Houba retrotransposon-based molecular markers: a tool for variation analysis in rice

Yüzbaşioğlu, Gözde; Yılmaz, Sevgi; Gözükırmızı, Nermin

doi:10.3906/tar-1509-2

Cited by 11 publications

(6 citation statements)

References 24 publications

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“…In addition to the human genome, retrotransposons have been identified in many organisms, especially in the plant kingdom, particularly in cereal genomes such as barley, maize, wheat and rice. In these cereals, the retrotransposon ratio is higher than in other plants [1,6].…”

Section: Introductionmentioning

confidence: 84%

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Sukkularetrotransposon movements in the human genome

Cakmak

Marakli

Gözükırmızı

2017

Biotechnology & Biotechnological Equipment

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Retrotransposons, a subclass of mobile genetic elements, have been discovered in many organisms. In this study, we identified a plant-specific retrotransposon (Sukkula) in the human genome (24 different DNA samples) by using retrotransposon-based molecular marker technique: interretrotransposon amplified polymorphism. There were five different groups related to the ages of the subjects. The polymorphism ratios were 8%-100% among all samples, 10%-91% among females (12 subjects) and 13%-100% among males (12 subjects). Moreover, we also observed 8%-91% polymorphism ratios when comparing males to females. To the best of our knowledge, this is one of the first reports on plant-specific retrotransposons in the human genome. The obtained findings are expected to contribute to broadening the knowledge about plant retrotransposons in the human genome and their role in human genome evolution.

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Section: Introductionmentioning

confidence: 84%

“…This way, the genomic distance between two LTRs is amplified [11]. This method has been used for investigation of specific retrotransposons in target genomes [6,7,12]. Moreover, some plant-specific retrotransposons have been found in other plants and animals [8,13].…”

Section: Introductionmentioning

confidence: 99%

Sukkularetrotransposon movements in the human genome

Cakmak

Marakli

Gözükırmızı

2017

Biotechnology & Biotechnological Equipment

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“…We report the soybean specific SIRE1 Retrotransposons in Barley Hordeum vulgare L. genome (Cakmak et al, 2015). Analysis on Hopi/Osr27 and Houba/Tos5/Osr13 retrotransposons in rice (Yuzbasioglu et al, 2016a, Yüzbaşıoğlu et al, 2016b and in Pinus nigra barley specific BAGY2, Nikita and Sukkula were analysed (Marakli et al, 2019). We also observed barley specific retrotransposons in endemic Colchium chalcedonicum (Karlık et al, 2019).…”

Section: Our Research With Transposonsmentioning

confidence: 82%

Transposons Continue the Amaze

Gözükırmızı

2019

International Journal of Science Letters

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Transposable elements (TEs) were first discovered in maize plants. However, they exist almost in all species with a few exceptions (Plasmodium falciparum, Ashbya gossypii and Kluveromuyces lactis). They are the most important contributors to genome plasticity and evolution and even epigenetic genome regulation. Organisms with large genomes have high transposon percentages. For example, Arabidopsis thaliana has a genome size of 125 Mb which comprises 14% transposons, Homo sapiens (3000 Mb) 45-48.5%, and Hordeum vulgare genome (5300 Mb) has 80%. TEs are classified into two major groups based on their transposition mechanisms: Class I (RNA transposonsretrotransposons) and Class II (DNA transposons). Recent progress in whole-genome sequencing and long-read assembly have resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. All TEs in a cell are named as transposome (mobilome), and transposomics is a new area to work with transposome. Although a number of bioinformatics softwares have recently been developed for the annotation of TEs in sequenced genomes, there are very few computational tools strictly dedicated to the identification of active TEs using genome-wide approaches. In this review article, after a brief introduction and review of the transposable elements, I discussed their effects in gene expression, evolution, recent applications and also share our research on retrotransposons with different organisms.

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“…Cömertpay et al (2011) used combined SSR and iPBS‐retrotransposon markers for 81 rice varieties including some Turkish rice varieties. Additionally, there are a few studies for diversity detection of Turkish rice cultivars by RAPD (Bay, 2009) and IRAP (Yüzbaşıoğlu et al 2016) markers. However, a study which was performed to comprehensively investigate genetic diversity and characterization of Turkish polished rice market has not been found.…”

Section: Introductionmentioning

confidence: 99%

Diversity analysis of the rice cultivars ( Oryza sativa L.) by utilizing SSRs rice diversity by SSRs

Beşer

Mutafçılar

Hasançebi

2021

J. Food Process. Preserv.

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This study was carried out to analysis of genetic diversity of rice marketed in Turkey. Sixty rice varieties used as a material. A total of 50 SSR markers distributed to all 12 rice chromosomes were used for the diversity analysis of the genotypes. Out of these, 43 SSRs produced clear, distinct polymorphic bands among the rice varieties, and a total of 227 alleles were obtained. The number of alleles per locus ranged from 9 to 1. The mean number of alleles per locus was 5.25, and 22 markers (51%) had 6 or more alleles. Clustering of 60 varieties based on 43 SSR markers was carried out. While aromatic varieties were placed into an out‐group Rocca and Baldo which are parents of many rice varieties and 47 varieties were placed into the same clusters. This SSR polymorphism analysis revealed genomic relationships in rice marketed in Turkey. Practical applications Results of this study could be used to diversity analysis of rice and other crops and rice breeding programs. It could be used to study genetic diversity of polished rice at the market and consumer preference by countries.

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Houba retrotransposon-based molecular markers: a tool for variation analysis in rice

Cited by 11 publications

References 24 publications

Sukkularetrotransposon movements in the human genome

Sukkularetrotransposon movements in the human genome

Transposons Continue the Amaze

Diversity analysis of the rice cultivars ( Oryza sativa L.) by utilizing SSRs rice diversity by SSRs

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