Genetic consequences of chronic gamma irradiation on agro morphological traits in chili under hydrogel enhance media.

Induced mutation for the creation of desirable traits through chronic gamma irradiation provides an opportunity for the selection and development of new chili varieties. This study was conducted to assess the effects of different doses of chronic gamma irradiation on morpho-physiological traits in chili. Ten plants from each variety were exposed to different doses of chronic gamma irradiation for 277.02 h at three weeks after germination under gamma greenhouse facilities, with accumulative dose; 185.61Gy, 83.11Gy, 47.096Gy, 30.474Gy, 19.4Gy, 13.9Gy, 11.1Gy, 8.31Gy, 5.54Gy) and 2.77Gy respectively. Highly significant differences were observed among doses (Rings) of chronic gamma irradiation expressed in mean values for all investigated traits. Relatively moderate doses of chronic gamma irradiation represented by doses 47.096 Gy (Ring 4) and 19.40 Gy (Ring 6) resulted in significant stimulation for most of the studied characters. The highest heritability was recorded in days to flowering at 99.88 while the lowest was observed in fruit dry weight at 34.66 %. High genetic advance were recorded for most of the quantitative traits studied. In addition, a highly significant positive correlation was observed between total fruit per plant, total number of fruit per plant, plant height, fruit fresh weight, number of secondary branches, chlorophyll a, fruit dry weight, total chlorophyll content, stem diameter, fruit length and fruit girth. With increasing chronic gamma dose, mutagenic efficiency and efficacy generally increased. Induced variety of desirable features will considerably increase the chilli's amelioration through mutation breeding, leading to the development of improved varieties. The results of this research offer valuable information for the use of chronic gamma radiation in the mutations breeding of Capsicum annuum L., which will be advantageous for future breeding programs.

Integrating Biomarker Outcomes into Clinical Trials for Alzheimer's Disease in Down Syndrome.

The NIH-funded Alzheimer's Biomarker Consortium Down Syndrome (ABC-DS) and the European Horizon 21 Consortium are collecting critical new information on the natural history of Alzheimer's Disease (AD) biomarkers in adults with Down syndrome (DS), a population genetically predisposed to developing AD. These studies are also providing key insights into which biomarkers best represent clinically meaningful outcomes that are most feasible in clinical trials. This paper considers how these data can be integrated in clinical trials for individuals with DS. The Alzheimer's Clinical Trial Consortium - Down syndrome (ACTC-DS) is a platform that brings expert researchers from both networks together to conduct clinical trials for AD in DS across international sites while building on their expertise and experience.

The Trial-Ready Cohort for Preclinical/Prodromal Alzheimer's Disease (TRC-PAD) Project: An Overview.

The Trial-Ready Cohort for Preclinical/prodromal Alzheimer's Disease (TRC-PAD) project is a collaborative effort to establish an efficient mechanism for recruiting participants into very early stage Alzheimer's disease trials. Clinically normal and mildly symptomatic individuals are followed longitudinally in a web-based component called the Alzheimer's Prevention Trial Webstudy (APT Webstudy), with quarterly assessment of cognition and subjective concerns. The Webstudy data is used to predict the likelihood of brain amyloid elevation; individuals at relatively high risk are invited for in-person assessment in the TRC screeing phase, during which a cognitive battery is administered and Apolipoprotein E genotype is obtained followed by reassessment of risk of amyloid elevation. After an initial validation study, plasma amyloid peptide ratios will be included in this risk assessment. Based on this second risk calculation, individuals may have amyloid testing by PET scan or lumbar puncture, with those potentially eligible for trials followed in the TRC, while the rest are invited to remain in the APT Webstudy. To date, over 30,000 individuals have participated in the Webstudy; enrollment in the TRC is in its early stage.

Recruitment into the Alzheimer Prevention Trials (APT) Webstudy for a Trial-Ready Cohort for Preclinical and Prodromal Alzheimer's Disease (TRC-PAD).

BACKGROUND: The Alzheimer Prevention Trials (APT) Webstudy is the first stage in establishing a Trial-ready Cohort for Preclinical and Prodromal Alzheimer's disease (TRC-PAD). This paper describes recruitment approaches for the APT Webstudy. OBJECTIVES: To remotely enroll a cohort of individuals into a web-based longitudinal observational study. Participants are followed quarterly with brief cognitive and functional assessments, and referred to Sites for in-clinic testing and biomarker confirmation prior to enrolling in the Trial-ready Cohort (TRC). DESIGN: Participants are referred to the APT Webstudy from existing registries of individuals interested in brain health and Alzheimer's disease research, as well as through central and site recruitment efforts. The study team utilizes Urchin Tracking Modules (UTM) codes to better understand the impact of electronic recruitment methods. SETTING: A remotely enrolled online study. PARTICIPANTS: Volunteers who are at least 50 years old and interested in Alzheimer's research. MEASUREMENTS: Demographics and recruitment source of participant where measured by UTM. RESULTS: 30,650 participants consented to the APT Webstudy as of April 2020, with 69.7% resulting from referrals from online registries. Emails sent by the registry to participants were the most effective means of recruitment. Participants are distributed across the US, and the demographics of the APT Webstudy reflect the referral registries, with 73.1% female, 85.0% highly educated, and 92.5% Caucasian. CONCLUSIONS: We have demonstrated the feasibility of enrolling a remote web-based study utilizing existing registries as a primary referral source. The next priority of the study team is to engage in recruitment initiatives that will improve the diversity of the cohort, towards the goal of clinical trials that better represent the US population.

TRC-PAD: Accelerating Recruitment of AD Clinical Trials through Innovative Information Technology.

BACKGROUND: The Trial-Ready Cohort for Preclinical/Prodromal Alzheimer's Disease (TRC-PAD) Informatics Platform (TRC-PAD IP) was developed to facilitate the efficient selection, recruitment, and assessment of study participants in support of the TRC-PAD program. OBJECTIVES: Describe the innovative architecture, workflows, and components of the TRC-PAD IP. DESIGN: The TRC-PAD IP was conceived as a secure, scalable, multi-tiered information management platform designed to facilitate high-throughput, cost-effective selection, recruitment, and assessment of TRC-PAD study participants and to develop a learning algorithm to select amyloid-bearing participants to participate in trials of early-stage Alzheimer's disease. SETTING: TRC-PAD participants were evaluated using both web-based and in-person assessments to predict their risk of amyloid biomarker abnormalities and eligibility for preclinical and prodromal clinical trials. Participant data were integrated across multiple stages to inform the prediction of amyloid biomarker elevation. PARTICIPANTS: TRC-PAD participants were age 50 and above, with an interest in participating in Alzheimer's research. MEASUREMENTS: TRC-PAD participants' cognitive performance and subjective memory concerns were remotely assessed on a longitudinal basis to predict participant risk of biomarker abnormalities. Those participants determined to be at the highest risk were invited to an in-clinic screening visit for a full battery of clinical and cognitive assessments and amyloid biomarker confirmation using positron emission tomography (PET) or lumbar puncture (LP). RESULTS: The TRC-PAD IP supported growth in recruitment, screening, and enrollment of TRC-PAD participants by leveraging a secure, scalable, cost-effective cloud-based information technology architecture. CONCLUSIONS: The TRC-PAD program and its underlying information management infrastructure, TRC-PAD IP, have demonstrated feasibility concerning the program aims. The flexible and modular design of the TRC-PAD IP will accommodate the introduction of emerging diagnostic technologies.

The Trial-Ready Cohort for Preclinical and Prodromal Alzheimer's Disease (TRC-PAD): Experience from the First 3 Years.

BACKGROUND: The Trial-Ready Cohort for Preclinical and Prodromal Alzheimer's disease (TRC-PAD) aims to accelerate enrollment for Alzheimer's disease (AD) clinical trials by remotely identifying and tracking individuals who are at high risk for developing symptoms of AD, and referring these individuals to in-person cognitive and biomarker evaluation with the purpose of engaging them in clinical trials. A risk algorithm using statistical modeling to predict brain amyloidosis will be refined as TRC-PAD advances with a maturing data set. OBJECTIVES: To provide a summary of the steps taken to build this Trial-Ready cohort (TRC) and share results of the first 3 years of enrollment into the program. DESIGN: Participants are remotely enrolled in the Alzheimer Prevention Trials (APT) Webstudy with quarterly assessments, and through an algorithm identified as potentially at high risk, referred to clinical sites for biomarker confirmation, and enrolled into the TRC. SETTING: Both an online study and in-clinic non-interventional cohort study. PARTICIPANTS: APT Webstudy participants are aged 50 or older, with an interest in participation in AD therapeutic trials. TRC participants must have a study partner, stable medical condition, and elevated brain amyloid, as measured by amyloid positron emission tomography or cerebrospinal fluid analysis. Additional risk assessments include apolipoprotein E genotyping. MEASUREMENTS: In the APT Webstudy, participants complete the Cognitive Function Index and Cogstate Brief Battery. The TRC includes the Preclinical Alzheimer's Cognitive Composite, comprised of the Free and Cued Selective Reminding Test, the Delayed Paragraph Recall score on the Logical Memory IIa test from the Wechsler Memory Scale, the Digit-Symbol Substitution test from the Wechsler Adult Intelligence Scale-Revised, and the Mini Mental State Examination total score (1). RESULTS: During the first 3 years of this program, the APT Webstudy has 30,650 consented participants, with 23 sites approved for in person screening, 112 participants have been referred for in-clinic screening visits with eighteen enrolled to the TRC. The majority of participants consented to APT Webstudy have a family history of AD (62%), identify as Caucasian (92.5%), have over twelve years of formal education (85%), and are women (73%). Follow up rates for the first quarterly assessment were 38.2% with 29.5% completing the follow up Cogstate Battery. CONCLUSIONS: After successfully designing and implementing this program, the study team's priority is to improve diversity of participants both in the APT Webstudy and TRC, to continue enrollment into the TRC to our target of 2,000, and to improve longitudinal retention, while beginning the process of referring TRC participants into clinical trials.

Author Correction: De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Novel SNPs in the SPAG11 gene and association with testicular biometric variables in Boer goats and application of the levelled-container technique.

Testicular volume (TV) is one of the most important traits used in evaluation of the reproductive capacity of male animals. The levelled-container used in the present study was found to be reliable instrument to measure TV, based on a water displacement method. Sperm-associated antigen 11 (SPAG11) is an important gene that affects male reproductive performance. An objective of the present study, therefore, was to determine if single nucleotide polymorphisms (SNPs) in a fragment of the SPAG11 gene could be used to determine associations with values of testicular biometric variables in Boer goats. Primers were designed to amplify the full length of the first two exons of SPAG11. The targeted fragment was generated using a molecular cloning technique. As the result, four SNPs, [g.1256A > G(ss19199134542), g.1270C > T(ss19199134541), g.1325A > G(ss19199134540) and g.1327 G > A (ss19199134543)], were detected using a single-base extension (SBE) method. Two of these SNPs were synonymous (ss19199134540 and ss19199134542). The other two SNPs were nonsynonymous, thus, there were changes in amino acid in the resulting protein: threonine to isoleucine (for ss19199134541) and arginine to glutamine (for ss19199134543). The SNP ss19199134543 was the only locus detected that was associated with TV (P = 0.002). None of the testes dimensions nor TW were associated with detected SPAG11 gene SNPs. Most likely, the ss19199134543 locus affects tissue structures adjacent to the testes, causing the change in TV. In conclusion, among the studied testicular biometric variables, TV had the greatest potential for preselecting of bucks with desirable semen quality. The use of the levelled-container as a TV measurement approach was an accurate and reliable method.

Molecular insights into the regulation of rice kernel elongation.

A large number of rice agronomic traits are complex, multi factorial and polygenic. As the mechanisms and genes determining grain size and yield are largely unknown, the identification of regulatory genes related to grain development remains a preeminent approach in rice genetic studies and breeding programs. Genes regulating cell proliferation and expansion in spikelet hulls and participating in endosperm development are the main controllers of rice kernel elongation and grain size. We review here and discuss recent findings on genes controlling rice grain size and the mechanisms, epialleles, epigenomic variation, and assessment of controlling genes using genome-editing tools relating to kernel elongation.

Genetic Diversity of Torch Ginger (Etlingera elatior) Germplasm Revealed by ISSR and SSR Markers.

Fifty-seven accessions of torch ginger (Etlingera elatior) collected from seven states in Peninsular Malaysia were evaluated for their molecular characteristics using ISSR and SSR markers to assess the pattern of genetic diversity and association among the characteristics. Diversity study through molecular characterization showed that high variability existed among the 57 torch ginger accessions. ISSR and SSR molecular markers revealed the presence of high genetic variability among the torch ginger accessions. The combination of different molecular markers offered reliable and convincing information about the genetic diversity of torch ginger germplasm. This study found that SSR marker was more informative compared to ISSR marker in determination of gene diversity, polymorphic information content (PIC), and heterozygosity in this population. SSR also revealed high ability in evaluating diversity levels, genetic structure, and relationships of torch ginger due to their codominance and rich allelic diversity. High level of genetic diversity discovered by SSR markers showed the effectiveness of this marker to detect the polymorphism in this germplasm collection.

De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing.

Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, 'Chiang Mai Pink' and 'UB Snow 701', to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.

Bacterial leaf blight resistance in rice: a review of conventional breeding to molecular approach.

Breeding for disease resistant varieties remains very effective and economical in controlling the bacterial leaf blight (BLB) of rice. Breeders have played a major role in developing resistant rice varieties against the BLB infection which has been adjudged to be a major disease causing significant yield reduction in rice. It would be difficult to select rice crops with multiple genes of resistance using the conventional approach alone. This is due to masking effect of genes including epistasis. In addition, conventional breeding takes a lot of time before a gene of interest can be introgressed. Linkage drag is also a major challenge in conventional approach. Molecular breeding involving markers has facilitated the characterization and introgression of BLB disease resistance genes. Biotechnology has brought another innovation in form of genetic engineering (transgenesis) of rice. Although, molecular breeding cannot be taken as a substitute for conventional breeding, molecular approach for combating BLB disease in rice is worthwhile given the demand for increased production of rice in a fast growing population of our society. This present article highlights the recent progress from conventional to molecular approach in breeding for BLB disease resistant rice varieties.

Improvement of Drought Tolerance in Rice (Oryza sativa L.): Genetics, Genomic Tools, and the WRKY Gene Family.

Drought tolerance is an important quantitative trait with multipart phenotypes that are often further complicated by plant phenology. Different types of environmental stresses, such as high irradiance, high temperatures, nutrient deficiencies, and toxicities, may challenge crops simultaneously; therefore, breeding for drought tolerance is very complicated. Interdisciplinary researchers have been attempting to dissect and comprehend the mechanisms of plant tolerance to drought stress using various methods; however, the limited success of molecular breeding and physiological approaches suggests that we rethink our strategies. Recent genetic techniques and genomics tools coupled with advances in breeding methodologies and precise phenotyping will likely reveal candidate genes and metabolic pathways underlying drought tolerance in crops. The WRKY transcription factors are involved in different biological processes in plant development. This zinc (Zn) finger protein family, particularly members that respond to and mediate stress responses, is exclusively found in plants. A total of 89 WRKY genes in japonica and 97 WRKY genes in O. nivara (OnWRKY) have been identified and mapped onto individual chromosomes. To increase the drought tolerance of rice (Oryza sativa L.), research programs should address the problem using a multidisciplinary strategy, including the interaction of plant phenology and multiple stresses, and the combination of drought tolerance traits with different genetic and genomics approaches, such as microarrays, quantitative trait loci (QTLs), WRKY gene family members with roles in drought tolerance, and transgenic crops. This review discusses the newest advances in plant physiology for the exact phenotyping of plant responses to drought to update methods of analysing drought tolerance in rice. Finally, based on the physiological/morphological and molecular mechanisms found in resistant parent lines, a strategy is suggested to select a particular environment and adapt suitable germplasm to that environment.

Genotypic and Phenotypic Relationship among Yield Components in Rice under Tropical Conditions.

The associations among yield-related traits and the pattern of influence on rice grain yield were investigated. This evaluation is important to determine the direct and indirect effects of various traits on yield to determine selection criteria for higher grain yield. Fifteen rice genotypes were evaluated under tropical condition at five locations in two planting seasons. The experiment was laid out in a randomized complete block design with three replications across the locations. Data were collected on vegetative and yield components traits. The pooled data based on the analysis of variance revealed that there were significant differences (p < 0.001) among the fifteen genotypes for all the characters studied except for panicle length and 100-grain weight. Highly significant and positive correlations at phenotypic level were observed in grain weight per hill (0.796), filled grains per panicle (0.702), panicles per hill (0.632), and tillers per hill (0.712) with yield per hectare, while moderate positive correlations were observed in flag leaf length to width ratio (0.348), days to flowering (0.412), and days to maturity (0.544). By contrast, unfilled grains per panicle (-0.225) and plant height (-0.342) had a negative significant association with yield per hectare. Filled grains per panicle (0.491) exhibited the maximum positive direct effect on yield followed by grain weight per hill (0.449), while unfilled grain per panicle (-0.144) had a negative direct effect. The maximum indirect effect on yield per hectare was recorded by the tillers per hill through the panicles per hill. Therefore, tillers per hill, filled grains per panicle, and grain weight per hill could be used as selection criteria for improving grain yield in rice.

Relationship between High Temperature and Formation of Chalkiness and Their Effects on Quality of Rice.

Occurrence of chalkiness in rice is attributed to genetic and environmental factors, especially high temperature (HT). The HT induces heat stress, which in turn compromises many grain qualities, especially transparency. Chalkiness in rice is commonly studied together with other quality traits such as amylose content, gel consistency, and protein storage. In addition to the fundamental QTLs, some other QTLs have been identified which accelerate chalkiness occurrence under HT condition. In this review, some of the relatively stable chalkiness, amylose content, and gel consistency related QTLs have been presented well. Genetically, HT effect on chalkiness is explained by the location of certain chalkiness gene in the vicinity of high-temperature-responsive genes. With regard to stable QTL distribution and availability of potential material resources, there is still feasibility to find out novel stable QTLs related to chalkiness under HT condition. A better understanding of those achievements is essential to develop new rice varieties with a reduced chalky grain percentage. Therefore, we propose the pyramiding of relatively stable and nonallelic QTLs controlling low chalkiness endosperm into adaptable rice varieties as pragmatic approach to mitigate HT effect.

Antioxidant Enzyme Activities and Secondary Metabolite Profiling of Oil Palm Seedlings Treated with Combination of NPK Fertilizers Infected with Ganoderma boninense.

Oil palm (Elaeis guineensis Jacq) is one of the major sources of edible oil. Reducing the effect of Ganoderma, main cause of basal stem rot (BSR) on oil palm, is the main propose of this study. Understanding the oil palm defense mechanism against Ganoderma infection through monitoring changes in the secondary metabolite compounds levels before/after infection by Ganoderma under different fertilizing treatment is required. Oil palm requires macro- and microelements for growth and yield. Manipulating the nutrient for oil palm is a method to control the disease. The 3-4-month-old oil palm seedlings were given different macronutrient treatments to evaluate induction of defense related enzymes and production of secondary metabolite compounds in response to G. boninense inoculation. The observed trend of changes in the infected and uninfected seedlings was a slightly higher activity for ß-1,3-glucanases, chitinase, peroxidase, and phenylalanine ammonia-lyase during the process of pathogenesis. It was found that PR proteins gave positive response to the interaction between oil palm seedlings and Ganoderma infection. Although the responses were activated systematically, they were short-lasting as the changes in enzymes activities appeared before the occurrence of visible symptoms. Effect of different nutrients doses was obviously observed among the results of the secondary metabolite compounds. Many identified/unidentified metabolite compounds were presented, of which some were involved in plant cell defense mechanism against pathogens, mostly belonging to alkaloids with bitter-tasting nitrogenous-compounds, and some had the potential to be used as new markers to detect basal stem rot at the initial step of disease.

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers.

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon's information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He ) of 0.60 and mean Nei's gene diversity index of 0.36. The dendrogram based on UPGMA and Nei's genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.