Shannon's Information Index Research Articles

Genetic diversity and structure among natural populations of Sindora glabra in Hainan Island, China as revealed by ISSR markers

Sindora glabra, one of the second-class national protective plants in China, has important ecological and commercial values. To understand the genetic diversity and structure of S. glabra, eleven natural populations from four areas of Hainan Island in China were analyzed by inter-simple sequence repeat (ISSR) markers. Thirteen primers were screened out and used to amplify 157 DNA samples. A total of 122 bands were obtained, among which 114 (93.4%) bands were polymorphic. Genetic parameters including average number of effective alleles (1.547), Nei's gene diversity (0.321), Shannon's information index (0.482), and gene differentiation coefficient (0.1944) revealed a high level of genetic diversity maintained in S. glabra populations. The variation within populations accounted for 85.6% of total variation based on analysis of molecular variance. Genetic distance analysis showed that 11 populations could be divided into three groups and populations from the same areas were classified as one group, suggesting that high genetic diversity of S. glabra was attributable to geographic isolation. Together, introduction of germplasm from distant natural distribution areas would be a sound strategy for germplasm resource conservation of S. glabra and selection of elite individuals from populations of far relationship for hybridization is of great importance for breeding improvement programs in future.

Applicability of start codon targeted (SCoT) and inter-simple sequence repeat (ISSR) markers for genetic diversity analysis in durum wheat genotypes

ABSTRACTDurum wheat (Triticum turgidum var. durum) is one of the most important cereal crops widely cultivated all over the world with high economic value. In the present study, genetic variation in a mini-core collection of durum wheat germplasm, including 25 breeding lines and 18 landraces, was evaluated using 15 inter-simple sequence repeat (ISSR) and six start codon targeted (SCoT) markers. High levels of polymorphism were observed; 98.70% (ISSR) and 100% (SCoT), which indicated that these markers are useful tools for detection of genetic variation in the collection. Analysis of molecular variance revealed that the major part of genetic variations (90% and 93% for ISSR and SCoT, respectively) occurred within genotypes set. Comparing the genetic variation of breeding lines and landraces based on genetic parameters showed that effective number of alleles (Ne), Nei's gene diversity (He) and Shannon's Information index (I) in landraces were higher than in breeding lines. Although cluster analysis, based on both markers, separated the genotypes in five groups, the dendrogram obtained from SCoT provided the best clustering pattern. Inter-population differentiation (Gst) estimated on the basis of two marker systems representing that a vast portion of the total genetic diversity refers to variation within two sets of genotypes. In conclusion, the results verified a high level of genetic variation among the durum wheat mini-core collection, particularly among landraces, which can be interesting for future breeding programmes.

Genetic differentiation between cultured and wild populations of Paralichthys olivaceus based on AFLP markers

Paralichthys olivaceus is a warm-temperature benthic species distributed in the western Pacific Ocean from the Kuril Islands, Japan to the South China Sea. In the present study AFLP (amplified fragment length polymorphism) marker was employed to examine the genetic differences between cultured and wild populations of P. olivaceus. The results showed that the gene diversity and Shannon's information index of cultured populations (h = 0.130–0.150; I = 0.201–0.236) were similar with wild populations (h = 0.123–0.136; I = 0.199–0.220). Pairwise Fst and AMOVA revealed significant genetic differentiation among them, indicating cultured populations exhibited distinctive heterogeneity with wild populations. The results of present study suggested that broods of this study should not be released into natural sea areas due to its genetic alterations.

Use of ISSR markers to assess the genetic diversity in wild medicinal Ziziphus spina-christi (L.) Willd. collected from different regions of Saudi Arabia

ABSTRACTZiziphus spina-christi (sidr) is a shrub, sometimes a tree, native to a vast area of Africa stretching from Mauritania to West Africa. In the Kingdom of Saudi Arabia, it is an exotic medicinal plant for many diseases. The aim of this study was to assess the genetic diversity within and among 34 accessions of Z. spina-christi collected from different regions of Saudi Arabia. The amplification of genomic DNA with 11 inter-simple sequence repeat (ISSR) primers yielded 105 scorable loci, of which 93.4% were found to be polymorphic. The observed number of alleles (na), effective number of alleles (ne), Nei's gene diversity (h) and genetic diversity estimated by Shannon's information index (I) were 1.93, 1.44, 0.26 and 0.41, respectively. The total genetic diversity, Ht (0.266 ± 0.0289) was close to the average intrapopulation genetic diversity, Hs (0.2199 ± 0.0216). A high level of gene flow (Nm = 2.37) between populations, reflecting high genetic differentiation (Gst = 0.1739). The analysis of molecular variance showed that the maximum value of genetic variation was found within populations (90%), whereas a low value of genetic variance was observed among populations. The analysis using the unweighted pair-group method with arithmetic averages clustered the population from Farasan Island as an out-group due to its geographical origin. The obtained results demonstrate that the ISSR markers may be used for evaluation of the genetic diversity due to their efficiency in revealing polymorphism even in closely related germplasm and may help in Ziziphus genome analysis.

Impact of alkaline dust pollution on genetic variation of Usnea subfloridana populations

Very little is known whether and how air pollution impacts genetic diversity of lichenized fungi that are well-known indicators of environmental quality. We studied the genetic variation of eight Usnea subfloridana populations in Pinus sylvestris-dominated boreal forest stands in southern Estonia, Northern Europe; four of these populations were exposed to long-term dust pollution released from unpaved road. The mean bark pH of lichen phorophyte differed considerably between polluted and unpolluted forest stands. We genotyped 274 Usnea thalli using nine specific fungal microsatellite markers. Genetic variation measures were calculated and compared between populations from different habitats. Allelic richness, Shannon's information index, and genetic diversity of lichen populations were significantly higher in unpolluted forest sites than in polluted forest sites. We conclude that environmental disturbances caused by alkaline dust pollution had negative impact on the genetic variation of U. subfloridana, a common species of lichenized fungi.

Genetic structure and diversity of Glehnia littoralis, an endangered medicinal plant in China

The medicinal plant Glehnia littoralis has become increasingly endangered in China. To assist in the formulation of conservation strategies for this species, we assessed the genetic diversity of G. littoralis with a total of 172 samples from 10 populations using SRAP markers. The results showed that Nei's gene diversity (H) per locus ranged from 0.04 to 0.2504, with an average of 0.245, and that Shannon's information index (I) ranged from 0.233 to 0.6253, averaging 0.5516 at the population level. The total genetic diversity (Ht) was 0.2471, and 66.5% (Hs = 0.1643) of the total genetic variation was attributed to within-population diversity (P < 0.05), with the rest (33.5%) due to differences between populations (Gst = 0.3353), indicating that gene flow was restricted among populations (Nm = 0.9911). AMOVA also suggested that the main source of variation was within populations (77.8%), whereas 22.2% of differentiation was found among populations. Estimates of genetic distance were not correlated with geographic distance according to a Mantel test (r = 0.0792, P = 0.329). These results show that high levels of genetic variation are present within and among populations. The endangered status of this species is likely due to the destruction of the habitats of the wild populations, rather than a loss of genetic diversity.

Characterization of microsatellites in Fusicladium effusum, cause of pecan scab

SummaryPecan scab, caused by the plant pathogenic fungus Fusicladium effusum, is the most destructive disease of pecan. Little is known of the population genetic diversity of this pathogen. In this study, microsatellites were mined from the F. effusum genome, and flanking primers were subsequently designed. A total of 275 microsatellites were screened, and 33 selected primers produced reliable, polymorphic markers against 46 isolates of F. effusum from 11 diverse locations in the southeastern USA. The number of alleles per microsatellite locus ranged from two to 17, and the polymorphic information content (PIC) from 0.475 to 0.911. A unique pattern informative combination (UPIC) analysis of three groups of 12 isolates each and 33 primers consistently showed a minimum number of markers required for the maximum discrimination of isolates equal to 3. The characteristics of the unique patterns (UP) and informative contents (IC) were very similar. However, the primers that were selected by UPIC were not necessarily the same for each of the three groups. Using all 46 isolates showed each locus was polymorphic, with a single‐population level Shannon's information index of 1.516, indicating substantial diversity. These markers show a range in polymorphic content and power of discrimination that will be valuable tools for studies of genetic diversity in F. effusum.

Nucleotide polymorphisms and protein structure changes in the Fg16 gene of Fusarium graminearum sensu stricto

Fusarium graminearum is one of the most important causes of wheat scab in different parts of the world. This fungus is able to produce widespread trichothecene mycotoxins such as nivalenol (NIV) and deoxynivalenol (DON) which are harmful for both human and animals. The Fg16 target is located in chromosome 1 of the F. graminearum genome coding for a hypothetical protein whose function is not yet known. The Fg16 gene is involved in lipid biosynthesis and leads to sexual development during colonization in wheat stalks. This gene is used to detect F. graminearum and determine the lineage of F. graminearum complex species. In the present study, polymerase chain reaction–single strand conformational polymorphism (PCR–SSCP) and DNA sequencing methods were employed in screening for genetic variation in 172 F. graminearum s.s. isolates. The PCR reaction forced the amplification of 410-bp fragments of Fg16. Two single nucleotide polymorphisms (T82C and A352T) and one amino acid exchange (C65S) with three patterns (TA/TA, CT/CT and TA/CT genotypes) were found in the Fg16 gene fragment. Two haplotypes, 1A and 1B, were identified within F. graminearum s.s. populations in northern and western regions of Iran. Two different secondary structures of protein were predicted for CT/CT and TA/CT genotypes of Fg16 gene. The average diversity levels detected were relatively high (He: 0.3238; Heu: 0.334; Ho: 0.2894; mean PIC: 0.514; mean Shannon's information index: 0.4132; mean number of alleles per locus: 1.473). On the basis of the obtained results, it was revealed that the Fg16 gene had a high degree of polymorphism that can be considered for future control programming strategies and thus the associations between the SSCP patterns with different traits of F. graminearum such as wheat colonization, perithecium formation on stalk tissues and lineage discrimination should be investigated.

The genetic diversity of triticale genotypes involved in Polish breeding programs.

Genetic diversity analysis of triticale populations is useful for breeding programs, as it helps to select appropriate genetic material for classifying the parental lines, heterotic groups and predicting hybrid performance. In our study 232 breeding forms were analyzed using diversity arrays technology markers. Principal coordinate analysis followed by model-based Bayesian analysis of population structure revealed the presence of weak data structuring with three groups of data. In the first group, 17 spring and 17 winter forms were clustered. The second and the third groups were represented by 101 and 26 winter forms, respectively. Polymorphic information content values, as well as Shannon’s Information Index, were higher for the first (0.319) and second (0.309) than for third (0.234) group. AMOVA analysis demonstrated a higher level of within variation (86 %) than among populations (14 %). This study provides the basic information on the presence of structure within a genetic pool of triticale breeding forms.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-1997-8) contains supplementary material, which is available to authorized users.

Evaluation of fire recurrence effect on genetic diversity in maritime pine (Pinus pinaster Ait.) stands using Inter-Simple Sequence Repeat profiles

The management of maritime pine in fire-prone habitats is a challenging task and fine-scale population genetic analyses are necessary to check if different fire recurrences affect genetic variability. The objective of this study was to assess the effect of fire recurrence on maritime pine genetic diversity using inter-simple sequence repeat markers (ISSR). Three maritime pine (Pinus pinaster Ait.) populations from Northern Portugal were chosen to characterize the genetic variability among populations. In relation to fire recurrence, Seirós population was affected by fire both in 1990 and 2005 whereas Vila Seca-2 population was affected by fire just in 2005. The Vila Seca-1 population has been never affected by fire. Our results showed the highest Nei's genetic diversity (He=0.320), Shannon information index (I=0.474) and polymorphic loci (PPL=87.79%) among samples from twice burned populations (Seirós site). Thus, fire regime plays an important role affecting genetic diversity in the short-term, although not generating maritime pine genetic erosion.

Correlation analysis of genetic diversity and population structure of Houttuynia cordata Thunb with regard to environment.

To study the levels of genetic diversity, and population structure, of Houttuynia cordata Thunb, the genetic background and relationships of populations were analyzed in terms of environmental factors. The genetic diversity and population structure of H. cordata were investigated using sequence-related amplified polymorphisms and correlation with environmental factors was analyzed using the SPSS software. Two thousand one hundred sixty-three sites were amplified from 41 pairs of primers, 1825 of which were polymorphic, and the percentage of polymorphic loci was 84.37%; the percentage of polymorphic sites was 72.14 and 67.77% at the species and population level, respectively. The observed number of alleles was 1.52 and 1.30 at species and population level, respectively. The effective number of alleles was 1.38 and 1.24 at species and population level, respectively. The Nei's diversity was 0.26 and 0.15 at species and population level, respectively. The Shannon's information index was 0.87 and 0.63 at species and population level, respectively. The genetic differentiation coefficient of populations was 0.51, and 12 populations were divided into three classes based on D = 0.20; the genetic diversities of different populations are correlated at different significance levels (P < 0.05) with environmental factors. Genetic differentiation existed among populations and the populations exhibited heteroplasmy.

内蒙古荒漠草原植物遗传多样性对模拟增温处理的响应

PDF HTML阅读 XML下载 导出引用 引用提醒 内蒙古荒漠草原植物遗传多样性对模拟增温处理的响应 DOI: 10.5846/stxb201504220826 作者: 作者单位: 中国农业科学院草原研究所;内蒙古农业大学生命科学学院,中国农业科学院草原研究所：内蒙古农业大学生命科学学院,中国农业科学院草原研究所,中国农业科学院草原研究所,内蒙古农业大学生态与环境学院,中国农业科学院草原研究所;内蒙古农业大学生命科学学院 作者简介: 通讯作者: 中图分类号: 基金项目: 内蒙古自治区自然科学基金资助项目（2015MS0305）；中国科学院西部之光“人才培养”项目；中国农业科学院草原研究所科技创新工程资助项目 The response of genetic diversity in desert steppe plants to simulated warming in Inner Mongolia, China Author: Affiliation: Institute of Grassland Research, Chinese Academy of Agricultural Sciences;College of Life Sciences, Inner Mongolia Agricultural University,,,,,Institute of Grassland Research, Chinese Academy of Agricultural Sciences;College of Life Science, Inner Mongolia Agricultural University, Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:为探究全球变暖对温带荒漠草原地上种群的遗传影响，对已经接受模拟增温处理6年的短花针茅草原4种不同生活型植物，即半灌木、多年生禾草、多年生杂类草和一年生植物，应用AFLP分子标记方法研究了其遗传多样性和遗传结构。结果显示，对照处理与增温处理下的木地肤、短花针茅、细叶葱、猪毛菜4种植物的多态位点百分率（PPB）分别为11.32%，11.32%；40.83%，39.91%；14.29%，13.10%；19.85%，19.12%。Nei's基因多样性指数（He）分别为0.0274，0.0259；0.0812，0.0899；0.0131，0.0084；0.0506，0.0456。Shannon's信息指数值（I）分别为0.0447，0.0430；0.1354，0.1466；0.0267，0.0182；0.0811，0.0733。分子方差分析（AMOVA）显示4种植物的变异主要来源于实验处理内部，木地肤为85.03%，短花针茅为66.35%，细叶葱为70.00%，猪毛菜为66.52%；增温处理间的变异分别占-2.81%，-5.47%，-3.60%，2.53%（P>0.05）。4种植物增温处理与变异程度之间在统计学上并无相关性。研究表明虽然短时间的模拟增温并不足以使4种生活型植物种群遗传多样性和遗传结构发生显著变化，但相对于3种多年生植物，一年生植物猪毛菜更容易受到增温影响。多年生和一年生植物对增温具有不同的遗传响应。 Abstract:Climate is the most important factor that determines vegetation types and the distribution of species, and, accordingly, these features are two of the most prominent indicators of climate change. Currently, scientists generally agree that climate change will inevitably lead to changes in plant community structure and function, and if this change continues, the effects will be profound and enduring. Existing research shows that simulated warming causes an increase in biomass in Deschampsia caespitosa, Carex alrofusca, and Leymus chinensis; as climates change, these constructive species and their main companion species within a Kobresia humilis meadow have experienced an advancement in their spring phenology and a delay in their autumn phenophase. In addition, the photosynthetic rate of Deschampsia caespitosa in a Northwest Sichuan alpine meadow has increased. Although the change in stomatal conductance was irregular, a significant decrease has also been observed in the sodium, potassium, and phosphorus content of leaves. However, relatively little research has been conducted on the effects of simulated warming on the genetic structure and diversity of plant populations. Against the background of global climate change, the temperatures of the Inner Mongolian desert steppe have become unevenly elevated, with average annual temperatures increasing from 8.1℃ in the 1950s to 9.0℃ in the 1990s. The present study explores the effects of global warming on the genetics of wild forage plant populations with different life forms in desert steppe habitat, in an effort to elucidate their potential to adapt to environmental change. The study site was located in the desert steppe in Siziwangqi territory of Inner Mongolia. Suspension infrared radiators were used to create a controlled warming experiment under otherwise natural field conditions. Warming began on May 3, 2006. The average soil temperature at depths of 0, 7.5, 15, 30, and 50 cm increased by 1.32, 0.92, 0.88, 0.80, and 0.74℃, respectively, after warming for 1 year compared with the average in plots not exposed to warming. For this study, changes in genetic diversity and structure were analyzed in four plant populations: (1) small half shrubs, represented by Kochia prostrata; (2) perennial grasses, represented by Stipa breviflora; (3) perennial forbs, represented by Allium tenuissimum; and (4) annuals and biennials, represented by Salsola collina). The study was conducted under simulated warming pressure and genetic analysis was performed using amplified fragment length polymorphism. The percentages of polymorphic loci in K. prostrata, S. breviflora, A. tenuissimum, and S. collina under non-warming were 11.32%, 40.83%, 14.29%, and 19.85%, whereas those under simulated warming were 11.32%, 39.91%, 13.10%, and 19.12%, respectively. The genetic diversity of the four populations measured under control and simulated warming, measured by the Shannon's information index, were as follows: K. prostrata (0.0274, 0.0259), S. breviflora (0.0812, 0.0899), Allium tenuissimum (0.0131, 0.0084), and S. collina (0.0506, 0.0456). These findings exhibited the same distributional pattern as that of Nei's genetic diversity index for K. prostrata (0.0447, 0.0430), S. breviflora (0.1354, 0.1466), Allium tenuissimum (0.0267, 0.0182), and S. collina (0.0811, 0.0733). Cluster analysis of these four species showed that known of the species reacted significantly to the warming process, and that inter-individual clusters were not significantly different. The results of an analysis of molecular variance (AMOVA) indicated that the main source of variation among the four life form populations was within-population variation: K. prostrata (85.03%), S. breviflora (66.35%), A. tenuissimum (70.00%), and S. collina (66.52%). The among-groups variation was not significant and accounted for the following percentages of variation: K. prostrata (-2.81%), S. breviflora (-5.47%), Allium tenuissimum (-3.60%), and S. collina (2.53%). No statistically significant correlation was found between simulated warming and genetic differentiation. This study shows that a short period of simulated warming was not sufficient to create a significant change in genetic diversity and structure for the four life form populations studied here; however, compared with the three types of perennials studied, the annual plant S. collina, is more susceptible to the effects of warming. Perennials and annuals have different genetic responses to warming. This study provides experimental evidence that can reveal the potential adaptation of plants to environmental change for different life forms of wild forage plants of the desert steppe, and will help researchers to predict forage yield and changes in forage quality. 参考文献 相似文献 引证文献

Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea.

Population Structure and Genetic Variation in Indian and African Eleusine coracana (L.) Gaertn

Population structure and genetic variation was estimated for 40 Indian and African finger millet genotypes using 237 random amplified polymorphic DNA (RAPD) and 16 morphological markers revealing differences between African and Indian groups. African genotypes showed 53.59%; 0.17±0.19; 0.27±0.27 compared to 48.10%; 0.15±0.19; 0.24±0.27 polymorphism, Nei's gene diversity and Shannon's Information index, respectively in Indian genotypes. Primers OPM-20, OPW-04, OPX-11 were identified as the most informative primers in terms of high % polymorphism and Nei's gene diversity values. Population structure analysis revealed the existence of two distinct sub-groups, correlated well with primary and secondary centers of finger millet diversity and can be utilized to enhance and widen finger millet germplasm base.

Morphological and AFLP-Based Genetic Diversity in Rosa platyacantha Population in Eastern Tianshan Mountains of Northwestern China

Morphological and AFLP-based genetic analyses of six natural populations of Rosa platyacantha in the Eastern Tianshan Mountains of Xinjiang in Northwestern China were performed. Nested analysis of variance models (ANOVA) showed that there were significant differences (P > 0.05) in morphological traits among and within the populations of R. platyacantha. The phenotypic variation coefficient (CV) of the traits varied from 9.78% to 37.71%, confirming the abundant phenotypic variations in the species. The average value of the phenotypic differentiation coefficient (Vst) was 27.50%, indicating a lower phenotypic diversity among populations than within populations. Principal component analysis (PCA) showed that the two decisive traits of ANH and TAW contributed to the proportion of 97.19% in the 1st principal component (PC), suggesting that the phenotypic variations of the traits primarily originated from the achene characters. The percentages of polymorphic loci (PPL), Nei's genetic diversity index (h) and Shannon information index (I) were highly similar among populations, with average values of 63.96%, 0.2361 and 0.3506, respectively. Moreover, the gene differentiation (Gst) and estimated value of gene flow (Nm) were 8.10% and 5.6766, respectively, indicating very low genetic diversity among populations. Clustering analysis based on morphological traits and AFLP markers showed that the populations were mainly grouped with similar altitudes and geographic distances, respectively. The Mantel test revealed that there was no significant correlation between the phenotypic and genetic diversity among populations, implying a possible influence of environments on the genotypes of R. platyacantha.

Genetic diversity and population structure of the narrow endemic and endangered species Heteroplexis microcephala Y. L. Chen. in China revealed by random amplified polymorphic DNA markers

Heteroplexis microcephala Y. L. Chen. is an endemic and endangered species found only in karst limestone regions in the Yangshuo County of the Guangxi Zhuang Autonomous Region in China: it is a habitat representative of species in the Heteroplexis genus. To provide basic genetic information for its conservation, in this study we evaluated the genetic variation and differentiation among six wild populations of H. microcephala by random amplified polymorphic DNA markers (RAPD). The leaves of 141 individuals were sampled. Based on 12 primers, 113 DNA fragments were generated. Genetic diversity was low at the population level (Nei?s gene diversity (h)=0.0579; Shannon information index (I)=0.0924; percentage of polymorphic bands (PPB)=23.30%), but relatively high at the species level (h=0.1701; I=0.2551; PPB=46.34%). The coefficient of genetic differentiation based on Nei?s genetic diversity analysis (0.6661) was high, indicating that there was significant genetic differentiation among populations, which was confirmed by AMOVA analysis exhibiting population differentiation among populations of 68.77%. Low gene flow among populations (0.2507) may result from several factors, such as a harsh pollination environment, population isolation and low seed dispersal distance. Limited gene flow and self-compatibility are the primary reasons for the high genetic differentiation observed for this species. We propose the collection of seeds from more populations with fewer individuals and core populations for ex situ conservation and suggest methods to increase seed germination rates.

Analysis of population structure and genetic diversity of Egyptian and exotic rice (Oryza sativa L.) genotypes

Understanding the population structure and genetic diversity is a very important goal to improve the economic value of crops. In rice, a loss of genetic diversity in the last few centuries is observed. To address this challenge, a set of 22 lines from three different regions – India (two), and Philippines (six), and Egypt (14) – were used to assess the genetic diversity and the features of population structure. These genotypes were analyzed using 106 SSR alleles that showed a clear polymorphism among the lines. Genetic diversity was estimated based on the number of different alleles, polymorphism information content (PIC), and gene diversity. A total of 106 SSR alleles was identified from the 23 SSR loci and used to study the population structure and carry out a cluster analysis. All SSR loci showed a wide range of the number of different alleles extended from two (one loci) to seven alleles (three loci). Five and eight loci showed high PIC and gene diversity (≥0.70), respectively. The results of population structure are in agreement with cluster analysis results. Both analyses revealed two different subpopulations (G1 and G2) with different genetic properties in number of private alleles, number of different alleles (Na), number of effective alleles (Ne), expected heterozygosity (He), and Shannon's Information Index (SII). Our findings indicate that five SSR loci (RM 111, RM 307, RM 22, RM 19, and RM 271) could be used in breeding programs to enhance the marker-assisted selection through QTL mapping and association studies. A high genetic diversity found between genotypes which can be exploited to improve and produce rice cultivars for important traits (e.g. high agronomic features and tolerance to biotic or/and abiotic stresses).

Genetic diversity of bottle gourd (Lagenaria siceraria (Molina) Standl.) landraces of South Africa assessed by morphological traits and simple sequence repeat markers

Bottle gourd (Lagenaria siceraria (Molina) Standl.) is an important crop in rural communities in South Africa but it remains under-researched. The objective of this study was to assess the genetic diversity present amongst bottle gourd landraces grown by smallholder farmers in South Africa using morphological traits and 11 selected polymorphic simple sequence repeat (SSR) markers. Marked phenotypic differences were observed amongst bottle gourd landraces. Principal component analysis on quantitative traits identified seven principal components, which accounted for 87% of the total variation. Number of alleles varied from 3 to 9 with a mean of 6 per SSR locus. Number of effective alleles ranged from 1.99 to 6.72 with a mean of 3.75. Shannon's information index varied from 0.95 to 2.01 with a mean of 1.41. Expected heterozygosity values ranged from 0.5 to 0.87 with a mean of 0.71 with polymorphic information content values of 0.5 to 0.85 and a mean of 0.7. Morphological traits and SSR marker analyses showed a significant correlation in clustering the landraces. The present study demonstrated the presence of genetic diversity amongst bottle gourd landrace collections from South Africa useful for strategic improvement, direct production or conservation.

Natural variation of selenium concentration in diverse tea plant (Camellia sinensis) accessions at seedling stage

Selenium (Se) is a dietary essential trace element for humans and animals. Owing to Se being obtained from food or other source of supplementation, Se-enriched tea is a possible source of supplemental Se and thus has been drawing much attention. This study aimed to identify the variation of the Se concentrations among 14 elite Camellia sinensis cultivars against two-Se-levels supplementation at seedling stage. In the present study, the genetic diversity was assessed by 93 alleles revealed by 12 SSR primers in the C. sinensis accessions. Among the scored 93 alleles, 81 (87.10%) were polymorphic, and the average Nei's gene diversity (He) was 0.253 and average shannon information index (I) was 0.394, indicating a relatively high genetic variation. Significant variations were observed for the Se concentration among the accessions in both treatments (P<0.01), ranging from 0.300–0.445mgkg−1 and 0.357–0.537mgkg−1 in control (0) and Se-supplied (4mgkg−1) treatments respectively. The quality components content, tea polyphenols and amino acid, were sensitive to Se-supplement in a few of accessions, whereas soluble sugar and aqueous extract content appeared unchanged between the contrast treatments. In addition, the genetic variation among the tea plant cultivars was not well correlated with the Se concentration. Even then, the genetic variation in Se concentration across the 14 accessions indicated the possibility of utilizing tea plant accessions to develop optimized cultivars for Se-enriched tea. For the relative high Se concentration in the tea, tea plant is supposed to be a Se-enriched species. These results may enhance our understanding the genetic variation in tea plant.

An analysis of genetic diversity in Marphysa sanguinea from different geographic populations using ISSR polymorphisms

The genetic diversity of five wild populations of marine polychaete Marphysa sanguinea found in China was investigated using Inter-Simple Sequence Repeat-PCR (ISSR-PCR) polymorphisms. The results of the ISSR-PCR showed that 108 (90.8%) of the 119 ISSR loci tested were polymorphic. The Shannon's information index value was 0.4981, Nei's gene diversity was 0.3418, and the coefficient of gene differentiation (Gst) was 0.3671, which indicated that the among-population component accounted for 36.7% of the total variation, while the within-population component accounted for 63.3%. A UPGMA tree showed that the five populations clustered into two branches. Populations from Dalian, Xingcheng, and Rushan clustered together, while the two Guangxi populations, A and B, clustered into a unique group. The results indicated that the genetic diversity among the five populations of M. sanguinea is high, which will provide useful information for the protection of biodiversity among marine polychaetes.