Estimation of the Present Status of the Species Based on the Theoretical Bounds of Environmental Noise Intensity: An Illustration Through a Big Abundance Data and Simulation

Sibly et al. (2005) described that most species have a fundamental characteristic to follow the theta-logistic growth trait with the convex downward trend. The fundamental yardstick of this research work builds under the deterministic setup, whereas the involvement of the external noise in any growth system is inevitable. But, the involvement of external affairs in any species growth can't be well judged only through its density dependence; it requires a further assessment. So, we frame the theta-logistic model with the stochastic analog in two directions, i.e., the discrete and continuous setup. The analysis of the discrete stochastic model is manifested by the bifurcation analysis, which shows that the attainment of the chaotic regime enhances with the increase in noise intensity level. Although the role of chaos in species extinction is debatable, a literature survey suggests that chaos with stochasticity accelerates the extinction of species. Similarly, in the case of the continuous version, we performed a theoretical study on the stochastic theta-logistic model to provide a critical value of the noise intensity parameter. This threshold magnitude act as the sustainability criteria of any species environmental tolerability. In this connection, we use the data of four major taxonomic groups, i.e., Bird, Insect, Mammal, and Fish, from the GPDD database and classify the species based on environmental sensitivity. The high sensitive species have a low tolerance level, associated with the small magnitude of environmental noise intensity parameter. Moreover, the simulation prediction model on these four taxonomic classes also shows that the overall extinction probability of the Bird is almost negligible for the current time window.

A novel locus (Bnsdt2) in a TFL1 homologue sustaining determinate growth in Brassica napus

Background The determinate growth habits is beneficial for plant architecture modification and the development of crops cultivars suited to mechanized production systems. Which play an important role in the genetic improvement of crops. In Brassica napus, a determinate inflorescence strain (4769) has been discovered among doubled haploid (DH) lines obtained from a spring B. napus × winter B. napus cross, but there are few reports on it. We fine mapped a determinate inflorescence locus, and evaluated the effect of the determinate growth habit on agronomic traits. Results In this study, we assessed the effect of the determinate growth habit on agronomic traits. The results showed that determinacy is beneficial for reducing plant height and flowering time, advancing maturity, enhancing lodging resistance, increasing plant branches and maintaining productivity. Genetic analysis in the determinate (4769) and indeterminate (2982) genotypes revealed that two independently inherited recessive genes (Bnsdt1, Bnsdt2) are responsible for this determinate growth trait. Bnsdt2 was subsequently mapped in BC2 and BC3 populations derived from the combination 2982 × 4769. Bnsdt2 could be delimited to an approximately 122.9 kb region between 68,586.2 kb and 68,709.1 kb on C09. BLAST analysis of these candidate intervals showed that chrC09g006434 (BnaC09.TFL1) is homologous to TFL1 of A. thaliana. Sequence analysis of two alleles identified two non-synonymous SNPs (T136C, G141C) in the first exon of BnaC09.TFL1, resulting in two amino acid substitutions (Phe46Leu, Leu47Phe). Subsequently, qRT-PCR revealed that BnaC09.TFL1 expression in shoot apexes was significantly higher in NIL-4769 than in 4769, suggesting its essential role in sustaining the indeterminate growth habit. Conclusions In this study, the novel locus Bnsdt2, a recessive genes for determinate inflorescence in B. napus, was fine-mapped to a 68,586.2 kb - 68,709.1 kb interval on C09. The annotated genes chrC09g006434 (BnaC09.TFL1) that may be responsible for inflorescence traits were found.

Effectiveness of K2siO3 on growth and physio-biochemical changes of banana seedlings grown under tropical climate as influenced by application frequency

Slow growth rate of tissue-cultured banana seedling’s performance and high post-transplanting mortality rate are commonly due to low rate mineral content in the soil, climate change and soil-borne disease. This study aimed to evaluate the effects of potassium silicate (K2SiO3) on growth, physio-biochemical changes on Berangan banana seedlings grown under tropical climate conditions. The experiment was conducted under a rain shelter and all treatments were arranged in a randomized complete block (RCBD) design. The plants were soil drenched with K2SiO3 at constant 0.0901 M by 25 mL/plant after two weeks of transplanting with different frequencies application: 0-day interval (DI) served as control, 7 DI (12×), 15 DI (6×) and 30 DI (3×) throughout three months experimental period. Results showed that K2SiO3 (13% SiO2, 20% K2O) applied on healthy banana seedlings at 15 days interval significantly improved morphological growth trait (plant height, pseudo-stem diameter size, total leaf area, root length, and dry matter biomass) and physiological traits characters, but reduced proline and MDA content in plant tissues of banana. Hence, the results confirmed that each banana seedlings that received K2SiO3 at optimum frequency rate (15DI) had successfully enhanced the growth performance with better quality of Berangan banana seedlings at commercial-scale production.

Protective Factors Associated With Post-traumatic Outcomes in Individuals With Experiences of Psychosis

Trauma and trauma-specific mental health difficulties (e.g., post-traumatic stress disorder) are highly prevalent in people with psychosis. However, not everyone develops post-traumatic symptoms, and some people even experience post-traumatic growth (PTG) following trauma. It is important to identify which protective factors are associated with less severe trauma symptoms and/or positive outcomes to inform the development and implementation of interventions fostering these variables. Eighty-five patients with experiences of psychosis took part in a cross-sectional study. They were administered questionnaires measuring exposure to traumatic events, symptoms of PTSD and complex PTSD and potential protective factors assumed to be associated with lower vulnerability for post-traumatic symptoms and higher post-traumatic growth (trait resilience, secure attachment, social support, adaptive coping, optimism, general self-efficacy). Multiple hierarchical regression showed that some of these protective factors, in particular optimism, were associated with lower post-traumatic symptoms, explaining 21% of the variance in complex PTSD symptoms and 16% of the variance in PTSD symptoms. However, the hypothesized protective factors, in particular resilience and adaptive coping, explained a considerably larger proportion of variance in PTG (44%). Our results suggest that whilst these variables provide only moderate protection from the vulnerability to experience post-traumatic stress, they may play an important role in allowing people to find meaning despite multiple traumas and subsequently lead more fulfilling lives. Therapies targeting the emotional and psychological consequences of trauma in people with psychosis might benefit from the integration of intervention strategies to enhance these additional psychological protective factors, which in turn may lead to positive treatment outcomes beyond the mere reduction of post-traumatic stress symptoms.

Polymorphism of Insulin-induced gene 1 (INSIG1) of three local beef cattle in Indonesia

Insulin-induced gene 1 (INSIG1) encoded protein that blocked of proteolysis activity from protein sterol regulatory element binding proteins (SREBP). The role gene plays of cholesterol, fatty acid, and glucose metabolism. Indonesia has many several beef cattle which has good quality of growth trait. The aim of this study was to identify polymorphism of INSIG1 gene (SNP 4366 (A>G) and 4534 (T>C)) of three local beef cattle in Indonesia (Bali, Pasundan and Ongole Decendent). One hundred and twenty seven samples were used in this study consisting of Bali cattle (46) from Pulukan Bali Island, Pasundan (36) from UPTD BPPT Beef cattle Ciamis West Java and Ongole Grade (OD) (45). DNA was extracted from whole blood using High Salt method then genotyping used PCR-RFLP method with RsaI and TaqI enzymes. Parameters in this study were genotype and allele frequencies, heterozigosity observed (Ho), expected (He), Hardy-Weinberg Equilibrium (HWE) and Polymorphism Information Content (PIC). Result showed that a 428 bp of DNA fragment was successfully amplified and digested. Three variant of genotypes with two alleles were identified. For SNP 4366 (A>G) were AA, AG and GG with dominant of G allele while SNP 4534 (T>C) were CC, CT and TT with dominant C allele. Both of SNPs in each of breed populations was in Hardy-Weinberg Equilibrium and polymorphic. Additionally, PIC value reached moderate. In conclusion, polymorphism was found in beef cattle and it could be early study for genetic diversity

Detection of GHR|AluI gene polymorphism and its association with body weight of Madura cattle in Indonesian Beef Cattle Research Station

Madura cattle is a one of the native cattle that are genetically tolerant of tropical climates. Madura cattle are one of the beef cattle breeds in Indonesia. Madura cattle can be a superior breed, but improving growth trait in Madura cattle needs to be conducted. The early step that was needed was for detecting the genes which were involved in growth traits. The purpose of this research was for detecting GHR gene polymorphisms and its association with body weight of Madura cattle population in Indonesian Beef Cattle Research Station. This study used 110 DNA samples of Madura cattle that was collected from the experimental barn at Indonesian Beef Cattle Research Station. DNA samples were extracted by DNA extraction kit. Genotype of GHR gene was detected by PCR-RFLP method using AluI restriction enzymes. In this study, association genotype and body weight was analysed by univariate GLM method. The birth weight, weaning weight, yearling weight and 18 months weight of Madura cattle were 16.8±0.3 kg; 82.4±2.3 kg; 124.6±3.7 kg and 166.7±5.0 kg, respectively. The GHR genes of Madura cattle had 3 genotypes AA, AG and GG and genotype frequencies of GHR gene were 0.273 (AA), 0.373 (AG), 0.355 (GG), respectively. Whereas the allele frequencies of A was 0.459 and the allele frequencies of G was 0.541. Based on Chi-square (X2) analysis showed that the population sample was not disequilibrium. The result of association analysis was significant (P <0.05) on weaning weight, yearling weight and 18 month weight. It was concluded that the GHR gene has potential as a genetic marker for growth traits and can be used as MAS in Madura cattle in Indonesian Beef Cattle Research Station.

Betaine supplementation to adequate nutrient diet does not affect the growth performance of quails divergently selected based on bodyweight

This study aimed to determine the effect of body weight clustering and betaine supplementation to adequate nutrient diet on the growth performance of quails. Nine hundred seven-day-old quails (Coturnix coturnix japonica) were allotted to a 3×2 factorial completely randomized design. Three bodyweight clusters included Random (21.1±1.2 g), Low (17.9±0.4 g), and High (22.4±0.4 g). Each bodyweight cluster was fed a diet without (0%) and with betaine supplementation (0.14%), resulting in six combination treatments. Each treatment consisted of five replicates of 30 quails. The basal diet was formulated with sufficient protein (22%) and metabolizable energy (2800 kcal/kg). The observed variables included feed intake, body weight, feed conversion, and protein and energy efficiency ratio. The results revealed that there was no interaction between body weight and betaine supplementation on all variables. The High body weight group consumed more feed and produced a higher body weight on 42 days of age than other treatments (p<0.05). However, betaine supplementation did not affect all growth trait variables. In conclusion, betaine supplementation to nutrient adequate diet is not effective in improving growth performance of quails divergently selected based on body weight.

44 Accuracy of Genomic Predictions over Time in Broilers

The objectives of this research were to investigate trends for accuracy of genomic predictions over time in a broiler population accumulating data, and to test if data from distant generations are useful in maintaining the accuracy of genomic predictions in selection candidates. The data contained 820k phenotypes for a growth trait (GROW), 200k for two feed efficiency traits (FE1 and FE2), and 42k for a dissection trait (DT). The pedigree included 1.2M animals across 7 years, over 100k from the last 4 years were genotyped. Accuracy was calculated by the linear regression method. Before genotypes became available for training populations, accuracy was nearly stable despite the accumulation of phenotypes and pedigrees. When the first year of genomic data was included in the training population, accuracy increased 56, 77, 39, and 111% for GROW, FE1, FE2, and DT, respectively. With genomic information, the accuracies increased every year except the last one, when they declined for GROW and FE2. The decay of accuracy over time was evaluated in progeny, grand-progeny, and great-grand-progeny of training populations. Without genotypes, the average decline in accuracy across traits was 41% from progeny to grand-progeny, and 19% from grand-progeny to great-grand-progeny. Whit genotypes, the average decline across traits was 14% from progeny to grand-progeny, and 2% from grand-progeny to great-grand-progeny. The accuracies in the last 3 generations were the same when the training population included 5 or 2 years of data, and a marginal decrease was observed when the training population included only 1 year of data. Training sets including genomic information provided an increased accuracy and persistence of genomic predictions compared to training sets without genomic data. The two most recent years of data were enough to maintain the accuracy of predictions in selection candidates.

Phytochrome contributes to blue-light-mediated stem elongation and flower initiation in mature Arabidopsis thaliana plants

To examine whether phytochromes contribute to blue-light-mediated stem elongation, plant phenotypic responses were investigated in wild type Arabidopsis thaliana (Col-0), and its quintuple phytochrome (phyA phyB phyC phyD phyE) mutant plants under the following light treatments: (1) R, a pure red light from 660-nm LED; (2) B, a pure blue light from 455-nm LED; (3) BR, a impure blue light from LED combination of 94% B and 6% R; and (4) BRF, another impure blue light from LED combination of BR and 6 µmol m−2 s−1 of FR (735 nm). A photosynthetic photon flux density of ≈100 μmol m−2 s−1 was provided for all the light treatments. The calculated phytochrome photoequilibrium was 0.89, 0.50, 0.69, and 0.60 for R, B, BR, and BRF, respectively, indicating a higher phytochrome activity under R and BR than B and BRF. After 18 days of light treatment, B or BRF increased main stem length in wild-type plants compared with R, but BR had an inhibition effect similar to R. Also, B and BRF relative to R or BR induced earlier flowering and reduced leaf size in wild type plants, showing typical shade-avoidance responses. In phytochrome-deficient mutant plants, the above shade-avoidance responses were inhibited under B or BRF. However, hypocotyl length, a growth trait characterizing the de-etiolation stage, was reduced under B, BR and BRF vs. R regardless of phytochrome absence. These findings suggest that for mature Arabidopsis plants, phytochrome plays a role in blue-light-mediated stem elongation and the associated shade-avoidance responses.

A high-quality chromosome-scale assembly of the centipedegrass [Eremochloa ophiuroides (Munro) Hack.] genome provides insights into chromosomal structural evolution and prostrate growth habit

Centipedegrass [Eremochloa ophiuroides (Munro) Hack.], a member of the Panicoideae subfamily, is one of the most important warm-season turfgrasses originating from China. This grass has an extremely developed prostrate growth habit and has been widely used in transitional and warm climatic regions. To better understand the genetic basis of important biological characteristics, such as prostrate growth and seed yield, in warm-season turfgrasses, we present a high-quality reference genome for centipedegrass and use PacBio, BioNano, and Hi-C technologies to anchor the 867.43 Mb genome assembly into nine pseudochromosomes, with a scaffold N50 of 86.05 Mb and 36,572 annotated genes. Centipedegrass was most closely related to sorghum and diverged from their common ancestor ~16.8 Mya. We detected a novel chromosome reshuffling event in centipedegrass, namely, the nest chromosome fusion event in which fusion of chromosomes 8 and 10 of sorghum into chromosome 3 of centipedegrass likely occurred after the divergence of centipedegrass from sorghum. The typical prostrate growth trait in centipedegrass may be linked to the expansion of candidate PROSTRATE GROWTH 1 (PROG1) genes on chromosome 2. Two orthologous genes of OsPROG1, EoPROG1, and EoPROG2, were confirmed to increase the stem number and decrease the stem angle in Arabidopsis. Collectively, our assembled reference genome of centipedegrass offers new knowledge and resources to dissect the genome evolution of Panicoideae and accelerate genome-assisted breeding and improvement of plant architecture in turf plants.