）, Jiulong was mainly in the second cluster （87.1%）, Zhongdian was primarily in the third cluster （83%）, and the other yak breeds were distributed in two to three clusters. The Gayal was positively left in the fourth cluster （99.3%）.

Plant diversity, population structure, and regeneration status in disturbed tropical forests in Assam, northeast India

We investigated the plant population structure and the phy- tosociological and regeneration status in two disturbed tropical forests in Assam Province, the Hojai Reserve Forest and Kumorakata Reserve Forest. A total of 166 species （80 trees, 20 shrubs and 66 herbs） of 136 genera and 63 families were recorded in both study sites. The disturbance index at the two sites, Kumorakata Reserve Forest and Hojai Reserve Forest, were recorded at 11.4% and 3.70% respectively. Reverse J-shaped population curve and exploitation of tree species in higher girth classes were recorded at both study sites. In the girth classes （10-30 cm, 30-60 cm, 60-90 cm and 90-120 cm in size） the percentage of cut stump density was higher than the percentage of individual living trees. The 18% （Kumorakata Reserve Forest） and 7% （Hojai Reserve Forest） spe- cies were recorded as not regenerating. Illegal felling and over-exploitation of forest resources may lead to species-specific changes in the population structure and can alter the future structure and composi- tion of the forests.

ISSR Analysis on Genetic Diversity of the 34 Populations of Oryza meyeriana Distributing in Yunnan Province,China

The genetic diversity of the 34 populations of wild rice Oryza meyeriana Baill. distributed in Yunnan Province, China was analyzed using 13 inter-simple sequence repeat （ISSR） markers. A total of 168 bands were amplified, of which 135 polymorphic bands were discovered and the percentage of polymorphic bands （PPB） was 80.36%. A genetic diversity was revealed as Nei＇s gene diversity （H） = 0.2666 and Shannon information index （I） = 0.4028 at population level. The 34 populations were divided into different groups based on administrative regions, latitude and longitudes, river areas, altitudes of their origins, and their indexes such as Na （number of alleles）, Ne （effective number of alleles）, H, I and PPB were calculated. Richer genetic diversity was found in the wild rice populations distributed in Simao Prefecture than that in Lingcang Prefecture or Xishuangbanna Prefecture whereas the least genetic diversity was in Baoshan Prefecture or Dehong Prefecture. Rich genetic diversity was also discovered in the wild rice populations originated from higher than 710 m altitude around the middle and lower reaches of the Lancang River belonging to the Pacific Ocean drainage system. The 34 populations could be classified into two groups, one group covered the wild rice distributing in Simao Prefecture only while the other group covered ones in Lingcang, Xishuangbanna and Dehong Prefectures. The issue on how to effectively conserve the wild rice germplasm was discussed.

Genetic Diversity of Natural Myrica rubra Sieb.et Zucc Populations in Guangxi Revealed by ISSR Markers

The present study was conducted to assess the molecular characterization and genetic diversity amongst natural populations of Myrica rubra in Guangxi Zhuang Autonomous Region, China, thus to provide scientific evidence for germplasm conservation and exploitation. Using ISSR （inter-simple sequence repeats） markers, the level of genetic variation and the molecular characterization of 10 natural populations of M. rubra, originated from Guangxi Zhuang Autonomous Region in China, were performed. Based on 11 primers, 123 clear and reproducible DNA fragments were generated, of which 95 （77.24%） were polymorphic. The average value of Nei＇s gene diversity （He） was 0.268. The coefficient of genetic differentiation （Gst） was 0.341, revealing that 34.1% of the total molecular variance existed among populations. The Mantel statistical testing showed that the genetic distance was correlated to the geographic distance, but the correlation was not significant. Ten populations were divided into two big clusters according to unweighted pair group method with arithmetic mean （UPGMA） analysis. One consisted of populations of Rongxian （RX）, Hepu （HP）, Liangqing （LQ）, Marshan （MS）, Lingshan （LS） and Shansi （SS）, which originated from the southern Guangxi, while the other was composed of Guanyang （GY） and Lingui （LG） populations of northern Guangxi, Huanjiang （HJ） populations of northwestern Guangxi and Shanglin （SL） populations of southern Guangxi. The level of genetic variation in wild M. rubra population distributed in Guangxi is high. Gene drift within the population was responsible for genetic variation in wild M. rubra in Guangxi, and the effect of the genetic flow among inter-populations was not significant. Classification of wild M. rubra populations was correlated to climate and environment. The molecular characterization and diversity assessment of M. rubra is of immense value for planning conservation of its genetic resources and their exploitation for further studies.