Editorial: Innovative applications of sequencing technologies in plant science

Kalendar, Ruslan; Hunter, Charles; Orbović﻿﻿﻿, Vladimir

doi:10.3389/fpls.2022.1058347

Cited by 3 publications

(4 citation statements)

References 8 publications

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“…Markers can then be used for various applications, such as population genetics, association studies, and GWAS. The discovery of high-throughput genetic markers and the use of restriction enzymes for genotyping have several advantages and will become the methods of choice for marker research ( Kalendar et al., 2022b ). One of the advantages of these methods is that they can be used both for model organisms with high-quality reference genome sequences and for non-model species that do not have existing genomic data.…”

Section: Prospects Challenges and Discussionmentioning

confidence: 99%

“…On the contrary, many LTR retrotransposons include evolutionarily conserved PBS sequences. The most significant advantage of this method is that it does not need TE sequence information for primer design ( Kalendar et al., 2022b ). Many studies on TEs are on the determination of relationships using these marker techniques ( Monden et al., 2014 ).…”

Section: Applications Of Inter-retrotransposon Amplified Polymorphismsmentioning

confidence: 99%

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The power of retrotransposons in high-throughput genotyping and sequencing

et al. 2023

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The use of molecular markers has become an essential part of molecular genetics through their application in numerous fields, which includes identification of genes associated with targeted traits, operation of backcrossing programs, modern plant breeding, genetic characterization, and marker-assisted selection. Transposable elements are a core component of all eukaryotic genomes, making them suitable as molecular markers. Most of the large plant genomes consist primarily of transposable elements; variations in their abundance contribute to most of the variation in genome size. Retrotransposons are widely present throughout plant genomes, and replicative transposition enables them to insert into the genome without removing the original elements. Various applications of molecular markers have been developed that exploit the fact that these genetic elements are present everywhere and their ability to stably integrate into dispersed chromosomal localities that are polymorphic within a species. The ongoing development of molecular marker technologies is directly related to the deployment of high-throughput genotype sequencing platforms, and this research is of considerable significance. In this review, the practical application to molecular markers, which is a use of technology of interspersed repeats in the plant genome were examined using genomic sources from the past to the present. Prospects and possibilities are also presented.

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Section: Prospects Challenges and Discussionmentioning

confidence: 99%

Section: Applications Of Inter-retrotransposon Amplified Polymorphismsmentioning

confidence: 99%

The power of retrotransposons in high-throughput genotyping and sequencing

et al. 2023

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“…With the recent remarkable development of next-generation sequencing (NGS) technology, it has become possible to obtain whole-genome information of the various rice lines at relatively low cost, enabling genetic and molecular biological analysis ( Guo et al., 2014 ; Nguyen et al., 2019 ; Kalendar et al., 2022 ). In such a situation, the low frequency of spontaneous mutation could be an advantage in finding causative genes involved in traits that differ from the parental varieties.…”

Section: Introductionmentioning

confidence: 99%

Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences

Suganami,

Kojima,

Yoshida

et al. 2024

Front. Plant Sci.

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In the early 1900s, mutation breeding to select varieties with desirable traits using spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.25. Although this low mutation rate was a major problem for breeding in those days, in the modern era with the development of next-generation sequencing (NGS) technology, it was conversely considered to be an advantage for efficient gene identification. In this paper, we proposed an in silico approach using NGS to compare the whole genome sequence of a spontaneous mutant with that of a closely related strain with a nearly identical genome, to find polymorphisms that differ between them, and to identify the causal gene by predicting the functional variation of the gene caused by the polymorphism. Using this approach, we found four causal genes for the dwarf mutation, the round shape grain mutation and the awnless mutation. Three of these genes were the same as those previously reported, but one was a novel gene involved in awn formation. The novel gene was isolated from Bozu-Aikoku, a mutant of Aikoku with the awnless trait, in which nine polymorphisms were predicted to alter gene function by their whole-genome comparison. Based on the information on gene function and tissue-specific expression patterns of these candidate genes, Os03g0115700/LOC_Os03g02460, annotated as a short-chain dehydrogenase/reductase SDR family protein, is most likely to be involved in the awnless mutation. Indeed, complementation tests by transformation showed that it is involved in awn formation. Thus, this method is an effective way to accelerate genome breeding of various crop species by enabling the identification of useful genes that can be used for crop breeding with minimal effort for NGS analysis.

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“…These markers can be specific genes or sequences with unknown functions. Currently, the analysis of genetic polymorphisms in genome sequences is typically performed using several approaches: detection of polymorphisms using various PCR-based genome profiling techniques; the use of hybridization systems on various platforms and microarrays; and the use of next-generation sequencing (NGS) or Third Generation Sequencing (TGS) for comprehensive analysis [24,25]. Molecular genetic markers are becoming widely used in environmental forensics.…”

Section: Introductionmentioning

confidence: 99%

Genetic Uniqueness and Genetic Structure of Populations of Picea obovata Ledeb. and Larix sibirica Ledeb. in the Northern and Middle Urals

Zhulanov,

Chertov,

Nechaeva

et al. 2023

Forests

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Establishing sustainable plantations with genetic diversity equivalent to that of natural populations is vital for successful reforestation efforts. In this study, we present an innovative approach for selecting populations suitable for reforestation, taking into account their genetic uniqueness using Inter Simple Sequence Repeats (ISSR) markers. Our investigation focused on six populations of Picea obovata Ledeb and six populations of Larix sibirica Ledeb, collected from the Northern and Middle Urals. We found that the indicators of genetic diversity were significantly higher in L. sibirica compared to P. obovata, while the number of rare alleles was greater in Siberian spruce (R = 19). Among the P. obovata populations, the Cherdyn’s forestry exhibited notably high genetic diversity, and for L. sibirica, the Gainy’s forestry stood out in this regard. Moreover, the genetic subdivision of the six P. obovata populations (GST = 0.331) was higher than that of the six L. sibirica populations (GST = 0.177). To ensure optimal seed selection considering the genetic originality coefficient (GOC) and population differentiation, we recommend utilizing the P. obovata population from Gainy’s forestry with a GOC of 0.554 and the L. sibirica population from Cherdyn’s forestry with a GOC of 0.372. These populations harbor typical alleles characteristic of the research region, making them ideal candidates for seed selection. Furthermore, the specific alleles identified can serve as valuable markers for determining the geographic origin of P. obovata and L. sibirica wood, aiding in efforts to trace the sources of these species in forestry and trade practices.

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Editorial: Innovative applications of sequencing technologies in plant science

Cited by 3 publications

References 8 publications

The power of retrotransposons in high-throughput genotyping and sequencing

The power of retrotransposons in high-throughput genotyping and sequencing

Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences

Genetic Uniqueness and Genetic Structure of Populations of Picea obovata Ledeb. and Larix sibirica Ledeb. in the Northern and Middle Urals

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