High genetic diversity and small genetic variation among populations of Magnolia wufengensis (Magnoliaceae), revealed by ISSR and SRAP markers

BackgroundGenetic diversity and genetic variation of 10 populations and subpopulations of Magnolia wufengensis, a new and endangered endemic species, were examined by inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) molecular markers. Compared with other endangered endemic Magnolia taxa, M. wufengensis holds a relatively high level of genetic variation.ResultTotal genetic diversity was found to be 87.7% for ISSR and 88.0% for SRAP markers. For polymorphic loci (P), the effective mean number of alleles (Ae) was 1.414 for ISSR markers and 1.458 for SRAP markers, while the mean expected heterozygosity (H) was 0.256 using ISSR and 0.291 for SRAP markers. Within-population variation was estimated for P as 74.9% using ISSR and 74.6% with SRAP markers; the number of alleles Ae was 1.379 with ISSR and 1.397 for SRAP and H 0.235 with ISSR and 0.247 for SRAP markers.ConclusionThe analysis of molecular variation of both ISSR and SRAP marker systems indicated that most genetic variation is within populations, with values of 90.64% and 82.92% respectively. Mantel tests indicated a moderate association between the two marker systems and a low correlation between genetic and geographic distances. High levels of genetic diversity and low levels of population divergence suggest that genetic drift is not currently of great concern for this species. Severe habitat loss and fragmentation, predominantly ascribed to anthropogenic pressures, caused in-situ developing restriction of this species. Action for conserving this rare species for its long-term survival should be taken immediately.     

Assessment of somaclonal variation in somatic embryo-derived plants of yacon [Smallanthus sonchifolius (Poepp. and Endl.) H. Robinson] using inter simple sequence repeat analysis and flow cytometry

BackgroundYacon (Smallanthus sonchifolius) is a root crop native to the Andean region. Low sexual reproductive capacity is a major constraint facing the genetic breeding of this crop. Biotechnological techniques offer alternative ways to widen genetic variability. We investigated somaclonal variation in regenerants of yacon derived from in vitro somatic embryogenesis using simple sequence repeat (ISSR) analysis and flow cytometry.ResultsTwenty tested ISSR primers provided a total of 7848 bands in 60 in vitro regenerants and control plant. The number of bands for each primer varied from 3 to 10, and an average of 6.95 bands was obtained per ISSR primer. Eight primers were polymorphic and generated 10 polymorphic bands with 7.19% mean polymorphism. ISSR analysis revealed genetic variability in 6 plants under study. These regenerants had Jaccard's distances 0.104, 0.020, 0.040, 0.106, 0.163 and 0.040. Flow cytometric analysis did not reveal changes of relative nuclear DNA content in regenerants suggesting that the plants obtained via somatic embryogenesis had maintained stable octoploid levels.ConclusionsOur findings show that indirect somatic embryogenesis could be used in yacon improvement to widen genetic variability, especially when low sexual reproductive capacity hinders classical ways of breeding.     

Efficiency of RAPD,ISSR, AFLP and ISTR markers for the detection of polymorphisms and genetic relationships in camote de cerro (Dioscorea spp.)

BackgroundAt present, species known as camote de cerro (Dioscorea spp.) are found only in the wilderness in Mexico, but their populations are extremely depleted because they are indiscriminately collected, it is urgent to evaluate the conservation status of these plants in order to design conservation genetics programs. In this study, genetic diversity parameters along with cluster analysis based on Jaccard's coefficient were estimated with the objective to assess the efficiency of Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR), Amplified Fragment Length Polymorphism (AFLP) and Inverse Sequence Tagged Repeat (ISTR) molecular DNA markers in the Dioscorea genus.ResultsThe polymorphic information contents were quite similar for all markers (≈ 0.48). Genetic variation of Dioscorea spp., in terms of average heterozygosity was lower with ISTR (0.36), and higher when other markers were used (RAPD = 0.43; ISSR = 0.45 and AFLP = 0.47).ConclusionThis indicates an important level of genetic differences despite the fact that the plant is asexually propagated. Based on the diversity statistics, any marker tested in present work can be recommended for use in large-scale genetic studies of populations. However, the low correlations among different molecular marker systems show the importance of the complementarity of the information that is generated by different markers for genetic studies involving estimation of polymorphism and relationships.     

不同来源葛根遗传多样性ISSR分析

对采自广西、云南、江西、湖北4省共11份葛根种质资源进行了ISSR多态性及聚类分析。结果表明,从90个ISSR引物中筛选出12个引物,共扩增到98条带,平均每个引物可扩增5.67条多态性DNA片段,其中多态性带有68条,多态性比率为69.39%,遗传相似性系数范围为0.65-1.00。经UPCMA聚类分析,将11份葛根资源分为2个大组,4个亚组。11份葛根材料的遗传相似性较高,可为葛根种质鉴别、选育及合理利用提供参考。     

Genetic variability of Sargassum liebmannii on the coast of Jalisco in the central Mexican Pacific revealed by molecular markers and morphological traits

BackgroundSargassum liebmannii is widely distributed throughout rocky, coastal upwelling areas in the tropical Mexican Pacific. This brown algae is of great environmental and industrial importance. However, no information is available that documents the genetic or phenotypic variability of the species, which is needed to determine how it may react to environmental variation related to climate change. In this study, S. liebmannii specimens were collected from the coast of Jalisco, Mexico, and molecular and morphological characterization was conducted. Intraspecific variability was estimated according to the study areas.ResultsThe inter-simple sequence repeat (ISSR) markers indicated a polymorphism percentage of 95%. The Shannon index and Nei index showed relatively low values among the populations (0.3569 and 0.081, respectively). On the other hand, the genetic differentiation coefficient indicated inter- and intrapopulation values of 36.69% and 63.31%, respectively. The Jaccard similarity coefficient was used to determine the degree of similarity among individuals by geographical area. The morphological characteristics and environmental variables that were used to correlate phenotypes and genotypes indicated that S. liebmannii showed low genetic flow because of the presence of geographical barriers due to substrate that was not optimal for algal development.ConclusionsThe ISSR markers were useful for detecting genetic differences among S. liebmannii individuals. The results indicate that a coupled genotypic-phenotypic study is beneficial for documenting the variation present in the little-studied algal species. These studies may be used in future research to clarify taxonomic controversies while generating additional genomic information.How to cite: Jung-Kim HW, Hernández-Herrera RM, Enciso-Padilla I, et al. Genetic variability of Sargassum liebmannii on the coast of Jalisco in the central Mexican Pacific revealed by molecular markers and morphological traits. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2021.08.003     

Identification and genetic diversity analysis of Memecylon species using ISSR,RAPD and Gene-based DNA barcoding tools

BackgroundMemecylon species are commonly used in Indian ethnomedical practices. The accurate identification is vital to enhance the drug's efficacy and biosafety. In the present study, PCR based techniques like RAPD, ISSR and DNA barcoding regions, such as 5s, psbA-trnH, rpoC1, ndh and atpF-atpH, were used to authenticate and analyze the diversity of five Memecylon species collected from Western Ghats of India.ResultsPhylogenetic analysis clearly distinguished Memecylon malabaricum from Memecylon wightii and Memecylon umbellatum from Memecylon edule and clades formed are in accordance with morphological keys. In the RAPD and ISSR analyses, 27 accessions representing five Memecylon species were distinctly separated into three different clades. M. malabaricum and M. wightii grouped together and M. umbellatum, M. edule and Memecylon talbotianum grouped in the same clade with high Jaccard dissimilarity coefficient and bootstrap support between each node, indicating that these grouped species are phylogenetically similar.ConclusionData from the present study reveals that chloroplast psbA-trnH region could be used as a potential candidate region for identifying Memecylon species, and ISSR marker system could be used for estimating genetic diversity since it has high percent polymorphism compared to RAPD marker.     

Analysis of the genetic relationships and diversity among 11 populations of Xanthoceras sorbifolia using phenotypic and microsatellite marker data

BackgroundAssessments of genetic diversity are essential for germplasm characterization and exploitation. Molecular markers are valuable tools for exploring genetic variation and identifying germplasm. They play key roles in a Xanthoceras sorbifolia breeding program.ResultsWe analyzed the genetic diversity of populations of this species using 23 simple sequence repeat (SSR) loci and data on kernel oil content. The 11 populations included in the study were distributed across a large geographic range in China. The kernel oil content differed significantly among populations. The SSR marker analysis detected high genetic diversity among the populations. All SSRs were polymorphic, and we identified 80 alleles across the populations. The number of alleles at each locus ranged from two to six, averaging 3.48 per primer pair. The polymorphism information content values ranged from 0.35 to 0.70, averaging 0.51. Expected heterozygosity, observed heterozygosity, and Shannon's information index calculations detected large genetic variations among populations of different provenance. The high average number of alleles per locus and the allelic diversity observed in the set of genotypes analyzed indicated that the genetic base of this species was relatively wide. The statistically significant positive correlation between genetic and geographic distances suggested adaptations to local conditions.ConclusionsMicrosatellite markers can be used to efficiently distinguish X. sorbifolia populations and assess their genetic diversity. The information we have provided will contribute to the conservation and management of this important plant genetic resource.     

11种金花茶植物的RAPD分析及其系统学意义

 利用随机扩增多态性DNA(RAPD)技术分析了11种金花茶植物,即:龙州金花茶Camellia longzhouensis J.Y．Luo,弄岗金花茶C．longgangensis C.F.Liang et S．L. Mo,大样金花茶 C．grandis(C. F. Liang et S．L．Mo)H．T,Chang et S．Y.Liang,扶绥金花茶 C.fusuiensis S．Y. Liang et X．J.Dong,中东金花茶C．achrysantha H．T．Chang et S．Y．Liang,小花金花茶C. micrantha S．Y. Liang et Y．C．Zhong,薄叶金花茶C．chrysanthoides H．T．Chang,毛籽金花茶C．ptilosperma S．Y．Liang et Q．D．Chen,陇瑞金花茶C．longruiensis S．Y．Liang et X．J．Dong,凹脉金花茶C．impressinervis H．T．Chang et S．Y．Liang和夏石金花茶C．xiashiensis S. Y．Liang et C．Z. Deng。选用14个引物(10 bp)扩增出201个DNA片段,用于种间遗传相似性分析,构建系统发育树图。分析结果表明:(1)小花金花茶、扶绥金花茶与中东金花茶之间的关系较近;(2)大样金花茶、薄叶金花茶和夏石金花茶之间的关系较近;(3)龙州金花茶、毛籽金花茶、陇瑞金花茶和弄岗金花茶之间的关系较近;(4)凹脉金花茶与其他各种关系相对较远。     

用RAPD探讨毛白杨起源

利用RAPD分子标记对山杨、欧洲山杨、银白杨、响叶杨及毛白杨的5个不同类型，即抱头毛白杨、截叶毛白杨、易县毛白杨、陕西毛白杨和南京栽培的毛白杨进行了分析，并进行了银白杨×响叶杨正反交实验，研究杂种后代与毛白杨的关系。RAPD分析说明，毛白杨的亲缘关系与银白杨和响叶杨较近，而与山杨和欧洲山杨的亲缘关系则较远。毛白杨在聚类图上首先是与银白杨和响叶杨聚为一类，再与山杨和欧洲山杨聚在一起。通过比较毛白杨与银白杨和响叶杨的正反交子代，发现毛白杨更接近银白杨×响叶杨的子代，而与反交子代有所区别。由此可见，毛白杨为天然杂种是没有疑义的，而且很可能是银白杨×响叶杨的杂种。本研究筛选出的13个引物，产生了78条谱带，覆盖了基因组的一定区域，其可靠性是较高的。     

DNA分子标记技术在水生动物遗传多样性研究中的应用

简要阐述了几种常见DNA分子标记技术,如限制性片断长度多态性(restriction fragment length polymorphism,RFLP)、随机扩增多态性DNA(random amplified polymorphie DNA,RAPD)、扩增片断长度多态性(amplified fragment length polymorphism,AFLP)、简单重复序列或微卫星标记(simpie sequencerepeat,SSR)、内部简单重复序列(inter-simple sequence repeat,ISSR)和单核苷酸多态性(single nucleotidepelymorphisms,SNP)等的基本原理、技术上的优缺点及其在水生动物遗传多样性研究中的应用,包括遗传多样性的鉴定、品种亲缘关系与分类的研究和种质资源的鉴定等.最后,对DNA分子标记技术在水生动物遗传多样性应用中的存在问题进行了简单的讨论.     

Genome-wide development of polymorphic microsatellite markers and their application in peanut breeding program

BackgroundCultivated peanut (Arachis hypogaea. L) represents one of the most important oil crops in the world. Although much effort has been expended to characterize microsatellites or Simple Sequence Repeats (SSRs) in peanut, the quantity and quality of the markers in breeding applications remain limited. Here, genome-wide SSR characterization and marker development were performed using the recently assembled genome of the cultivar Tifrunner.ResultsIn total, 512,900 microsatellites were identified from 2556.9-Mb genomic sequences. Based on the flanking sequences of the identified microsatellites, 7757 primer pairs (markers) were designed, and further evaluated in the assembled genomic sequences of the tetraploid Arachis cultivars, Tifrunner and Shitouqi, and the diploid ancestral species, A. duranensis and A. ipaensis. In silico PCR analysis showed that the SSR markers had high amplification efficiency and polymorphism in four Arachis genotypes. Notably, nearly 60% of these markers were single-locus SSRs in tetraploid Arachis species, indicating they are more specific in distinguishing the alleles of the A and B sub-genomes of peanut. In addition, two markers closely related with purple testa color and 27 markers near to FAD2 genes were identified, which could be used for breeding varieties with purple testa and high-oleic acid content, respectively. Moreover, the potential application of these SSR markers in tracking introgressions from Arachis wild relatives was discussed.ConclusionsThis study reported the development of genomic SSRs from assembled genomic sequences of the tetraploid Arachis Tifrunner, which will be useful for diversity analysis, genetic mapping and functional genomics studies in peanut.How to cite: Ma J, Zhao Y, Chen H, et al. Genome-wide development of polymorphic microsatellite markers and their application in peanut breeding program. Electron J Biotechnol 2020;44. https://doi.org/10.1016/j.ejbt.2020.01.004.     

Analysis of the population structure and genetic diversity of the red swamp crayfish (Procambarus clarkii) in China using SSR markers

BackgroundProcambarus clarkii produces high-quality, delicious meat that is high in protein, low in fat, and rich in calcium and phosphorus. It has become an important aquatic resource in China. Our objectives are (i) to analyze the level of genetic diversity of P. clarkii populations; (ii) to explore the genetic differentiation (Gst); and (iii) to propose appropriate strategies for the conservation.ResultsIn this study, Shannon's index (I) and Nei's gene diversity index (H) for P. clarkii were high (I = 0.3462 and H = 0.2325 on average and I = 0.6264, H = 0.4377 at the species level) based on the SSR markers. The expected heterozygosity value of 17 microsatellite loci in 25 crayfish populations was 0.9317, the observed heterozygosity value was 0.9121, and the observed number of alleles per locus was 2.000; and the effective number of alleles per locus was 1.8075. Among the P. clarkii populations, the inbreeding coefficient within populations (Fis) was 0.2315, overall inbreeding coefficient (Fit) was 0.4438, genetic differentiation coefficient among populations (Fst) was 0.3145 and gene differentiation (Gst) was 0.4785 based on SSR analyses. The cluster analysis results obtained by unweighted pair-group method with arithmetic mean (UPGMA) analysis, principal coordinate analysis (PCoA) and STRUCTURE analysis were similar. A mantel test showed that the isolation-by-distance pattern was not significant.ConclusionsThe high Gst among P. clarkii populations is attributed to genetic drift and geographic isolation. The results indicated that more P. clarkii populations should be collected when formulating conservation and aquaculture strategies.How to citeLiu F, Qu Y-K, Geng C, et al. Analysis of the population structure and genetic diversity of the red swamp crayfish (Procambarus clarkii) in China using SSR markers. Electron J Biotechnol 2020;47. https://doi.org/10.1016/j.ejbt.2020.06.007.     

Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

BackgroundAvailability of related rice species is critical for rice breeding and improvement. Two distinct species of domesticated rice exist in the genus Oryza: Oryza sativa (Asian rice) and Oryza glaberrima (African rice). New rice for Africa (NERICA) is derived from interspecific crosses between these two species. Molecular profiling of these germplasms is important for both genetics and breeding studies. We used 30 polymorphic SSR markers to assess the genetic diversity and molecular fingerprints of 53 rice genotypes of O. sativa, O. glaberrima, and NERICA.ResultsIn total, 180 alleles were detected. Average polymorphism information content and Shannon's information index were 0.638 and 1.390, respectively. Population structure and neighbor-joining phylogenetic tree revealed that 53 genotypes grouped into three distinct subpopulations conforming to the original three groups, except three varieties (IR66417, WAB450-4, MZCD74), and that NERICA showed a smaller genetic distance from O. sativa genotypes (0.774) than from O. glaberrima genotypes (0.889). A molecular fingerprint map of the 53 accessions was constructed with a novel encoding method based on the SSR polymorphic alleles. Ten specific SSR markers displayed different allelic profiles between the O. glaberrima and O. sativa genotypes.ConclusionsGenetic diversity studies revealed that 50 rice types were clustered into different subpopulations whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice breeding and molecular classification of O. sativa and O. glaberrima germplasms.     

广西产三种地钱RAPD分子鉴定初步研究

目的:建立广西产地钱(Marchantia polymorpha L.)拳卷地钱(Marchantia convoluta gao et chang.)和粗裂地钱(Marchantia paleacea Bertol.)的分子鉴别方法。方法:利用RAPD(random amplified polymorphic DNA)技术。结果:采用改良的CTAB法提取地钱、拳卷地钱、粗裂地钱3种植物的总DNA均适用于22引物对供试材料DNA进行随机扩增,共扩增出145条谱带,多态性条带128条,占扩增总条带的88.3%,平均多态性百分率为89.8%;三种地钱遗传距离为0.3713-0.4107、Nei′s遗传一致度为0.5893-0.6287。结论:RAPD技术对广西产地钱、拳卷地钱、粗裂地钱进行分子鉴定是有效的。RAPD分析。     

利用RAPD分子标记评价仲彬草属的种间关系

利用随机扩增多态性DNA(RAPD)技术分析了14种仲彬草属Kengyilia植物的种间关系。对34个OPRON公司十聚体随机引物进行多态性筛选,20个(58．8％)能产生多态性。14个引物产生的112个DNA片断,用于计算种间Jaccard遗传相似性系数分析,在NTSYS程序中利用UPGMA构建系统发育树状图。分析结果表明：(1)14个Kengyilia物种存在较大的遗传多样性;(2)青藏高原的物种与新疆的物种 的RAPD变异极大;(3)形态相似、地理分布一致的物种有一定的亲缘关系,聚类在一起;(4)RAPD结果与形态学和细胞学等分析结果一致。RAPD分析方法将为Kengyilia系统分类提供DNA水平上丰富的资料。     

用RAPD技术探讨中国枣的种下划分

利用随机扩增多态性DNA(RAPD)技术对14个枣Ziziphus jujuba 品种和1个野生种——泰山酸枣Z．spinosus的遗传变异进行了研究。从120个10-碱基随机引物中筛选出37个多态性引物用于正式扩增，共扩增出429条DNA带，其中多态性带214条，占49．88％。根据DNA扩增结果计算了品种及类型间遗传距离，并用UPGMA构建了聚类树状图。分析结果表明：龙爪枣 Z．jujuba var．tortuosa、葫芦枣 Z. jujuba var．lageniformis、无核枣 Z.jujuba var．anucleatus 等几个变种内的遗传距离大于变种间遗传距离，认为枣的变种划分是不自然的，宜并入其原变种；枣种下不宜设变种，对枣种下的众多品种，应根据品种间的遗传关系，直接划分品种群。     

Genetic diversity and differentiation of nine populations of the hard clam (Meretrix petechialis) assessed by EST-derived microsatellites

BackgroundMeretrix petechialis is one of the commercially important marine bivalves. In this study, we selected six highly polymorphic EST-derived microsatellite markers to assess the genetic diversity and population differentiation on nine wild populations of Meretrix petechialis.ResultsThe number of alleles detected per locus ranged from 4 to 30 (mean N_A = 27.5) with a total of 165 alleles. The mean value of observed and expected heterozygosities varied from 0.717 to 0.861 and from 0.797 to 0.856, respectively. Meanwhile, the result of Neighbor-joining and overall F_ST = 0.214 (P < 0.01) reveled that M. petechialis populations from GX are the farthest populations, a certain degree of genetic variation among individuals in each population and the genetic differentiation is significant.ConclusionsGX population has high genetic diversity among individual, and there are certain differences in genetic characteristics among different populations. This study will provide a basis for the domestication and cultivation of genetic diversity of M. petechialis population and the protection of clam germplasm resources.How to citeXu Q, Zheng J, Yan X, et al. Genetic diversity and differentiation of nine populations of the hard clam (Meretrix petechialis) assessed by EST-derived microsatellites. Electron J Biotechnol 2020;48. https://doi.org/10.1016/j.ejbt.2020.09.003     

浙闽香鱼4个群体遗传多样性的RAPD分析

采用RAPD分子标记技术对采自福建东张水库(DZ)、浙江楠溪江(N8、N9)和浙江省海洋水产养殖研究所清江试验场(QJ)的香鱼4个群体进行遗传多样性和遗传关系分析.筛选出15条RAPD引物在4个群体72个样品中共检测到106个稳定清晰的位点,其中多态性位点47个,多态位点比例(PPL)为44.34％.群体遗传多样性分析...