RETRACTED ARTICLE: Elucidate genetic diversity and population structure of Olea europaea L. germplasm in Iran using AFLP and IRAP molecular markers

Khaleghi, Esmaeil; Sorkheh, Karim; Chaleshtori, Maryam Hosseni; Erċışlı, Sezai

doi:10.1007/s13205-017-0669-x

Cited by 10 publications

(7 citation statements)

References 60 publications

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“…The CCC of 0.88 obtained from the dendrogram based on Jaccard coefficient is suggestive of this. In a previous report on 200 tree accessions in the 20 groups of Olea europaea using IRAP markers, CCC value was 0.96, indicating a good fit between the similarity matrix and the dendrogram [94].…”

Section: Genetic Diversity Of Asian Bamboo Speciesmentioning

confidence: 66%

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Ramakrishnan

Vinod

et al. 2019

Forests

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Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos.

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Section: Genetic Diversity Of Asian Bamboo Speciesmentioning

confidence: 66%

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Ramakrishnan

Vinod

et al. 2019

Forests

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“…Dendrogram was constructed using unweighted pair group method with arithmetic averages (UPGMA) algorithm based on the genetic distance of Nei and Li [19]. Polymorphism information content (PIC) was calculated using EIGEN module of NTSYSpc 2.02 to confirm primer efficiency according to the formula given by Khaleghi et al [20].…”

Section: Methodsmentioning

confidence: 99%

Assessment of genetic diversity in Colletotrichum falcatum Went accessions based on RAPD and ISSR markers

Patel

Rajkumar

Parmar

et al. 2018

Journal of Genetic Engineering and Biotechnology

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Sugarcane is susceptible to red rot disease caused by phytopathogenic fungus Colletotrichum falcatum Went which ultimately affect the economy of farmers as well as sugar based industry. One of the various ways to control this devastating disease is to develop disease resistance sugarcane cultivar and this requires the complete understanding of genetic makeup of pathogen. Although South Gujarat is well known sugarcane cultivating area, less published data can be found about PCR-based genetic diversity in prevalent C. falcatum accessions. So, present investigation aims at finding molecular variation among the ten accessions of C. falcatum using RAPD and ISSR molecular markers. A total of 35 RAPD and 39 ISSR primers were screened across 10 C. falcatum accessions, of which 15 RAPD and 21 ISSR primers have showed consistent amplification. Statistics related to genetic variation were estimated using NTSYS-PC by means of Dice’s coefficient. The results revealed 80.6% and 68.07% polymorphism and similarity coefficient ranged from 0.43 to 0.91 and 0.73 to 0.93 in RPAD and ISSR analysis respectively. The dendrogram generated using RAPD, ISSR and combined RAPD-ISSR grouped accessions into different clusters which reveal considerable level molecular variation among the C. falcatum accessions. It is also evident from PCA plots that accessions are rather dispersed with tested marker systems indicating good genetic base. So, in nut shell, we found considerable genetic variation and relatedness within C. falcatum accessions collected from different areas of south Gujarat, India using RAPD and ISSR markers.

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“…The phenomenon of synonyms, homonyms, and unclear genetic relationship still exists among olive germplasms [ 10 , 11 ]. Researchers have done lots of studies on the molecular markers to distinguish different olive accessions, such as the amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), and single nucleotide polymorphism (SNP) [ 12 , 13 , 14 ]. D’Agostino et al [ 15 ] and Zhu et al [ 16 ] conducted whole-genome level SNP exploration for 97 and 57 olive cultivars, respectively.…”

Section: Introductionmentioning

confidence: 99%

Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L.

Niu

Cheng-ying

Wang

et al. 2020

Genes

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Olive (Olea europaea L.) is a very important woody tree and favored by consumers because of the fruit’s high-quality olive oil. Chloroplast genome analysis will provide insights into the chloroplast variation and genetic evolution of olives. The complete chloroplast genomes of three accessions (O. europaea subsp. cuspidata isolate Yunnan, O. europaea subsp. europaea var. sylvestris, and O. europaea subsp. europaea var. frantoio) were obtained by next-generation sequencing technology. A total of 133 coding regions were identified in the three chloroplast genomes without rearrangement. O. europaea subsp. europaea var. sylvestris and O. europaea subsp. europaea var. frantoio had the same sequences (155,886 bp), while O. europaea subsp. cuspidata isolate Yunnan (155,531 bp) presented a large gap between rps16 and trnQ-UUG genes with six small gaps and fewer microsatellites. The whole chloroplast genomes of 11 O. europaea were divided into two main groups by a phylogenetic tree and O. europaea subsp. cuspidata formed a separate group (Cuspidata group) with the other subspecies (Mediterranean/North African group). Identification of consistency and diversity among O. europaea subspecies will benefit the exploration of domestication events and facilitate molecular-assisted breeding for O. europaea.

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RETRACTED ARTICLE: Elucidate genetic diversity and population structure of Olea europaea L. germplasm in Iran using AFLP and IRAP molecular markers

Cited by 10 publications

References 60 publications

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Assessment of genetic diversity in Colletotrichum falcatum Went accessions based on RAPD and ISSR markers

Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L.

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