Genetic diversity in local barley accessions collected from different geographical regions of Tunisia

2009 ◽  
Vol 7 (02) ◽  
pp. 169-176 ◽  
Author(s):  
M. A. Ould Med Mahmoud ◽  
S. Hamza
Keyword(s):  
Genetic Diversity ◽  
Geographical Origin ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
North West ◽  
The North ◽  
Geographical Regions ◽  
The Impact ◽  
Expressed Sequence ◽  
Simple Sequence

To assess the genetic diversity among Tunisian local barley, a set of 120 barley accessions representing five distinct geographical regions (North-West, Littoral, South, Jerba and Kerkennah Islands) was characterized with 20 simple sequence repeats (SSR) and 8 expressed sequence tag (EST)-SSR markers. The 28 loci revealed a total of 98 alleles, with an average of 3.76 alleles per locus (range 2–10). Gene diversity averaged 0.50 (range 0.09–0.84). Partitioning analysis of genetic diversity showed that about 95% of the total variation was within regions and no geographical differentiation could be found except for the North-West population. Similarly, neighbour joining clustering of the genotypes did not indicate any clear pattern of division among the barley accessions based on geographical origin. These results may reflect the impact of seed exchange between farmers which is likely to limit highlighting favourable alleles due to local adaptation.

scholarly journals Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars

2021 ◽  
Vol 12 ◽  
Author(s):  
Haftom Brhane ◽  
Teklehaimanot Haileselassie ◽  
Kassahun Tesfaye ◽  
Cecilia Hammenhag ◽  
Rodomiro Ortiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Finger Millet ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
Geographic Regions ◽  
Landrace Accessions ◽  
Expressed Sequence ◽  
Simple Sequence

Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.

scholarly journals Genetic diversity of mutant napiergrass using Expressed Sequence Tag Simple Sequence Repeat (EST-SSR)

2019 ◽  
Vol 20 (8) ◽  
Author(s):  
Mansyur M Mansyur ◽  
Panca Dewi MH Karti ◽  
Luki Abdullah ◽  
Ali Husni ◽  
Puji Lestari
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
Mutation Breeding ◽  
Sequence Repeat ◽  
Average Value ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract. Mansyur, Karti PMH, Abdullah L, Husni A, Lestari P. 2019. Genetic diversity of mutant napiergrass using Expressed Sequence Tag Simple Sequence Repeat (EST-SSR). Biodiversitas 20: 2403-2409. Napiergrass is one of the tropical grasses which has a very important role in developing ruminant livestock, its productivity is high and its nutritional content is quite good. Plant breeding to produce new varieties that have better productivity continues. One of them is through mutation breeding and in vitro culture. The purpose of this research was to look at the genetic diversity among napiergrasses using the Expressed Sequence Tag Simple Sequence Repeat (EST-SSR). This study used 14 SSR molecular markers. The results showed that mutant DNA of napiergrass can be clearly amplified by all the EST-SSR primers used. The average number of alleles was 4.57, the average frequency of the main allele was 42%, and the average value of gene diversity was 0.66. While the PIC average value was 0.60. There were five markers that were very informative and have PIC values ​​above 0.7, among others, namely ICMP3045, ICMP3018, PSMP2090, PSMP2209, and PSMP2019. Phylogenetic analysis shows that 37 numbers of napiergrass mutants split into two main clusters at a coefficient of 0.56. The first cluster consists of 26 lines while the second cluster consists of 11 mutants. The parent napiergrass is in the first cluster. There are two pairs of mutants that have the same diversity, namely R20-11 with R 20-20-3 and R100-1 with R100-3.

scholarly journals Does the genetic diversity among pubescent white oaks in southern Italy, Sicily and Sardinia islands support the current taxonomic classification?

2020 ◽  
Author(s):  
Romeo Di Pietro ◽  
Antonio Luca Conte ◽  
Piera Di Marzio ◽  
Paola Fortini ◽  
Emmanuele Farris ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Expressed Sequence Tag ◽  
Taxonomic Classification ◽  
Genetic Assignment ◽  
Molecular Analyses ◽  
Genetic Groups ◽  
Ecological Features ◽  
Weak Separation ◽  
Expressed Sequence ◽  
Simple Sequence

AbstractMolecular diversity analysis of deciduous pubescent oaks was conducted for populations from Calabria, Sicily and Sardinia. The aims of this study were twofold. First, to provide data on the genetic diversity of pubescent oaks from an understudied area which currently exhibits one of the highest concentrations of pubescent oak species in Europe. Second, to verify if these groups of oaks are genetically distinct and if their identification is in accordance with the current taxonomic classification. Molecular analyses of leaf material of 480 trees from seventeen populations belonging to putatively different pubescent oak species (Quercus amplifolia, Q. congesta, Q. dalechampii, Q. ichnusae, Q. leptobalanos, Q. virgiliana) were performed. Twelve gene-based Expressed Sequence Tag-Simple Sequence Repeat markers were selected, and genetic diversity and differentiation were calculated. The results showed relatively high values of allelic richness, heterozygosity and number of private alleles for the populations investigated. A weak but positive correlation between geographical and genetic distance was detected. Genetic assignment (STRUCTURE) and principle coordinate analyses exhibited a weak separation into two genetic groups which, however, did not correspond to the taxonomic, chorological and ecological features of the populations investigated. Sardinian populations formed one group which was separated from the Calabrian and Sicilian populations. In light of the results obtained, the taxonomic classification for the pubescent white oaks currently reported in the major Italian floras and checklists for the study area was not confirmed by molecular analyses.

A comparative assessment of genetic diversity in cultivated barley collected in different decades of the last century in Austria, Albania and India by using genomic and genic simple sequence repeat (SSR) markers

2006 ◽  
Vol 4 (2) ◽  
pp. 125-133 ◽  
Author(s):  
Elena K. Khlestkina ◽  
Rajeev K. Varshney ◽  
Marion S. Röder ◽  
Andreas Graner ◽  
Andreas Börner
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Polymorphic Information Content ◽  
Time Interval ◽  
Slight Reduction ◽  
Geographical Regions ◽  
Cultivated Barley ◽  
Quantitative Changes ◽  
Expressed Sequence

Molecular investigations of qualitative and quantitative changes in the genetic diversity of cultivated crops are useful for plant breeding and the management of crop genetic resources. A genotyping study, based on 28 genomic (g-SSR) and 13 expressed sequence tag-derived (e-SSR) microsatellite markers uniformly distributed across the barley genome, was conducted on samples of cultivated barley (Hordeum vulgare L.) collected at intervals of 40–50 years in three comparable geographical regions in Austria, Albania and India. The analysis indicated an absence of any significant differences either in the total number of alleles per locus or in g-SSR and e-SSR polymorphic information content (PIC) values from the Indian and Austrian materials. However, a slight reduction in genetic diversity was noted among the materials collected in Albania. The trend in numbers of collection mission-specific SSR alleles suggests significant allele flow over the time interval sampled. The g-SSRs yielded a higher mean number of alleles per locus and a superior PIC than the e-SSR markers. We conclude that a qualitative, rather than a quantitative shift in diversity has taken place over time, and that g-SSR markers detect more diversity than do e-SSR markers.

Evaluation of genetic diversity of Rubus hyrcanus using Inter Simple Sequence Repeat (ISSR) and morphological markers

Biologia ◽  
2015 ◽  
Vol 70 (3) ◽  
Author(s):  
Ehsan Sedighi ◽  
Mehdi Rahimmalek
Keyword(s):  
Genetic Diversity ◽  
Caspian Sea ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Morphological Markers ◽  
The Caspian Sea ◽  
Geographical Regions ◽  
North Eastern ◽  
North Western ◽  
Simple Sequence

AbstractRubus hyrcanus is considered as an important wild blackberry species scattered around the Caspian Sea. In this research, ISSR and morphological markers were used to assess genetic diversity in several populations of R. hyrcanus from various geographical regions of Caspian Sea in Iran. Twenty-five populations of R. hyrcanus from three regions (North- Western (NW), North- Eastern (NE) and Central (C)) and one population from R. discolor were applied in this research. Ten primers were used to amplify bands out of which 157 (77.13%) were polymorphic. Cluster and Principle coordinate analyses (PCoA) showed the higher similarity of NE and NW populations. Analysis of molecular variance (AMOVA) revealed that the differences among three collection regions only accounted for 28.09% of the total variation, whereas differences among populations within groups were 66.03%. Analyses among three regions showed that the minimum gene diversity over loci was observed in NW (0.16) and NE (0.17), while the highest one was found in C (0.238) region. Furthermore, narrow genetic base and relatively high genetic differentiation obtained for studied R. hyrcanus genotypes. The results of morphological analysis in most cases corresponded to those obtained through molecular analyses.

Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 731-737 ◽  
Author(s):  
N A Barkley ◽  
M L Newman ◽  
M L Wang ◽  
M W Hotchkiss ◽  
G A Pederson
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Phylogenetic Relationships ◽  
Expressed Sequence Tag ◽  
Genetic Distances ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Expressed Sequence ◽  
Simple Sequence

Polymorphic expressed sequence tag - simple sequence repeat (EST-SSR) markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number of alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pairwise combinations and assessing differences in character data. The resulting dendrograms (unweighted pair group method with arithmetic means (UPGMA) and parsimony) clustered the accessions into 2 main clades, which corresponded to accessions characterized morphologically as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their current taxonomic classification. These markers were also beneficial in identifying contaminated and (or) misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera.Key words: bamboo germplasm, genetic diversity, phylogeny.

Genetic diversity of Crotalaria germplasm assessed through phylogenetic analysis of EST-SSR markers

Genome ◽  
2006 ◽  
Vol 49 (6) ◽  
pp. 707-715 ◽  
Author(s):  
M L Wang ◽  
J A Mosjidis ◽  
J B Morris ◽  
R E Dean ◽  
T M Jenkins ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Germplasm Collection ◽  
High Similarity ◽  
Ssr Primers ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Crotalaria Spectabilis

The genetic diversity of the genus Crotalaria is unknown even though many species in this genus are economically valuable. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago and soybean were used to assess the genetic diversity of the Crotalaria germplasm collection. This collection consisted of 26 accessions representing 4 morphologically characterized species. Phylogenetic analysis partitioned accessions into 4 main groups generally along species lines and revealed that 2 accessions were incorrectly identified as Crotalaria juncea and Crotalaria spectabilis instead of Crotalaria retusa. Morphological re-examination confirmed that these 2 accessions were misclassified during curation or conservation and were indeed C. retusa. Some amplicons from Crotalaria were sequenced and their sequences showed a high similarity (89% sequence identity) to Medicago truncatula from which the EST-SSR primers were designed; however, the SSRs were completely deleted in Crotalaria. Highly distinguishing markers or more sequences are required to further classify accessions within C. juncea.Key words: Crotalaria germplasm, EST-SSR, genetic diversity, phylogeny.

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