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

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

Development and deployment of high-throughput retrotransposon-based markers reveal genetic diversity and population structure of Asian bamboo

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. Inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput method to study the genetic diversity of plant species. Till date, there are no markers based on Transposable Elements (TEs) for the bamboo genome and no reports on bamboo genetic diversity using the IRAP method. Phyllostachys is an Asian bamboo, the largest group in the bamboo subfamily, Bambusoideae, and it is of great economic value due to its fast growth. The structure of LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, were analysed in the bamboo genome using LTRharvest and LTRdigest software. A total of 98,850 LTR retrotransposons with both ends of intact LTR sequences were identified, grouped into 64,281 clusters/scaffolds, using CD-HIT software. Among the total of 64,281 clusters, 13 clusters had more than 30 copy numbers of LTR sequences and at least one copy had all intact protein domains such as gag protein and polyprotein. Based on the high copy numbers of conserved LTR sequences, a total of 16 IRAP primers were developed. All these IRAP primers were used to study the genetic diversity and population structure of the Asian bamboo. AMOVA analysis was done for 58 Asian bamboo species collected from nine different provinces of China, from Italy and America. In the bamboo species, these IRAP primers produced a total of 3340 amplicons with an average of 98% polymorphism. The 58 Asian bamboo species were grouped into two major clusters and four sub-clusters, based on UPGMA analysis. UPGMA cluster analysis was corroborated by statistical analyses of genetic similarity coefficients. Structure analysis showed that the bamboo species could be divided into four subpopulations (K = 4): SP1, SP2, SP3 and SP4. All SPs had an admixture of alleles. AMOVA analysis showed that higher genetic variations occurred within populations (75%) rather than among populations (25%). The study highlights the usability of IRAP in Asian bamboo to determine inter-species variability using retrotransposon markers.Peer reviewe

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

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

Microstructure evolution and mechanical property of a new multi-component β titanium alloy with ultrahigh strength above 1350 MPa

The microstructure evolution and precipitation behavior of a multi-component β titanium alloy (namely TB17) were investigated through various characterization methods. The results show that with the increase of the solution temperature, the coarse lamellar α phase (αl) and fine secondary α phase (αs) existed in the original as-forged TB17 alloy decrease. At the same time, the molybdenum equivalent value of the β matrix also decreases gradually, leading to the increase of αs phase during the following aging process. For the aged samples, the micro-strain accumulated in the β matrix resulted from phase transformation strain exhibits an increasing trend as the solution treatment temperature rises, highly depending on the volume fraction of αs phase. When the alloy is subjected to a solution treatment at temperature of 805 °C plus aging, it can achieve a good combination of high strength of 1375 MPa and considerable ductility due to mixed microstructure of suitable amount of micro-scale αl and nano-scale αs precipitates. The strength is further improved by increasing the solution temperature (from α+β to β field), which is attributed to higher volume fraction of fine αs precipitates formed during aging that can effectively hinder dislocation slip and induce micro-strain. Morphological features of the fracture surfaces are also discussed against the different microstructural morphologies, revealing the fracture mechanism of TB17 alloy under different heat treatment conditions. The current work could contribute to a better understanding of phase transformation behavior and strengthening mechanism in TB17 alloy

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

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

Research on the Algorithm Model for Measuring Ocean Waves Based on Satellite GPS Signals in China

In recent years, the GPS wave buoy has been developed for in situ wave monitoring based on satellite GPS signals. Many research works have been completed on the GPS-based wave measurement technology and great progress has been achieved. The basic principle of the GPS wave buoy is to calculate the movement velocity of the buoy using the Doppler frequency shift of satellite GPS signals, and then to calculate the wave parameters from the movement velocity according to ocean wave theory. The shortage of the GPS wave buoy is the occasional occurrence of some unusual values in the movement velocity. This is mainly due to the fact that the GPS antenna is occasionally covered by sea water and cannot normally receive high-quality satellite GPS signals. The traditional solution is to remove these unusual movement velocity values from the records, which requires furthering extend the acquisition time of satellite GPS signals to ensure there is a large enough quantity of effective movement velocity values. Based on the traditional GPS wave measurement technology, this paper presents the algorithmic flow and proposes two improvement measures. On the one hand, the neural network algorithm is used to correct the unusual movement velocity data so that extending the acquisition time of satellite GPS signals is not necessary and battery power is saved. On the other hand, the Gaussian low-pass filter is used to correct the raw directional wave spectrum, which can further eliminate the influence of noise spectrum energy and improve the measurement accuracy. The on-site sea test of the SBF7-1A GPS wave buoy, developed by the National Ocean Technology Center in China, and the gravity-acceleration-type DWR-MKIII Waverider buoy are highlighted in this article. The wave data acquired by the two buoys are analyzed and processed. It can be seen from the processed results that the ocean wave parameters from the two kinds of wave buoys, such as wave height, wave period, wave direction, wave frequency spectrum, and directional wave spectrum, are in good consistency, indicating that the SBF7-1A GPS wave buoy is comparable to the traditional gravity-acceleration-type wave buoy in terms of its accuracy. Therefore, the feasibility and validity of the two improvement measures proposed in this paper are confirmed

Investigation of Dynamic Mechanical Behavior and Damage Characteristics in TC32 Alloy

The dynamic shearing experiment was been done by using split Hopkinson pressure bar(SHPB) technique in TC32 alloy with lamellar, bimodal and basket microstructures. The damage Characteristics of TC32 alloy was investigated by using optical microscope(OP) and scanning electron microscopy(SEM). The results show that the critical fracture velocity is 2400 s-1, 2700 s-1, and 2600 s-1 for lamellar, bimodal, and basket microstructures respectively. The bimodal microstructure exhibit the best Dynamic mechanical behavior compared with the other two microstructures. Adiabatic shear bands(ASBs) and microvoids initiation, growth, and coalescence to damage in adiabatic shear bands(ASBs) were observed in all of three microstructures. Also, microvoids initiation and growth are prior to the interface between ASBs and matrix. Investigation indicated that plastic flow characteristic is not obvious at the interface between ASBs and matrix, which observed long crack in lamellar microstructure. In bimodal microstructure, fibrous a adiabatic shear bands(ASBs) and surrounding region are shown. Because of strong shear deformation, the plastic flow characteristic appears clearly, and primary α phase was elongated. Microvoids initiation is also prior to the α/β phase boundaries. The damage characteristics of basket microstructure are similar to bimodal microstructure. But unlike lamellar and basket microstructures, the microvoids are initiatied when the acicular primary α phase arranged in order is perpendicular to the adiabatic shear bands(ASBs) in lamellar microstructure. ASBs is mostly consisted of equiaxed grains, and the deformation mechanism still wasn't defined

Research and Application of New Type of High Performance Titanium Alloy

With the continuous extension of the application quantity and range for titanium alloy in the fields of national aviation, space, weaponry, marine and chemical industry, etc., even more critical requirements to the comprehensive mechanical properties, low cost and process technological properties of titanium alloy have been raised. Through the alloying based on the microstructure parameters design, and the comprehensive strengthening and toughening technologies of fine grain strengthening, phase transformation and process control of high toughening, the new type of high performance titanium alloy which has good comprehensive properties of high strength and toughness, anti-fatigue, failure resistance and anti-impact has been researched and manufactured. The new titanium alloy has extended the application quantity and application level in the high end field, realized the industrial upgrading and reforming, and met the application requirements of next generation equipment

Distributionally Robust Unit Commitment with N-<i>k</i> Security Criterion and Operational Flexibility of CSP

In order to reduce the conservatism of the robust optimization method and the complexity of the stochastic optimization method and to enhance the ability of power systems to deal with occasional line fault disturbance, this paper proposes a distributionally robust unit commitment (DRUC) model with concentrating solar power (CSP) operational flexibility and N-k safety criterion under distributed uncertainty. According to the limited historical sample data, under the condition of satisfying a certain confidence level, based on the imprecise Dirichlet model (IDM), an ambiguity set is constructed to describe the uncertainty of transmission line fault probability. Through the identification of the worst probability distribution in the ambiguity set, the adaptive robust optimal scheduling problem is transformed into a two-stage robust optimization decision model under the condition of deterministic probability distribution. The CSP flexibility column and constraint generation (C&CG) algorithm is used to process the model and the main problem and subproblem are solved by using the Big-M method, linearization technique, and duality principle. Then, a mixed integer linear programming problem (MILP) model is obtained, which effectively reduces the difficulty of solving the model. Finally, case studies on the IEEE 14 bus system and the IEEE 118 bus system demonstrate the efficiency of the proposed method, such as enhancing the ability of power systems to cope with occasional line fault disturbances and reducing the conservatism of the robust optimization method