Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome

Neolamarckia cadamba (or locally known as kelampayan) is an important fast growing plantation tree species that confers various advantages for timber industry as a strategy for reducing the logging pressure on natural forests for wood production to an acceptable level. Hence, attempts were made to develop a set of EST-SSR markers for kelampayan trees based on the EST sequences of kelampayan (NcdbEST) and further assessed the polymorphisms and transferability of the markers to other species. In this study, 155 (2.34%) out of 6,622 EST sequences which contain 232 SSRs were mined from NcdbEST. Of these, 97 ESTs were assigned with putative functions and gene ontology terms. Eighteen EST-SSR markers were developed according to the criteria, and further characterized and validated by using 50 individuals of kelampayan from two selected mother trees. The markers exhibited a considerable high level of polymorphism in kelampayan trees with an average of 4.17 and 4.11 alleles per locus, and PIC values of 0.465 and 0.537, respectively for mother trees T1 and T2. Parentage assignment analysis suggests a high probability for kelampayan trees to be predominantly outcrossed. The transferability rate was ranging from 16.7-94.4% among the five cross-genera species of kelampayan. The present study is the first report of the development of EST-SSR markers in kelampayan. These markers will be valuable genomic resources that could pave the way for exploiting the genotype data for comparative genome mapping, association genetics, population genetics studies and molecular breeding of kelampayan and other indigenous tropical tree species in future

Resequencing And Nucleotide Variation Of Sucrose Synthase (Nmsusy1) Gene In A Tropical Timber Tree Neolamarckia Macrophylla

Sucrose synthase (SuSy) is a key enzyme that catalyses the reversible synthesis and degradation of sucrose. It provides greater impact in regulating the photosynthetic processes and environmental stresses in plants. Thus, the nucleotide variation of partial NmSusy1 genomic DNAs (750 bp) generated through PCR amplification was examined in this study, and this followed by resequencing from 15 selected Neolamarckia macrophylla clones. The consensus sequences were aligned to detect the presence of single nucleotide polymorphisms (SNPs). In total, five SNPs were detected at nucleotide 1, 2, 34, 35 and 397. Of these, four SNPs were located at the predicted coding region while one SNP was located at the predicted non-coding region. Interestingly, one single base pair InDel polymorphism was also detected at nucleotide 17. On average, one SNP at every 150 bp was detected based on the 15 NmSusy1 sequences. There was one non-synonymous mutation detected, whereby amino acid glutamic acid (E) was replaced by arginine (R) in one of the 15 samples tested. This non-synonymous SNP might change the structural, functional or biochemical properties of the enzyme being produced and therefore possibly lead to changes in phenotypic characteristic of the trees. Overall, this study has demonstrated that resequencing is an effective technique for classifying molecular diversity or nucleotide variation in the Susy gene of N. macrophylla. Those SNPs, once validated, could potentially be used as a tool in marker-assisted selection (MAS) that enables more precise and accurate in the selection and prediction of yield or performance at the early developmental stages, such as at the seedling stage

Genetic diversity of Neolamarckia cadamba using dominant DNA markers based on inter-simple sequence repeats (ISSRs) in Sarawak

Neolamarckia cadamba or commonly known as kelampayan has been selected as one of the important plantation tree species in Malaysia. Thus, the molecular characterization of this indigenous tropical tree species is needed to maintain its high quality. Inter simple sequence repeats (ISSR) markers were used in this study to determine the genetic diversity and relatedness of N. cadamba in two planted forests and six natural forests in Sarawak. Three ISSR primers had generated atotal of 239 loci, of which 32.6% - 59.4% of the loci were polymorphic among236N. cadamba treesin eight populations. The mean Shannon’s diversity index (I)ranged from 0.1399 to 0.2354. The coefficient of population differentiation was low for planted forests (Gst = 0.0871) and natural forests (Gst = 0.2013`). Both UPGMA dendrogram and NJ-tree generated by ISSR markers had divided natural forests and planted forests into two distinct clusters. Natural forests were grouped in one cluster while planted forests were grouped in another cluster. This study shows that N. cadamba trees are closely related within its own population and its designated forest type. In future, several specific loci can be sequenced and developed into SCAR (sequence characterized amplification region) markers for tree improvement and conservation programme of N. cadamba

Search for gravitational waves from Scorpius X-1 in the second Advanced LIGO observing run with an improved hidden Markov model

We present results from a semicoherent search for continuous gravitational waves from the low-mass x-ray binary Scorpius X-1, using a hidden Markov model (HMM) to track spin wandering. This search improves on previous HMM-based searches of LIGO data by using an improved frequency domain matched filter, the J-statistic, and by analyzing data from Advanced LIGO's second observing run. In the frequency range searched, from 60 to 650 Hz, we find no evidence of gravitational radiation. At 194.6 Hz, the most sensitive search frequency, we report an upper limit on gravitational wave strain (at 95% confidence) of h095%=3.47×10-25 when marginalizing over source inclination angle. This is the most sensitive search for Scorpius X-1, to date, that is specifically designed to be robust in the presence of spin wandering. © 2019 American Physical Society

Search for Tensor, Vector, and Scalar Polarizations in the Stochastic Gravitational-Wave Background

The detection of gravitational waves with Advanced LIGO and Advanced Virgo has enabled novel tests of general relativity, including direct study of the polarization of gravitational waves. While general relativity allows for only two tensor gravitational-wave polarizations, general metric theories can additionally predict two vector and two scalar polarizations. The polarization of gravitational waves is encoded in the spectral shape of the stochastic gravitational-wave background, formed by the superposition of cosmological and individually unresolved astrophysical sources. Using data recorded by Advanced LIGO during its first observing run, we search for a stochastic background of generically polarized gravitational waves. We find no evidence for a background of any polarization, and place the first direct bounds on the contributions of vector and scalar polarizations to the stochastic background. Under log-uniform priors for the energy in each polarization, we limit the energy densities of tensor, vector, and scalar modes at 95% credibility to Ω0T<5.58×10-8, Ω0V<6.35×10-8, and Ω0S<1.08×10-7 at a reference frequency f0=25 Hz. © 2018 American Physical Society

Search for Gravitational Waves Associated with Gamma-Ray Bursts Detected by Fermi and Swift during the LIGO-Virgo Run O3b

We search for gravitational-wave signals associated with gamma-ray bursts (GRBs) detected by the Fermi and Swift satellites during the second half of the third observing run of Advanced LIGO and Advanced Virgo (2019 November 1 15:00 UTC-2020 March 27 17:00 UTC). We conduct two independent searches: A generic gravitational-wave transients search to analyze 86 GRBs and an analysis to target binary mergers with at least one neutron star as short GRB progenitors for 17 events. We find no significant evidence for gravitational-wave signals associated with any of these GRBs. A weighted binomial test of the combined results finds no evidence for subthreshold gravitational-wave signals associated with this GRB ensemble either. We use several source types and signal morphologies during the searches, resulting in lower bounds on the estimated distance to each GRB. Finally, we constrain the population of low-luminosity short GRBs using results from the first to the third observing runs of Advanced LIGO and Advanced Virgo. The resulting population is in accordance with the local binary neutron star merger rate. © 2022. The Author(s). Published by the American Astronomical Society

Narrowband Searches for Continuous and Long-duration Transient Gravitational Waves from Known Pulsars in the LIGO-Virgo Third Observing Run

Isolated neutron stars that are asymmetric with respect to their spin axis are possible sources of detectable continuous gravitational waves. This paper presents a fully coherent search for such signals from eighteen pulsars in data from LIGO and Virgo's third observing run (O3). For known pulsars, efficient and sensitive matched-filter searches can be carried out if one assumes the gravitational radiation is phase-locked to the electromagnetic emission. In the search presented here, we relax this assumption and allow both the frequency and the time derivative of the frequency of the gravitational waves to vary in a small range around those inferred from electromagnetic observations. We find no evidence for continuous gravitational waves, and set upper limits on the strain amplitude for each target. These limits are more constraining for seven of the targets than the spin-down limit defined by ascribing all rotational energy loss to gravitational radiation. In an additional search, we look in O3 data for long-duration (hours-months) transient gravitational waves in the aftermath of pulsar glitches for six targets with a total of nine glitches. We report two marginal outliers from this search, but find no clear evidence for such emission either. The resulting duration-dependent strain upper limits do not surpass indirect energy constraints for any of these targets. © 2022. The Author(s). Published by the American Astronomical Society

Erratum: "A Gravitational-wave Measurement of the Hubble Constant Following the Second Observing Run of Advanced LIGO and Virgo" (2021, ApJ, 909, 218)

[no abstract available