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ML tree using 14 flax cultivars. The ML tree was built using a general time reversible model for binary data and 1000 bootstrap replicates (bootstrap support is shown for each branch). The colored groupings reflect different flax types: orange (fiber spring -FS), purple (fiber winter - FW), green (oil spring -OS), blue (oil winter -OW). Two biological replicates were used per cultivar with the exception of Bethune with eight replicates
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Background
Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The pol...
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Citations
... /2023 integrated elsewhere within the genome, they can greatly increase their copy number and genome size. They have been shown to alter gene expression thus leading to diversification between individuals, populations and species (Haas et al., 2021;Galindo-González et al., 2016;Kalendar et al., 2000). It is thus possible that Z. latifolia applies the same mechanisms in order to adapt to the colder north and hot south zones and that the overall genome divergence could partly be due to LTR retrotransposons response to climatic conditions. ...
The rapid climate change poses considerable threat to biodiversity by constantly alter-ing species distribution, phenotypic variation and allele frequencies. Understanding the interplay between the climate and species phenotypic and genetic variation is thus cru-cial to inform conservation strategies. In this study, we investigated local adaptation of a widespread aquatic species in China, Zizania latifolia .
We performed restriction-site associated DNA sequencing (RAD-seq) for 66 wild samples composed of 10 populations, two populations in each of the five major eco-geographical regions of China and 6 cultivated samples derived from three culti-vars found in central China. We assessed genetic diversity and structure, genetic-envi-ronmental association, and genome-wide association studies for the 60 wild samples.
Low levels of genetic variability were found in the Z. latifolia populations rang-ing from H E = 0.08 to H E = 1.52. Population structure showed that samples belonged to two major groups, north and south clades, split along a temperature boundary. It was estimated that the two groups diverged during the 8.2kiloyear event and later experi-enced severe genetic bottlenecks with advancement of agriculture and increase in hu-man population some 2k years later.
Landscape analysis using SNP and trait data showed that environment was more important in shaping the genetic structure than geography, but the combined effect of environment and geography explained >90% of both genetic and morphological varia-tion. Several loci were found to be correlated with environmental variables as well as morphological traits, most of which were annotated as retrotransposons. Considering the abundance of transposable elements in the Z. latifolia genome, differentiation and local adaptation was inferred to be partly driven by temperature-induced transposable elements activity.
... Ty1-copia retrotransposons are the most abundant class of transposon and have the main domains (GAG), protease (PR), integrase (INT), reverse transcriptase (RT), and ribonuclease H (RNase HI) which were all found in the insertion using NCBI conserved domains (Galindo-González et al. 2016). The sequence is also flanked by LTRs as seen in Supplementary File 2 (GenBank ID: MT633125). ...
Key message
A previously identified soybean maturity locus, E6, is discovered to be J, with the long juvenile allele in Paranagoiana now deemed j−x.
Abstract
Soybean grown at latitudes of ~20° or lower can produce lower grain yields due to the short days. This limitation can be overcome by using the long juvenile trait (LJ) which delays flowering under short day conditions. Two LJ loci have been mapped to the same location on Gm04, J and E6. The objective of this research was to investigate the e6 allele in ‘Paranagoiana’ and determine if E6 and J are the same locus or linked loci. KASP markers showed that e6 lines did not have the j−1 allele of LJ PI 159925. A population fixed for E1 but segregating for E6, with e6 introgressed from Paranagoiana, showed single gene control for flowering and maturity under short days. Sequencing Glyma.04G050200, the J gene, with long amplification Taq found that the e6 line ‘Paranagoiana’ contains a Ty1-copia retrotransposon of ~10,000 bp, inserted within exon 4. PCR amplification of the cDNA of Glyma.04G050200 also showed differences between the mRNA sequences (presence of insertion in j−x). Hence, we conclude that the loci E6 and J are one locus and deem this new variation found in Paranagoiana as j−x.
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Transposable elements (TEs) are common mobile genetic elements comprising several classes and making up the majority of eukaryotic genomes. The movement and accumulation of TEs has been a major force shaping the genes and genomes of most organisms. Most eukaryotic genomes are dominated by retrotransposons and minimal DNA transposon accumulation. The 'copy and paste' lifecycle of replicative transposition produces new genome insertions without excising the original element. Horizontal TE transfer among lineages is rare. TEs represent a reservoir of potential genomic instability and RNA-level toxicity. Many TEs appear static and nonfunctional, but some are capable of replicating and mobilising to new positions, and somatic transposition events have been observed. The overall structure of retrotransposons and the domains responsible for the phases of their replication are highly conserved in all eukaryotes. TEs are important drivers of species diversity and exhibit great variety in their structure, size and transposition mechanisms, making them important putative actors in evolution. Because TEs are abundant in plant genomes, various applications have been developed to exploit polymorphisms in TE insertion patterns, including conventional or anchored PCR, and quantitative or digital PCR with primers for the 5 0 or 3 0 junction. Alternatively, the retrotransposon junction can be mapped using high-throughput next-generation sequencing and bioinformatics. With these applications, TE insertions can be rapidly, easily and accurately identified, or new TE insertions can be found. This review provides an overview of the TE-based applications developed for plant species and assesses the contributions of TEs to the analysis of plants' genetic diversity.
... Основным фактором, лимитирующим рост растений на кислых почвах, считается токсичное действие алюминия [1-3], однако механизмы устойчивости льна к действию ионов алюминия практически не изучены [4]. Геном льна к настоящему времени секвенирован [5], изучен полиморфизм видов и сортов [6][7][8][9], а также определены изменения экспрессии генов при некоторых видах стресса [10][11][12]. Ранее нами было показано, что гены, кодирующие переносчики малата, ABC-транспортеры, аквапорины и пероксидазы, участвующие в ответе различных видов растений на алюминий [2,13], вероятно, не играют ключевой роли в ответе льна на алюминий. ...
Understanding the molecular mechanisms of plant response to unfavorable conditions is necessary for the effective selection of tolerant genotypes. Earlier, using high-throughput transcriptome sequencing of flax plants after exposure to aluminum ions (Al^(3+)) and high soil acidity, we detected stress-induced alteration in the expression of several genes, including CAX3, which encodes Ca^(2+)/H^(+)-exchanger involved in calcium ion transport. Here we describe CAX3 mRNA levels in flax cultivars either tolerant (Hermes and TMP1919) or sensitive (Lira and Orshanskiy) to Al^(3+). Stress-induced increased expression of CAX3 was detected only in aluminum-tolerant flax cultivars. The product of CAX3 gene may participate in flax response to high soil acidity and high Al^(3+) concentration through Ca^(2+)-mediated intracellular regulation.
... However, the mechanisms of flax's tolerance to the influence of aluminum ions are poorly studied [4]. Today, the flax genome has been sequenced [5], the polymorphism of its species and cultivars has been analyzed [6][7][8][9], and changes in the flax gene expression have been investigated under several types of stress [10][11][12]. It was shown earlier that genes encoding malate transporters, ABC-transporters, aquaporins, and peroxidases, and that are involved in the response of different plant species to the influence of aluminum [2,13], apparently do not play a key role in the response of flax to treatment with aluminum. ...
Understanding the molecular mechanisms of plant response to unfavorable conditions is necessary for the effective selection of tolerant genotypes. Earlier, using high-throughput transcriptome sequencing of flax plants after exposure to aluminum ions (Al³⁺) and high soil acidity, we detected stress-induced alteration in the expression of several genes, including CAX3, which encodes Ca²⁺/H⁺-exchanger involved in calcium ion transport. Here we describe CAX3 mRNA levels in flax cultivars either tolerant (Hermes and TMP1919) or sensitive (Lira and Orshanskiy) to Al³⁺. Stress-induced increased expression of CAX3 was detected only in aluminum-tolerant flax cultivars. The product of CAX3 gene may participate in flax response to high soil acidity and high Al³⁺ concentration through Ca²⁺-mediated intracellular regulation.
... Keywords: Linum usitatissimum, Flax, Biotic stress, Fusarium oxysporum, High-throughput sequencing, ROS, 1,3-betaglucanase, Cell wall, Background Flax (Linum usitatissimum L.) is a widely distributed crop, which is used for fiber and oil production [1]. Genetic polymorphism of L. usitatissimum and related species is well characterized [2][3][4][5][6][7] and could be used for the breeding of improved cultivars. Although potentially highyielding flax varieties have previously been developed, biotic and abiotic stresses can markedly decrease flax production. ...
Background:
Flax (Linum usitatissimum L.) is a crop plant used for fiber and oil production. Although potentially high-yielding flax varieties have been developed, environmental stresses markedly decrease flax production. Among biotic stresses, Fusarium oxysporum f. sp. lini is recognized as one of the most devastating flax pathogens. It causes wilt disease that is one of the major limiting factors for flax production worldwide. Breeding and cultivation of flax varieties resistant to F. oxysporum is the most effective method for controlling wilt disease. Although the mechanisms of flax response to Fusarium have been actively studied, data on the plant response to infection and resistance gene candidates are currently very limited.
Results:
The transcriptomes of two resistant and two susceptible flax cultivars with respect to Fusarium wilt, as well as two resistant BC2F5 populations, which were grown under control conditions or inoculated with F. oxysporum, were sequenced using the Illumina platform. Genes showing changes in expression under F. oxysporum infection were identified in both resistant and susceptible flax genotypes. We observed the predominant overexpression of numerous genes that are involved in defense response. This was more pronounced in resistant cultivars. In susceptible cultivars, significant downregulation of genes involved in cell wall organization or biogenesis was observed in response to F. oxysporum. In the resistant genotypes, upregulation of genes related to NAD(P)H oxidase activity was detected. Upregulation of a number of genes, including that encoding beta-1,3-glucanase, was significantly greater in the cultivars and BC2F5 populations resistant to Fusarium wilt than in susceptible cultivars in response to F. oxysporum infection.
Conclusions:
Using high-throughput sequencing, we identified genes involved in the early defense response of L. usitatissimum against the fungus F. oxysporum. In response to F. oxysporum infection, we detected changes in the expression of pathogenesis-related protein-encoding genes and genes involved in ROS production or related to cell wall biogenesis. Furthermore, we identified genes that were upregulated specifically in flax genotypes resistant to Fusarium wilt. We suggest that the identified genes in resistant cultivars and BC2F5 populations showing induced expression in response to F. oxysporum infection are the most promising resistance gene candidates.
One of the biggest challenges for a more widespread utilization of plant fibers is to better understand the different molecular factors underlying the variability in fineness and mechanical properties of both elementary and scutched fibers. Accordingly, we analyzed genome-wide transcription profiling from bast fiber bearing tissues of seven different flax varieties (4 spring, 2 winter fiber varieties and 1 winter linseed) and identified 1041 differentially expressed genes between varieties, of which 97 were related to cell wall metabolism. KEGG analysis highlighted a number of different enriched pathways. Subsequent statistical analysis using Partial Least-Squares Discriminant Analysis showed that 73% of the total variance was explained by the first 3 X-variates corresponding to 56 differentially expressed genes. Calculation of Pearson correlations identified 5 genes showing a strong correlation between expression and morphometric data. Two-dimensional gel proteomic analysis on the two varieties showing the most discriminant and significant differences in morphometrics revealed 1490 protein spots of which 108 showed significant differential abundance. Mass spectrometry analysis successfully identified 46 proteins representing 32 non-redundant proteins. Statistical clusterization based on the expression level of genes corresponding to the 32 proteins showed clear discrimination into three separate clusters, reflecting the variety type (spring-/winter-fiber/oil). Four of the 32 proteins were also highly correlated with morphometric features. Examination of predicted functions for the 9 (5 + 4) identified genes highlighted lipid metabolism and senescence process. Calculation of Pearson correlation coefficients between expression data and retted fiber mechanical measurements (strength and maximum force) identified 3 significantly correlated genes. The genes were predicted to be connected to cell wall dynamics, either directly (Expansin-like protein), or indirectly (NAD(P)-binding Rossmann-fold superfamily protein). Taken together, our results have allowed the identification of molecular actors potentially associated with the determination of both in-planta fiber morphometrics, as well as ex-planta fiber mechanical properties, both of which are key parameters for elementary fiber and scutched fiber quality in flax.
Plant breeding through conventional methods with classical markers (morphological, cytological, and biochemical) has substantially contributed to crop productivity and germplasm conservation for sustenance of food security, but integration of molecular markers has potentially revolutionized plant breeding. Molecular markers, genes or DNA sequences controlling traits within chromosomal locations, when fully deployed in plant breeding including underutilized crops, will facilitate identification of novel traits that are phenotypically associated with expressed characters for high yields, early maturity, wide genetic base, resistance to abiotic and biotic stressors in under-utilized crops even at the seedling stage. Molecular markers are more sensitive, reliable, accurate, reproducible and devoid of environmental interferences unlike morphological traits. Some gel-based microsatellite/minisatellite markers and non-gel-based markers that require sequencing and high-throughput genotyping approaches are widely applicable in breeding programmes to assuage the bottlenecks in conventional agriculture and to enhance rapid selection of agronomically significant traits. Utilization of these markers has recorded tremendous breeding progress in many well-known crops but not fully in orphan crops. Parental or varietal genepools with traits of interest can be harnessed through these informative molecular markers and strategically implementing them in underutilized crops will accelerate identification and association of useful traits for breeding, germplasm conservation and food security.
Several soybean (Glycine max L.) germplasms, such as Nishiyamahitashi 98-5 (NH), have an intense seaweed-like flavor after cooking because of their high seed S-methylmethionine (SMM) content. In this study, we compared the amounts of amino acids in the phloem sap, leaves, pods, and seeds between NH and the common soybean cultivar Fukuyutaka (FY). This revealed a comparably higher SMM content alongside a higher free methionine (Met) content in NH seeds, suggesting that the SMM-hyperaccumulation phenotype of NH soybean was related to Met metabolism in seeds. To investigate the molecular mechanism behind SMM hyperaccumulation, we examined the phenotype-associated gene locus in NH plants. Analyses of the quantitative trait loci in segregated offspring of the cross between NH and the common soybean cultivar Williams82 indicated that one locus on chromosome 10 explains 71.4% of SMM hyperaccumulation. Subsequent fine-mapping revealed that a transposon insertion into the intron of a gene, Glyma.10g172700, is associated with the SMM-hyperaccumulation phenotype. The Glyma.10g172700-encoded recombinant protein showed Met-γ-lyase (MGL) activity in vitro, and the transposon-insertion mutation in NH efficiently suppressed Glyma.10g172700 expression in developing seeds. Exogenous administration of Met to sections of developing soybean seeds resulted in transient increases in Met levels, followed by continuous increases in SMM concentrations, which was likely caused by Met methyltransferase activity in the seeds. Accordingly, we propose that the SMM-hyperaccumulation phenotype is caused by suppressed MGL expression in developing soybean seeds resulting in transient accumulation of Met, which is converted into SMM to avoid the harmful effects caused by excess free Met.
Transposable element (TE) marker system was developed considering the useful properties of the transposable elements such as their large number in the animal and plant genomes, high rate of insertion polymorphism, and ease of detection. Various methods have been employed for developing a large number of TE markers in several crop plants for genomics studies. Here we describe some of these methods including the recent whole genome search. We also review the application of TE markers in molecular breeding.
