Genetic Diversity and Population Structure of Dendrobium Nobile in Southwest of China Based On Genotyping-by-Sequencing

Abstract Dendrobium nobile Lindl. is one of the most important Orchid plants worldwide. The genotype-by-sequencing (GBS) method has now been widely used to access genetic diversity because of its high-throughput and cost-effective in molecular markers. The goal of this study was to employ the GBS technique for diversity evaluation of D. nobile and determine genetic differences between populations. A total of 129 accessions of D. nobile collected originally between 2019 and 2020 from 10 imitation-wild cultivated populations growing in Sichuan, Guizhou and Yunnan of southwestern China were sequenced, a total of 135G clean reads and a total of 836,786 SNPs of high quality data was yielded and were used for final analysis of genetic diversity and population structure. The quality value 20(Q20) ≥ 92.61%, the quality value 30(Q30) ≥ 82.38%. The GC contents distributed between 37.58% and 38.82%. It was also found that more transitions than transversions, and the ratio of transition/transversion varied from 1.804 to 1.911. By the methods of STRUCTURE, the most appropriate number was found to be k=3, all accessions of D. nobile were classified into three groups, excepts for 14 accessions belonging to admixed group. Phylogenetic tree and principal component analysis (PCA) were consistent with the result. The first two principal components explained a total of 23.25% of the variation by PCA. The genetic diversity of ML population showed the lower genetic diversity as indicated by the effective number of alleles (Ne) = 1.287, polymorphism information content (PIC) = 0.141, and Shannon's information index (I) = 0.205, while WT population showed slightly higher genetic diversity by the Ne =1.512, PIC =0.256, and I =0.360. ML population and other nine populations (FB, FM, FX, LJ, SJ, SP, WL, WT and XM) were the most divergent between them respectively owing to all pairwise Fst values above 0.25, while FM population and FX population were considered identical because the pairwise Fst value was 0.0 between the two populations. Correlation analysis showed that highly significant correlation was observed between genetic distance and actual geographical distance (r = 0.854, P < 0.0001), indicating that the genetic differentiation of the 10 D.nobile populations conformed to the geographical isolation model. Analysis of molecular variance (AMOVA) revealed that the genetic variation was greater within populations (87.8%) than among populations (12.2%). This confirmed that intra-population variation was the main source of genetic variation in 10 D. nobile populations. The results also showed that Nm = 1.799 > 1, indicating that there was gene exchange between different populations. Analysis of unweighted pair-group method with arithmetic mean (UPGMA) suggested that the 10 populations were classified into three groups (Group I, Group II and Group III), Group III could be further divided into two subgroups (Group IIIa and Group IIIb). The results will not only provide valuable information for the level of genetic diversity of D.nobile growing in southwestern of China but also help for formulation of strategies for resource protection and utilization. Moreover, GBS appears as an efficient tool to detect intra-population variation.

Download Full-text

Analyses of the genetic diversity and population structures ofHistoplasma capsulatumclinical isolates from Mexico, Guatemala, Colombia and Argentina, using a randomly amplified polymorphic DNA-PCR assay

Epidemiology and Infection ◽

10.1017/s0950268819000931 ◽

2019 ◽

Vol 147 ◽

Cited By ~ 1

Author(s):

J. H. Sahaza ◽

E. Duarte-Escalante ◽

C. Canteros ◽

G. Rodríguez-Arellanes ◽

M. R. Reyes-Montes ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Geographic Origin ◽

The United States ◽

Group Method ◽

Randomly Amplified Polymorphic Dna ◽

Pcr Assay ◽

Cophenetic Correlation ◽

Group I ◽

Rapd Pcr

AbstractWe studied the genetic diversity and the population structure of human isolates ofHistoplasma capsulatum, the causative agent of histoplasmosis, using a randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) assay to identify associations with the geographic distribution of isolates from Mexico, Guatemala, Colombia and Argentina. The RAPD-PCR pattern analyses revealed the genetic diversity by estimating the percentage of polymorphic loci, effective number of alleles, Shannon's index and heterozygosity. Population structure was identified by the index of association (IA) test. Thirty-seven isolates were studied and clustered into three groups by the unweighted pair-group method with arithmetic mean (UPGMA). Group I contained five subgroups based on geographic origin. The consistency of the UPGMA dendrogram was estimated by the cophenetic correlation coefficient (CCCr= 0.94,P= 0.001). Isolates from Mexico and Colombia presented higher genetic diversity than isolates from Argentina. Isolates from Guatemala grouped together with the reference strains from the United States of America and Panama. TheIAvalues suggest the presence of a clonal population structure in the ArgentinianH. capsulatumisolates and also validate the presence of recombining populations in the Colombian and Mexican isolates. These data contribute to the knowledge on the molecular epidemiology of histoplasmosis in Latin America.

Download Full-text

Population Structure and Genetic Diversity of Phytophthora nicotianae from Tobacco in Georgia

Plant Disease ◽

10.1094/pdis-01-17-0142-re ◽

2017 ◽

Vol 101 (7) ◽

pp. 1113-1118 ◽

Cited By ~ 5

Author(s):

Yonggang Li ◽

Karen Harris-Shultz ◽

Hongliang Wang ◽

Phillip A. Wadl ◽

Pingsheng Ji

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Mating Type ◽

Geographical Location ◽

Phytophthora Nicotianae ◽

Group Method ◽

Group I ◽

Tobacco Production ◽

Group Ii

Black shank, caused by Phytophthora nicotianae, occurs worldwide and is responsible for significant yield loss in tobacco production in Georgia. Management of the disease has primarily relied on utilization of tobacco cultivars with resistance to race 0 of the pathogen and application of the fungicide mefenoxam. Races of P. nicotianae currently prevalent in tobacco production in Georgia, their sensitivity to mefenoxam, and genetic diversity of the pathogen are largely unknown. To determine population structure and genetic diversity of the pathogen, simple sequence repeat (SSR) markers were used. Three races of P. nicotianae (races 0, 1, and 3) were isolated from infected tobacco plants, with race 3 identified in Georgia for the first time. The majority of isolates were identified as A2 mating type and all isolates were sensitive or intermediately sensitive to mefenoxam at 1 or 10 μg/ml, with effective concentration of mefenoxam for 50% mycelial growth reduction values ranging from <0.01 to 0.12 μg/ml. Bayesian and unweighted pair group method with arithmetic means analyses of 59 isolates using SSR markers grouped the isolates in two major groups. Group I contained 20 isolates, of which 19 isolates were collected from Berrien County. Group II contained 39 isolates collected from Bacon, Cook, Tift, and Toombs Counties as well as one sample from Berrien County. Genetic diversity of the isolates was associated with geographical location of collection, and isolates in group I were primarily (75%) race 1, whereas isolates in group II were primarily (69%) race 0. The presence of a single pathogen mating type at most of the locations implies low probability of sexual recombination that may have contributed to the low genetic diversity at a particular geographical location. Sensitivity of the isolates to mefenoxam indicates that the fungicide remains to be a potent tool for growers to combat the disease. Information generated in the study advances our knowledge about diversity and population structure of P. nicotianae, which facilitates development and implementation of effective disease management programs.

Download Full-text

Molecular Genetic Variability of Spigelia marilandica and S. gentianoides

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.140.2.120 ◽

2015 ◽

Vol 140 (2) ◽

pp. 120-128

Author(s):

Amanda J. Hershberger ◽

Tracie M. Jenkins ◽

Carol Robacker

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Variability ◽

Gene Diversity ◽

Molecular Genetic ◽

Genetic Distances ◽

Population Variation ◽

Group Method ◽

Polymorphism Analysis ◽

Two Samples

Despite the ecologic and ornamental potential of southeastern U.S. native Spigelia, little is known about the intraspecific or the interpopulation genetic variation. The southeastern U.S. native Spigelia habitat is becoming more and more fragmented as a result of human activity, making it imperative to gain an understanding of natural genetic variation among and within species and populations for the purpose of obtaining variability for plant breeding and preserve the genetic variability in Spigelia. Therefore, the objective of this study was to use amplified fragment length polymorphism analysis to determine interspecific and intraspecific genetic variation and to evaluate gene flow. Thirteen populations of two species of native Spigelia, S. marilandica (SM), S. gentianoides var. gentianoides (SGG), and S. gentianoides var. alabamensis (SGA), were analyzed using four primer pairs that amplified a total of 269 bands. Based on analysis of molecular variance and estimates of Nei’s coefficients of gene diversity (percentage of polymorphic loci, average genetic diversity within populations, average genetic diversity within species, and proportion of species genetic diversity attributed to among population variation), the majority of variation found in Spigelia occurs within populations. Both among-species and among-population variation was low, likely the effect of common ancestry as well as relatively frequent introgression among individuals (and populations) of Spigelia. When all individuals were evaluated using Nei’s unbiased genetic distances and viewed as a unweighted pair group method with arithmetic mean phenogram, three main groups were shown, one with two samples of SGG from one population, one with 13 individuals from both SGG populations used in this study, and one with all of the SM, SGA, and remaining SGG individuals. Further evaluation using STRUCTURE software showed introgression between populations and species, although all allele clusters have not entirely introgressed into all populations. The significance of these results is discussed in relation to breeding in Spigelia.

Download Full-text

Assessment of the Genetic Diversity and Population Structure of Lotus Cultivars Grown in China by Amplified Fragment Length Polymorphism

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.136.5.339 ◽

2011 ◽

Vol 136 (5) ◽

pp. 339-349 ◽

Cited By ~ 8

Author(s):

Jie Fu ◽

Qiaoyan Xiang ◽

Xianbao Zeng ◽

Mei Yang ◽

Ying Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Amplified Fragment Length Polymorphism ◽

Group I ◽

Population Structure Analysis ◽

Morphological Criteria

To assess the genetic diversity among lotus (Nelumbo) accessions and evaluate the correlation between genetic variation and morphological classification, we sampled 138 accessions: two of N. lutea, 112 of N. nucifera, 17 of hybrids between N. nucifera and N. lutea, and seven Japanese cultivars. The 11 selected combinations of amplified fragment length polymorphism (AFLP) primers produced 138 polymorphic loci, and the percentage of polymorphism was 28.7%. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram clustered all the accessions into two groups: Group I comprised N. lutea and its hybrids with N. nucifera; Group II included N. nucifera and its hybrids with N. lutea and Japanese cultivars. Population structure analysis identified four main clusters: N. lutea clustered mainly in C1, whereas N. nucifera clustered in C2, C3, and C4, which was consistent with the UPGMA and principal coordinate analysis results. The Japanese cultivars were related more closely to N. nucifera (genetic similarity coefficient = 0.74) than to N. lutea (0.46); hence, the Japanese cultivars can be classified as N. nucifera. Moreover, rhizome lotuses formed a separate subclade, whereas seed lotuses were interspersed among flower lotuses, which demonstrated that rhizome lotuses were distinct from flower and seed lotuses. Plant size, flower color, and other morphological criteria used commonly to classify lotuses were correlated with genetic variation to a certain extent but not sufficiently for accurate classification. It appears that it is necessary to use both DNA markers and morphological characteristics to classify lotus species and cultivars.

Download Full-text

Detection of DNA and Ploidy Variation within Vegetatively Propagated Zoysiagrass Cultivars

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.139.5.547 ◽

2014 ◽

Vol 139 (5) ◽

pp. 547-552 ◽

Cited By ~ 5

Author(s):

Karen R. Harris-Shultz ◽

Susana Milla-Lewis ◽

Aaron J. Patton ◽

Kevin Kenworthy ◽

Ambika Chandra ◽

...

Keyword(s):

Genetic Variability ◽

Reference Sample ◽

Warm Season ◽

The United States ◽

Group Method ◽

Group Iii ◽

Climatic Regions ◽

Pair Group ◽

Group I ◽

Two Samples

Zoysiagrass (Zoysia sp.) is used as a warm-season turfgrass for lawns, parks, and golf courses in the warm, humid and transitional climatic regions of the United States. Zoysiagrass is an allotetraploid species (2n = 4x = 40) and some cultivars are known to easily self- and cross-pollinate. Previous studies showed that genetic variability in the clonal cultivars Emerald and Diamond was likely the result of contamination (seed production or mechanical transfer) or mislabeling. To determine the extent of genetic variability of vegetatively propagated zoysiagrass cultivars, samples were collected from six commercially available zoysiagrass cultivars (Diamond, Emerald, Empire, JaMur, Meyer, Zeon) from five states (Arkansas, Florida, Georgia, North Carolina, Texas). Two of the newest cultivar releases (Geo and Atlantic) were to serve as outgroups. Where available, one sample from university research plots and two samples from sod farms were collected for each cultivar per state. Forty zoysiagrass simple sequence repeat (SSR) markers and flow cytometry were used to compare genetic and ploidy variation of each collected sample to a reference sample. Seventy-five samples were genotyped and an unweighted pair group method with arithmetic mean clustering revealed four groups. Group I (Z. japonica) included samples of ‘Meyer’ and Empire11 (‘Empire’ sample at location #11), Group II (Z. japonica × Z. pacifica) included samples of ‘Emerald’ and ‘Geo’, Group III (Z. matrella) included samples of ‘Diamond’ and ‘Zeon’, and Group IV (Z. japonica) consisted of samples from ‘Empire’, ‘JaMur’, ‘Atlantic’, and Meyer3 (‘Meyer’ at sample location #3). Samples of ‘Empire’, ‘Atlantic’, and ‘JaMur’ were indistinguishable with the markers used. Four samples were found to have alleles different from the respective reference cultivar, including two samples of ‘Meyer’, one sample of ‘Empire’, and one sample of ‘Emerald’. Three of these samples were from Texas and one of these samples was from Florida. Three of the four samples that were different from the reference cultivar were university samples. In addition, one sample, Empire11, was found to be an octoploid (2n = 8x = 80). For those samples that had a fingerprint different from the reference cultivar, contamination, selfing, and/or hybridization with other zoysiagrasses may have occurred.

Download Full-text

Genome-wide genetic diversity, population structure and admixture analysis in Eritrean Indigenous Cattle

South African Journal of Animal Science ◽

10.4314/sajas.v49i6.12 ◽

2020 ◽

Vol 49 (6) ◽

pp. 1083-1092

Author(s):

S Goitom ◽

M.G. Gicheha ◽

F.K. Njonge ◽

N Kiplangat

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Population Differentiation ◽

Principal Component ◽

Vital Role ◽

Group Method ◽

Indigenous Cattle ◽

Ecological Zones ◽

Genome Wide

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes. Keywords: genetic variability, molecular characterization, population differentiation

Download Full-text

The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species

PeerJ ◽

10.7717/peerj.10274 ◽

2020 ◽

Vol 8 ◽

pp. e10274 ◽

Cited By ~ 1

Author(s):

Mirella Pupo Santos ◽

João V.S. Rabelo Araujo ◽

Arthur V. Sant’anna Lopes ◽

Julio Cesar Fiorio Vettorazzi ◽

Marcela Santana Bastos Boechat ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Geographical Location ◽

Inter Simple Sequence Repeat ◽

Shannon Index ◽

Conservation Strategies ◽

Amazon Forest ◽

Mass Extinctions ◽

Effective Conservation

Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.

Download Full-text

Genetic diversity and population structure of the rice false smut pathogen Ustilaginoidea virens in Sichuan-Chongqing region

Plant Disease ◽

10.1094/pdis-04-21-0750-re ◽

2021 ◽

Author(s):

Anfei Fang ◽

Zhuangyuan Fu ◽

Zexiong Wang ◽

Yuhang Fu ◽

Yubao Qin ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Recombination ◽

Resistance Breeding ◽

Ustilaginoidea Virens ◽

Breeding Lines ◽

Rice False Smut ◽

Geographical Populations ◽

False Smut

Rice false smut caused by Ustilaginoidea virens is currently one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from SNP-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in Sichuan-Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. The groups Ⅰ and Ⅵ were the largest including 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. AMOVA showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup. The UPGMA dendrogram and population structure revealed that the genetic composition of isolates collected from ST (Santai), NC (Nanchong), YC (Yongchuan), and WS (Wansheng) dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

Download Full-text

Genetic diversity and differentiation in populations of invasive Eurasian (Myriophyllum spicatum) and hybrid (Myriophyllum spicatum × Myriophyllum sibiricum) watermilfoil

Invasive Plant Science and Management ◽

10.1017/inp.2020.12 ◽

2020 ◽

Vol 13 (2) ◽

pp. 59-67

Author(s):

Ryan A. Thum ◽

Gregory M. Chorak ◽

Raymond M. Newman ◽

Jasmine A. Eltawely ◽

Jo Latimore ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Population Genetic ◽

Myriophyllum Spicatum ◽

Population Variation ◽

Efficacy Evaluation ◽

Submerged Aquatic Plant ◽

Myriophyllum Sibiricum ◽

Control Response ◽

Herbicide Response

AbstractPopulation genetic studies of within- and among-population genetic variability are still lacking for managed submerged aquatic plant species, and such studies could provide important information for managers. For example, the extent of within-population genetic variation may influence the potential for managed populations to locally adapt to environmental conditions and control tactics. Similarly, among-population variation may influence whether specific control tactics work equally effectively in different locations. In the case of invasive Eurasian watermilfoil (Myriophyllum spicatum L.), including interspecific hybrids with native northern watermilfoil (Myriophyllum sibiricum Kom.), managers recognize that there is genetic variation for growth and herbicide response. However, it is unclear how much overall genetic variation there is, and how it is structured within and among populations. Here, we studied patterns of within- and among-lake genetic variation in 41 lakes in Michigan and 62 lakes in Minnesota using microsatellite markers. We found that within-lake genetic diversity was generally low, and among-lake genetic diversity was relatively high. However, some lakes were genetically diverse, and some genotypes were shared across multiple lakes. For genetically diverse lakes, managers should explicitly recognize the potential for genotypes to differ in control response and should account for this in monitoring and efficacy evaluation and using pretreatment herbicide screens to predict efficacy. Similarly, managers should consider differences in genetic composition among lakes as a source of variation in the growth and herbicide response of lakes with similar control tactics. Finally, laboratory or field information on control efficacy from one lake may be applied to other lakes where genotypes are shared among lakes.

Download Full-text

How diverse can rare species be on the margins of genera distribution?

AoB Plants ◽

10.1093/aobpla/plz037 ◽

2019 ◽

Vol 11 (4) ◽

Author(s):

Alice Backes ◽

Geraldo Mäder ◽

Caroline Turchetto ◽

Ana Lúcia Segatto ◽

Jeferson N Fregonezi ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Variability ◽

Habitat Loss ◽

Evolutionary History ◽

Founder Effects ◽

Geographical Isolation ◽

Genetic Diversity And Structure ◽

Genetic Patterns

Abstract Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.

Download Full-text