scholarly journals Genetic diversity by ISSR of two endemic quillworts (Isoetes L.) species from Amazon Iron Rocky Outcrops, Isoetes cangae e I. serracarajensis

2019 ◽  
Author(s):  
Mirella Pupo Santos ◽  
João Victor da Silva Rabelo Araújo ◽  
Arthur Vinícius de Sant’anna Lopes ◽  
Julio Cesar Fiorio Vettorazzi ◽  
Rodrigo Nunes da Fonseca ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Species Conservation ◽  
Principal Component ◽  
Shannon Index ◽  
Conservation Strategies ◽  
Amazon Forest ◽  
The North ◽  
Species Specific ◽  
High Level ◽  
Issr Molecular Markers

AbstractTwo lycophytes endemic species have been recently described at the State of Pará, in the Amazon forest located in the North of Brazil. Genetic diversity and population structure of Isoetes cangae and I. serracarajensis were investigated through ISSR molecular markers. These analyses aim to establish strategies for future attempts for species conservation. From sixteen primers, 115 gel bands were identified from which 87% were polymorphic. A high level of polymorphic loci (81,74 % e 68,48 %) and a high Shannon index for intra populational genetic diversity was observed for each species (Sh=0.376 e 0.289) I. cangae and I. serracarajensis, respectively. The largest genetic diversity of both species relies in their own populations. The coefficient of genetic differentiation between population areas (GST) was higher in I. serracarajensis (0.5440) than in I. cangae (0.2250). Gene flow was high between I. cangae populations (1.7142) and very low in I. serracarajensis (0.4190). Principal Component Analysis (PCoA) showed that individual plants were allocated into species-specific and population groups. Overall, the results further show that I. serracarajensis (0.5440) and I. cangae are two species with considerable genetic variation. These results should be considered for effective conservation strategies of both species.

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

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10274 ◽  
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.

scholarly journals Phenotypic Characterisation for Growth and Nut Characteristics Revealed the Extent of Genetic Diversity in Wild Macadamia Germplasm

Agriculture ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 680
Author(s):  
Thuy T. P. Mai ◽  
Craig M. Hardner ◽  
Mobashwer M. Alam ◽  
Robert J. Henry ◽  
Bruce L. Topp
Keyword(s):  
Genetic Diversity ◽  
Growth Traits ◽  
Principal Component ◽  
Conservation Strategies ◽  
Wild Germplasm ◽  
Phenotypic Characterisation ◽  
Wide Range ◽  
Genetic And Environmental Factors ◽  
Positive Correlations ◽  
Wild Accessions

Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing diversity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased sampling within sites to capture wide genetic diversity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.

scholarly journals Chloroplast microsatellites reveal genetic diversity and population structure in natural populations of Himalayan Cedar (Cedrus deodara (Roxb.) G. Don) in India

2020 ◽  
Vol 69 (1) ◽  
pp. 86-93
Author(s):  
H. S. Ginwal ◽  
Rajesh Sharma ◽  
Priti Chauhan ◽  
Kirti Chamling Rai ◽  
Santan Barthwal
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Natural Populations ◽  
Conservation Strategies ◽  
Restricted Gene Flow ◽  
Chloroplast Microsatellites ◽  
Timber Species ◽  
Western Himalayas ◽  
Cedrus Deodara ◽  
High Level

AbstractHimalayan cedar (Cedrus deodara) is one of the most important temperate timber species of Western Himalayas and is considered to be among the endangered conifer species in the region. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Ten polymorphic chloroplast microsatellites (cpSSR) were used to study genetic diversity and population structure in twenty one natural populations of C. deodara throughout its entire distribution range in Western Himalayas. When alleles at each of the 10 loci were jointly analysed, 254 different haplotypes were identified among 1050 individuals. The cpSSRs indicate that C. deodara forests maintain a moderately high level of genetic diversity (mean h = 0.79 ). AMOVA analysis showed that most of the diversity in C. deodara occurs within populations. Bayesian analysis for population structure (BAPS) revealed spatial structuration of the variation (22 % of the total variation) and substructuring captured nineteen genetic clusters in the entire divisions of the populations. Most of the populations were clustered independently with minor admixtures. The distribution of genetic diversity and sub-structuring of C. deodara may be due to restricted gene flow due to geographic isolation, genetic drift, and natural selection. These findings indicated existence of genetically distinct and different high diversity and low diversity clusters, which are potential groups of populations that require attention for their conservation and management. The results are interpreted in context of future conservation plans for C. deodara.

scholarly journals Diversity of virulence phenotypes of Puccinia triticinain different agroclimatic zones of the North Caucasus

2019 ◽  
pp. 23-26 ◽  
Author(s):  
G. V. Volkova ◽  
O. A. Kudinova ◽  
O. F. Vaganova
Keyword(s):  
Puccinia Triticina ◽  
Shannon Index ◽  
Population Diversity ◽  
North Caucasus ◽  
Climatic Zones ◽  
The North ◽  
Dominant Phenotype ◽  
Northern Zone ◽  
High Level ◽  
Agroclimatic Zones

The phenotypic composition of the North Caucasian population of wheat leaf rust pathogen (Puccinia triticina Erikks.) in various agro-climatic zones of the region in 2016-2018 is analyzed. 233 single pustule isolates were studied, of which 212 virulence phenotypes were identified. In all the years of research, a high level of population diversity was established (the Shannon index (Sh) was 0.92-0.99). The dominant phenotype in 2016 was the PHRS phenotype, which was identified in the southern foothill, western Azov and eastern steppe agro-climatic zones. In the population of 2016, phenotypes with a high and medium number of virulence genes prevailed. In 2017, the most represented are the phenotypes of DCRL, LBLL (Western Azov zone) and PCQB (Northern zone). Avirulent phenotype BBBB was common for populations of 20162018. In 2016, a phenotype with virulence to Lr9 (TLGS) was first detected. In 2017 and 2018, phenotypes virulent to the Lr24 gene (PKTT, SFGQ, CFPQ, TKTS, MKTT, LKSR) were detected in the populations of the fungus. A high level of population differences in phenotypic composition between the years of research was established (Rogers index (R) was 0.96 -0.99).

scholarly journals Testing the breeding strategy of Hungarian Bronze turkey strains for maintaining genetic diversity with microsatellites

2011 ◽  
Vol 54 (4) ◽  
pp. 419-429
Author(s):  
S. Kusza ◽  
S. Mihók ◽  
L. Czeglédi ◽  
A. Jávor ◽  
M. Árnyasi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Mating System ◽  
Breeding Strategy ◽  
Shannon Index ◽  
Inbreeding Coefficient ◽  
Control Population ◽  
Conservation Strategies ◽  
The Mean ◽  
Two Populations

Abstract. The aim of the study was to provide information on the genetic variability of the Hungarian Bronze turkey gene reserve population and its difference from the Broad-breasted turkey, and offer guidance and proposals for its future conservation strategies. Altogether, 239 Hungarian Bronze turkeys from 10 strains and 13 Broad-breasted turkeys as a control population were genotyped for 15 microsatellites. All loci were polymorphic with the average number of alleles per locus 3.20±1.146 in the Hungarian Bronze turkey. The mean expected (Hexp) and observed heterozygosity (Hobs) were not different (0.392 and 0.376, respectively) in the overall population, and similar values were obtained for hens and bucks and among hen strains. Inbreeding coefficient (FIS) and Shannon index (I) indicated that there was low inbreeding within hens and bucks. Our results confirm that the genetic diversity in the Hungarian Bronze turkey population has been preserved by the rotational mating system. Differences between the Hungarian Bronze turkey and the Broad-breasted turkey populations were determined. Nei’s unbiased values clearly indicated that the two populations are highly genetically differentiated.

scholarly journals De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

2020 ◽  
Author(s):  
Duy Dinh Vu ◽  
Syed Noor Muhammad Shah ◽  
Mai Phuong Pham ◽  
Van Thang Bui ◽  
Minh Tam Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
De Novo ◽  
Average Length ◽  
Species Conservation ◽  
Illumina Hiseq ◽  
Bottleneck Analysis ◽  
Genetic Diversity And Structure ◽  
Geographical Distances ◽  
High Level

Abstract Background: Understanding the genetic diversity in endangered species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeqTM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

scholarly journals Genetic diversity in natural populations of Hancornia speciosa Gomes: Implications for conservation of genetic resources

2018 ◽  
Vol 42 (6) ◽  
pp. 623-630
Author(s):  
Cristiane Gouvêa Fajardo ◽  
Daniel Ferreira da Costa ◽  
Kyvia Pontes Teixeira das Chagas ◽  
Fábio de Almeida Vieira
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
In Situ Conservation ◽  
Natural Populations ◽  
Allelic Diversity ◽  
Shannon Index ◽  
Conservation Strategies ◽  
Effective Population ◽  
Infinite Allele Model ◽  
Hancornia Speciosa

ABSTRACT The continuing fragmentation of forests has been a threat to the maintenance of genetic resources. Genetic diversity is fundamental to the survival of species in natural environments in the long term, as well as being the basis for genetic improvement. The objective of this study was to evaluate the genetic diversity in natural populations of Hancornia speciosa and to contribute to the development of conservation strategies. We sampled 105 individuals of H. speciosa, distributed in seven populations. The ISSR (Inter-Simple Sequence Repeat) markers provided 70 loci, of which 81% were polymorphic. The mean genetic diversity of Nei (h) was 0.19, and the Shannon index (I) was 0.27. The h and I diversity indices ranged respectively from 0.16 to 0.24 in the PAD (Parque das Dunas) population and from 0.21 to 0.29 in MAC (Macaíba) population. Resulting from a Bayesian analysis, the genotypes were divided into four groups (K = 4). The allelic diversity patterns observed indicated the occurrence of the genetic bottleneck in all populations, according to the stepwise mutation model (SMM). The infinite allele model (IAM) revealed an imbalance between mutation and genetic drift only in the PAD population. Genetic conservation strategies for H. speciosa should cover each genetic group that was differentially structured. We recommend in situ conservation and the creation of germplasm banks, especially with the PAD population which demonstrated the lower genetic diversity and decreased effective population size according to the two mutational models.

Genetic diversity of arctic bramble (Rubus arcticus L. subsp. arcticus) as measured by amplified fragment length polymorphism

2003 ◽  
Vol 81 (8) ◽  
pp. 805-813 ◽  
Author(s):  
Hannele Lindqvist-Kreuze ◽  
Hilkka Koponen ◽  
Jari P.T Valkonen
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Fragment Length ◽  
Natural Habitat ◽  
Genotypic Variation ◽  
Natural Populations ◽  
Shannon Index ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
High Level

The levels of genotypic and genetic variation were estimated in six natural populations of arctic bramble (Rubus arcticus L. subsp. arcticus) in Finland. Using three primer combinations, a total of 117 amplified fragment length polymorphisms (AFLP) were found. The results were highly reproducible and allowed identification of 78 genets among the 122 plants of arctic bramble studied. Genotypic variation measured as Simpson index (D) was high in all populations, ranging from 0.72 to 0.94. Also, the level of genetic variation measured as Shannon index was relatively high in all populations, ranging from 0.19 to 0.32 (average 0.26). The high levels of genetic diversity indicate that sexual reproduction has played a significant role in these populations. The hierarchical analysis of molecular variance (AMOVA) partitioned 48% of the genetic variation among populations, suggesting a high level of population differentiation and a low level of interpopulation gene flow. Genetic diversity among ten currently grown cultivars of arctic bramble and hybrid arctic bramble (R. arcticus subsp. arcticus × R. arcticus subsp. stellatus) was large, and the subspecies were clearly distinguished from each other based on the AFLP marker data.Key words: AFLP, AMOVA, population, natural habitat, Rubus arcticus subsp. arcticus, Rubus arcticus subsp. stellatus.

scholarly journals Genetic diversity of Polish cultivars of common wheat (Triticum aestivum L.) based on molecular and protein markers

2020 ◽  
Vol 48 (2) ◽  
pp. 535-548
Author(s):  
Ewa FILIP ◽  
Aleksandra STROŃSKA ◽  
Magdalena SZENEJKO ◽  
Waldemar PLUTA
Keyword(s):  
Genetic Diversity ◽  
Common Wheat ◽  
Similarity Index ◽  
Principal Component ◽  
Shannon Index ◽  
Qualitative Assessment ◽  
Wheat Cultivars ◽  
Protein Markers ◽  
Binary Matrix ◽  
Sds Page

Knowledge of the composition subunits of proteins glutenins makes it much easier to determine the quality and suitability of the final product obtained from gluten. It is important to remember that not only molecular processes model gluten protein polymorphism. In this study, the genetic diversity of Polish common wheat cultivars was examined at the level of DNA and glutenin’s proteins HMW-GS. The SDS-PAGE and RAPD bands were evaluated in binary matrix, which was the basis for further analysis of results, using appropriate measures of variability: Q-Cochran  test (Cochran, 1950), p < 0.05; I-Shannon index; Si-Similarity index; PIC-Polymorphism Information Content; (PCA-Principal component analysis). Both types of markers proved to be useful in the overall assessment of genetic variability between tested of common wheat cultivars. The general genetic diversity indicates that good candidates with unique composition of HMW-GS subunits were selected among the examined cultivars and three OPA-02, OPA-03, OPB-08 primers with the highest power differentiating for the studied genotypes were selected. Results of the research revealed the potentials of RAPD and SDS-PAGE technique in determining genetical diversity and make a suitable qualitative assessment of common wheat cultivars.

Analysis of genetic diversity and spatial structure in Tunisian populations of Hordeum marinum ssp. marinum based on molecular markers

2019 ◽  
Vol 157 (5) ◽  
pp. 399-412 ◽  
Author(s):  
W. Saoudi ◽  
M. Badri ◽  
M. Gandour ◽  
A. Smaoui ◽  
C. Abdelly ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Conservation Strategies ◽  
Entire Collection ◽  
High Discrimination ◽  
High Level ◽  
Dna Primers ◽  
Altitudinal Difference

AbstractHordeum marinum commonly known as sea barley is a salinity-tolerant species of grass. In the current study, 150 lines from ten populations of H. marinum ssp. marinum collected from five Tunisian bioclimatic sites were screened for polymorphism with 13 selected random amplified polymorphic DNA primers. Results exhibited a high level of polymorphism (160 polymorphic bands with an average of 12.46 per primer) and a high level of genetic diversity in all the studied populations (on average UHe = 0.247 and I = 0.358). High discrimination capacity was found for the 13 primers and a combination of three allowed assignation of a unique profile for each of the 150 lines. The partition of genetic diversity with Analysis of Molecular Variance suggested that the majority of genetic variation (67%) was within populations. The components between-populations within ecoregions and between-ecoregions explained 21 and 12%, respectively, of the total genetic variance. There was no significant association of population differentiation (ФPT) with geographical distance or altitudinal difference. Results also showed that the 150 lines grouped into three clusters with no respect to geographic origin. A sub-set of 13 lines was identified, which captured the maximum genetic diversity of the entire collection. The genetic variation found in this collection of H. marinum is deemed to be useful in formulating conservation strategies for this species.

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