scholarly journals Simple sequence repeat markers revealed genetic divergence and population structure of okra [Abelmoschus esculentus] collections of diverse geographic origin

2020 ◽  
pp. 1032-1041
Author(s):  
Wassu Mohammed ◽  
Beyene Amelework ◽  
Hussein Shimelis
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Geographic Origin ◽  
Population Divergence ◽  
Sequence Repeat ◽  
Germplasm Exchange ◽  
Geographic Regions ◽  
Simple Sequence

The study was carried out to assess the genetic diversity and population structure of okra collections from diverse geographic origin using selected polymorphic simple sequence repeat (SSR) markers. Thirty-two okra accessions collected from three geographic regions were genotyped using 16 selected SSR markers. The SSR markers generated a total of 71 loci of which 67% were polymorphic. Genetic distances among accessions ranged from 2.2 to 7.1, with a mean of 4.65. Gene diversity ranged from 0.10 to 0.78 with a mean of 0.52. Genetic clustering classified the accessions into three major clusters and four sub-clusters. Each cluster and sub-cluster consisted of accessions derived from different sources. Analysis of molecular variance revealed that 67%, 81% and 83% of the total genetic variation detected was found within populations of geographic origin, altitude and collection district, respectively. The observed moderate to high population differentiation could partly be attributed to limited germplasm exchange, agro-ecological differences, and partly by selection pressure. The present study revealed the presence of high genetic diversity and population divergence among okra collections from Ethiopia. The study demonstrated that a collection strategy for conservation of okra genetic resources should focus on sampling of representative genotypes covering wide geographic regions and altitudinal ranges of target agro-ecologies.

scholarly journals Genetic Diversity and Population Structure of Traditional Greek and Cypriot Melon Cultigens (Cucumis melo L.) Based on Simple Sequence Repeat Variability

HortScience ◽  
2009 ◽  
Vol 44 (7) ◽  
pp. 1820-1824 ◽  
Author(s):  
Emmanouil N. Tzitzikas ◽  
Antonio J. Monforte ◽  
Abdelhak Fatihi ◽  
Zacharias Kypriotakis ◽  
Tefkros A. Iacovides ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Simple Sequence Repeat ◽  
Cucumis Melo ◽  
Sequence Repeat ◽  
Population Structure Analysis ◽  
Simple Sequence

Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure among traditional Greek and Cypriot melon cultigens (Cucumis melo L.). All SSR markers were polymorphic with a total number of 81 alleles, whereas all cultigens could be distinguished with at least one SSR, except cultigens 43 and 41. Reference accessions showed larger genetic variability with an average of four alleles per locus and 0.65 gene of diversity compared with an average of 2.47 alleles per locus and 0.30 of gene diversity for the Greek/Cypriot cultigens. Observed heterozygosity was very low, indicating a lack of outcrossing, at least in recent times. Unrooted neighbor-joining tree analysis and population structure analysis clustered the cultigens and the reference genotypes into five groups. All cultigens could be distinguished; the Cypriot cultigens were more closely related to the inodorus ‘Piel de Sapo’, whereas the Greek cultigens were located in an intermediate position between the inodorus ‘Piel de Sapo’ and the cantalupensis ‘Védrantais’. The cultigen ‘Kokkini’ was the most divergent among the Greek and Cypriot cultigens. This association between geographic origin and genetic similarity among Greek and Cypriot cultigens indicates geographic isolation. Most of the cultivars from the same cultivar group (i.e., inodorus, cantalupensis) clustered together, but some exceptions were found, suggesting that former inodorus landraces would have been transformed to cantalupensis as a result of intercrossing and further selection by farmers. Results of population structure analysis support mixing between cantalupensis and inodorus. ‘Agiou Basileiou’, an inodorus cultigen, was assigned to the subpopulation IV/II of which II is a pure cantalupensis subpopulation. Greek and Cypriot melon cultigens were developed from a broader germplasm base than western Mediterranean cultivars and exhibited useful for melon breeding programs genetic variability.

scholarly journals Genetic diversity and population structure analysis of Ghanaian and exotic cassava accessions using simple sequence repeat (SSR) markers

Heliyon ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. e03154
Author(s):  
Joseph Adjebeng-Danquah ◽  
Joseph Manu-Aduening ◽  
Isaac Kwadwo Asante ◽  
Richard Yaw Agyare ◽  
Vernon Gracen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Population Structure Analysis ◽  
Simple Sequence

scholarly journals Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species

2019 ◽  
Author(s):  
Jun Hyoung Bang ◽  
Chi Eun Hong ◽  
Sebastin Raveendar ◽  
Kyong Hwan Bang ◽  
Kyung Ho Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Sequence Repeat ◽  
Molecular Studies ◽  
Simple Sequence ◽  
Genomic Simple Sequence Repeat

Background. Licorice (Glycyrrhiza spp. L.) is used as a natural sweetener and medicinal herb. Molecular studies have been conducted to find differences between wild and cultivated species because most wild species are highly resistant to abiotic and biotic stresses compared with their cultivated counterparts. However, few molecular markers have been developed for studying the genetic diversity and population structure of licorice species and to identify differences between cultivars. Thus, the present study aimed to develop a set of genomic simple sequence repeat (SSR) markers for molecular studies of these species. Methods. We designed 100 SSR markers based on the whole-genome sequence data of wild Glycyrrhiza lepidota and selected 62 SSR markers. Results. The genetic diversity analysis using these markers identified 2–23 alleles, and the major allele frequency, observed heterozygosity, genetic diversity, and polymorphism information content were 0.11–0.91, 0–0.90, 0.17–0.94, and 0.15–0.93, respectively. Interspecies transferability values were 93.5%, 91.6%, and 91.1% for G. echinata, G. glabra, and G. uralensis, respectively. Phylogenetic analysis clustered cultivated (group 1) and wild (group 2) species into three and two subgroups, respectively. The SSR markers developed here can be applied to genetic diversity, population structure, and cultivar differentiation studies, as well as to breeding of licorice varieties.

scholarly journals Genetic diversity and population structure of Urochloa grass accessions from Tanzania using simple sequence repeat (SSR) markers

2018 ◽  
Vol 41 (3) ◽  
pp. 699-709 ◽  
Author(s):  
S. O. Kuwi ◽  
M. Kyalo ◽  
C. K. Mutai ◽  
A. Mwilawa ◽  
J. Hanson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Simple Sequence

scholarly journals Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species

2019 ◽  
Author(s):  
Jun Hyoung Bang ◽  
Chi Eun Hong ◽  
Sebastin Raveendar ◽  
Kyong Hwan Bang ◽  
Kyung Ho Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Sequence Repeat ◽  
Molecular Studies ◽  
Simple Sequence ◽  
Genomic Simple Sequence Repeat

Background. Licorice (Glycyrrhiza spp. L.) is used as a natural sweetener and medicinal herb. Molecular studies have been conducted to find differences between wild and cultivated species because most wild species are highly resistant to abiotic and biotic stresses compared with their cultivated counterparts. However, few molecular markers have been developed for studying the genetic diversity and population structure of licorice species and to identify differences between cultivars. Thus, the present study aimed to develop a set of genomic simple sequence repeat (SSR) markers for molecular studies of these species. Methods. We designed 100 SSR markers based on the whole-genome sequence data of wild Glycyrrhiza lepidota and selected 62 SSR markers. Results. The genetic diversity analysis using these markers identified 2–23 alleles, and the major allele frequency, observed heterozygosity, genetic diversity, and polymorphism information content were 0.11–0.91, 0–0.90, 0.17–0.94, and 0.15–0.93, respectively. Interspecies transferability values were 93.5%, 91.6%, and 91.1% for G. echinata, G. glabra, and G. uralensis, respectively. Phylogenetic analysis clustered cultivated (group 1) and wild (group 2) species into three and two subgroups, respectively. The SSR markers developed here can be applied to genetic diversity, population structure, and cultivar differentiation studies, as well as to breeding of licorice varieties.

scholarly journals Discovery, Characterization, and Linkage Mapping of Simple Sequence Repeat Markers In Hazelnut

2018 ◽  
Vol 143 (5) ◽  
pp. 347-362 ◽  
Author(s):  
Gehendra Bhattarai ◽  
Shawn A. Mehlenbacher
Keyword(s):  
Genetic Diversity ◽  
Linkage Map ◽  
Ssr Markers ◽  
Genome Sequence ◽  
Simple Sequence Repeat ◽  
Genomic Sequence ◽  
Geographic Origin ◽  
Null Alleles ◽  
Sequence Repeat ◽  
Simple Sequence

From the genome sequence of hazelnut (Corylus avellana), 192 new polymorphic simple sequence repeat (SSR) markers were developed, characterized, and used to investigate genetic diversity in 50 accessions. Next-generation sequencing allows inexpensive sequencing of plant genomes and transcriptomes, and efficient development of polymorphic SSR markers, also known as microsatellite markers, at low cost. A search of the genome sequence of ‘Jefferson’ hazelnut identified 9094 fragments with long repeat motifs of 4, 5, or 6 base pairs (bp), from which polymorphic SSR markers were developed. The repeat regions in the ‘Jefferson’ genome were used as references to which genomic sequence reads of seven additional cultivars were aligned in silico. Visual inspection for variation in repeat number among the aligned reads identified 246 as polymorphic, for which primer pairs were designed. Polymerase chain reaction (PCR) amplification followed by agarose gel separation indicated polymorphism at 195 loci, for which fluorescent forward primers were used to amplify the DNA of 50 hazelnut accessions. Amplicons were post-PCR multiplexed for capillary electrophoresis, and allele sizes were determined for 50 accessions. After eliminating three, 192 were confirmed as polymorphic, and 169 showed only one or two alleles in each of the 50 cultivars, as expected in a diploid. At these 169 SSRs, a total of 843 alleles were found, for an average of 4.99 and a range of 2 to 17 alleles per locus. The mean observed heterozygosity, expected heterozygosity, polymorphism information content, and the frequency of null alleles were 0.51, 0.53, 0.47, and 0.03, respectively. An additional 25 primer pairs produced more than two bands in some accessions with an average of 6.8 alleles. The UPGMA dendrogram revealed a wide genetic diversity and clustered the 50 accessions according to their geographic origin. Of the new SSRs, 132 loci were placed on the linkage map. These new markers will be useful for diversity and parentage studies, cultivar fingerprinting, marker-assisted selection, and aligning the linkage map with scaffolds of the genome sequence.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

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