Genetics polymorphism of poplars from Moscow region based on high-throughput sequencing of ITS

Borkhert, Elena V.; Krasnov, George S.; Bolsheva, Nadezhda L.; Kezimana, Parfait; Yurkevich, Olga Yu.; Муравенко, О. В.; Kudryavtseva, Anna V.; Melnikova, N. V.

doi:10.18699/vj18.391

Cited by 5 publications

(4 citation statements)

References 21 publications

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“…To study the genetic relationship of poplar species and hybrids from sections Aigeiros and Tacamahaca , we chose an approach based on targeted deep sequencing of amplicons. This method drastically reduces the cost of analysis per sample compared to whole genome sequencing, has incomparable accuracy in the study of heterozygous genotypes and multicopy sequences, as well as less laboriousness in the analysis of large sample sets for a significant number of loci compared to Sanger sequencing ( McCormack et al., 2013 ; Cruaud et al., 2017 ; Borkhert et al., 2018 ; Melnikova et al., 2019 ; Dmitriev et al., 2020 ; Novakovskiy et al., 2020 ; Povkhova et al., 2022 ). However, effective application of targeted deep sequencing requires the selection of the most informative loci.…”

Section: Discussionmentioning

confidence: 99%

“…Compared to the previous studies on Populus species based on the analysis of multicopy and single-copy sequences of nuclear and chloroplast genomes ( Schmidt et al., 1994 ; Leskinen and Alström-Rapaport, 1999 ; Page, 2000 ; Huson and Scornavacca, 2011 ; Schroeder et al., 2012 ; Huang et al., 2014 ; Wang et al., 2014 ; Alexandrov and Karlov, 2018 ; Borkhert et al., 2018 ; Zhou et al., 2018 ; Wang et al., 2019 ), we sequenced regions of the SDR and the ARR17 gene, which is the key gene in sex determination in the genus Populus ( Muller et al., 2020 ). The SDR allowed us to reveal the origin of the examined genotypes in the male lineage and significantly complemented the results obtained in the analysis of the DNA sequences traditionally used in poplar studies.…”

Section: Discussionmentioning

confidence: 99%

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Sex-determining region complements traditionally used in phylogenetic studies nuclear and chloroplast sequences in investigation of Aigeiros Duby and Tacamahaca Spach poplars (genus Populus L., Salicaceae)

Borkhert,

Pushkova,

Nasimovich

et al. 2023

Front. Plant Sci.

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Members of the genus Populus L. play an important role in the formation of forests in the northern hemisphere and are used in urban landscaping and timber production. Populus species of closely related sections show extensive hybridization. Therefore, the systematics of the genus is rather complicated, especially for poplars of hybrid origin. We aimed to assess the efficiency of application of the sex-determining region (SDR) in addition to the nuclear and chloroplast genome loci traditionally used in phylogenetic studies of poplars to investigate relationships in sections Aigeiros Duby and Tacamahaca Spach. Targeted deep sequencing of NTS 5S rDNA, ITS, DSH 2, DSH 5, DSH 8, DSH 12, DSH 29, 6, 15, 16, X18, trnG-psbK-psbI, rps2-rpoC2, rpoC2-rpoC1, as well as SDR and ARR17 gene was performed for 379 poplars. The SDR and ARR17 gene together with traditionally used multicopy and single-copy loci of nuclear and chloroplast DNA allowed us to obtain a clustering that is most consistent with poplar systematics based on morphological data and to shed light on several controversial hypotheses about the origin of the studied taxa (for example, the inexpediency of separating P. koreana, P. maximowiczii, and P. suaveolens into different species). We present a scheme of relationships between species and hybrids of sections Aigeiros and Tacamahaca based on molecular genetic, morphological, and geographical data. The geographical proximity of species and, therefore, the possibility of hybridization between them appear to be more important than the affiliation of species to the same section. We speculate that sections Aigeiros and Tacamahaca are distinguished primarily on an ecological principle (plain and mountain poplars) rather than on a genetic basis. Joint analysis of sequencing data for the SDR and chloroplast genome loci allowed us to determine the ancestors of P. × petrovskoe – P. laurifolia (female tree) × P. × canadensis (male tree), and P. × rasumovskoe – P. nigra (female tree) × P. suaveolens (male tree). Thus, the efficiency of using the SDR for the study of poplars of sections Aigeiros and Tacamahaca and the prospects of its use for the investigation of species of the genus Populus were shown.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Sex-determining region complements traditionally used in phylogenetic studies nuclear and chloroplast sequences in investigation of Aigeiros Duby and Tacamahaca Spach poplars (genus Populus L., Salicaceae)

Borkhert,

Pushkova,

Nasimovich

et al. 2023

Front. Plant Sci.

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“…This approach significantly reduces the cost of sequencing per genotype compared to the whole genome analysis and allows the sequencing of dozens and hundreds of genome regions in hundreds and thousands of samples. It also overcomes the difficulties of Sanger sequencing associated with polyploidy of plant genomes and a high degree of duplication of their genes [ 18 , 97 , 98 , 99 , 100 , 101 ]. Therefore, the third approach, developed by us, for the identification of the three low-LIN mutations in the FAD3A and FAD3B genes in flax genotypes was based on targeted deep sequencing.…”

Section: Discussionmentioning

confidence: 99%

Development and Complex Application of Methods for the Identification of Mutations in the FAD3A and FAD3B Genes Resulting in the Reduced Content of Linolenic Acid in Flax Oil

Povkhova

Pushkova

Rozhmina

et al. 2022

Plants

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Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. Inactivating mutations in the FAD3A and FAD3B genes lead to a decrease in the LIN content and an increase in the LIO content. For the identification of the three most common low-LIN mutations in flax varieties (G-to-A in exon 1 of FAD3A substituting tryptophan with a stop codon, C-to-T in exon 5 of FAD3A leading to arginine to a stop codon substitution, and C-to-T in exon 2 of FAD3B resulting in histidine to tyrosine substitution), three approaches were proposed: (1) targeted deep sequencing, (2) high resolution melting (HRM) analysis, (3) cleaved amplified polymorphic sequences (CAPS) markers. They were tested on more than a thousand flax samples of various types and showed promising results. The proposed approaches can be used in marker-assisted selection to choose parent pairs for crosses, separate heterogeneous varieties into biotypes, and select genotypes with desired homozygous alleles of the FAD3A and FAD3B genes at the early stages of breeding for the effective development of varieties with a particular LIN and LIO content, as well as in basic studies of the molecular mechanisms of fatty acid synthesis in flax seeds to select genotypes adequate to the tasks.

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“…Poplar (dicotyledon, Salicaceae, Populus) is a perennial deciduous tree species widely cultivated in China and an important shelterbelt, timber stand, and city tree species. It has been used to improve ecological structures and provides photosynthates that purify the air [1]. Due to its rapid growth and high productivity, poplar has become a model for studying woody plants [2].…”

Section: Introductionmentioning

confidence: 99%

Identification of Differentially Expressed lncRNAs in Response to Blue Light and Expression Pattern Analysis of Populus tomentosa Hybrid Poplar 741

Li,

Zhang,

Lan

et al. 2023

Plants

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Poplar is an important shelterbelt, timber stand, and city tree species that has been the focus of forestry research. The regulatory role of the long non-coding RNA molecule (lncRNA; length > 200 nt) has been a research hotspot in plants. In this study, seedlings of 741 poplar were irradiated with LED blue and white light, and the Illumina HiSeq 2000 sequencing platform was used to identify lncRNAs. |logFC| > 1 and p < 0.05 were considered to indicate differentially expressed lncRNAs, and nine differentially expressed lncRNAs were screened, the target genes of which were predicted, and three functionally annotated target genes were obtained. The differentially expressed lncRNAs were identified as miRNA targets. Six lncRNAs were determined to be target sites for twelve mRNAs in six miRNA families. LncRNAs and their target genes, including lncRNA MSTRG.20413.1-ptc-miR396e-5p-GRF9, were verified using quantitative real-time polymerase chain reaction analysis, and the expression patterns were analyzed. The analysis showed that the ptc-miR396e-5p expression was downregulated, while lncRNA MSTRG.20413.1 and GRF9 expression was upregulated, after blue light exposure. These results indicate that lncRNAs interact with miRNAs to regulate gene expression and affect plant growth and development.

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Genetics polymorphism of poplars from Moscow region based on high-throughput sequencing of ITS

Cited by 5 publications

References 21 publications

Sex-determining region complements traditionally used in phylogenetic studies nuclear and chloroplast sequences in investigation of Aigeiros Duby and Tacamahaca Spach poplars (genus Populus L., Salicaceae)

Sex-determining region complements traditionally used in phylogenetic studies nuclear and chloroplast sequences in investigation of Aigeiros Duby and Tacamahaca Spach poplars (genus Populus L., Salicaceae)

Development and Complex Application of Methods for the Identification of Mutations in the FAD3A and FAD3B Genes Resulting in the Reduced Content of Linolenic Acid in Flax Oil

Identification of Differentially Expressed lncRNAs in Response to Blue Light and Expression Pattern Analysis of Populus tomentosa Hybrid Poplar 741

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