Molecular variability and phylogenetic relationships of guava (Psidium guajava L.) cultivars using inter-primer binding site (iPBS) and microsatellite (SSR) markers

Mehmood, Asim; Luo, Shuming; Ahmad, Nabil; Dong, Chongmei; Mahmood, T.; Sajjad, Yasar; Jaskani, Muhammad Jafar; Sharp, P. J.

doi:10.1007/s10722-015-0322-7

Cited by 38 publications

(42 citation statements)

References 38 publications

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“…used in this study were not likely to be conserved. This finding supported previous reports in other species, such as saffron (Gedik et al, 2017), common bean (Nemli et al, 2015), grape (Guo et al, 2014), guava (Mehmood et al, 2016), and those investigated by Kalendar et al (2010). There were a total of 204 alleles with an average of 20.4 per primer.…”

Section: Polymorphism Revealed By Ipbs Primerssupporting

confidence: 91%

Genetic structure and diversity of Adonis L. (Ranunculaceae) populations collected from Turkey by inter-primer binding site (iPBS) retrotransposon markers

Türkoğlu¹,

Karahan²,

İlhan³

et al. 2019

Turk J Bot

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The genus Adonis L. is a member of Ranunculaceae and consists of perennial and annual herbaceous plants included in the tribe Adonideae under the subfamily Ranunculoideae. Botanically, Ranunculaceae comprises vital medicinal plants. Molecular markers are one of the most effective tools for exploring genetic variation that can enhance breeding efficiency. To identify the genetic diversity of 62 Adonis ecotypes collected from different regions in Turkey, the interprimer binding site (iPBS) retrotransposon system was used. Of the 83 iPBS primers used, 10 provided sufficient polymorphic data, generating a total of 204 alleles. The number of iPBS bands per individual was 3.29, and the number of alleles per polymorphic locus ranged from 8 to 35, with an average of 20.30. The average polymorphism percentage was 99.50%, and polymorphic information content ranged from 0.16 to 0.39. The highest average number of alleles, Nei's genetic diversity (h), and Shannon's information index (I) were obtained from A. volgensis species (1.64, 0.39, and 0.58, respectively), whereas the lowest values (1.41, 0.29, and 0.46, respectively) were found in A. flammea species. The analysis of molecular variance revealed significant variance within the population (71%), whereas no significant genetic variation was observed among the different species (29%). Cluster analysis according to unweighted pair-group mean average (UPGMA) divided 62 Adonis ecotypes into four major clusters. According to the principal coordinate analysis, the first three principal coordinates accounted for 81.51% of total variation. Genetic structure analysis of the studied germplasm using the Bayesian method revealed four subpopulations with an average of 0.2634 for expected heterozygosity and 0.2154 for population differentiation measurements. The results of this study suggested that iPBS markers could be used in the identification of genetic diversity among the Adonis species.

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Section: Polymorphism Revealed By Ipbs Primerssupporting

confidence: 91%

Genetic structure and diversity of Adonis L. (Ranunculaceae) populations collected from Turkey by inter-primer binding site (iPBS) retrotransposon markers

Türkoğlu¹,

Karahan²,

İlhan³

et al. 2019

Turk J Bot

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“…Our earlier studies in wild emmer [8], pea [24], tobacco [25], common bean [48], pepper [50] and safflower [51] also found this marker system highly robust, and trustable, which can be used for the investigation of genetic diversity in any crop. Similarly, Mehmood et al [41] also found this marker system highly reproducible, robust and trustable. Moreover, trustbility of this marker compared to another marker system has been proven by earlier studies as well.…”

Section: Polymorphism In Turkish Laurel Germplasm Revealed By Ipb-retmentioning

confidence: 78%

“…Previous studies have proven iPBS-retrotransposon a highly reproducible, robust and trustable marker system [22,23,40,41]. Our earlier studies in wild emmer [8], pea [24], tobacco [25], common bean [48], pepper [50] and safflower [51] also found this marker system highly robust, and trustable, which can be used for the investigation of genetic diversity in any crop.…”

Section: Polymorphism In Turkish Laurel Germplasm Revealed By Ipb-retmentioning

confidence: 90%

Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System

Karik¹,

Nadeem

Habyarimana

et al. 2019

Agronomy

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Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon's information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant.

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“…Accurate identification of accessions in a germplasm collection is an important first step in crop improvement. Molecular marker systems, including SSRs, can more accurately differentiate germpalsm than methods based on morphological traits or isoenzymes because they are objective, reproducible and independent of environmental influences (Al-Najm et al, 2016;Mehmood et al, 2016). In the current study, seventeen polymorphic SSR markers discriminated a range of Phoenix dactylifera accessions including related species and provided valuable information on the genetic relationship amongst the accessions.…”

Section: Discussionmentioning

confidence: 99%

“…However, analysis among closely related cultivars using morphological characters alone is often unreliable and influenced by the environment (Mehmood et al, 2013;Luo et al, 2015;Borna et al, 2016). Isozyme markers were used as an alternative, although the method was limited by the number of informative data and gave no direct assessment of DNA genomic variation (see Akbari et al 2012;Al-Najm et al, 2016;Khanam et al, 2012;Mehmood et al, 2014;Mehmood et al, 2016;Sedra et al, 1993;Sedra et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

Molecular variability and population structure of a core collection of date palm (Phoenix dactylifera L.) cultivars from Australia and the Middle East

Al-Najm¹,

Luo²,

Ahmad³

et al. 2017

Aust J Crop Sci

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Understanding genetic relatedness in date palm (Phoenix dactylifera L.) germplasm is important for effective plant improvement. Microsatellite (SSR) markers were used to assess the molecular variation and population structure of 60 Australian locally selected and exotic genotypes (24 female, 30 male and 6 related species), 12 Iraqi female cultivars and 10 female cultivars from Jordan. The main objectives were to survey genetic diversity and determine population structure in this core date palm collection which includes the most important and widely distributed cultivars in Australia. These Australian accessions were then compared to those originating from the date palm center of origin in the Middle East. PCR of 17 SSR primers (co-dominant markers) produced a total of 313 alleles ranging from 5 to 31 with an average of 18.4 alleles per locus. The PIC value for these 17 primers ranged from 0.4771 to 0.8199 with a mean of 0.670. The mean expected heterozygosity (0.841), mean observed heterozygosity (0.946) and Shannon's information index (2.067) indicated a high level of genetic diversity among the accessions. Multi-locus DNA fingerprints based on the 17 SSR loci unambiguously differentiated all accessions and revealed an absence of duplicated samples. Ordination and cluster analyses showed that the Australian accessions did not group together geographically; instead separate male and female groups differentiated among the six clusters. A Bayesian cluster analysis also partitioned the accessions into six groups and this result was largely compatible with the result of ordination analysis. The Australian date palm germplasm is highly diverse and thus provides an effective platform for plant improvement, enhancement of date production and the conservation of genetic resources.

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Molecular variability and phylogenetic relationships of guava (Psidium guajava L.) cultivars using inter-primer binding site (iPBS) and microsatellite (SSR) markers

Cited by 38 publications

References 38 publications

Genetic structure and diversity of Adonis L. (Ranunculaceae) populations collected from Turkey by inter-primer binding site (iPBS) retrotransposon markers

Genetic structure and diversity of Adonis L. (Ranunculaceae) populations collected from Turkey by inter-primer binding site (iPBS) retrotransposon markers

Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System

Molecular variability and population structure of a core collection of date palm (Phoenix dactylifera L.) cultivars from Australia and the Middle East

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